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#444;text-decoration: none;} + +.icn3d-text {font-family: Verdana, Arial, Helvetica, sans-serif; font-size:12px!important;} + +.ui-dialog { font-size: 12px;} +.ui-dialog .ui-dialog-title { font-size: 16px; height: 18px; } +.ui-dialog .ui-button { width: 12px; height:12px; margin: -5px 0px 0px 0px;} +.ui-dialog .ui-dialog-titlebar { padding: 0px 1em 2px 1em; } + +.ui-accordion .ui-accordion-icons { padding-left: 0; text-align: center; } + +.icn3d-menu {float:left; width:110px;} +.icn3d-menu-color {color:#1c94c4; font-weight:bold; font-size: 14px!important;} + +accordion {font-size: 14px!important; z-index:1999; } +accordion h3 {width: 100px; font-size: 14px!important;} +accordion h3 > .ui-icon { display: none !important; } +accordion ul ul {width: 160px} +@media screen and (max-device-width: 480px) { + accordion ul ul {width: 110px} +} +accordion ul ul ul {width: 160px} +accordion ul li {cursor:default!important; white-space:nowrap;} +/*accordion ul .icn3d-link, div .icn3d-link, accordion li input, accordion li label, button {cursor:pointer!important; } */ +.icn3d-link, accordion li input, accordion li label, button {cursor:pointer!important; } +.icn3d-blue {color:blue!important;} + +/*.icn3d-dl_sequence {background: white; padding-left:10px;}*/ +.icn3d-dl_sequence {background: white;} +.icn3d-highlightSeq {background-color: #FFFF00;} +.icn3d-highlightSeqBox {border:3px solid #FFA500;} + +/* used to identify a residue when clicking a residue in sequence*/ +.icn3d-residue {font-weight:regular;} +.icn3d-residueNum {color: green; width:40px!important; text-align:center; white-space:nowrap;} + +.icn3d-dl_sequence span {display:inline-block; font-size:11px; width:10px; text-align:center;} +/*.icn3d-dl_2ddgm {} */ +.icn3d-chemical {width:30px!important;} + +button, select, input { font-size: 10px; } + +.icn3d-hidden {display: none;} +.icn3d-shown {display: block;} + +.icn3d-seqTitle, .icn3d-seqTitle2, .icn3d-annoTitle {display:inline-block; font-size:11px; font-weight:bold; width:60px;} +.icn3d-annotation {white-space: nowrap;} +.icn3d-annotation .icn3d-seqTitle, .icn3d-annotation .icn3d-seqTitle2, .icn3d-annotation .icn3d-annoTitle {display:inline-block; font-size:11px; font-weight:bold; width:120px;} +.icn3d-seqLine {white-space:nowrap;} +.icn3d-annoLargeTitle {font-size:14px; font-weight:bold; background-color: #DDDDDD;} +.icn3d-large {font-size:14px; font-weight:bold;} + +.icn3d-dialog {font-family: Verdana, Arial, Helvetica, sans-serif; color: #666666;} +.icn3d-commandTitle {font-size: 12px; font-weight:bold; font-family: Verdana, Arial, Helvetica, sans-serif; color: #666666;} +.icn3d-modeselection {color: #f8b84e!important;} +/*.icn3d-viewselection {color: #800000!important;}*/ +.icn3d-viewselection {color: #f8b84e!important;} + +.icn3d-middleIcon {opacity: 1.0} +.icn3d-endIcon {opacity: 0.2} + +.icn3d-box {border: solid 1px #ccc; padding: 5px; margin: 5px;} + +/* +//sequence alignent, 'cons' means aligned and conserved, 'ncons' means aligned and not conserved, 'nalign' means not aligned +.icn3d-cons {} +.icn3d-ncons {} +.icn3d-nalign {} +*/ + +.icn3d-node, .icn3d-ctnode {cursor:pointer!important; } +.icn3d-interaction {cursor:pointer!important; } + +/* force-directed graph node text */ +.icn3d-node-text0 {font-size: 0px; font-weight: bold} +.icn3d-node-text4 {font-size: 4px; font-weight: bold} +.icn3d-node-text8 {font-size: 8px; font-weight: bold} +.icn3d-node-text12 {font-size: 12px; font-weight: bold} +.icn3d-node-text16 {font-size: 16px; font-weight: bold} +.icn3d-node-text24 {font-size: 24px; font-weight: bold} +.icn3d-node-text32 {font-size: 32px; font-weight: bold} + +.ui-dialog .ui-resizable-se { + width: 14px; + height: 14px; + right: 3px; + bottom: 3px; + background-position: -80px -224px; +} + +.ui-menu-icon { + float: right; +} + +/* toggle button: http://www.w3schools.com/howto/howto_css_switch.asp */ +.icn3d-switch { + position: relative; + display: inline-block; + width: 33px; + height: 18px; +} + +.icn3d-switch input {display:none;} + +.icn3d-slider { + position: absolute; + cursor: pointer; + top: 0; + left: 0; + right: 0; + bottom: 0; + background-color: #ccc; + -webkit-transition: .4s; + transition: .4s; +} + +.icn3d-slider:before { + position: absolute; + content: ""; + height: 13px; + width: 13px; + left: 4px; + bottom: 3px; + background-color: white; + -webkit-transition: .4s; + transition: .4s; +} + +input:checked + .icn3d-slider { + background-color: #f8b84e; +} + +input:focus + .icn3d-slider { + box-shadow: 0 0 1px #f8b84e; +} + +input:checked + .icn3d-slider:before { + -webkit-transform: translateX(13px); + -ms-transform: translateX(13px); + transform: translateX(13px); +} + +.icn3d-slider.icn3d-round { + border-radius: 18px; +} + +.icn3d-slider.icn3d-round:before { + border-radius: 50%; +} + +/* jquery UI 1.13.2 + for jquery tooltip */ +.icn3d-tooltip { + display: inline-block; + width: 200px; +} + +.snptip { + max-height: 150px; + overflow:auto; +} + +.ui-widget { + font-family: Arial,Helvetica,sans-serif; + font-size: 12px!important; /* 0.9em is a little too large */ +} +.ui-menu-item { + position: relative; + padding: 3px 1em 3px .4em; +} + +.icn3d-clinvar {color:green; font-size:12px; font-weight:bold;} +.icn3d-clinvar-path {color:red; font-size:12px; font-weight:bold;} + +/*.icn3d-sheet {background-image: linear-gradient(transparent, transparent 25%, #FFC800 25%, #FFC800 75%, transparent 75%, transparent 100%);} */ +.icn3d-sheet {background-image: linear-gradient(transparent, transparent 25%, #008000 25%, #008000 75%, transparent 75%, transparent 100%);} +.icn3d-sheet2 {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/ssimages/trig.png"); background-size: contain; background-repeat: no-repeat;} + +.icn3d-sheety {background-image: linear-gradient(transparent, transparent 25%, #FFC800 25%, #FFC800 75%, transparent 75%, transparent 100%);} +.icn3d-sheet2y {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/ssimages/triy.png"); background-size: contain; background-repeat: no-repeat;} + +.icn3d-helix {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/ssimages/helix.png"); background-size: contain; background-repeat: no-repeat;} +.icn3d-helix2 {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/ssimages/helix2.png"); background-size: contain; background-repeat: no-repeat;} + +.icn3d-coil {background-image: linear-gradient(transparent, transparent 45%, #6080FF 45%, #6080FF 55%, transparent 55%, transparent 100%);} +.icn3d-other {background-image: linear-gradient(transparent, transparent 45%, #DDDDDD 45%, #DDDDDD 55%, transparent 55%, transparent 100%);} + +.icn3d-helix-color {color: #FF0080;} + +.icn3d-sheet-color {color: #008000;} +.icn3d-sheet-colory {color: #FFC800;} + +.icn3d-fixed-pos {position:fixed;} +/*.icn3d-space-title {width:160px; display:inline-block;} */ + +.icn3d-bkgd {background-color:#eee;} + +/* remove the extra bar in the menu */ + /* background: #eee url(images/ui-bg_highlight-soft_100_eeeeee_1x100.png) 50% top repeat-x; */ +.ui-widget-content { + border: 1px solid #ddd; + background: #eee; + color: #333; +} + +.icn3d-rad > input{ /* HIDE RADIO */ + visibility: hidden; /* Makes input not-clickable */ + position: absolute; /* Remove input from document flow */ +} +.icn3d-rad > input + .ui-icon{ /* IMAGE STYLES */ + cursor:pointer; + /*border:2px solid transparent;*/ +} +.icn3d-rad > input:checked + .ui-icon{ /* (RADIO CHECKED) IMAGE STYLES */ + /*border:2px solid #f00;*/ + background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_222222_256x240.png"); + background-position: -64px -144px; /*ui-icon-check */ +} +.icn3d-rad > input:not(:checked) + .ui-icon{ /* (RADIO NOT CHECKED) IMAGE STYLES */ + /*border:2px solid #f00;*/ + background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_222222_256x240.png"); + background-position: -160px 0px; /*empty */ +} + +.ui-menu-icons .ui-menu-item-wrapper, .ui-menu-icons .ui-menu-item { + padding-left: 0.4em!important; +} + +.icn3d-rad-text, .icn3d-color-rad-text { + padding-left: 1.2em; +} + +.icn3d-popup {display:none; position:absolute; z-index:99; top:-1000px; left:-1000px; background-color:#DDDDDD; text-align:center; width:80px; height:18px; padding:3px;} + +.icn3d-legend {display:none; position:absolute; z-index:99; bottom:-20px; right:20px; background-color:#DDDDDD; width:100px; height:35px; padding:6px;} + +.icn3d-legend2 {display:none; position:absolute; z-index:99; bottom:50px; right:20px; background-color:#DDDDDD; width:200px; height:60px; padding:6px;} + +.icn3d-saveicon {cursor:pointer; position:absolute; top:8px; right:20px; } +.icn3d-hideicon {cursor:pointer; position:absolute; top:8px; right:40px; } + +.icn3d-border tr th, .icn3d-border tr td {border-right: solid 1px;} + +.icn3d-sticky thead th { + position: -webkit-sticky; /* for Safari */ + position: sticky; + background-color: rgba(255, 255, 255, 1); + top: 0; +} + +.icn3d-sticky tbody th { + position: -webkit-sticky; /* for Safari */ + position: sticky; + background-color: rgba(255, 255, 255, 1); + left: 0; +} + +.icn3d-snplink {text-decoration: underline; cursor:pointer;} + +.icn3d-wifi {width:16px; display:inline-block; background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/ssimages/wifi.png"); background-size: contain; background-repeat: no-repeat;} +.icn3d-license {width:16px; display:inline-block; background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/ssimages/license.png"); background-size: contain; background-repeat: no-repeat;} + +.icn3d-square { display:inline-block; width:15px;} + +.icn3d-distance {color:#1c94c4; cursor: pointer;} + +.icn3d-menupd {padding-left:1.5em!important;} + +.icn3d-nbclose {cursor:pointer; background-color:white;} + +.color-picker, +.color-picker:before, +.color-picker:after, +.color-picker *, +.color-picker *:before, +.color-picker *:after { + -webkit-box-sizing:border-box; + -moz-box-sizing:border-box; + box-sizing:border-box; +} +.color-picker { + position:absolute; + top:0; + left:0; + z-index:9999; + width:172px; +} +.color-picker-control { + border:1px solid #000; + -webkit-box-shadow:1px 5px 10px rgba(0,0,0,.5); + -moz-box-shadow:1px 5px 10px rgba(0,0,0,.5); + box-shadow:1px 5px 10px rgba(0,0,0,.5); +} +.color-picker-control *, +.color-picker-control *:before, +.color-picker-control *:after {border-color:inherit} +.color-picker-control:after { + content:" "; + display:table; + clear:both; +} +.color-picker i {font:inherit} +.color-picker-h { + position:relative; + width:20px; + height:150px; + float:right; + border-left:1px solid; + border-left-color:inherit; + cursor:ns-resize; + background:transparent no-repeat 50% 50%; /*url('color-picker-h.png')*/ + background-image:-webkit-linear-gradient(to top,#f00 0%,#ff0 17%,#0f0 33%,#0ff 50%,#00f 67%,#f0f 83%,#f00 100%); + background-image:-moz-linear-gradient(to top,#f00 0%,#ff0 17%,#0f0 33%,#0ff 50%,#00f 67%,#f0f 83%,#f00 100%); + background-image:linear-gradient(to top,#f00 0%,#ff0 17%,#0f0 33%,#0ff 50%,#00f 67%,#f0f 83%,#f00 100%); + -webkit-background-size:100% 100%; + -moz-background-size:100% 100%; + background-size:100% 100%; + overflow:hidden; +} +.color-picker-h i { + position:absolute; + top:-3px; + right:0; + left:0; + z-index:3; + display:block; + height:6px; +} +.color-picker-h i:before { + content:""; + position:absolute; + top:0; + right:0; + bottom:0; + left:0; + display:block; + border:3px solid; + border-color:inherit; + border-top-color:transparent; + border-bottom-color:transparent; +} +.color-picker-sv { + position:relative; + width:150px; + height:150px; + float:left; + background:transparent no-repeat 50% 50%; /*url('color-picker-sv.png')*/ + background-image:-webkit-linear-gradient(to top,#000,rgba(0,0,0,0)),linear-gradient(to right,#fff,rgba(255,255,255,0)); + 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CIFTools,$NGL_shaderTextHash={};$NGL_shaderTextHash["SphereImpostor.frag"]=["#define STANDARD","#define IMPOSTOR","","uniform vec3 diffuse;","uniform vec3 emissive;","uniform float roughness;","uniform float metalness;","uniform float opacity;","uniform float nearClip;","uniform mat4 projectionMatrix;","uniform float ortho;","","varying float vRadius;","varying float vRadiusSq;","varying vec3 vPoint;","varying vec3 vPointViewPosition;","","#ifdef PICKING"," uniform float objectId;"," varying vec3 vPickingColor;","#else"," #include common"," #include color_pars_fragment"," #include fog_pars_fragment"," #include bsdfs"," #include lights_pars_begin"," #include lights_physical_pars_fragment","#endif","","bool flag2 = false;","bool interior = false;","vec3 cameraPos;","vec3 cameraNormal;","","// Calculate depth based on the given camera position.","float calcDepth( in vec3 cameraPos ){"," vec2 clipZW = cameraPos.z * projectionMatrix[2].zw + projectionMatrix[3].zw;"," return 0.5 + 0.5 * clipZW.x / clipZW.y;","}","","float calcClip( vec3 cameraPos ){"," return dot( vec4( cameraPos, 1.0 ), vec4( 0.0, 0.0, 1.0, nearClip - 0.5 ) );","}","","bool Impostor( out vec3 cameraPos, out vec3 cameraNormal ){",""," vec3 cameraSpherePos = -vPointViewPosition;"," cameraSpherePos.z += vRadius;",""," vec3 rayOrigin = mix( vec3( 0.0, 0.0, 0.0 ), vPoint, ortho );"," vec3 rayDirection = mix( normalize( vPoint ), vec3( 0.0, 0.0, 1.0 ), ortho );"," vec3 cameraSphereDir = mix( cameraSpherePos, rayOrigin - cameraSpherePos, ortho );",""," float B = dot( rayDirection, cameraSphereDir );"," float det = B * B + vRadiusSq - dot( cameraSphereDir, cameraSphereDir );",""," if( det < 0.0 ){"," discard;"," return false;"," }"," float sqrtDet = sqrt( det );"," float posT = mix( B + sqrtDet, B + sqrtDet, ortho );"," float negT = mix( B - sqrtDet, sqrtDet - B, ortho );",""," cameraPos = rayDirection * negT + rayOrigin;",""," #ifdef NEAR_CLIP","if( calcDepth( cameraPos ) <= 0.0 ){"," cameraPos = rayDirection * posT + rayOrigin;"," interior = true;"," return false;","}else if( calcClip( cameraPos ) > 0.0 ){"," cameraPos = rayDirection * posT + rayOrigin;"," interior = true;"," flag2 = true;"," return false;","}else{"," cameraNormal = normalize( cameraPos - cameraSpherePos );","}"," #else","if( calcDepth( cameraPos ) <= 0.0 ){"," cameraPos = rayDirection * posT + rayOrigin;"," interior = true;"," return false;","}else{"," cameraNormal = normalize( cameraPos - cameraSpherePos );","}"," #endif",""," cameraNormal = normalize( cameraPos - cameraSpherePos );"," cameraNormal *= float(!interior) * 2.0 - 1.0;"," return !interior;","","}","","void main(void){",""," bool flag = Impostor( cameraPos, cameraNormal );",""," #ifdef NEAR_CLIP"," if( calcClip( cameraPos ) > 0.0 )"," discard;"," #endif",""," // FIXME not compatible with custom clipping plane"," //Set the depth based on the new cameraPos."," gl_FragDepthEXT = calcDepth( cameraPos );"," if( !flag ){",""," // clamp to near clipping plane and add a tiny value to"," // make spheres with a greater radius occlude smaller ones"," #ifdef NEAR_CLIP","if( flag2 ){"," gl_FragDepthEXT = max( 0.0, calcDepth( vec3( - ( nearClip - 0.5 ) ) ) + ( 0.0000001 / vRadius ) );","}else if( gl_FragDepthEXT >= 0.0 ){"," gl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius );","}"," #else","if( gl_FragDepthEXT >= 0.0 ){"," gl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius );","}"," #endif",""," }",""," // bugfix (mac only?)"," if (gl_FragDepthEXT < 0.0)"," discard;"," if (gl_FragDepthEXT > 1.0)"," discard;",""," #ifdef PICKING",""," gl_FragColor = vec4( vPickingColor, objectId );",""," #else",""," vec3 vNormal = cameraNormal;"," vec3 vViewPosition = -cameraPos;",""," vec4 diffuseColor = vec4( diffuse, opacity );"," ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) );"," vec3 totalEmissiveLight = emissive;",""," #include color_fragment"," #include roughnessmap_fragment"," #include metalnessmap_fragment",""," // don't use include normal_fragment"," vec3 normal = normalize( vNormal );",""," #include lights_physical_fragment"," //include lights_template"," #include lights_fragment_begin"," #include lights_fragment_end",""," vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveLight;",""," gl_FragColor = vec4( outgoingLight, diffuseColor.a );"," //gl_FragColor = vec4( reflectedLight.directSpecular, diffuseColor.a );",""," #include premultiplied_alpha_fragment"," #include tonemapping_fragment"," #include encodings_fragment"," //include fog_fragment"," #ifdef USE_FOG"," #ifdef USE_LOGDEPTHBUF_EXT"," float depth = gl_FragDepthEXT / gl_FragCoord.w;"," #else"," float depth = gl_FragCoord.z / gl_FragCoord.w;"," #endif"," #ifdef FOG_EXP2"," float fogFactor = whiteCompliment( exp2( - fogDensity * fogDensity * depth * depth * LOG2 ) );"," #else"," float fogFactor = smoothstep( fogNear, fogFar, depth );"," #endif"," gl_FragColor.rgb = mix( gl_FragColor.rgb, fogColor, fogFactor );"," #endif",""," #endif","","}"].join("\n"),$NGL_shaderTextHash["SphereImpostor.vert"]=["uniform mat4 projectionMatrixInverse;","uniform float nearClip;","","varying float vRadius;","varying float vRadiusSq;","varying vec3 vPoint;","varying vec3 vPointViewPosition;","varying float fogDepth;","varying float fogNear;","varying float fogFar;","","attribute vec2 mapping;","//attribute vec3 position;","attribute float radius;","","#ifdef PICKING"," #include unpack_clr"," attribute float primitiveId;"," varying vec3 vPickingColor;","#else"," #include color_pars_vertex","#endif","","//include matrix_scale","float matrixScale( in mat4 m ){"," vec4 r = m[ 0 ];"," return sqrt( r[ 0 ] * r[ 0 ] + r[ 1 ] * r[ 1 ] + r[ 2 ] * r[ 2 ] );","}","","const mat4 D = mat4("," 1.0, 0.0, 0.0, 0.0,"," 0.0, 1.0, 0.0, 0.0,"," 0.0, 0.0, 1.0, 0.0,"," 0.0, 0.0, 0.0, -1.0",");","","mat4 transposeTmp( in mat4 inMatrix ) {"," vec4 i0 = inMatrix[0];"," vec4 i1 = inMatrix[1];"," vec4 i2 = inMatrix[2];"," vec4 i3 = inMatrix[3];",""," mat4 outMatrix = mat4("," vec4(i0.x, i1.x, i2.x, i3.x),"," vec4(i0.y, i1.y, i2.y, i3.y),"," vec4(i0.z, i1.z, i2.z, i3.z),"," vec4(i0.w, i1.w, i2.w, i3.w)"," );"," return outMatrix;","}","","//------------------------------------------------------------------------------","// Compute point size and center using the technique described in:","// 'GPU-Based Ray-Casting of Quadratic Surfaces'","// by Christian Sigg, Tim Weyrich, Mario Botsch, Markus Gross.","//","// Code based on","/*=========================================================================",""," Program: Visualization Toolkit"," Module: Quadrics_fs.glsl and Quadrics_vs.glsl",""," Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen"," All rights reserved."," See Copyright.txt or http://www.kitware.com/Copyright.htm for details.",""," This software is distributed WITHOUT ANY WARRANTY; without even"," the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR"," PURPOSE. See the above copyright notice for more information.",""," =========================================================================*/","","// .NAME Quadrics_fs.glsl and Quadrics_vs.glsl","// .SECTION Thanks","// ","//","// This file is part of the PointSprites plugin developed and contributed by","//","// Copyright (c) CSCS - Swiss National Supercomputing Centre","// EDF - Electricite de France","//","// John Biddiscombe, Ugo Varetto (CSCS)","// Stephane Ploix (EDF)","//","// ","//","// Contributions by Alexander Rose","// - ported to WebGL","// - adapted to work with quads","void ComputePointSizeAndPositionInClipCoordSphere(){",""," vec2 xbc;"," vec2 ybc;",""," mat4 T = mat4("," radius, 0.0, 0.0, 0.0,"," 0.0, radius, 0.0, 0.0,"," 0.0, 0.0, radius, 0.0,"," position.x, position.y, position.z, 1.0"," );",""," mat4 R = transposeTmp( projectionMatrix * modelViewMatrix * T );"," float A = dot( R[ 3 ], D * R[ 3 ] );"," float B = -2.0 * dot( R[ 0 ], D * R[ 3 ] );"," float C = dot( R[ 0 ], D * R[ 0 ] );"," xbc[ 0 ] = ( -B - sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );"," xbc[ 1 ] = ( -B + sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );"," float sx = abs( xbc[ 0 ] - xbc[ 1 ] ) * 0.5;",""," A = dot( R[ 3 ], D * R[ 3 ] );"," B = -2.0 * dot( R[ 1 ], D * R[ 3 ] );"," C = dot( R[ 1 ], D * R[ 1 ] );"," ybc[ 0 ] = ( -B - sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );"," ybc[ 1 ] = ( -B + sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );"," float sy = abs( ybc[ 0 ] - ybc[ 1 ] ) * 0.5;",""," gl_Position.xy = vec2( 0.5 * ( xbc.x + xbc.y ), 0.5 * ( ybc.x + ybc.y ) );"," gl_Position.xy -= mapping * vec2( sx, sy );"," gl_Position.xy *= gl_Position.w;","","}","","void main(void){",""," #ifdef PICKING"," vPickingColor = unpackColor( primitiveId );"," #else"," #include color_vertex"," #endif",""," vRadius = radius * matrixScale( modelViewMatrix );",""," vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );"," // avoid clipping, added again in fragment shader"," mvPosition.z -= vRadius;",""," gl_Position = projectionMatrix * vec4( mvPosition.xyz, 1.0 );"," ComputePointSizeAndPositionInClipCoordSphere();","",""," vRadiusSq = vRadius * vRadius;"," vec4 vPoint4 = projectionMatrixInverse * gl_Position;"," vPoint = vPoint4.xyz / vPoint4.w;"," vPointViewPosition = -mvPosition.xyz / mvPosition.w;","","}"].join("\n"),$NGL_shaderTextHash["CylinderImpostor.frag"]=["#define STANDARD","#define IMPOSTOR","","// Open-Source PyMOL is Copyright (C) Schrodinger, LLC.","//","// All Rights Reserved","//","// Permission to use, copy, modify, distribute, and distribute modified","// versions of this software and its built-in documentation for any","// purpose and without fee is hereby granted, provided that the above","// copyright notice appears in all copies and that both the copyright","// notice and this permission notice appear in supporting documentation,","// and that the name of Schrodinger, LLC not be used in advertising or","// publicity pertaining to distribution of the software without specific,","// written prior permission.","//","// SCHRODINGER, LLC DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,","// INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN","// NO EVENT SHALL SCHRODINGER, LLC BE LIABLE FOR ANY SPECIAL, INDIRECT OR","// CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS","// OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE","// OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE","// USE OR PERFORMANCE OF THIS SOFTWARE.","","// Contributions by Alexander Rose","// - ported to WebGL","// - dual color","// - pk color","// - custom clipping","// - three.js lighting","","uniform vec3 diffuse;","uniform vec3 emissive;","uniform float roughness;","uniform float metalness;","uniform float opacity;","uniform float nearClip;","uniform mat4 projectionMatrix;","uniform float ortho;","","varying vec3 axis;","varying vec4 base_radius;","varying vec4 end_b;","varying vec3 U;","varying vec3 V;","varying vec4 w;","","#ifdef PICKING"," uniform float objectId;"," varying vec3 vPickingColor;","#else"," varying vec3 vColor1;"," varying vec3 vColor2;"," #include common"," #include fog_pars_fragment"," #include bsdfs"," #include lights_pars_begin"," #include lights_physical_pars_fragment","#endif","","bool interior = false;","","float distSq3( vec3 v3a, vec3 v3b ){"," return ("," ( v3a.x - v3b.x ) * ( v3a.x - v3b.x ) +"," ( v3a.y - v3b.y ) * ( v3a.y - v3b.y ) +"," ( v3a.z - v3b.z ) * ( v3a.z - v3b.z )"," );","}","","// Calculate depth based on the given camera position.","float calcDepth( in vec3 cameraPos ){"," vec2 clipZW = cameraPos.z * projectionMatrix[2].zw + projectionMatrix[3].zw;"," return 0.5 + 0.5 * clipZW.x / clipZW.y;","}","","float calcClip( vec3 cameraPos ){"," return dot( vec4( cameraPos, 1.0 ), vec4( 0.0, 0.0, 1.0, nearClip - 0.5 ) );","}","","void main(){",""," vec3 point = w.xyz / w.w;",""," // unpacking"," vec3 base = base_radius.xyz;"," float vRadius = base_radius.w;"," vec3 end = end_b.xyz;"," float b = end_b.w;",""," vec3 end_cyl = end;"," vec3 surface_point = point;",""," vec3 ray_target = surface_point;"," vec3 ray_origin = vec3(0.0);"," vec3 ray_direction = mix(normalize(ray_origin - ray_target), vec3(0.0, 0.0, 1.0), ortho);"," mat3 basis = mat3( U, V, axis );",""," vec3 diff = ray_target - 0.5 * (base + end_cyl);"," vec3 P = diff * basis;",""," // angle (cos) between cylinder cylinder_axis and ray direction"," float dz = dot( axis, ray_direction );",""," float radius2 = vRadius*vRadius;",""," // calculate distance to the cylinder from ray origin"," vec3 D = vec3(dot(U, ray_direction),"," dot(V, ray_direction),"," dz);"," float a0 = P.x*P.x + P.y*P.y - radius2;"," float a1 = P.x*D.x + P.y*D.y;"," float a2 = D.x*D.x + D.y*D.y;",""," // calculate a dicriminant of the above quadratic equation"," float d = a1*a1 - a0*a2;"," if (d < 0.0)"," // outside of the cylinder"," discard;",""," float dist = (-a1 + sqrt(d)) / a2;",""," // point of intersection on cylinder surface"," vec3 new_point = ray_target + dist * ray_direction;",""," vec3 tmp_point = new_point - base;"," vec3 _normal = normalize( tmp_point - axis * dot(tmp_point, axis) );",""," ray_origin = mix( ray_origin, surface_point, ortho );",""," // test caps"," float front_cap_test = dot( tmp_point, axis );"," float end_cap_test = dot((new_point - end_cyl), axis);",""," // to calculate caps, simply check the angle between"," // the point of intersection - cylinder end vector"," // and a cap plane normal (which is the cylinder cylinder_axis)"," // if the angle < 0, the point is outside of cylinder"," // test front cap",""," #ifndef CAP"," vec3 new_point2 = ray_target + ( (-a1 - sqrt(d)) / a2 ) * ray_direction;"," vec3 tmp_point2 = new_point2 - base;"," #endif",""," // flat"," if (front_cap_test < 0.0)"," {"," // ray-plane intersection"," float dNV = dot(-axis, ray_direction);"," if (dNV < 0.0)"," discard;"," float near = dot(-axis, (base)) / dNV;"," vec3 front_point = ray_direction * near + ray_origin;"," // within the cap radius?"," if (dot(front_point - base, front_point-base) > radius2)"," discard;",""," #ifdef CAP"," new_point = front_point;"," _normal = axis;"," #else"," new_point = ray_target + ( (-a1 - sqrt(d)) / a2 ) * ray_direction;"," dNV = dot(-axis, ray_direction);"," near = dot(axis, end_cyl) / dNV;"," new_point2 = ray_direction * near + ray_origin;"," if (dot(new_point2 - end_cyl, new_point2-base) < radius2)"," discard;"," interior = true;"," #endif"," }",""," // test end cap","",""," // flat"," if( end_cap_test > 0.0 )"," {"," // ray-plane intersection"," float dNV = dot(axis, ray_direction);"," if (dNV < 0.0)"," discard;"," float near = dot(axis, end_cyl) / dNV;"," vec3 end_point = ray_direction * near + ray_origin;"," // within the cap radius?"," if( dot(end_point - end_cyl, end_point-base) > radius2 )"," discard;",""," #ifdef CAP"," new_point = end_point;"," _normal = axis;"," #else"," new_point = ray_target + ( (-a1 - sqrt(d)) / a2 ) * ray_direction;"," dNV = dot(-axis, ray_direction);"," near = dot(-axis, (base)) / dNV;"," new_point2 = ray_direction * near + ray_origin;"," if (dot(new_point2 - base, new_point2-base) < radius2)"," discard;"," interior = true;"," #endif"," }",""," gl_FragDepthEXT = calcDepth( new_point );",""," #ifdef NEAR_CLIP"," if( calcClip( new_point ) > 0.0 ){"," dist = (-a1 - sqrt(d)) / a2;"," new_point = ray_target + dist * ray_direction;"," if( calcClip( new_point ) > 0.0 )"," discard;"," interior = true;"," gl_FragDepthEXT = calcDepth( new_point );"," if( gl_FragDepthEXT >= 0.0 ){"," gl_FragDepthEXT = max( 0.0, calcDepth( vec3( - ( nearClip - 0.5 ) ) ) + ( 0.0000001 / vRadius ) );"," }"," }else if( gl_FragDepthEXT <= 0.0 ){"," dist = (-a1 - sqrt(d)) / a2;"," new_point = ray_target + dist * ray_direction;"," interior = true;"," gl_FragDepthEXT = calcDepth( new_point );"," if( gl_FragDepthEXT >= 0.0 ){"," gl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius );"," }"," }"," #else"," if( gl_FragDepthEXT <= 0.0 ){"," dist = (-a1 - sqrt(d)) / a2;"," new_point = ray_target + dist * ray_direction;"," interior = true;"," gl_FragDepthEXT = calcDepth( new_point );"," if( gl_FragDepthEXT >= 0.0 ){"," gl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius );"," }"," }"," #endif",""," // this is a workaround necessary for Mac"," // otherwise the modified fragment won't clip properly"," if (gl_FragDepthEXT < 0.0)"," discard;"," if (gl_FragDepthEXT > 1.0)"," discard;",""," #ifdef PICKING",""," gl_FragColor = vec4( vPickingColor, objectId );",""," #else",""," vec3 vViewPosition = -new_point;"," vec3 vNormal = _normal;"," vec3 vColor;",""," if( distSq3( new_point, end_cyl ) < distSq3( new_point, base ) ){"," if( b < 0.0 ){"," vColor = vColor1;"," }else{"," vColor = vColor2;"," }"," }else{"," if( b > 0.0 ){"," vColor = vColor1;"," }else{"," vColor = vColor2;"," }"," }",""," vec4 diffuseColor = vec4( diffuse, opacity );"," ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) );"," vec3 totalEmissiveLight = emissive;",""," #include color_fragment"," //ifdef USE_COLOR"," //diffuseColor.r *= vColor[0];"," //diffuseColor.g *= vColor[1];"," //diffuseColor.b *= vColor[2];"," //endif"," #include roughnessmap_fragment"," #include metalnessmap_fragment",""," // don't use include normal_fragment"," vec3 normal = normalize( vNormal );",""," #include lights_physical_fragment"," //include lights_template"," #include lights_fragment_begin"," #include lights_fragment_end",""," vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveLight;",""," gl_FragColor = vec4( outgoingLight, diffuseColor.a );"," //gl_FragColor = vec4( reflectedLight.directSpecular, diffuseColor.a );",""," #include premultiplied_alpha_fragment"," #include tonemapping_fragment"," #include encodings_fragment"," //include fog_fragment"," #ifdef USE_FOG"," #ifdef USE_LOGDEPTHBUF_EXT"," float depth = gl_FragDepthEXT / gl_FragCoord.w;"," #else"," float depth = gl_FragCoord.z / gl_FragCoord.w;"," #endif"," #ifdef FOG_EXP2"," float fogFactor = whiteCompliment( exp2( - fogDensity * fogDensity * depth * depth * LOG2 ) );"," #else"," float fogFactor = smoothstep( fogNear, fogFar, depth );"," #endif"," gl_FragColor.rgb = mix( gl_FragColor.rgb, fogColor, fogFactor );"," #endif",""," #endif","","}"].join("\n"),$NGL_shaderTextHash["CylinderImpostor.vert"]=["// Open-Source PyMOL is Copyright (C) Schrodinger, LLC.","//","// All Rights Reserved","//","// Permission to use, copy, modify, distribute, and distribute modified","// versions of this software and its built-in documentation for any","// purpose and without fee is hereby granted, provided that the above","// copyright notice appears in all copies and that both the copyright","// notice and this permission notice appear in supporting documentation,","// and that the name of Schrodinger, LLC not be used in advertising or","// publicity pertaining to distribution of the software without specific,","// written prior permission.","//","// SCHRODINGER, LLC DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,","// INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN","// NO EVENT SHALL SCHRODINGER, LLC BE LIABLE FOR ANY SPECIAL, INDIRECT OR","// CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS","// OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE","// OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE","// USE OR PERFORMANCE OF THIS SOFTWARE.","","// Contributions by Alexander Rose","// - ported to WebGL","// - dual color","// - pk color","// - shift","","attribute vec3 mapping;","attribute vec3 position1;","attribute vec3 position2;","attribute float radius;","","varying vec3 axis;","varying vec4 base_radius;","varying vec4 end_b;","varying vec3 U;","varying vec3 V;","varying vec4 w;","varying float fogDepth;","varying float fogNear;","varying float fogFar;","","#ifdef PICKING"," #include unpack_clr"," attribute float primitiveId;"," varying vec3 vPickingColor;","#else"," //attribute vec3 color;"," attribute vec3 color2;"," varying vec3 vColor1;"," varying vec3 vColor2;","#endif","","uniform mat4 modelViewMatrixInverse;","uniform float ortho;","","//include matrix_scale","float matrixScale( in mat4 m ){"," vec4 r = m[ 0 ];"," return sqrt( r[ 0 ] * r[ 0 ] + r[ 1 ] * r[ 1 ] + r[ 2 ] * r[ 2 ] );","}","","void main(){",""," #ifdef PICKING"," vPickingColor = unpackColor( primitiveId );"," #else"," vColor1 = color;"," vColor2 = color2;"," #endif",""," // vRadius = radius;"," base_radius.w = radius * matrixScale( modelViewMatrix );",""," //vec3 center = position;"," vec3 center = ( position2 + position1 ) / 2.0;"," vec3 dir = normalize( position2 - position1 );"," float ext = length( position2 - position1 ) / 2.0;",""," // using cameraPosition fails on some machines, not sure why"," // vec3 cam_dir = normalize( cameraPosition - mix( center, vec3( 0.0 ), ortho ) );"," vec3 cam_dir;"," if( ortho == 0.0 ){"," cam_dir = ( modelViewMatrixInverse * vec4( 0, 0, 0, 1 ) ).xyz - center;"," }else{"," cam_dir = ( modelViewMatrixInverse * vec4( 0, 0, 1, 0 ) ).xyz;"," }"," cam_dir = normalize( cam_dir );",""," vec3 ldir;",""," float b = dot( cam_dir, dir );"," end_b.w = b;"," // direction vector looks away, so flip"," if( b < 0.0 )"," ldir = -ext * dir;"," // direction vector already looks in my direction"," else"," ldir = ext * dir;",""," vec3 left = normalize( cross( cam_dir, ldir ) );"," left = radius * left;"," vec3 up = radius * normalize( cross( left, ldir ) );",""," // transform to modelview coordinates"," axis = normalize( normalMatrix * ldir );"," U = normalize( normalMatrix * up );"," V = normalize( normalMatrix * left );",""," vec4 base4 = modelViewMatrix * vec4( center - ldir, 1.0 );"," base_radius.xyz = base4.xyz / base4.w;",""," vec4 top_position = modelViewMatrix * vec4( center + ldir, 1.0 );"," vec4 end4 = top_position;"," end_b.xyz = end4.xyz / end4.w;",""," w = modelViewMatrix * vec4("," center + mapping.x*ldir + mapping.y*left + mapping.z*up, 1.0"," );",""," gl_Position = projectionMatrix * w;",""," // avoid clipping (1.0 seems to induce flickering with some drivers)"," gl_Position.z = 0.99;","","}"].join("\n"),$NGL_shaderTextHash["SphereInstancing.frag"]=$NGL_shaderTextHash["SphereImpostor.frag"],$NGL_shaderTextHash["SphereInstancing.vert"]=["uniform mat4 projectionMatrixInverse;","uniform float nearClip;","","varying float vRadius;","varying float vRadiusSq;","varying vec3 vPoint;","varying vec3 vPointViewPosition;","varying float fogDepth;","varying float fogNear;","varying float fogFar;","","attribute vec2 mapping;","//attribute vec3 position;","attribute float radius;","attribute vec4 matrix1;","attribute vec4 matrix2;","attribute vec4 matrix3;","attribute vec4 matrix4;","","#ifdef PICKING"," #include unpack_clr"," attribute float primitiveId;"," varying vec3 vPickingColor;","#else"," #include color_pars_vertex","#endif","","//include matrix_scale","float matrixScale( in mat4 m ){"," vec4 r = m[ 0 ];"," return sqrt( r[ 0 ] * r[ 0 ] + r[ 1 ] * r[ 1 ] + r[ 2 ] * r[ 2 ] );","}","","const mat4 D = mat4("," 1.0, 0.0, 0.0, 0.0,"," 0.0, 1.0, 0.0, 0.0,"," 0.0, 0.0, 1.0, 0.0,"," 0.0, 0.0, 0.0, -1.0",");","","mat4 transposeTmp( in mat4 inMatrix ) {"," vec4 i0 = inMatrix[0];"," vec4 i1 = inMatrix[1];"," vec4 i2 = inMatrix[2];"," vec4 i3 = inMatrix[3];",""," mat4 outMatrix = mat4("," vec4(i0.x, i1.x, i2.x, i3.x),"," vec4(i0.y, i1.y, i2.y, i3.y),"," vec4(i0.z, i1.z, i2.z, i3.z),"," vec4(i0.w, i1.w, i2.w, i3.w)"," );"," return outMatrix;","}","","//------------------------------------------------------------------------------","// Compute point size and center using the technique described in:","// 'GPU-Based Ray-Casting of Quadratic Surfaces'","// by Christian Sigg, Tim Weyrich, Mario Botsch, Markus Gross.","//","// Code based on","/*=========================================================================",""," Program: Visualization Toolkit"," Module: Quadrics_fs.glsl and Quadrics_vs.glsl",""," Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen"," All rights reserved."," See Copyright.txt or http://www.kitware.com/Copyright.htm for details.",""," This software is distributed WITHOUT ANY WARRANTY; without even"," the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR"," PURPOSE. See the above copyright notice for more information.",""," =========================================================================*/","","// .NAME Quadrics_fs.glsl and Quadrics_vs.glsl","// .SECTION Thanks","// ","//","// This file is part of the PointSprites plugin developed and contributed by","//","// Copyright (c) CSCS - Swiss National Supercomputing Centre","// EDF - Electricite de France","//","// John Biddiscombe, Ugo Varetto (CSCS)","// Stephane Ploix (EDF)","//","// ","//","// Contributions by Alexander Rose","// - ported to WebGL","// - adapted to work with quads","void ComputePointSizeAndPositionInClipCoordSphere(vec4 updatePosition){",""," vec2 xbc;"," vec2 ybc;",""," mat4 T = mat4("," radius, 0.0, 0.0, 0.0,"," 0.0, radius, 0.0, 0.0,"," 0.0, 0.0, radius, 0.0,"," updatePosition.x, updatePosition.y, updatePosition.z, 1.0"," );",""," mat4 R = transposeTmp( projectionMatrix * modelViewMatrix * T );"," float A = dot( R[ 3 ], D * R[ 3 ] );"," float B = -2.0 * dot( R[ 0 ], D * R[ 3 ] );"," float C = dot( R[ 0 ], D * R[ 0 ] );"," xbc[ 0 ] = ( -B - sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );"," xbc[ 1 ] = ( -B + sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );"," float sx = abs( xbc[ 0 ] - xbc[ 1 ] ) * 0.5;",""," A = dot( R[ 3 ], D * R[ 3 ] );"," B = -2.0 * dot( R[ 1 ], D * R[ 3 ] );"," C = dot( R[ 1 ], D * R[ 1 ] );"," ybc[ 0 ] = ( -B - sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );"," ybc[ 1 ] = ( -B + sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );"," float sy = abs( ybc[ 0 ] - ybc[ 1 ] ) * 0.5;",""," gl_Position.xy = vec2( 0.5 * ( xbc.x + xbc.y ), 0.5 * ( ybc.x + ybc.y ) );"," gl_Position.xy -= mapping * vec2( sx, sy );"," gl_Position.xy *= gl_Position.w;","","}",""," mat4 computeMat(vec4 v1, vec4 v2, vec4 v3, vec4 v4) {"," return mat4("," v1.x, v1.y, v1.z, v1.w,"," v2.x, v2.y, v2.z, v2.w,"," v3.x, v3.y, v3.z, v3.w,"," v4.x, v4.y, v4.z, v4.w"," );"," }","","void main(void){",""," #ifdef PICKING"," vPickingColor = unpackColor( primitiveId );"," #else"," #include color_vertex"," #endif",""," vRadius = radius * matrixScale( modelViewMatrix );",""," mat4 matrix = computeMat(matrix1, matrix2, matrix3, matrix4);"," vec4 updatePosition = matrix * vec4(position, 1.0);","","// vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );"," vec4 mvPosition = modelViewMatrix * vec4( updatePosition.xyz, 1.0 );"," // avoid clipping, added again in fragment shader"," mvPosition.z -= vRadius;","","// gl_Position = projectionMatrix * vec4( mvPosition.xyz, 1.0 );"," gl_Position = projectionMatrix * vec4( mvPosition.xyz, 1.0 );"," ComputePointSizeAndPositionInClipCoordSphere(updatePosition);","",""," vRadiusSq = vRadius * vRadius;"," vec4 vPoint4 = projectionMatrixInverse * gl_Position;"," vPoint = vPoint4.xyz / vPoint4.w;"," vPointViewPosition = -mvPosition.xyz / mvPosition.w;","","}"].join("\n"),$NGL_shaderTextHash["CylinderInstancing.frag"]=$NGL_shaderTextHash["CylinderImpostor.frag"],$NGL_shaderTextHash["CylinderInstancing.vert"]=["// Open-Source PyMOL is Copyright (C) Schrodinger, LLC.","//","// All Rights Reserved","//","// Permission to use, copy, modify, distribute, and distribute modified","// versions of this software and its built-in documentation for any","// purpose and without fee is hereby granted, provided that the above","// copyright notice appears in all copies and that both the copyright","// notice and this permission notice appear in supporting documentation,","// and that the name of Schrodinger, LLC not be used in advertising or","// publicity pertaining to distribution of the software without specific,","// written prior permission.","//","// SCHRODINGER, LLC DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,","// INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN","// NO EVENT SHALL SCHRODINGER, LLC BE LIABLE FOR ANY SPECIAL, INDIRECT OR","// CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS","// OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE","// OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE","// USE OR PERFORMANCE OF THIS SOFTWARE.","","// Contributions by Alexander Rose","// - ported to WebGL","// - dual color","// - pk color","// - shift","","attribute vec3 mapping;","attribute vec3 position1;","attribute vec3 position2;","attribute float radius;","attribute vec4 matrix1;","attribute vec4 matrix2;","attribute vec4 matrix3;","attribute vec4 matrix4;","","varying vec3 axis;","varying vec4 base_radius;","varying vec4 end_b;","varying vec3 U;","varying vec3 V;","varying vec4 w;","varying float fogDepth;","varying float fogNear;","varying float fogFar;","","#ifdef PICKING"," #include unpack_clr"," attribute float primitiveId;"," varying vec3 vPickingColor;","#else"," //attribute vec3 color;"," attribute vec3 color2;"," varying vec3 vColor1;"," varying vec3 vColor2;","#endif","","uniform mat4 modelViewMatrixInverse;","uniform float ortho;","","//include matrix_scale","float matrixScale( in mat4 m ){"," vec4 r = m[ 0 ];"," return sqrt( r[ 0 ] * r[ 0 ] + r[ 1 ] * r[ 1 ] + r[ 2 ] * r[ 2 ] );","}",""," mat4 computeMat(vec4 v1, vec4 v2, vec4 v3, vec4 v4) {"," return mat4("," v1.x, v1.y, v1.z, v1.w,"," v2.x, v2.y, v2.z, v2.w,"," v3.x, v3.y, v3.z, v3.w,"," v4.x, v4.y, v4.z, v4.w"," );"," }","","void main(){",""," #ifdef PICKING"," vPickingColor = unpackColor( primitiveId );"," #else"," vColor1 = color;"," vColor2 = color2;"," #endif",""," // vRadius = radius;"," base_radius.w = radius * matrixScale( modelViewMatrix );",""," //vec3 center = ( position2 + position1 ) / 2.0;",""," mat4 matrix = computeMat(matrix1, matrix2, matrix3, matrix4);"," vec4 updatePosition1 = matrix * vec4(position1, 1.0);"," vec4 updatePosition2 = matrix * vec4(position2, 1.0);"," vec3 center = ( updatePosition2.xyz + updatePosition1.xyz ) / 2.0;",""," //vec3 dir = normalize( position2 - position1 );"," vec3 dir = normalize( updatePosition2.xyz - updatePosition1.xyz );"," float ext = length( position2 - position1 ) / 2.0;",""," // using cameraPosition fails on some machines, not sure why"," // vec3 cam_dir = normalize( cameraPosition - mix( center, vec3( 0.0 ), ortho ) );"," vec3 cam_dir;"," if( ortho == 0.0 ){"," cam_dir = ( modelViewMatrixInverse * vec4( 0, 0, 0, 1 ) ).xyz - center;"," }else{"," cam_dir = ( modelViewMatrixInverse * vec4( 0, 0, 1, 0 ) ).xyz;"," }"," cam_dir = normalize( cam_dir );",""," vec3 ldir;",""," float b = dot( cam_dir, dir );"," end_b.w = b;"," // direction vector looks away, so flip"," if( b < 0.0 )"," ldir = -ext * dir;"," // direction vector already looks in my direction"," else"," ldir = ext * dir;",""," vec3 left = normalize( cross( cam_dir, ldir ) );"," left = radius * left;"," vec3 up = radius * normalize( cross( left, ldir ) );",""," // transform to modelview coordinates"," axis = normalize( normalMatrix * ldir );"," U = normalize( normalMatrix * up );"," V = normalize( normalMatrix * left );",""," vec4 base4 = modelViewMatrix * vec4( center - ldir, 1.0 );"," base_radius.xyz = base4.xyz / base4.w;",""," vec4 top_position = modelViewMatrix * vec4( center + ldir, 1.0 );"," vec4 end4 = top_position;"," end_b.xyz = end4.xyz / end4.w;",""," w = modelViewMatrix * vec4("," center + mapping.x*ldir + mapping.y*left + mapping.z*up, 1.0"," );",""," gl_Position = projectionMatrix * w;",""," // avoid clipping (1.0 seems to induce flickering with some drivers)"," gl_Position.z = 0.99;","","}"].join("\n"),$NGL_shaderTextHash["Instancing.frag"]=["#define STANDARD","uniform vec3 diffuse;","uniform vec3 emissive;","uniform float roughness;","uniform float metalness;","uniform float opacity;","uniform float nearClip;","uniform float clipRadius;","uniform mat4 projectionMatrix;","uniform float ortho;","varying float bCylinder;","","#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || ( !defined( PICKING ) && !defined( NOLIGHT ) )"," varying vec3 vViewPosition;","#endif","","#if defined( RADIUS_CLIP )"," varying vec3 vClipCenter;","#endif","","#if defined( PICKING )"," uniform float objectId;"," varying vec3 vPickingColor;","#elif defined( NOLIGHT )"," varying vec3 vColor;","#else"," #ifndef FLAT_SHADED"," varying vec3 vNormal;"," #endif"," #include common"," #include color_pars_fragment"," #include fog_pars_fragment"," #include bsdfs"," #include lights_pars_begin"," #include lights_physical_pars_fragment","#endif","","void main(){"," #include nearclip_fragment"," #include radiusclip_fragment",""," #if defined( PICKING )",""," gl_FragColor = vec4( vPickingColor, objectId );",""," #elif defined( NOLIGHT )",""," gl_FragColor = vec4( vColor, opacity );",""," #else",""," vec4 diffuseColor = vec4( diffuse, opacity );"," ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) );"," vec3 totalEmissiveLight = emissive;",""," #include color_fragment"," #include roughnessmap_fragment"," #include metalnessmap_fragment"," #include normal_flip"," #include normal_fragment_begin",""," //include dull_interior_fragment",""," #include lights_physical_fragment"," //include lights_template"," #include lights_fragment_begin"," #include lights_fragment_end",""," vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveLight;",""," #include interior_fragment",""," gl_FragColor = vec4( outgoingLight, diffuseColor.a );",""," #include premultiplied_alpha_fragment"," #include tonemapping_fragment"," #include encodings_fragment"," #include fog_fragment",""," #include opaque_back_fragment",""," #endif","","}"].join("\n"),$NGL_shaderTextHash["Instancing.vert"]=["#define STANDARD","","uniform mat4 projectionMatrixInverse;","uniform float nearClip;","uniform vec3 clipCenter;","attribute vec4 matrix1;","attribute vec4 matrix2;","attribute vec4 matrix3;","attribute vec4 matrix4;","attribute float cylinder;","varying float bCylinder;","","#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || ( !defined( PICKING ) && !defined( NOLIGHT ) )"," varying vec3 vViewPosition;","#endif","","#if defined( RADIUS_CLIP )"," varying vec3 vClipCenter;","#endif","","#if defined( PICKING )"," #include unpack_color"," attribute float primitiveId;"," varying vec3 vPickingColor;","#elif defined( NOLIGHT )"," varying vec3 vColor;","#else"," #include color_pars_vertex"," #ifndef FLAT_SHADED"," varying vec3 vNormal;"," #endif","#endif","","#include common",""," mat4 computeMat(vec4 v1, vec4 v2, vec4 v3, vec4 v4) {"," return mat4("," v1.x, v1.y, v1.z, v1.w,"," v2.x, v2.y, v2.z, v2.w,"," v3.x, v3.y, v3.z, v3.w,"," v4.x, v4.y, v4.z, v4.w"," );"," }","","void main(){"," bCylinder = cylinder;",""," mat4 matrix = computeMat(matrix1, matrix2, matrix3, matrix4);"," vec4 updatePosition = matrix * vec4(position, 1.0);",""," #if defined( PICKING )"," vPickingColor = unpackColor( primitiveId );"," #elif defined( NOLIGHT )"," vColor = color;"," #else"," #include color_vertex"," //include beginnormal_vertex"," //vec3 objectNormal = vec3( normal );"," vec3 objectNormal = vec3(matrix * vec4(normal,0.0));"," #include defaultnormal_vertex"," // Normal computed with derivatives when FLAT_SHADED"," #ifndef FLAT_SHADED"," vNormal = normalize( transformedNormal );"," #endif"," #endif",""," //include begin_vertex"," vec3 transformed = updatePosition.xyz;"," //include project_vertex"," vec4 mvPosition = modelViewMatrix * vec4( transformed, 1.0 );"," gl_Position = projectionMatrix * mvPosition;",""," #if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || ( !defined( PICKING ) && !defined( NOLIGHT ) )"," vViewPosition = -mvPosition.xyz;"," #endif",""," #if defined( RADIUS_CLIP )"," vClipCenter = -( modelViewMatrix * vec4( clipCenter, 1.0 ) ).xyz;"," #endif",""," #include nearclip_vertex","","}"].join("\n"),THREE.RenderableObject=function(){"use strict";this.id=0,this.object=null,this.z=0},THREE.RenderableFace=function(){"use strict";this.id=0,this.v1=new THREE.RenderableVertex,this.v2=new THREE.RenderableVertex,this.v3=new THREE.RenderableVertex,this.normalModel=new THREE.Vector3,this.vertexNormalsModel=[new THREE.Vector3,new THREE.Vector3,new THREE.Vector3],this.vertexNormalsLength=0,this.color=new THREE.Color,this.material=null,this.uvs=[new THREE.Vector2,new THREE.Vector2,new THREE.Vector2],this.z=0},THREE.RenderableVertex=function(){"use strict";this.position=new THREE.Vector3,this.positionWorld=new THREE.Vector3,this.positionScreen=new THREE.Vector4,this.visible=!0},THREE.RenderableVertex.prototype.copy=function(e){"use strict";this.positionWorld.copy(e.positionWorld),this.positionScreen.copy(e.positionScreen)},THREE.RenderableLine=function(){"use strict";this.id=0,this.v1=new THREE.RenderableVertex,this.v2=new THREE.RenderableVertex,this.vertexColors=[new THREE.Color,new THREE.Color],this.material=null,this.z=0},THREE.RenderableSprite=function(){"use strict";this.id=0,this.object=null,this.x=0,this.y=0,this.z=0,this.rotation=0,this.scale=new THREE.Vector2,this.material=null},THREE.Projector=function(){"use strict";var e,t,n,r,i,o,a,s,c,u,d,l=[],f=0,p=[],h=0,g=[],v=0,m=[],y=0,E=[],w=0,b={objects:[],lights:[],elements:[]},_=(new THREE.Vector3,new THREE.Vector3,new THREE.Vector3,new THREE.Vector3),T=new THREE.Vector4,S=new THREE.Box3(new THREE.Vector3(-1,-1,-1),new THREE.Vector3(1,1,1)),C=new THREE.Box3,x=new Array(3),R=(new Array(4),new THREE.Matrix4),A=new THREE.Matrix4,k=(new THREE.Matrix4,new THREE.Matrix3,new THREE.Frustum);new THREE.Vector4,new THREE.Vector4;this.projectVector=function(e,t){console.warn("THREE.Projector: .projectVector() is now vector.project()."),e.project(t)},this.unprojectVector=function(e,t){console.warn("THREE.Projector: .unprojectVector() is now vector.unproject()."),e.unproject(t)},this.pkRay=function(e,t){console.error("THREE.Projector: .pkRay() is now raycaster.setFromCamera().")};var I=new function(){var e=[],t=[],c=null,u=null,l=new THREE.Matrix3,f=function(e){var t=e.position,n=e.positionWorld,r=e.positionScreen;n.copy(t).applyMatrix4(d),r.copy(n).applyMatrix4(A);var i=1/r.w;r.x*=i,r.y*=i,r.z*=i,e.visible=r.x>=-1&&r.x<=1&&r.y>=-1&&r.y<=1&&r.z>=-1&&r.z<=1},E=function(e,t,n){return!0===e.visible||!0===t.visible||!0===n.visible||(x[0]=e.positionScreen,x[1]=t.positionScreen,x[2]=n.positionScreen,S.isIntersectionBox(C.setFromPoints(x)))},w=function(e,t,n){return(n.positionScreen.x-e.positionScreen.x)*(t.positionScreen.y-e.positionScreen.y)-(n.positionScreen.y-e.positionScreen.y)*(t.positionScreen.x-e.positionScreen.x)<0};return{setObject:function(n){u=(c=n).material,l.getNormalMatrix(c.matrixWorld),e.length=0,t.length=0},projectVertex:f,checkTriangleVisibility:E,checkBackfaceCulling:w,pushVertex:function(e,t,i){(n=function(){if(r===h){var e=new THREE.RenderableVertex;return p.push(e),h++,r++,e}return p[r++]}()).position.set(e,t,i),f(n)},pushNormal:function(t,n,r){e.push(t,n,r)},pushUv:function(e,n){t.push(e,n)},pushLine:function(e,t){var n=p[e],r=p[t];(a=function(){if(s===y){var e=new THREE.RenderableLine;return m.push(e),y++,s++,e}return m[s++]}()).id=c.id,a.v1.copy(n),a.v2.copy(r),a.z=(n.positionScreen.z+r.positionScreen.z)/2,a.material=c.material,b.elements.push(a)},pushTriangle:function(n,r,a){var s=p[n],d=p[r],f=p[a];if(!1!==E(s,d,f)&&(u.side===THREE.DoubleSide||!0===w(s,d,f))){(i=function(){if(o===v){var e=new THREE.RenderableFace;return g.push(e),v++,o++,e}return g[o++]}()).id=c.id,i.v1.copy(s),i.v2.copy(d),i.v3.copy(f),i.z=(s.positionScreen.z+d.positionScreen.z+f.positionScreen.z)/3;for(var h=0;h<3;h++){var m=3*arguments[h],y=i.vertexNormalsModel[h];y.set(e[m],e[m+1],e[m+2]),y.applyMatrix3(l).normalize();var _=2*arguments[h];i.uvs[h].set(t[_],t[_+1])}i.vertexNormalsLength=3,i.material=c.material,b.elements.push(i)}}}};function P(){if(u===w){var e=new THREE.RenderableSprite;return E.push(e),w++,u++,e}return E[u++]}function N(e,t){return e.z!==t.z?t.z-e.z:e.id!==t.id?e.id-t.id:0}this.projectScene=function(n,i,a,p){o=0,s=0,u=0,b.elements.length=0,!0===n.autoUpdate&&n.updateMatrixWorld(),void 0===i.parent&&i.updateMatrixWorld(),R.copy(i.matrixWorldInverse.copy(i.matrixWorld).invert()),A.multiplyMatrices(i.projectionMatrix,R),k.setFromMatrix(A),t=0,b.objects.length=0,b.lights.length=0,n.traverseVisible(function(n){if(n instanceof THREE.Light)b.lights.push(n);else if(n instanceof THREE.Mesh||n instanceof THREE.Line||n instanceof THREE.Sprite){if(!1===n.material.visible)return;!1!==n.frustumCulled&&!0!==k.intersectsObject(n)||((e=function(){if(t===f){var e=new THREE.RenderableObject;return l.push(e),f++,t++,e}return l[t++]}()).id=n.id,e.object=n,_.setFromMatrixPosition(n.matrixWorld),_.applyProjection(A),e.z=_.z,b.objects.push(e))}}),!0===a&&b.objects.sort(N);for(var h=0,g=b.objects.length;h0)for(h=0;h=-1&&T.z<=1&&((c=P()).id=v.id,c.x=T.x*H,c.y=T.y*H,c.z=T.z,c.object=v,c.rotation=v.rotation,c.scale.x=v.scale.x*Math.abs(c.x-(T.x+i.projectionMatrix.elements[0])/(T.w+i.projectionMatrix.elements[12])),c.scale.y=v.scale.y*Math.abs(c.y-(T.y+i.projectionMatrix.elements[5])/(T.w+i.projectionMatrix.elements[13])),c.material=v.material,b.elements.push(c))}}return!0===p&&b.elements.sort(N),b}},THREE.TrackballControls=function(e,t,n){"use strict";var r=this;this.STATE={NONE:-1,ROTATE:0,ZOOM:1,PAN:2,TOUCH_ROTATE:3,TOUCH_ZOOM_PAN:4},this.object=e,this.domElement=void 0!==t?t:document,this.enabled=!0,this.screen={left:0,top:0,width:0,height:0},this.rotateSpeed=1,this.zoomSpeed=1.2,this.panSpeed=.3,this.noRotate=!1,this.noZoom=!1,this.noPan=!1,this.noRoll=!1,this.staticMoving=!1,this.dynamicDampingFactor=.2,this.minDistance=0,this.maxDistance=1/0,this.keys=[65,83,68],this.target=new THREE.Vector3;var i=new THREE.Vector3;this._state=this.STATE.NONE;var o=this.STATE.NONE,a=new THREE.Vector3;this._rotateStart=new THREE.Vector3,this._rotateEnd=new THREE.Vector3,this._zoomStart=new THREE.Vector2,this._zoomEnd=new THREE.Vector2;var s=0,c=0;this._panStart=new THREE.Vector2,this._panEnd=new THREE.Vector2,this.target0=this.target.clone(),this.position0=this.object.position.clone(),this.up0=this.object.up.clone();var u={type:"change"},d={type:"start"},l={type:"end"};this.handleResize=function(){if(this.domElement===document)this.screen.left=0,this.screen.top=0,this.screen.width=window.innerWidth,this.screen.height=window.innerHeight;else if(this.domElement){var e=this.domElement.getBoundingClientRect(),t=this.domElement.ownerDocument.documentElement;this.screen.left=e.left+window.pageXOffset-t.clientLeft,this.screen.top=e.top+window.pageYOffset-t.clientTop,this.screen.width=e.width,this.screen.height=e.height}},this.handleEvent=function(e){"function"==typeof this[e.type]&&this[e.type](e)};var f,p,h,g,v,m,y,E,w,b=(f=new THREE.Vector2,function(e,t){return f.set((e-r.screen.left)/r.screen.width,(t-r.screen.top)/r.screen.height),f}),_=(p=new THREE.Vector3,h=new THREE.Vector3,g=new THREE.Vector3,function(e,t){g.set((e-.5*r.screen.width-r.screen.left)/(.5*r.screen.width),(.5*r.screen.height+r.screen.top-t)/(.5*r.screen.height),0);var n=g.length();return r.noRoll?n1?g.normalize():g.z=Math.sqrt(1-n*n),a.copy(r.object.position).sub(r.target),p.copy(r.object.up).setLength(g.y),p.add(h.copy(r.object.up).cross(a).setLength(g.x)),p.add(a.setLength(g.z)),p});function T(e){!1===r.enabled||Object.keys(window).length<2||(window.removeEventListener("keydown",T),o=r._state,r._state===r.STATE.NONE&&(e.keyCode!==r.keys[r.STATE.ROTATE]||r.noRotate?e.keyCode!==r.keys[r.STATE.ZOOM]||r.noZoom?e.keyCode!==r.keys[r.STATE.PAN]||r.noPan||(r._state=r.STATE.PAN):r._state=r.STATE.ZOOM:r._state=r.STATE.ROTATE))}function S(e){!1===r.enabled||Object.keys(window).length<2||(e.stopPropagation(),r._state!==r.STATE.ROTATE||r.noRotate?r._state!==r.STATE.ZOOM||r.noZoom?r._state!==r.STATE.PAN||r.noPan||r._panEnd.copy(b(e.pageX,e.pageY)):r._zoomEnd.copy(b(e.pageX,e.pageY)):r._rotateEnd.copy(_(e.pageX,e.pageY)))}function C(e){!1===r.enabled||Object.keys(window).length<2||(e.stopPropagation(),r._state=r.STATE.NONE,document.removeEventListener("mousemove",S),document.removeEventListener("mouseup",C),r.dispatchEvent(l))}function x(e){if(!(!1===r.enabled||Object.keys(window).length<2)){e.stopPropagation();var t=0;e.wheelDelta?t=e.wheelDelta/40:e.detail&&(t=-e.detail/3),r._zoomStart.y=.005*t,r.dispatchEvent(d),r.dispatchEvent(l)}}this.rotateCamera=(v=new THREE.Vector3,m=new THREE.Quaternion,function(e,t){var i;void 0===e&&(i=Math.acos(r._rotateStart.dot(r._rotateEnd)/r._rotateStart.length()/r._rotateEnd.length())),(i||void 0!==e)&&(void 0===e?(v.crossVectors(r._rotateStart,r._rotateEnd).normalize(),i*=r.rotateSpeed,m.setFromAxisAngle(v,-i)):m.copy(e),void 0===n||void 0===n.quaternion||void 0!==t&&!0!==t||n.quaternion.multiplyQuaternions(m,n.quaternion),a.applyQuaternion(m),r.object.up.applyQuaternion(m),r._rotateEnd.applyQuaternion(m),r.staticMoving?r._rotateStart.copy(r._rotateEnd):(m.setFromAxisAngle(v,i*(r.dynamicDampingFactor-1)),r._rotateStart.applyQuaternion(m)))}),this.zoomCamera=function(e,t){var i;r._state===r.STATE.TOUCH_ZOOM_PAN?(void 0!==e?i=e:(i=s/c,s=c),a.multiplyScalar(i),void 0===n||void 0===n._zoomFactor||void 0!==t&&!0!==t||(n._zoomFactor*=i,n.fogCls.setFog())):(i=void 0!==e?e:1+(r._zoomEnd.y-r._zoomStart.y)*r.zoomSpeed,void 0===n||void 0===n._zoomFactor||void 0!==t&&!0!==t||(n._zoomFactor*=i,n.fogCls.setFog()),1!==i&&(a.multiplyScalar(i),r.staticMoving?r._zoomStart.copy(r._zoomEnd):r._zoomStart.y+=(r._zoomEnd.y-r._zoomStart.y)*this.dynamicDampingFactor))},this.panCamera=(y=new THREE.Vector2,E=new THREE.Vector3,w=new THREE.Vector3,function(e,t){void 0!==e?(y=e,void 0===n||void 0===n.mouseChange||void 0!==t&&!0!==t||n.mouseChange.add(e)):(y.copy(r._panEnd).sub(r._panStart),void 0===n||void 0===n.mouseChange||void 0!==t&&!0!==t||n.mouseChange.add(r._panEnd).sub(r._panStart)),y.lengthSq()&&(y.multiplyScalar(a.length()*r.panSpeed),w.copy(a).cross(r.object.up).setLength(y.x),w.add(E.copy(r.object.up).setLength(y.y)),r.object.position.add(w),r.target.add(w),r.staticMoving?r._panStart.copy(r._panEnd):r._panStart.add(y.subVectors(r._panEnd,r._panStart).multiplyScalar(r.dynamicDampingFactor)))}),this.checkDistances=function(){r.noZoom&&r.noPan||(a.lengthSq()>r.maxDistance*r.maxDistance&&r.object.position.addVectors(r.target,a.setLength(r.maxDistance)),a.lengthSq()1e-6&&(r.dispatchEvent(u),i.copy(r.object.position))},this.reset=function(){r._state=r.STATE.NONE,o=r.STATE.NONE,r.target.copy(r.target0),r.object.position.copy(r.position0),r.object.up.copy(r.up0),a.subVectors(r.object.position,r.target),r.object.lookAt(r.target),r.dispatchEvent(u),i.copy(r.object.position)},Object.keys(window).length>=2&&this.domElement&&(this.domElement.addEventListener("contextmn",function(e){},!1),this.domElement.addEventListener("mousedown",function(e){!1===r.enabled||Object.keys(window).length<2||(e.stopPropagation(),r._state===r.STATE.NONE&&(r._state=e.button),r._state!==r.STATE.ROTATE||r.noRotate?r._state!==r.STATE.ZOOM||r.noZoom?r._state!==r.STATE.PAN||r.noPan||(r._panStart.copy(b(e.pageX,e.pageY)),r._panEnd.copy(r._panStart)):(r._zoomStart.copy(b(e.pageX,e.pageY)),r._zoomEnd.copy(r._zoomStart)):(r._rotateStart.copy(_(e.pageX,e.pageY)),r._rotateEnd.copy(r._rotateStart)),document.addEventListener("mousemove",S,!1),document.addEventListener("mouseup",C,!1),r.dispatchEvent(d))},!1),this.domElement.addEventListener("mousewheel",x,!1),this.domElement.addEventListener("DOMMouseScroll",x,!1),this.domElement.addEventListener("touchstart",function(e){if(!(!1===r.enabled||Object.keys(window).length<2)){switch(e.touches.length){case 1:r._state=r.STATE.TOUCH_ROTATE,r._rotateStart.copy(_(e.touches[0].pageX,e.touches[0].pageY)),r._rotateEnd.copy(r._rotateStart);break;case 2:r._state=r.STATE.TOUCH_ZOOM_PAN;var t=e.touches[0].pageX-e.touches[1].pageX,n=e.touches[0].pageY-e.touches[1].pageY;c=s=Math.sqrt(t*t+n*n);var i=(e.touches[0].pageX+e.touches[1].pageX)/2,o=(e.touches[0].pageY+e.touches[1].pageY)/2;r._panStart.copy(b(i,o)),r._panEnd.copy(r._panStart);break;default:r._state=r.STATE.NONE}r.dispatchEvent(d)}},!1),this.domElement.addEventListener("touchend",function(e){if(!(!1===r.enabled||Object.keys(window).length<2)){switch(e.touches.length){case 1:r._rotateEnd.copy(_(e.touches[0].pageX,e.touches[0].pageY)),r._rotateStart.copy(r._rotateEnd);break;case 2:s=c=0;var t=(e.touches[0].pageX+e.touches[1].pageX)/2,n=(e.touches[0].pageY+e.touches[1].pageY)/2;r._panEnd.copy(b(t,n)),r._panStart.copy(r._panEnd)}r._state=r.STATE.NONE,r.dispatchEvent(l)}},!1),this.domElement.addEventListener("touchmove",function(e){if(!(!1===r.enabled||Object.keys(window).length<2))switch(e.stopPropagation(),e.touches.length){case 1:r._rotateEnd.copy(_(e.touches[0].pageX,e.touches[0].pageY));break;case 2:var t=e.touches[0].pageX-e.touches[1].pageX,n=e.touches[0].pageY-e.touches[1].pageY;c=Math.sqrt(t*t+n*n);var i=(e.touches[0].pageX+e.touches[1].pageX)/2,o=(e.touches[0].pageY+e.touches[1].pageY)/2;r._panEnd.copy(b(i,o));break;default:r._state=r.STATE.NONE}},!1),Object.keys(window).length>=2&&window.addEventListener("keydown",T,!1),Object.keys(window).length>=2&&window.addEventListener("keyup",function(e){!1===r.enabled||Object.keys(window).length<2||(r._state=o,window.addEventListener("keydown",T,!1))},!1)),this.handleResize(),this.update()},THREE.TrackballControls.prototype=Object.create(THREE.EventDispatcher.prototype),THREE.TrackballControls.prototype.constructor=THREE.TrackballControls,THREE.OrthographicTrackballControls=function(e,t,n){this.icn3d;var r=this,i={NONE:-1,ROTATE:0,ZOOM:1,PAN:2,TOUCH_ROTATE:3,TOUCH_ZOOM_PAN:4};this.object=e,this.domElement=void 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l={type:"change"},f={type:"start"},p={type:"end"};this.handleResize=function(){if(this.domElement===document)this.screen.left=0,this.screen.top=0,this.screen.width=window.innerWidth,this.screen.height=window.innerHeight;else if(this.domElement){var e=this.domElement.getBoundingClientRect(),t=this.domElement.ownerDocument.documentElement;this.screen.left=e.left+window.pageXOffset-t.clientLeft,this.screen.top=e.top+window.pageYOffset-t.clientTop,this.screen.width=e.width,this.screen.height=e.height}this.left0=this.object.left,this.right0=this.object.right,this.top0=this.object.top,this.bottom0=this.object.bottom,this.center0.set((this.left0+this.right0)/2,(this.top0+this.bottom0)/2)},this.handleEvent=function(e){"function"==typeof this[e.type]&&this[e.type](e)};var h,g,v,m,y,E,w,b,_,T=(h=new THREE.Vector2,function(e,t){return h.set((e-r.screen.left)/r.screen.width,(t-r.screen.top)/r.screen.height),h}),S=(g=new THREE.Vector3,v=new THREE.Vector3,m=new 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0!==t&&!0!==t||n.mouseChange.add(e)):(w.copy(r._panEnd).sub(r._panStart),void 0===n||void 0===n.mouseChange||void 0!==t&&!0!==t||n.mouseChange.add(r._panEnd).sub(r._panStart)),w.lengthSq()&&(w.multiplyScalar(s.length()*r.panSpeed),_.copy(s).cross(r.object.up).setLength(w.x),_.add(b.copy(r.object.up).setLength(w.y)),r.object.position.add(_),r.target.add(_),r.staticMoving?r._panStart.copy(r._panEnd):r._panStart.add(w.subVectors(r._panEnd,r._panStart).multiplyScalar(r.dynamicDampingFactor)))}),this.update=function(e){s.subVectors(r.object.position,r.target),r.noRotate||(void 0!==e&&void 0!==e.quaternion?r.rotateCamera(e.quaternion,e.update):r.rotateCamera()),r.noZoom||(void 0!==e&&void 0!==e._zoomFactor?r.zoomCamera(e._zoomFactor,e.update):r.zoomCamera(),r.object.updateProjectionMatrix()),r.noPan||(void 0!==e&&void 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1:r._state=i.TOUCH_ROTATE,r._rotateStart.copy(S(e.touches[0].pageX,e.touches[0].pageY)),r._rotateEnd.copy(r._rotateStart);break;case 2:r._state=i.TOUCH_ZOOM_PAN;var t=e.touches[0].pageX-e.touches[1].pageX,n=e.touches[0].pageY-e.touches[1].pageY;d=u=Math.sqrt(t*t+n*n);var o=(e.touches[0].pageX+e.touches[1].pageX)/2,a=(e.touches[0].pageY+e.touches[1].pageY)/2;r._panStart.copy(T(o,a)),r._panEnd.copy(r._panStart);break;default:r._state=i.NONE}r.dispatchEvent(f)}},!1),this.domElement.addEventListener("touchend",function(e){if(!(!1===r.enabled||Object.keys(window).length<2)){switch(e.touches.length){case 1:r._rotateEnd.copy(S(e.touches[0].pageX,e.touches[0].pageY)),r._rotateStart.copy(r._rotateEnd);break;case 2:u=d=0;var t=(e.touches[0].pageX+e.touches[1].pageX)/2,n=(e.touches[0].pageY+e.touches[1].pageY)/2;r._panEnd.copy(T(t,n)),r._panStart.copy(r._panEnd)}r._state=i.NONE,r.dispatchEvent(p)}},!1),this.domElement.addEventListener("touchmove",function(e){if(!(!1===r.enabled||Object.keys(window).length<2))switch(e.stopPropagation(),e.touches.length){case 1:r._rotateEnd.copy(S(e.touches[0].pageX,e.touches[0].pageY));break;case 2:var t=e.touches[0].pageX-e.touches[1].pageX,n=e.touches[0].pageY-e.touches[1].pageY;d=Math.sqrt(t*t+n*n);var o=(e.touches[0].pageX+e.touches[1].pageX)/2,a=(e.touches[0].pageY+e.touches[1].pageY)/2;r._panEnd.copy(T(o,a));break;default:r._state=i.NONE}},!1),window.addEventListener("keydown",C,!1),window.addEventListener("keyup",function(e){!1===r.enabled||Object.keys(window).length<2||(r._state=a,window.addEventListener("keydown",C,!1))},!1)),this.handleResize(),this.update()},THREE.OrthographicTrackballControls.prototype=Object.create(THREE.EventDispatcher.prototype),THREE.OrthographicTrackballControls.prototype.constructor=THREE.OrthographicTrackballControls,function(e){var t,n,r,i;e.VERSION={number:"1.1.7",date:"Oct 30 2018"},function(e){function t(e,t,n){(t|=0)<=0&&(t=1);var r=t*n,i=e(r);return{elementSize:n,chunkSize:r,creator:e,current:i,parts:[i],currentIndex:0,elementCount:0}}e.is=function(e){return e.creator&&e.chunkSize},e.add4=function(e,t,n,r,i){return 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i{constructor(e){this.icn3dui=e,this.glycanHash={GLC:{c:"1E90FF",s:"sphere"},BGC:{c:"1E90FF",s:"sphere"},NAG:{c:"1E90FF",s:"cube"},NDG:{c:"1E90FF",s:"cube"},GCS:{c:"1E90FF",s:"cube"},PA1:{c:"1E90FF",s:"cube"},GCU:{c:"1E90FF",s:"cone"},BDP:{c:"1E90FF",s:"cone"},G6D:{c:"1E90FF",s:"cone"},DDA:{c:"1E90FF",s:"cylinder"},B6D:{c:"1E90FF",s:"cylinder"},XXM:{c:"1E90FF",s:"cylinder"},MAN:{c:"00FF00",s:"sphere"},BMA:{c:"00FF00",s:"sphere"},BM3:{c:"00FF00",s:"cube"},"95Z":{c:"00FF00",s:"cube"},MAV:{c:"00FF00",s:"cone"},BEM:{c:"00FF00",s:"cone"},RAM:{c:"00FF00",s:"cone"},RM4:{c:"00FF00",s:"cone"},TYV:{c:"00FF00",s:"cylinder"},ARA:{c:"00FF00",s:"cylinder"},ARB:{c:"00FF00",s:"cylinder"},KDN:{c:"00FF00",s:"cylinder"},KDM:{c:"00FF00",s:"cylinder"},"6PZ":{c:"00FF00",s:"cylinder"},GMH:{c:"00FF00",s:"cylinder"},BDF:{c:"00FF00",s:"cylinder"},GAL:{c:"FFFF00",s:"sphere"},GLA:{c:"FFFF00",s:"sphere"},NGA:{c:"FFFF00",s:"cube"},A2G:{c:"FFFF00",s:"cube"},X6X:{c:"FFFF00",s:"cube"},"1GN":{c:"FFFF00",s:"cube"},ADA:{c:"FFFF00",s:"cone"},GTR:{c:"FFFF00",s:"cone"},LDY:{c:"FFFF00",s:"cylinder"},KDO:{c:"FFFF00",s:"cylinder"},T6T:{c:"FFFF00",s:"cylinder"},GUP:{c:"A52A2A",s:"sphere"},GL0:{c:"A52A2A",s:"sphere"},LGU:{c:"A52A2A",s:"cone"},ABE:{c:"A52A2A",s:"cylinder"},XYS:{c:"A52A2A",s:"cylinder"},XYP:{c:"A52A2A",s:"cylinder"},SOE:{c:"A52A2A",s:"cylinder"},PZU:{c:"FF69B4",s:"cylinder"},RIP:{c:"FF69B4",s:"cylinder"},"0MK":{c:"FF69B4",s:"cylinder"},ALL:{c:"8A2BE2",s:"sphere"},AFD:{c:"8A2BE2",s:"sphere"},NAA:{c:"8A2BE2",s:"cube"},SIA:{c:"8A2BE2",s:"cylinder"},SIB:{c:"8A2BE2",s:"cylinder"},AMU:{c:"8A2BE2",s:"cylinder"},X0X:{c:"1E90FF",s:"cone"},X1X:{c:"1E90FF",s:"cone"},NGC:{c:"1E90FF",s:"cylinder"},NGE:{c:"1E90FF",s:"cylinder"},"4N2":{c:"A0522D",s:"sphere"},HSQ:{c:"A0522D",s:"cube"},IDR:{c:"A0522D",s:"cone"},MUR:{c:"A0522D",s:"cylinder"},FUC:{c:"FF0000",s:"cone"},FUL:{c:"FF0000",s:"cone"}},this.nucleotidesArray=[" G"," A"," T"," C"," U"," DG"," DA"," DT"," DC"," DU","G","A","T","C","U","DG","DA","DT","DC","DU"],this.ionsArray=[" K"," NA"," MG"," AL"," CA"," TI"," MN"," FE"," NI"," CU"," ZN"," AG"," BA"," F"," CL"," BR"," I","K","NA","MG","AL","CA","TI","MN","FE","NI","CU","ZN","AG","BA","F","CL","BR","I"],this.cationsTrimArray=["K","NA","MG","AL","CA","TI","MN","FE","NI","CU","ZN","AG","BA"],this.anionsTrimArray=["F","CL","BR","I"],this.ionCharges={K:1,NA:1,MG:2,AL:3,CA:2,TI:3,MN:2,FE:3,NI:2,CU:2,ZN:2,AG:1,BA:2},this.vdwRadii={H:1.08,HE:1.34,LI:1.75,BE:2.05,B:1.47,C:1.49,N:1.41,O:1.4,F:1.39,NE:1.68,NA:1.84,MG:2.05,AL:2.11,SI:2.07,P:1.92,S:1.82,CL:1.83,AR:1.93,K:2.05,CA:2.21,SC:2.16,TI:1.87,V:1.79,CR:1.89,MN:1.97,FE:1.94,CO:1.92,NI:1.84,CU:1.86,ZN:2.1,GA:2.08,GE:2.15,AS:2.06,SE:1.93,BR:1.98,KR:2.12,RB:2.16,SR:2.24,Y:2.19,ZR:1.86,NB:2.07,MO:2.09,TC:2.09,RU:2.07,RH:1.95,PD:2.02,AG:2.03,CD:2.3,IN:2.36,SN:2.33,SB:2.25,TE:2.23,I:2.23,XE:2.21,CS:2.22,BA:2.51,LA:2.4,CE:2.35,PR:2.39,ND:2.29,PM:2.36,SM:2.29,EU:2.33,GD:2.37,TB:2.21,DY:2.29,HO:2.16,ER:2.35,TM:2.27,YB:2.42,LU:2.21,HF:2.12,TA:2.17,W:2.1,RE:2.17,OS:2.16,IR:2.02,PT:2.09,AU:2.17,HG:2.09,TL:2.35,PB:2.32,BI:2.43,PO:2.29,AT:2.36,RN:2.43,FR:2.56,RA:2.43,AC:2.6,TH:2.37,PA:2.43,U:2.4,NP:2.21,PU:2.56,AM:2.56,CM:2.56,BK:2.56,CF:2.56,ES:2.56,FM:2.56},this.covalentRadii={H:.31,HE:.28,LI:1.28,BE:.96,B:.84,C:.76,N:.71,O:.66,F:.57,NE:.58,NA:1.66,MG:1.41,AL:1.21,SI:1.11,P:1.07,S:1.05,CL:1.02,AR:1.06,K:2.03,CA:1.76,SC:1.7,TI:1.6,V:1.53,CR:1.39,MN:1.39,FE:1.32,CO:1.26,NI:1.24,CU:1.32,ZN:1.22,GA:1.22,GE:1.2,AS:1.19,SE:1.2,BR:1.2,KR:1.16,RB:2.2,SR:1.95,Y:1.9,ZR:1.75,NB:1.64,MO:1.54,TC:1.47,RU:1.46,RH:1.42,PD:1.39,AG:1.45,CD:1.44,IN:1.42,SN:1.39,SB:1.39,TE:1.38,I:1.39,XE:1.4,CS:2.44,BA:2.15,LA:2.07,CE:2.04,PR:2.03,ND:2.01,PM:1.99,SM:1.98,EU:1.98,GD:1.96,TB:1.94,DY:1.92,HO:1.92,ER:1.89,TM:1.9,YB:1.87,LU:1.87,HF:1.75,TA:1.7,W:1.62,RE:1.51,OS:1.44,IR:1.41,PT:1.36,AU:1.36,HG:1.32,TL:1.45,PB:1.46,BI:1.48,PO:1.4,AT:1.5,RN:1.5,FR:2.6,RA:2.21,AC:2.15,TH:2.06,PA:2,U:1.96,NP:1.9,PU:1.87,AM:1.8,CM:1.69},this.atomColors={H:this.thr(16777215),He:this.thr(16761035),HE:this.thr(16761035),Li:this.thr(11674146),LI:this.thr(11674146),B:this.thr(65280),C:this.thr(11184810),N:this.thr(255),O:this.thr(15728640),F:this.thr(14329120),Na:this.thr(255),NA:this.thr(255),Mg:this.thr(2263842),MG:this.thr(2263842),Al:this.thr(8421520),AL:this.thr(8421520),Si:this.thr(14329120),SI:this.thr(14329120),P:this.thr(16753920),S:this.thr(16762930),Cl:this.thr(65280),CL:this.thr(65280),Ca:this.thr(8421520),CA:this.thr(8421520),Ti:this.thr(8421520),TI:this.thr(8421520),Cr:this.thr(8421520),CR:this.thr(8421520),Mn:this.thr(8421520),MN:this.thr(8421520),Fe:this.thr(16753920),FE:this.thr(16753920),Ni:this.thr(10824234),NI:this.thr(10824234),Cu:this.thr(10824234),CU:this.thr(10824234),Zn:this.thr(10824234),ZN:this.thr(10824234),Br:this.thr(10824234),BR:this.thr(10824234),Ag:this.thr(8421520),AG:this.thr(8421520),I:this.thr(10494192),Ba:this.thr(16753920),BA:this.thr(16753920),Au:this.thr(14329120),AU:this.thr(14329120)},this.atomnames={H:"Hydrogen",HE:"Helium",LI:"Lithium",B:"Boron",C:"Carbon",N:"Nitrogen",O:"Oxygen",F:"Fluorine",NA:"Sodium",MG:"Magnesium",AL:"Aluminum",SI:"Silicon",P:"Phosphorus",S:"Sulfur",CL:"Chlorine",CA:"Calcium",TI:"Titanium",CR:"Chromium",MN:"Manganese",FE:"Iron",NI:"Nickel",CU:"Copper",ZN:"Zinc",BR:"Bromine",AG:"Silver",I:"Iodine",BA:"Barium",AU:"Gold"},this.defaultAtomColor=this.thr(13421772),this.stdChainColors=[this.thr(16711935),this.thr(255),this.thr(10053171),this.thr(65433),this.thr(16750848),this.thr(16737894),this.thr(3329330),this.thr(2003199),this.thr(16416882),this.thr(16753920),this.thr(52945),this.thr(16738740),this.thr(65280),this.thr(255),this.thr(16711680),this.thr(16776960),this.thr(65535),this.thr(16711935),this.thr(3978097),this.thr(4620980),this.thr(13458524),this.thr(16770229),this.thr(11529966),this.thr(15631086),this.thr(25600),this.thr(139),this.thr(9109504),this.thr(13468991),this.thr(35723),this.thr(9699539)],this.backgroundColors={black:this.thr(0),grey:this.thr(13421772),white:this.thr(16777215),transparent:this.thr(16777215)},this.residueColors={ALA:this.thr(13158600),ARG:this.thr(1334015),ASN:this.thr(56540),ASP:this.thr(15075850),CYS:this.thr(15132160),GLN:this.thr(56540),GLU:this.thr(15075850),GLY:this.thr(15461355),HIS:this.thr(8553170),ILE:this.thr(1016335),LEU:this.thr(1016335),LYS:this.thr(1334015),MET:this.thr(15132160),PHE:this.thr(3289770),PRO:this.thr(14456450),SER:this.thr(16422400),THR:this.thr(16422400),TRP:this.thr(11819700),TYR:this.thr(3289770),VAL:this.thr(1016335),ASX:this.thr(16738740),GLX:this.thr(16738740),G:this.thr(32768),A:this.thr(6324479),T:this.thr(16744448),C:this.thr(16711680),U:this.thr(16744448),DG:this.thr(32768),DA:this.thr(6324479),DT:this.thr(16744448),DC:this.thr(16711680),DU:this.thr(16744448)},this.residueArea={ALA:247,ARG:366,ASN:290,ASP:285,CYS:271,GLN:336,GLU:325,GLY:217,HIS:340,ILE:324,LEU:328,LYS:373,MET:346,PHE:366,PRO:285,SER:265,THR:288,TRP:414,TYR:387,VAL:293,ASX:290,GLX:336,G:520,A:507,T:515,C:467,U:482,DG:520,DA:507,DT:515,DC:467,DU:482},this.defaultResidueColor=this.thr(12492910),this.chargeColors={" G":this.thr(16711680)," A":this.thr(16711680)," T":this.thr(16711680)," C":this.thr(16711680)," U":this.thr(16711680)," DG":this.thr(16711680)," DA":this.thr(16711680)," DT":this.thr(16711680)," DC":this.thr(16711680)," DU":this.thr(16711680),G:this.thr(16711680),A:this.thr(16711680),T:this.thr(16711680),C:this.thr(16711680),U:this.thr(16711680),DG:this.thr(16711680),DA:this.thr(16711680),DT:this.thr(16711680),DC:this.thr(16711680),DU:this.thr(16711680),ARG:this.thr(255),LYS:this.thr(255),ASP:this.thr(16711680),GLU:this.thr(16711680),HIS:this.thr(8421631),GLY:this.thr(8947848),PRO:this.thr(8947848),ALA:this.thr(8947848),VAL:this.thr(8947848),LEU:this.thr(8947848),ILE:this.thr(8947848),PHE:this.thr(8947848),SER:this.thr(8947848),THR:this.thr(8947848),ASN:this.thr(8947848),GLN:this.thr(8947848),TYR:this.thr(8947848),MET:this.thr(8947848),CYS:this.thr(8947848),TRP:this.thr(8947848)},this.hydrophobicColors={" G":this.thr(16711680)," A":this.thr(16711680)," T":this.thr(16711680)," C":this.thr(16711680)," U":this.thr(16711680)," DG":this.thr(16711680)," DA":this.thr(16711680)," DT":this.thr(16711680)," DC":this.thr(16711680)," DU":this.thr(16711680),G:this.thr(16711680),A:this.thr(16711680),T:this.thr(16711680),C:this.thr(16711680),U:this.thr(16711680),DG:this.thr(16711680),DA:this.thr(16711680),DT:this.thr(16711680),DC:this.thr(16711680),DU:this.thr(16711680),ARG:this.thr(255),LYS:this.thr(255),ASP:this.thr(16711680),GLU:this.thr(16711680),HIS:this.thr(8421631),TRP:this.thr().setHSL(1/3,1,.5),PHE:this.thr().setHSL(1/3,1,.5909090909090908),LEU:this.thr().setHSL(1/3,1,.700956937799043),ILE:this.thr().setHSL(1/3,1,.7320574162679425),TYR:this.thr().setHSL(1/3,1,.5+.69/2.09),MET:this.thr().setHSL(1/3,1,.5+.71/2.09),VAL:this.thr().setHSL(1/3,1,.5+.815/2.09),CYS:this.thr().setHSL(1/3,1,.5+1.035/2.09),PRO:this.thr().setHSL(1/6,1,.9391304347826086),THR:this.thr().setHSL(1/6,1,.8913043478260869),SER:this.thr().setHSL(1/6,1,.8),ALA:this.thr().setHSL(1/6,1,.7826086956521738),GLN:this.thr().setHSL(1/6,1,.6652173913043478),ASN:this.thr().setHSL(1/6,1,.6304347826086956),GLY:this.thr().setHSL(1/6,1,.5)},this.normalizedHPColors={" G":this.thr(16777215)," A":this.thr(16777215)," T":this.thr(16777215)," C":this.thr(16777215)," U":this.thr(16777215)," DG":this.thr(16777215)," DA":this.thr(16777215)," DT":this.thr(16777215)," DC":this.thr(16777215)," DU":this.thr(16777215),G:this.thr(16777215),A:this.thr(16777215),T:this.thr(16777215),C:this.thr(16777215),U:this.thr(16777215),DG:this.thr(16777215),DA:this.thr(16777215),DT:this.thr(16777215),DC:this.thr(16777215),DU:this.thr(16777215),ARG:this.thr(16777215),LYS:this.thr(16777215),ASP:this.thr(16777215),GLU:this.thr(16777215),HIS:this.thr(16777215),TRP:this.thr().setHSL(1/3,1,.5),PHE:this.thr().setHSL(1/3,1,.558641975308642),LEU:this.thr().setHSL(1/3,1,.6296296296296295),ILE:this.thr().setHSL(1/3,1,.6496913580246912),TYR:this.thr().setHSL(1/3,1,.5+.69/3.24),MET:this.thr().setHSL(1/3,1,.5+.71/3.24),VAL:this.thr().setHSL(1/3,1,.5+.815/3.24),CYS:this.thr().setHSL(1/3,1,.5+1.035/3.24),PRO:this.thr().setHSL(1/3,1,.5+1.115/3.24),THR:this.thr().setHSL(1/3,1,.5+1.17/3.24),SER:this.thr().setHSL(1/3,1,.5+1.275/3.24),ALA:this.thr().setHSL(1/3,1,.5+1.295/3.24),GLN:this.thr().setHSL(1/3,1,.5+1.43/3.24),ASN:this.thr().setHSL(1/3,1,.5+1.47/3.24),GLY:this.thr().setHSL(1/3,1,1)},this.hydrophobicValues={" G":3," A":3," T":3," C":3," U":3," DG":3," DA":3," DT":3," DC":3," DU":3,G:3,A:3,T:3,C:3,U:3,DG:3,DA:3,DT:3,DC:3,DU:3,ARG:1.5,LYS:1.5,ASP:3,GLU:3,HIS:2,TRP:-2.09,PHE:-1.71,LEU:-1.25,ILE:-1.12,TYR:-.71,MET:-.67,VAL:-.46,CYS:-.02,PRO:.14,THR:.25,SER:.46,ALA:.5,GLN:.77,ASN:.85,GLY:1.15},this.residueAbbrev={ALA:"A (Ala)",ARG:"R (Arg)",ASN:"N (Asn)",ASP:"D (Asp)",CYS:"C (Cys)",GLN:"Q (Gln)",GLU:"E (Glu)",GLY:"G (Gly)",HIS:"H (His)",ILE:"I (Ile)",LEU:"L (Leu)",LYS:"K (Lys)",MET:"M (Met)",PHE:"F (Phe)",PRO:"P (Pro)",SER:"S (Ser)",THR:"T (Thr)",TRP:"W (Trp)",TYR:"Y (Tyr)",VAL:"V (Val)",ASX:"X (Asx)",GLX:"X (Glx)",G:"Guanine",A:"Adenine",T:"Thymine",C:"Cytosine",U:"Uracil",DG:"deoxy-Guanine",DA:"deoxy-Adenine",DT:"deoxy-Thymine",DC:"deoxy-Cytosine",DU:"deoxy-Uracil"},this.ssColors={helix:this.thr(16711680),sheet:this.thr(32768),coil:this.thr(6324479)},this.ssColors2={helix:this.thr(16711680),sheet:this.thr(16762880),coil:this.thr(6324479)},this.resn2restype={ALA:1,ARG:4,ASN:7,ASP:10,CYS:13,GLN:16,GLU:19,GLY:22,HIS:25,ILE:28,LEU:31,LYS:34,MET:37,PHE:40,PRO:43,SER:46,THR:49,TRP:52,TYR:55,VAL:58},this.nuclMainArray=["C1'","C1*","C2'","C2*","C3'","C3*","C4'","C4*","C5'","C5*","O3'","O3*","O4'","O4*","O5'","O5*","P","OP1","O1P","OP2","O2P"],this.b62ResArray=["A","R","N","D","C","Q","E","G","H","I","L","K","M","F","P","S","T","W","Y","V","B","Z","X","*"],this.b62Matrix=[[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0,-2,-1,0,-4],[-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3,-1,0,-1,-4],[-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3,3,0,-1,-4],[-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3,4,1,-1,-4],[0,-3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4],[-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2,0,3,-1,-4],[-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3,-1,-2,-1,-4],[-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3,0,0,-1,-4],[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3,-3,-3,-1,-4],[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,1,-4,-3,-1,-4],[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2,0,1,-1,-4],[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1,-3,-1,-1,-4],[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1,-3,-3,-1,-4],[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2,-2,-1,-2,-4],[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2,0,0,0,-4],[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0,-1,-1,0,-4],[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,1,-4,-3,-2,11,2,-3,-4,-3,-2,-4],[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1,-3,-2,-1,-4],[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4,-3,-2,-1,-4],[-2,-1,3,4,-3,0,1,-1,0,-3,-4,0,-3,-3,-2,0,-1,-4,-3,-3,4,1,-1,-4],[-1,0,0,1,-3,3,4,-2,0,-3,-3,1,-1,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2,0,0,-2,-1,-1,-1,-1,-1,-4],[-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,1]]}thr(e){return this.icn3dui,"#0"==e&&(e="#000"),new THREE.Color(e)}}class n{constructor(e){this.icn3dui=e}onId(e,t,s){if(this.icn3dui,!(Object.keys(window).length<2)&&("#"==e.substr(0,1)&&(e=e.substr(1)),document.getElementById(e))){t.split(" ").forEach((t=>{document.getElementById(e).addEventListener(t,s)}))}}onIds(e,t,s){let i=this.icn3dui;Array.isArray(e)?e.forEach((e=>{i.myEventCls.onId(e,t,s)})):i.myEventCls.onId(e,t,s)}}class l{constructor(e){this.icn3dui=e}getRmsdSuprCls(e,t,s){let i,n,l,r,o,a,d,c,h,p,m,u,g,f=this.icn3dui,C=new Array(9),b=new THREE.Vector3,y=new THREE.Vector3,v=[],_=[],w=new Array(3),S=new Array(3),A=new Array(3),x=new Array(3),k=new Array(3),O=new Array(3);if(i=0,s<=1)return{rot:void 0,trans1:void 0,trans2:void 0,rmsd:999};let R=s;for(n=0;n0?(C[0]=x[0]*w[0]+k[0]*S[0]+O[0]*A[0],C[1]=x[0]*w[1]+k[0]*S[1]+O[0]*A[1],C[2]=x[0]*w[2]+k[0]*S[2]+O[0]*A[2],C[3]=x[1]*w[0]+k[1]*S[0]+O[1]*A[0],C[4]=x[1]*w[1]+k[1]*S[1]+O[1]*A[1],C[5]=x[1]*w[2]+k[1]*S[2]+O[1]*A[2],C[6]=x[2]*w[0]+k[2]*S[0]+O[2]*A[0],C[7]=x[2]*w[1]+k[2]*S[1]+O[2]*A[1],C[8]=x[2]*w[2]+k[2]*S[2]+O[2]*A[2]):(C[0]=x[0]*w[0]+k[0]*S[0]-O[0]*A[0],C[1]=x[0]*w[1]+k[0]*S[1]-O[0]*A[1],C[2]=x[0]*w[2]+k[0]*S[2]-O[0]*A[2],C[3]=x[1]*w[0]+k[1]*S[0]-O[1]*A[0],C[4]=x[1]*w[1]+k[1]*S[1]-O[1]*A[1],C[5]=x[1]*w[2]+k[1]*S[2]-O[1]*A[2],C[6]=x[2]*w[0]+k[2]*S[0]-O[2]*A[0],C[7]=x[2]*w[1]+k[2]*S[1]-O[2]*A[1],C[8]=x[2]*w[2]+k[2]*S[2]-O[2]*A[2]),c=Math.sqrt(c),h=Math.sqrt(h),p=Math.sqrt(p),g=c+h+u*p,m=a+d-2*g,i=m>0?Math.sqrt(m):void 0,{rot:C,trans1:I,trans2:E,rmsd:i})}eigen_values(e){let t,s,i,n,l,r,o,a,d,c,h,p,m,u,g,f,C,b,y,v;if(this.icn3dui,t=e[0],s=e[1],i=e[2],n=e[3],l=e[4],r=e[5],o=e[6],a=e[7],d=e[8],c=-(t+l+d),h=t*l+(t+l)*d-r*a-s*n-i*o,p=-t*l*d+t*r*a+s*n*d-s*r*o-i*n*a+i*l*o,m=-c*c/3+h,u=c*c*c/13.5-c*h/3+p,g=.25*u*u+m*m*m/27,g<0){let e,t;e=Math.sqrt(.25*u*u-g),t=Math.acos(-.5*u/e),b=2*Math.cbrt(e)*Math.cos(t/3)}else f=Math.cbrt(-.5*u+Math.sqrt(g)),C=Math.cbrt(-.5*u-Math.sqrt(g)),b=f+C;return b-=c/3,c+=b,p/=-b,y=.5*(-c+Math.sqrt(c*c-4*p)),v=.5*(-c-Math.sqrt(c*c-4*p)),yw&&(w=Math.abs(d)),Math.abs(c)>w&&(w=Math.abs(c)),Math.abs(h)>w&&(w=Math.abs(h)),Math.abs(p)>w&&(w=Math.abs(p)),Math.abs(m)>w&&(w=Math.abs(m)),Math.abs(u)>w&&(w=Math.abs(u)),Math.abs(g)>w&&(w=Math.abs(g)),Math.abs(f)>w&&(w=Math.abs(f)),w<1e-10)return r=3,{k:r,v1:t,v2:s,v3:i};if(o=0,a/=w,d/=w,c/=w,h/=w,p/=w,m/=w,u/=w,g/=w,f/=w,Math.abs(a)w&&(_=a,a=h,h=_,_=d,d=p,p=_,_=c,c=m,m=_,w=Math.abs(d)),Math.abs(g)>w&&(_=a,a=u,u=_,_=d,d=g,g=_,_=c,c=f,f=_),y=m-p*c/d,v=f-g*c/d,Math.abs(y)w&&(_=a,a=h,h=_,_=d,d=p,p=_,_=c,c=m,m=_,w=Math.abs(a)),Math.abs(c)>w&&(_=a,a=u,u=_,_=d,d=g,g=_,_=c,c=f,f=_),C=p-h*d/a,b=m-h*c/a,y=g-u*d/a,v=f-u*c/a,Math.abs(C)0&&(1==o?(a=s[0],d=s[1],c=s[2],_=Math.sqrt(a*a+d*d+c*c),s[0]=a/_,s[1]=d/_,s[2]=c/_):2==o?(a=t[0],d=t[1],c=t[2],h=s[0],p=s[1],m=s[2],_=a*h+d*p+c*m,Math.abs(_)>=n&&(s[0]=a+_*h,s[1]=d+_*p,s[2]=c+_*m,h=s[0],p=s[1],m=s[2]),_=Math.sqrt(a*a+d*d+c*c),t[0]=a/_,t[1]=d/_,t[2]=c/_,_=Math.sqrt(h*h+p*p+m*m),s[0]=h/_,s[1]=p/_,s[2]=m/_):(a=t[0],d=t[1],c=t[2],_=Math.sqrt(a*a+d*d+c*c),t[0]=a/_,t[1]=d/_,t[2]=c/_)),{k:r,v1:t,v2:s,v3:i}}getEigenForSelection(e,t){let s,i=this.icn3dui,n=new THREE.Vector3,l=[];for(s=0;s0&&Math.abs(l[0].x-e[0].x)<=6&&Math.abs(l[0].y-e[0].y)<=6&&Math.abs(l[0].z-e[0].z)<=6?(p.push(l[0]),m=1):m=0,p.push(e[0]);for(let t=1,s=e.length-1;t0&&Math.abs(r[0].x-e[e.length-1].x)<=6&&Math.abs(r[0].y-e[e.length-1].y)<=6&&Math.abs(r[0].z-e[e.length-1].z)<=6&&(p.push(r[0]),++g),u>1&&Math.abs(r[0].x-r[1].x)<=6&&Math.abs(r[0].y-r[1].y)<=6&&Math.abs(r[0].z-r[1].z)<=6&&(p.push(r[1]),++g);let f=[],C=[],b=[];o&&(g=u>0?u-1:0);let y;for(let e=-1,n=p.length,l=1/s;e<=n-3;++e){y=e-m;let r=p[-1===e?0:e],o=p[e+1],u=p[e+2],v=p[e===n-3?n-1:e+3],_=0,w=a.subdivideCls.getKnot(1,_,r,o),S=a.subdivideCls.getKnot(1,w,o,u),A=a.subdivideCls.getKnot(1,S,u,v);w-_<1e-4&&(w=_+1),S-w<1e-4&&(S=w+1),A-S<1e-4&&(A=S+1),e>-1&&(void 0===i||i[y+1])&&e>=-1+m&&e<=n-3-g+1&&(d=d.concat(f),c=c.concat(C),h=h.concat(b)),f=[],C=[],b=[];let x=(S-w)*l;for(let l=0;l=-1+m&&e<=n-3-g&&i[y+1]&&l<=parseInt(s/2)&&(d.push(new THREE.Vector3(k,O,R)),c.push(i[y+1]),h.push(t[y+1])),e>=-1+m&&e<=n-3-g+1&&i[y+2]&&l>parseInt(s/2)&&(f.push(new THREE.Vector3(k,O,R)),C.push(i[y+2]),b.push(t[y+2]))):e>=-1+m&&e<=n-3-g&&(d.push(new THREE.Vector3(k,O,R)),c.push(y+1),h.push(t[y+1]))}}i&&!i[y+1]||(d=d.concat(f),c=c.concat(C),h=h.concat(b),d.push(p[p.length-1-g]),c.push(p.length-1-g),h.push(t[p.length-1-g])),f=[],C=[],b=[],p=[];let v=[];return v.push(d),v.push(c),v.push(h),v}getKnot(e,t,s,i){return this.icn3dui,s.distanceTo(i)+t}getValueFromKnot(e,t,s,i,n,l,r,o,a){this.icn3dui;let d,c,h=(r-l)/(s-t),p=(o-r)/(i-s),m=(a-o)/(n-i),u=(s+i)*(s+i)-4*(t*s+i*n-t*n);return 0==u?(d=9999,c=9999):(d=6*(3*p*s+2*h*n+m*s-2*h*s-2*p*n-p*i-m*s)/u,c=6*(3*p*i+2*m*t+h*s-2*p*t-2*m*i-h*i-p*s)/u),p*(e-s)+r+((2*d+c)/6/(s-i)*(e-s)*(e-i)*(e-i)+(2*c+d)/6/(i-s)*(e-s)*(e-s)*(e-i))}}class o{constructor(e){this.icn3dui=e}passFloat32(e,t){let s=this.icn3dui,i=e.length;t||(t=new Uint8Array(4*i));let n=s.convertTypeCls.getDataView(t);for(let t=0;t  Very high (pLDDT > 90)
  Confident (90 > pLDDT > 70)
  Low (70 > pLDDT > 50)
  Very low (pLDDT < 50)
'}setLegendHtml(e){let t=this.icn3dui.icn3d,s="
";if(e)s+=this.setAlphaFoldLegend();else{s+="
"+t.startValue+""+t.midValue+""+t.endValue+"
"}return s}SetChainsAdvancedMenu(){let e=this.icn3dui,t=e.icn3d;if(void 0===t.bSetChainsAdvancedMenu||!t.bSetChainsAdvancedMenu){let s=e.hashUtilsCls.cloneHash(t.hAtoms);t.definedSetsCls.setPredefinedInMenu(),t.bSetChainsAdvancedMenu=!0,t.hAtoms=e.hashUtilsCls.cloneHash(s)}}setSetsMenus(e,t){let s=this.icn3dui,i=s.icn3d;this.SetChainsAdvancedMenu();let n=e,l=e+"2",r=i.definedSetsCls.setAtomMenu(["protein"]);$("#"+s.pre+n).length&&$("#"+s.pre+n).html(" "+r),!t&&$("#"+s.pre+l).length&&$("#"+s.pre+l).html(" "+r),$("#"+s.pre+n).resizable(),t||$("#"+s.pre+l).resizable()}applyShownMenus(e){let t=this.icn3dui;t.icn3d;let s=[];for(let e in t.htmlCls.allMenus)t.htmlCls.shownMenus.hasOwnProperty(e)?$("#"+t.pre+e).parent().show():($("#"+t.pre+e).parent().hide(),s.push(e));Object.keys(t.htmlCls.shownMenus).length==Object.keys(t.htmlCls.allMenus).length?$(".icn3d-menusep").show():$(".icn3d-menusep").hide(),localStorage&&!e&&localStorage.setItem("hiddenmenus",JSON.stringify(s))}getHiddenMenusFromCache(){let e=this.icn3dui;e.icn3d,e.htmlCls.shownMenus={};let t=localStorage?localStorage.getItem("hiddenmenus"):"";if(t&&"[]"!=t){let s=JSON.parse(t);for(let t in e.htmlCls.allMenus)-1==s.indexOf(t)&&(e.htmlCls.shownMenus[t]=1)}else e.htmlCls.shownMenus=e.hashUtilsCls.cloneHash(e.htmlCls.allMenus)}displayShownMenus(){let e=this.icn3dui;e.icn3d;let t="
";t+="",t+="";for(let s in e.htmlCls.allMenusSel){if("uniclr"==s.substr(0,6)||"mn5_opacity"==s.substr(0,11)||"mn6_labelscale"==s.substr(0,14)||"faq_"==s.substr(0,4)||"dev_"==s.substr(0,4))continue;"mn1_searchgrooup"==s?t+="
FileSelectViewStyleColorAnalysisHelp
":("mn2_definedsets"==s||"mn2_show_selected"==s||"mn3_proteinwrap"==s||e.cfg.cid&&"mn3_ligwrap"==s||"mn4_clrwrap"==s||"mn6_selectannotations"==s||"abouticn3d"==s)&&(t+="");let i=e.htmlCls.shownMenus.hasOwnProperty(s)?"checked":"",n=e.htmlCls.allMenusSel[s];t+=""+e.htmlCls.allMenus[s]+"
"}t+="
",$("#"+e.pre+"menulist").html(t)}async setIgTemplate(e){let t=this.icn3dui.icn3d;t.bRunRefnumAgain=!0;let s=t.resid2specCls.atoms2residues(Object.keys(t.hAtoms));for(let e=0,i=s.length;e0?"_blank":"_self";window.open(n,l)})),e.myEventCls.onIds("#"+e.pre+"mn1_mmciffile","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_mmciffile","Please append mmCIF File")})),e.myEventCls.onIds("#"+e.pre+"mn1_mmcifid","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_mmcifid","Please input mmCIF ID")})),e.myEventCls.onIds("#"+e.pre+"mn1_mmdbid","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_mmdbid","Please input MMDB or PDB ID")})),e.myEventCls.onIds(["#"+e.pre+"mn1_mmdbafid",,"#"+e.pre+"tool_mmdbafid"],"click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_mmdbafid","Please input PDB/MMDB/AlphaFold UniProt IDs")})),e.myEventCls.onIds("#"+e.pre+"mn1_blast_rep_id","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_blast_rep_id","Align sequence to structure")})),e.myEventCls.onIds("#"+e.pre+"mn1_esmfold","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_esmfold","Sequence to structure prediction with ESMFold")})),e.myEventCls.onIds("#"+e.pre+"mn1_proteinname","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_proteinname","Please input protein or gene name")})),e.myEventCls.onIds("#"+e.pre+"mn1_cid","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_cid","Please input PubChem CID")})),e.myEventCls.onIds("#"+e.pre+"mn1_pngimage","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_pngimage","Please input the PNG image")})),e.myEventCls.onIds("#"+e.pre+"mn1_state","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_state","Please input the state file")})),e.myEventCls.onIds("#"+e.pre+"mn1_selection","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_selection","Please input the selection file")})),e.myEventCls.onIds("#"+e.pre+"mn1_collection","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_selectCollections","Select Collections")})),e.myEventCls.onIds("#"+e.pre+"mn1_dsn6","click",(function(t){e.icn3d,e.htmlCls.dialogCls.openDlg("dl_dsn6","Please input the map file to display electron density map")})),e.myEventCls.onIds(["#"+e.pre+"mn1_delphi","#"+e.pre+"mn1_delphi2","#"+e.pre+"tool_delphi"],"click",(function(t){e.icn3d.loadPhiFrom="delphi",$("#"+e.pre+"dl_delphi_tabs").tabs(),e.htmlCls.dialogCls.openDlg("dl_delphi","Please set parameters to display DelPhi potential map")})),e.myEventCls.onIds("#"+e.pre+"mn1_phi","click",(function(t){e.icn3d.loadPhiFrom="phi",$("#"+e.pre+"dl_phi_tabs").tabs(),$("#"+e.pre+"phitab1_tabs").tabs(),$("#"+e.pre+"phitab2_tabs").tabs(),e.htmlCls.dialogCls.openDlg("dl_phi","Please input local phi or cube file to display DelPhi potential 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"+s,l+=r+'
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☰

":l+="

☰

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        ",t+=this.getLink("mn1_opmid","OPM PDB ID "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_mmcifid","RCSB mmCIF ID "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_cid","PubChem CID "+e.htmlCls.wifiStr,1,2),t+="
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        ",t+=this.getMenuText("mn1_savepngimage","iCn3D PNG Image",void 0,1,2),t+="
          ",t+=this.getLink("mn1_exportCanvas","Original Size & HTML",1,3),t+=this.getLink("mn1_exportCanvas1","Original Size",void 0,3),t+=this.getLink("mn1_exportCanvas2","2X Large",void 0,3),t+=this.getLink("mn1_exportCanvas4","4X Large",void 0,3),t+=this.getLink("mn1_exportCanvas8","8X Large",void 0,3),t+="
        ",t+="",t+=this.getLink("mn1_exportState","State File",void 0,2),t+=this.getLink("mn1_exportSelections","Selection File",void 0,2),t+=this.getLink("mn1_exportSelDetails","Selection Details",void 0,2),t+=this.getLink("mn1_exportCounts","Residue Counts",void 0,2),t+=this.getLink("mn1_exportPdbRes","PDB",1,2),t+=this.getLink("profixpdb","PDB with Missing Atoms",void 0,2),void 0===e.cfg.cid&&(t+=this.getLink("mn1_exportSecondary","Secondary Structure",void 0,2)),t+=this.getMenuText("m1_exportrefnum","Reference Numbers",void 0,void 0,2),t+="
          ",t+=this.getLink("mn1_exportIgstrand","Ig Strand",void 0,3),t+=this.getLink("mn1_exportKabat","Kabat",void 0,3),t+=this.getLink("mn1_exportImgt","IMGT",void 0,3),t+="
        ",t+="

        • ",t+="
      ",t+="",t+=this.getLink("mn1_sharelink","Share Link "+e.htmlCls.wifiStr,1,1),t+=this.getLink("mn1_replayon","Replay Each Step",void 0,1),t+=this.getMenuSep(),t+=this.getMenuText("mn1_menuwrap","Customize Menus",void 0,1,1),t+="
        ",t+=this.getLink("mn1_menuall","All Menus",1,2),t+=this.getLink("mn1_menusimple","Simple Menus",1,2),t+=this.getMenuSep(),t+=this.getLink("mn1_menupref","Preferences",1,2),t+=this.getLink("mn1_menuloadpref","Load Preferences",1,2),t+="
      ",t+="",t+="

      • ",t+="
    ",t}setMenu2(){let e=this.icn3dui;if(e.bNode)return"";let t="";return t+="
    ",t+="",t+="

    Select

    ",t+="
    ",t+=this.setMenu2_base(),t+="
    ",t+="    ",t+="
    ",t}setMenu2_base(){let e=this.icn3dui;if(e.bNode)return"";let t="";return t+="
      ",t+=this.getLink("mn2_definedsets","Defined Sets",1,1),t+=this.getLink("mn2_selectall","All",void 0,1),t+=this.getLink("mn2_selectdisplayed","Displayed Set",void 0,1),t+=this.getLink("mn2_aroundsphere","by Distance",1,1),t+=this.getMenuText("mn2_selbyprop","by Property",void 0,void 0,1),t+="
        ",t+=this.getLink("mn2_propPos","Positive",void 0,2),t+=this.getLink("mn2_propNeg","Negative",void 0,2),t+=this.getLink("mn2_propHydro","Hydrophobic",void 0,2),t+=this.getLink("mn2_propPolar","Polar",void 0,2),t+=this.getLink("mn2_propBfactor","B-factor/pLDDT",void 0,2),t+=this.getLink("mn2_propSolAcc","Solvent Accessibility",void 0,2),t+="
      ",t+="",t+=this.getLink("mn2_selectcomplement","Inverse",void 0,1),t+=this.getLink("mn2_selectmainchains","Main Chains",void 0,1),t+=this.getLink("mn2_selectsidechains","Side Chains",void 0,1),t+=this.getLink("mn2_selectmainsidechains","Main & Side Chains",void 0,1),t+=this.getLink("mn2_command","Advanced",void 0,1),void 0===e.cfg.cid?(t+=this.getMenuText("mn2_selon3d","Select on 3D",void 0,1,1),t+="
        ",t+='
      • "Alt"+Click: start selection
        • ',t+='
      • "Ctrl"+Click: union selection
        • ',t+='
      • "Shift"+Click: range Selection
        • ',t+=this.getMenuSep(),t+=this.getRadio("mn2_pk","mn2_pkChain","Chain",void 0,1,2),void 0===e.cfg.mmdbid&&void 0===e.cfg.gi||(t+=this.getRadio("mn2_pk","mn2_pkDomain","3D Domain",void 0,void 0,2)),t+=this.getRadio("mn2_pk","mn2_pkStrand","Strand/Helix",void 0,void 0,2),t+=this.getRadio("mn2_pk","mn2_pkResidue","Residue",!0,1,2),t+=this.getRadio("mn2_pk","mn2_pkYes","Atom",void 0,1,2),t+=this.getRadio("mn2_pk","mn2_pkNo","None",void 0,void 0,2),t+="
      ",t+=""):e.utilsCls.isMobile()?t+="
    • Touch to pick
      • ":t+='
    • Picking with
      "Alt" + Click
      • ',t+=this.getMenuSep(),t+=this.getLink("mn2_saveselection","Save Selection",1,1),t+=this.getLink("clearall","Clear Selection",void 0,1),t+=this.getLink("mn2_saveresidue","Save Res. in Sel.",1,1),t+=this.getMenuSep(),t+=this.getMenuText("mn2_hlcolor","Highlight Color",void 0,void 0,1),t+="
        ",t+=this.getRadio("mn2_hl_clr","mn2_hl_clrYellow","Yellow",!0,void 0,2),t+=this.getRadio("mn2_hl_clr","mn2_hl_clrGreen","Green",void 0,void 0,2),t+=this.getRadio("mn2_hl_clr","mn2_hl_clrRed","Red",void 0,void 0,2),t+="
      ",t+="",t+=this.getMenuText("mn2_hlstyle","Highlight Style",void 0,void 0,1),t+="
        ",t+=this.getRadio("mn2_hl_style","mn2_hl_styleOutline","Outline",!0,void 0,2),t+=this.getRadio("mn2_hl_style","mn2_hl_styleObject","3D Objects",void 0,void 0,2),t+="
      ",t+="",t+=this.getLink("toggleHighlight2","Toggle Highlight",1,1),t+="

      • ",t+="
    ",t}setMenu2b(){let e=this.icn3dui;if(e.bNode)return"";let t="";return t+="
    ",t+="",t+="

    View

    ",t+="
    ",t+=this.setMenu2b_base(),t+="
    ",t+="    ",t+="
    ",t}setMenu2b_base(){let e=this.icn3dui;if(e.bNode)return"";let t="";return t+="
      ",t+=this.getLink("mn2_show_selected","View Selection",1,1),t+=this.getLink("mn2_hide_selected","Hide Selection",1,1),t+=this.getLink("mn2_selectedcenter","Zoom in Selection",1,1),t+=this.getLink("mn6_center","Center Selection",1,1),t+=this.getLink("mn2_fullstru","View Full Structure"),t+=this.getLinkWrapper("mn2_alternate",'Alternate(Key "a")',"mn2_alternateWrap",void 0,1),void 0!==e.cfg.opmid?t+=this.getLinkWrapper("togglemem","Toggle Membrane","togglememli",void 0,1):void 0===e.cfg.cid&&(t+=this.getLinkWrapper("togglemem","Toggle Membrane","togglememli",void 0,1,!0)),void 0!==e.cfg.opmid&&(t+=this.getLinkWrapper("adjustmem","Adjust Membrane","adjustmemli",void 0,1),t+=this.getLinkWrapper("selectplane","Select between
      Two X-Y Planes","selectplaneli",void 0,1)),t+=this.getMenuSep(),t+=this.getMenuText("mn2_vrarhints","VR & AR Hints",void 0,1,1),t+="
        ",t+=this.getMenuUrl("vrhint",e.htmlCls.baseUrl+"icn3d/icn3d.html#vr","VR: VR Headsets",1,2),t+=this.getMenuUrl("arhint",e.htmlCls.baseUrl+"icn3d/icn3d.html#ar","AR: Chrome in Android",1,2),t+="
      ",t+="",t+=this.getLink("mn6_sidebyside","Side by Side",1,1),t+=this.getMenuText("mn2_rotate","Rotate",void 0,1,1),t+="
        ",t+=this.getMenuText("mn2_rotate90","Rotate 90°",void 0,void 0,2),t+="
          ",t+=this.getRadio("mn6_rotate90","mn6_rotatex","rotate x",void 0,void 0,2),t+=this.getRadio("mn6_rotate90","mn6_rotatey","rotate y",void 0,void 0,2),t+=this.getRadio("mn6_rotate90","mn6_rotatez","rotate z",void 0,void 0,2),t+="
        ",t+="",t+=this.getMenuText("mn2_rotateauto","Auto Rotation",void 0,1,2),t+="
          ",t+=this.getRadio("mn6_rotate","mn6_rotateleft","Rotate Left",void 0,1,3),t+=this.getRadio("mn6_rotate","mn6_rotateright","Rotate Right",void 0,1,3),t+=this.getRadio("mn6_rotate","mn6_rotateup","Rotate Up",void 0,1,3),t+=this.getRadio("mn6_rotate","mn6_rotatedown","Rotate Down",void 0,1,3),t+="
        ",t+="",t+="
      ",t+="",t+=this.getLink("mn2_translate","Translate XYZ",void 0,1),t+=this.getLink("mn2_matrix","Rotate with Matrix",void 0,1),t+=this.getMenuText("mn2_camera","Camera",void 0,void 0,1),t+="
        ",t+=this.getRadio("mn6_camera","mn6_cameraPers","Perspective",!0,void 0,2),t+=this.getRadio("mn6_camera","mn6_cameraOrth","Orthographic",void 0,void 0,2),t+="
      ",t+="",t+=this.getMenuText("mn2_fog","Fog for Selection",void 0,void 0,1),t+="
        ",t+=this.getRadio("mn6_showfog","mn6_showfogYes","On",void 0,void 0,2),t+=this.getRadio("mn6_showfog","mn6_showfogNo","Off",!0,void 0,2),t+="
      ",t+="",t+=this.getMenuText("mn2_slab","Slab for Selection",void 0,void 0,1),t+="
        ",t+=this.getRadio("mn6_showslab","mn6_showslabYes","On",void 0,void 0,2),t+=this.getRadio("mn6_showslab","mn6_showslabNo","Off",!0,void 0,2),t+="
      ",t+="",t+=this.getMenuText("mn2_axes","XYZ-axes",void 0,void 0,1),t+="
        ",t+=this.getRadio("mn6_showaxis","mn6_showaxisYes","Original",void 0,void 0,2),t+=this.getRadio("mn6_showaxis","mn6_showaxisSel","Prin. Axes on Sel.",void 0,void 0,2),t+=this.getRadio("mn6_showaxis","mn6_showaxisNo","Hide",!0,void 0,2),t+="
      ",t+="",t+=this.getMenuSep(),t+=this.getMenuText("mn2_resetwrap","Reset",void 0,1,1),t+="
        ",t+=this.getRadio("mn6_reset","reset","All",void 0,1,2),t+=this.getRadio("mn6_reset","mn6_resetOrientation","Orientation",void 0,1,2),t+="
      ",t+="",t+=this.getLink("mn6_back","Undo",void 0,1),t+=this.getLink("mn6_forward","Redo",void 0,1),t+=this.getLink("mn6_fullscreen","Full Screen",void 0,1),t+="

      • ",t+="
    ",t}setMenu3(){let e=this.icn3dui;if(e.bNode)return"";let t="";return t+="
    ",t+="",t+="

    Style

    ",t+="
    ",t+=this.setMenu3_base(),t+="
    ",t+="    ",t+="
    ",t}setMenu3_base(){let e=this.icn3dui;if(e.bNode)return"";let t="";t+="
      ",void 0===e.cfg.cid&&(t+=this.getMenuText("mn3_proteinwrap","Proteins",void 0,1,1),t+="
        ",void 0!==e.cfg.align||void 0!==e.cfg.chainalign?t+=this.getRadio("mn3_proteins","mn3_proteinsRibbon","Ribbon",void 0,1,2):t+=this.getRadio("mn3_proteins","mn3_proteinsRibbon","Ribbon",!0,1,2),t+=this.getRadio("mn3_proteins","mn3_proteinsStrand","Strand",void 0,void 0,2),t+=this.getRadio("mn3_proteins","mn3_proteinsCylinder","Cylinder and Plate",void 0,void 0,2),t+=this.getRadio("mn3_proteins","mn3_proteinsSchematic","Schematic",void 0,1,2),void 0!==e.cfg.align||void 0!==e.cfg.chainalign?t+=this.getRadio("mn3_proteins","mn3_proteinsCalpha","C Alpha Trace",!0,1,2):t+=this.getRadio("mn3_proteins","mn3_proteinsCalpha","C Alpha Trace",void 0,1,2),t+=this.getRadio("mn3_proteins","mn3_proteinsBackbone","Backbone",void 0,void 0,2),t+=this.getRadio("mn3_proteins","mn3_proteinsBfactor","B-factor Tube",void 0,1,2),t+=this.getRadio("mn3_proteins","mn3_proteinsLines","Lines",void 0,1,2),t+=this.getRadio("mn3_proteins","mn3_proteinsStick","Stick",void 0,1,2),t+=this.getRadio("mn3_proteins","mn3_proteinsBallstick","Ball and Stick",void 0,1,2),t+=this.getRadio("mn3_proteins","mn3_proteinsSphere","Sphere",void 0,1,2),t+=this.getRadio("mn3_proteins","mn3_proteinsNo","Hide",void 0,1,2),t+="
      ",t+="",t+=this.getMenuText("mn3_sidecwrap","Side Chains",void 0,1,1),t+="
        ",t+=this.getRadio("mn3_sidec","mn3_sidecLines","Lines",void 0,1,2),t+=this.getRadio("mn3_sidec","mn3_sidecStick","Stick",void 0,1,2),t+=this.getRadio("mn3_sidec","mn3_sidecBallstick","Ball and Stick",void 0,1,2),t+=this.getRadio("mn3_sidec","mn3_sidecSphere","Sphere",void 0,1,2),t+=this.getRadio("mn3_sidec","mn3_sidecNo","Hide",!0,1,2),t+="
      ",t+="",t+=this.getMenuText("mn3_nuclwrap","Nucleotides",void 0,1,1),t+="
        ",t+=this.getRadio("mn3_nucl","mn3_nuclCartoon","Cartoon",!0,1,2),t+=this.getRadio("mn3_nucl","mn3_nuclPhos","O3' Trace",void 0,1,2),t+=this.getRadio("mn3_nucl","mn3_nuclBackbone","Backbone",void 0,void 0,2),t+=this.getRadio("mn3_nucl","mn3_nuclSchematic","Schematic",void 0,1,2),t+=this.getRadio("mn3_nucl","mn3_nuclLines","Lines",void 0,1,2),t+=this.getRadio("mn3_nucl","mn3_nuclStick","Stick",void 0,1,2),t+=this.getRadio("mn3_nucl","mn3_nuclBallstick","Ball and Stick",void 0,1,2),t+=this.getRadio("mn3_nucl","mn3_nuclSphere","Sphere",void 0,1,2),t+=this.getRadio("mn3_nucl","mn3_nuclNo","Hide",void 0,1,2),t+="
      ",t+="",t+=this.getMenuText("mn3_ntbasewrap","Nucl. Bases",void 0,1,1),t+="
        ",t+=this.getRadio("mn3_ntbase","mn3_ntbaseLines","Lines",void 0,1,2),t+=this.getRadio("mn3_ntbase","mn3_ntbaseStick","Stick",void 0,1,2),t+=this.getRadio("mn3_ntbase","mn3_ntbaseBallstick","Ball and Stick",void 0,1,2),t+=this.getRadio("mn3_ntbase","mn3_ntbaseSphere","Sphere",void 0,1,2),t+=this.getRadio("mn3_ntbase","mn3_ntbaseNo","Hide",!0,1,2),t+="
      ",t+=""),t+=this.getMenuText("mn3_ligwrap","Chemicals",void 0,1,1),t+="
        ",t+=this.getRadio("mn3_lig","mn3_ligLines","Lines",void 0,1,2),void 0===e.cfg.cid?(t+=this.getRadio("mn3_lig","mn3_ligStick","Stick",!0,1,2),t+=this.getRadio("mn3_lig","mn3_ligBallstick","Ball and Stick",void 0,1,2)):(t+=this.getRadio("mn3_lig","mn3_ligStick","Stick",void 0,1,2),t+=this.getRadio("mn3_lig","mn3_ligBallstick","BalHydrogensl and Stick",!0,1,2)),t+=this.getRadio("mn3_lig","mn3_ligSchematic","Schematic",void 0,1,2),t+=this.getRadio("mn3_lig","mn3_ligSphere","Sphere",void 0,1,2),t+=this.getRadio("mn3_lig","mn3_ligNo","Hide",void 0,1,2),t+="
      ",t+="",t+=this.getMenuText("mn3_hydrogenswrap","Hydrogens",void 0,1,1),t+="
        ",t+=this.getRadio("mn3_hydrogens","mn3_hydrogensYes","Show",!0,1,2),t+=this.getRadio("mn3_hydrogens","mn3_hydrogensNo","Hide",void 0,1,2),t+="
      ",t+="",void 0===e.cfg.cid&&(t+=this.getMenuText("mn3_glycanwrap","Glycans",void 0,void 0,1),t+="
        ",t+=this.getRadio("mn3_glycansCart","mn3_glycansCartYes","Show Cartoon",void 0,void 0,2),t+=this.getRadio("mn3_glycansCart","mn3_glycansCartNo","Hide Cartoon",!0,void 0,2),t+="
      ",t+=""),t+=this.getMenuText("mn3_ionswrap","Ions",void 0,1,1),t+="
        ",t+=this.getRadio("mn3_ions","mn3_ionsSphere","Sphere",!0,1,2),t+=this.getRadio("mn3_ions","mn3_ionsDot","Dot",void 0,1,2),t+=this.getRadio("mn3_ions","mn3_ionsNo","Hide",void 0,1,2),t+="
      ",t+="",t+=this.getMenuText("mn3_waterwrap","Water",void 0,1,1),t+="
        ",t+=this.getRadio("mn3_water","mn3_waterSphere","Sphere",void 0,1,2),t+=this.getRadio("mn3_water","mn3_waterDot","Dot",void 0,1,2),t+=this.getRadio("mn3_water","mn3_waterNo","Hide",!0,1,2),t+="
      ",t+="",t+=this.getLink("mn3_setThickness","Preferences",void 0,1),t+=this.getMenuSep(),t+=this.getLink("mn3_styleSave","Save Style",void 0,2),t+=this.getLink("mn3_styleApplySave","Apply Saved Style",void 0,2),t+=this.getMenuSep(),t+=this.getMenuText("mn5_surfacewrap","Surface Type",void 0,1,1),t+="
        ",t+=this.getRadio("mn5_surface","mn5_surfaceVDW","Van der Waals",void 0,1,2),t+=this.getRadio("mn5_surface","mn5_surfaceVDWContext","VDW with Context",void 0,void 0,2),t+=this.getRadio("mn5_surface","mn5_surfaceMolecular","Molecular Surface",void 0,1,2),t+=this.getRadio("mn5_surface","mn5_surfaceMolecularContext","MS with Context",void 0,void 0,2),t+=this.getRadio("mn5_surface","mn5_surfaceSAS","Solvent Accessible",void 0,1,2),t+=this.getRadio("mn5_surface","mn5_surfaceSASContext","SA with Context",void 0,void 0,2),t+="
      ",t+="",t+=this.getLink("mn5_surfaceNo","Remove Surface",1,1),t+=this.getMenuText("mn5_surfaceop","Surface Opacity",void 0,1,1),t+="
        ",t+=this.getMenuText("mn5_surfaceopfast","Fast Transparency",void 0,1,2),t+="
          ",t+=this.getRadio("mn5_opacity","mn5_opacity10","1.0",!0,1,3);for(let e=9;e>0;--e)t+=this.getRadio("mn5_opacity","mn5_opacity0"+e,"0."+e,1,3);t+="
        ",t+="",t+=this.getMenuText("mn5_surfaceopslow","Slow Transparency",void 0,void 0,2),t+="
          ",t+=this.getRadio("mn5_opacityslow","mn5_opacityslow10","1.0",!0,void 0,3);for(let e=9;e>0;--e)t+=this.getRadio("mn5_opacityslow","mn5_opacityslow0"+e,"0."+e,void 0,void 0,3);return t+="
        ",t+="",t+="
      ",t+=this.getMenuText("mn5_wireframewrap","Surface Wireframe",void 0,1,1),t+="
        ",t+=this.getRadio("mn5_wireframe","mn5_wireframeYes","Yes",void 0,1,2),t+=this.getRadio("mn5_wireframe","mn5_wireframeNo","No",!0,1,2),t+="
      ",t+="",t+=this.getMenuSep(),t+=this.getLink("mn5_cartoonshape","Cartoon for a Set",void 0,1),t+=this.getLink("mn5_linebtwsets","Line btw. Two Sets",void 0,1),void 0===e.cfg.cid&&void 0===e.cfg.align&&void 0===e.cfg.chainalign&&void 0===e.cfg.mmdbaf&&(t+=this.getMenuSep(),t+=this.getLinkWrapper2("mn5_map","Electron Density","mapWrapper1",void 0,1),t+="
        ",t+=this.getLink("mn5_elecmap2fofc","2Fo-Fc Map",void 0,2),t+=this.getLink("mn5_elecmapfofc","Fo-Fc Map",void 0,2),t+=this.getLinkWrapper("mn5_elecmapNo","Remove Map","mapWrapper2",void 0,2),t+="
      ",t+="",t+=this.getLinkWrapper2("mn5_map3","Map Wireframe","mapWrapper3",void 0,1),t+="
        ",t+=this.getRadio("mn5_mapwireframe","mn5_mapwireframeYes","Yes",!0,void 0,2),t+=this.getRadio("mn5_mapwireframe","mn5_mapwireframeNo","No",void 0,void 0,2),t+="
      ",t+="",void 0===e.cfg.mmtfid&&(t+=this.getLinkWrapper("mn5_emmap","EM Density Map","emmapWrapper1",void 0,1),t+=this.getLinkWrapper("mn5_emmapNo","Remove EM Map","emmapWrapper2",void 0,1),t+=this.getLinkWrapper2("mn5_emmap3","EM Map Wireframe","emmapWrapper3",void 0,1),t+="
        ",t+=this.getRadio("mn5_emmapwireframe","mn5_emmapwireframeYes","Yes",!0,void 0,2),t+=this.getRadio("mn5_emmapwireframe","mn5_emmapwireframeNo","No",void 0,void 0,2),t+="
      ",t+="")),t+=this.getMenuSep(),t+=this.getMenuText("mn6_bkgdwrap","Background",void 0,1,1),t+="
        ",t+=this.getRadio("mn6_bkgd","mn6_bkgdTransparent","Transparent",void 0,1,2),t+=this.getRadio("mn6_bkgd","mn6_bkgdBlack","Black",!0,1,2),t+=this.getRadio("mn6_bkgd","mn6_bkgdGrey","Gray",void 0,1,2),t+=this.getRadio("mn6_bkgd","mn6_bkgdWhite","White",void 0,1,2),t+="
      ",t+="",t+=this.getMenuText("mn6_themewrap","Dialog Color",void 0,void 0,1),t+="
        ",t+=this.getRadio("mn6_theme","mn6_themeBlue","Blue",!0,void 0,2),t+=this.getRadio("mn6_theme","mn6_themeOrange","Orange",void 0,void 0,2),t+=this.getRadio("mn6_theme","mn6_themeBlack","Black",void 0,void 0,2),t+="
      ",t+="",t+="

      • ",t+="
    ",t}setMenu4(){let e=this.icn3dui;if(e.bNode)return"";let t="";return t+="
    ",t+="",t+="

    Color

    ",t+="
    ",t+=this.setMenu4_base(),t+="
    ",t+="    ",t+="
    ",t}setMenu4_base(){let e=this.icn3dui;if(e.bNode)return"";let t="";return t+="
      ",t+=this.getMenuText("mn4_clrwrap","Unicolor","icn3d-menupd",1,1),t+="
        ",t+=this.getMenuText("uniclrRedwrap","Red",void 0,1,2),t+="
          ",t+=this.getRadClr("mn4_clr","uniclrRed1","Red","F00",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrRed2","Indian Red","CD5C5C",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrRed3","Light Coral","F08080",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrRed4","Salmon","FA8072",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrRed5","Dark Salmon","E9967A",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrRed6","Light Salmon","FFA07A",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrRed7","Crimson","DC143C",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrRed8","Fire Brick","B22222",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrRed9","Dark Red","8B0000",void 0,1,3),t+="
        ",t+=this.getMenuText("uniclrPinkwrap","Pink",void 0,1,2),t+="
          ",t+=this.getRadClr("mn4_clr","uniclrPink1","Pink","FFC0CB",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrPink2","Light Pink","FFB6C1",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrPink3","Hot Pink","FF69B4",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrPink4","Deep Pink","FF1493",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrPink5","Medium Violet Red","C71585",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrPink6","Pale Violet Red","DB7093",void 0,1,3),t+="
        ",t+=this.getMenuText("uniclrOrangewrap","Orange",void 0,1,2),t+="
          ",t+=this.getRadClr("mn4_clr","uniclrOran1","Orange","FFA500",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrOran2","Dark Orange","FF8C00",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrOran3","Orange Red","FF4500",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrOran4","Tomato","FF6347",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrOran5","Coral","FF7F50",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrOran6","Light Salmon","FFA07A",void 0,1,3),t+="
        ",t+=this.getMenuText("uniclrYellowwrap","Yellow",void 0,1,2),t+="
          ",t+=this.getRadClr("mn4_clr","uniclrYllw1","Yellow","FF0",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrYllw2","Gold","FFD700",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrYllw3","Light Yellow","FFFFE0",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrYllw4","Lemon Chiffon","FFFACD",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrYllw5","Light Golden Rod","FAFAD2",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrYllw6","Papaya Whip","FFEFD5",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrYllw7","Moccasin","FFE4B5",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrYllw8","Peach Puff","FFDAB9",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrYllw9","Pale Golden Rod","EEE8AA",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrYllw10","Khaki","F0E68C",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrYllw11","Dark Khaki","BDB76B",void 0,1,3),t+="
        ",t+=this.getMenuText("uniclrMagentawrap","Magenta",void 0,1,2),t+="
          ",t+=this.getRadClr("mn4_clr","uniclrMgnt1","Magenta","F0F",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt2","Orchid","DA70D6",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt3","Violet","EE82EE",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt4","Plum","DDA0DD",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt5","Thistle","D8BFD8",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt6","Lavender","E6E6FA",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt7","Medium Orchid","BA55D3",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt8","Medium Purple","9370DB",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt9","Rebecca Purple","663399",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt10","Blue Violet","8A2BE2",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt11","Dark Violet","9400D3",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt12","Dark Orchid","9932CC",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt13","Dark Magenta","8B008B",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt14","Purple","800080",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt15","Indigo","4B0082",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt16","Slat Blue","6A5ACD",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt17","Dark Slate Blue","483D8B",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrMgnt18","Medium Slat Blue","6A5ACD",void 0,1,3),t+="
        ",t+=this.getMenuText("uniclrGreenwrap","Green",void 0,1,2),t+="
          ",t+=this.getRadClr("mn4_clr","uniclrGrn1","Green","0F0",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn2","Dark Green","006400",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn3","Yellow Green","9ACD32",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn4","Olive Drab","6B8E23",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn5","Olive","808000",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn6","Dark Olive Green","556B2F",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn7","Medium Aquamarine","66CDAA",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn8","Dark Sea Green","8FBC8B",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn9","Lignt Sea Green","20B2AA",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn10","Dark Cyan","008B8B",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn11","Teal","008080",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn12","Forest Green","228B22",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn13","Sea Green","2E8B57",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn14","Medium Sea Green","3CB371",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn15","Spring Green","00FF7F",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn16","Medium Spring","00FA9A",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn17","Light Green","90EE90",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn18","Pale Green","98FB98",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn19","Lime Green","32CD32",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn20","Lawn Green","7CFC00",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn21","Chartreuse","7FFF00",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGrn22","Green Yellow","ADFF2F",void 0,1,3),t+="
        ",t+=this.getMenuText("uniclrCyanwrap","Cyan",void 0,1,2),t+="
          ",t+=this.getRadClr("mn4_clr","uniclrCyan1","Cyan","0FF",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrCyan2","Light Cyan","E0FFFF",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrCyan3","Pale Turquoise","AFEEEE",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrCyan4","Aquamarine","7FFFD4",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrCyan5","Turquoise","40E0D0",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrCyan6","Medium Turquoise","48D1CC",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrCyan7","Dark Turquoise","00CED1",void 0,1,3),t+="
        ",t+=this.getMenuText("uniclrBluewrap","Blue",void 0,1,2),t+="
          ",t+=this.getRadClr("mn4_clr","uniclrBlue1","Blue","00F",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue2","Medium Blue","0000CD",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue3","Dark Blue","00008B",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue4","Navy","000080",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue5","Midnight Blue","191970",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue6","Royal Blue","4169E1",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue7","Medium Slate Blue","7B68EE",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue8","Corn Flower Blue","6495ED",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue9","Dodger Blue","1E90FF",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue10","Deep Sky Blue","00BFFF",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue11","Light Sky Blue","87CEFA",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue12","Sky Blue","87CEEB",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue13","Light Blue","ADD8E6",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue14","Powder Blue","B0E0E6",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue15","Light Steel Blue","B0C4DE",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue16","Steel Blue","4682B4",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBlue17","Cadet Blue","5F9EA0",void 0,1,3),t+="
        ",t+=this.getMenuText("uniclrBrownwrap","Brown",void 0,1,2),t+="
          ",t+=this.getRadClr("mn4_clr","uniclrBrown1","Brown","A52A2A",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown2","Maroon","800000",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown3","Sienna","A0522D",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown4","Saddle Brown","8B4513",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown5","Chocolate","D2691E",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown6","Peru","CD853F",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown7","Dark Golden Rod","B8860B",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown8","Golden Rod","DAA520",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown9","Sandy Brown","F4A460",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown10","Rosy Brown","BC8F8F",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown11","Tan","D2B48C",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown12","Burlywood","DEB887",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown13","Wheat","F5DEB3",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown14","Navajo White","FFDEAD",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown15","Bisque","FFE4C4",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown16","Blanched Almond","FFEBCD",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrBrown17","Corn Silk","FFF8DC",void 0,1,3),t+="
        ",t+=this.getMenuText("uniclrWhitewrap","White",void 0,1,2),t+="
          ",t+=this.getRadClr("mn4_clr","uniclrWhite1","White","FFF",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite2","Snow","FFFAFA",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite3","Honey Dew","F0FFF0",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite4","Mint Cream","F5FFFA",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite5","Azure","F0FFFF",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite6","Alice Blue","F0F8FF",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite7","Ghost White","F8F8FF",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite8","White Smoke","F5F5F5",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite9","Sea Shell","FFF5EE",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite10","Beige","F5F5DC",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite11","Old Lace","FDF5E6",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite12","Floral White","FFFAF0",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite13","Ivory","FFFFF0",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite14","Antique White","FAEBD7",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite15","Linen","FAF0E6",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite16","Lavenderblush","FFF0F5",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrWhite17","Misty Rose","FFE4E1",void 0,1,3),t+="
        ",t+=this.getMenuText("uniclrGraywrap","Gray",void 0,1,2),t+="
          ",t+=this.getRadClr("mn4_clr","uniclrGray1","Gray","808080",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGray2","Dim Gray","696969",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGray3","Light Slate Gray","778899",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGray4","Slate Gray","708090",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGray5","Dark Slate Gray","2F4F4F",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGray6","Black","000000",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGray7","Dark Gray","A9A9A9",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGray8","Silver","C0C0C0",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGray9","Light Gray","D3D3D3",void 0,1,3),t+=this.getRadClr("mn4_clr","uniclrGray10","Gainsboro","DCDCDC",void 0,1,3),t+="
        ",t+="
      ",t+=this.getRadio("mn4_clr","mn4_clrCustom","Color Picker",void 0,void 0,1),t+=this.getMenuSep(),void 0===e.cfg.cid?(t+=this.getMenuText("mn4_clrRainbowwrap","Rainbow (R-V)","icn3d-menupd",1,1),t+="
        ",t+=this.getRadio("mn4_clr","mn4_clrRainbow","for Selection",void 0,1,2),t+=this.getRadio("mn4_clr","mn4_clrRainbowChain","for Chains",void 0,1,2),t+=this.getRadio("mn4_clr","mn4_clrRainbowSets","for Sets",void 0,void 0,2),t+=this.getRadio("mn4_clr","mn4_clrRainbowAcrossSets","across Sets",void 0,void 0,2),t+="
      ",t+=this.getMenuText("mn4_clrSpectrumwrap","Spectrum (V-R)","icn3d-menupd",1,1),t+="
        ",t+=this.getRadio("mn4_clr","mn4_clrSpectrum","for Selection",void 0,1,2),t+=this.getRadio("mn4_clr","mn4_clrSpectrumChain","for Chains",void 0,1,2),t+=this.getRadio("mn4_clr","mn4_clrSpectrumSets","for Sets",void 0,void 0,2),t+=this.getRadio("mn4_clr","mn4_clrSpectrumAcrossSets","across Sets",void 0,void 0,2),t+="
      ",t+=this.getMenuText("mn4_clrSSwrap","Secondary","icn3d-menupd",1,1),t+="
        ",t+=this.getRadio("mn4_clr","mn4_clrSSGreen","Sheet in Green",void 0,1,2),t+=this.getRadio("mn4_clr","mn4_clrSSYellow","Sheet in Yellow",void 0,1,2),t+=this.getRadio("mn4_clr","mn4_clrSSSpectrum","Spectrum",void 0,void 0,2),t+="
      ",t+=this.getRadio("mn4_clr","mn4_clrCharge","Charge",void 0,1,1),t+=this.getMenuText("mn4_hydrophobicwrap","Hydrophobicity","icn3d-menupd",1,1),t+="
        ",t+=this.getRadio("mn4_clr","mn4_clrNormalizedHP","Normalized",void 0,1,2),t+=this.getRadio("mn4_clr","mn4_clrHydrophobic","Wimley-White",void 0,void 0,2),t+="
      ",t+=this.getMenuText("mn4_clrBfactorwrap","B-factor","icn3d-menupd",1,1),t+="
        ",t+=this.getRadio("mn4_clr","mn4_clrBfactor","Original",void 0,1,2),t+=this.getRadio("mn4_clr","mn4_clrBfactorNorm","Percentile",void 0,1,2),t+="
      ",t+=this.getRadio("mn4_clr","mn4_clrArea",'Solvent
      Accessibility',void 0,void 0,1),t+=this.getRadio("mn4_clr","mn4_clrStructure","Structure",void 0,1,1),void 0!==e.cfg.align||void 0!==e.cfg.chainalign||void 0!==e.cfg.blast_rep_id?t+=this.getRadio("mn4_clr","mn4_clrChain","Chain",void 0,1,1):t+=this.getRadio("mn4_clr","mn4_clrChain","Chain",!0,1,1),t+=this.getRadio("mn4_clr","mn4_clrdomain","3D Domain",void 0,void 0,1),void 0===e.cfg.cid&&(t+=this.getMenuText("mn4_clrsetswrap","Defined Sets","icn3d-menupd",void 0,1),t+="
        ",t+=this.getRadio("mn4_clr","mn4_clrsets",'Rainbow for Selected Sets
        in "Analysis > Defined Sets"',void 0,void 0,2),t+="
      ",t+=""),t+=this.getMenuText("mn4_clrResiduewrap","Residue","icn3d-menupd",1,1),t+="
        ",t+=this.getRadio("mn4_clr","mn4_clrResidue","Default",void 0,1,2),t+=this.getRadio("mn4_clr","mn4_clrResidueCustom","Custom",void 0,void 0,2),t+="
      ",t+=this.getRadio("mn4_clr","mn4_clrAtom","Atom",void 0,1,1),void 0!==e.cfg.align||void 0!==e.cfg.chainalign?(t+=this.getRadio("mn4_clr","mn4_clrIdentity","Identity",!0,void 0,2),t+=this.getRadio("mn4_clr","mn4_clrConserved","Conservation",void 0,void 0,2)):void 0!==e.cfg.blast_rep_id?(t+=this.getRadio("mn4_clr","mn4_clrIdentity","Identity",void 0,void 0,2),t+=this.getRadio("mn4_clr","mn4_clrConserved","Conservation",!0,void 0,2)):(t+=this.getRadio("mn4_clr","mn4_clrIdentity","Identity",void 0,void 0,2),t+=this.getRadio("mn4_clr","mn4_clrConserved","Conservation",void 0,void 0,2)),t+=this.getRadio("mn4_clr","mn4_clrConfidence","pLDDT",void 0,1,1),t+=this.getRadio("mn4_clr","mn4_clrIgstrand","Ig Strand",void 0,void 0,2),t+=this.getRadio("mn4_clr","mn4_clrIgproto","Ig Protodomain",void 0,void 0,2)):t+=this.getRadio("mn4_clr","mn4_clrAtom","Atom",!0,1,1),t+=this.getMenuSep(),t+=this.getLink("mn4_clrSave","Save Color",void 0,1),t+=this.getLink("mn4_clrApplySave","Apply Saved Color",void 0,1),t+="

      • ",t+="
    ",t}setMenu5(){let e=this.icn3dui;if(e.bNode)return"";let t="";return t+="
    ",t+="",t+="

     Analysis

    ",t+="
    ",t+=this.setMenu5_base(),t+="
    ",t+="    ",t+="
    ",t}setMenu5_base(){let e=this.icn3dui;if(e.bNode)return"";let t="";t+="
      ",void 0===e.cfg.cid&&(t+=this.getLink("mn6_selectannotations","Seq. & Annotations "+e.htmlCls.wifiStr,1,1),t+=this.getLink("mn2_alignment","Aligned Seq. "+e.htmlCls.wifiStr,void 0,1),void 0===e.cfg.mmdbid&&void 0===e.cfg.gi&&void 0===e.cfg.blast_rep_id&&void 0===e.cfg.align&&void 0===e.cfg.chainalign||(t+=this.getLink("mn2_2ddgm","2D Diagram "+e.htmlCls.wifiStr,1,1)),t+=this.getMenuText("2dctnwrap","2D Cartoon",void 0,void 0,1),t+="
        ",t+=this.getLink("2dctn_chain","Chain Level",void 0,2),t+=this.getLink("2dctn_domain","Domain Level",void 0,2),t+=this.getLink("2dctn_secondary","Helix/Sheet Level",void 0,2),t+="
      ",t+="",t+=this.getLink("definedsets2","Defined Sets",1,1),t+=this.getMenuSep(),t+=this.getLink("mn6_hbondsYes","Interactions",1,1),t+=this.getMenuText("mn1_window","Bring to Front",void 0,void 0,1),t+="
        ",t+=this.getLink("mn1_window_table","Interaction Table",void 0,2),t+=this.getLink("mn1_window_linegraph","2D Interaction Network",void 0,2),t+=this.getLink("mn1_window_scatterplot","2D Interaction Map",void 0,2),t+=this.getLink("mn1_window_graph","2D Graph(Force-Directed)",void 0,2),t+="
      ",t+="",t+=this.getLink("mn6_contactmap","Contact Map",void 0,1),t+=this.getLink("mn1_mutation","Mutation "+e.htmlCls.wifiStr,1,1)),e.cfg.hidelicense||(t+=this.getMenuText("mn1_delphiwrap","DelPhi Potential",void 0,1,1),t+="
        ",t+=this.getLink("mn1_delphi","DelPhi Potential "+e.htmlCls.licenseStr,1,2),t+=this.getMenuText("mn1_phiwrap","Load PQR/Phi",void 0,void 0,2),t+="
          ",t+=this.getLink("mn1_phi","Local PQR/Phi/Cube File",void 0,3),t+=this.getLink("mn1_phiurl","URL PQR/Phi/Cube File",void 0,3),t+="
        ",t+="",t+=this.getLink("delphipqr","Download PQR",void 0,2),t+="
      ",t+=""),t+=this.getMenuSep(),t+=this.getMenuText("mn6_distancewrap","Distance",void 0,1,1),t+="
        ",t+=this.getRadio("mn6_distance","mn6_distanceYes","between Two Atoms",void 0,1,2),t+=this.getRadio("mn6_distance","mn6_distTwoSets","between Two Sets",void 0,void 0,2),t+=this.getRadio("mn6_distance","mn6_distManySets","Among Many Sets",void 0,void 0,2),t+=this.getRadio("mn6_distance","mn6_distanceNo","Hide",!0,1,2),t+="
      ",t+="",t+=this.getLink("mn6_area","Surface Area",1,1),t+=this.getMenuText("mn6_addlabelwrap","Label",void 0,1,1),t+="
        ",t+=this.getRadio("mn6_addlabel","mn6_addlabelYes","by Picking Atoms",void 0,void 0,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelSelection","per Selection",void 0,void 0,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelAtoms","per Atom",void 0,void 0,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelElements","per Atom Element",void 0,1,2),void 0===e.cfg.cid&&(t+=this.getRadio("mn6_addlabel","mn6_addlabelResidues","per Residue",void 0,1,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelResnum","per Residue & Number",void 0,1,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelRefnum","per Reference Number",void 0,1,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelIg","per Ig Domain",void 0,1,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelChains","per Chain",void 0,void 0,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelTermini","N- & C-Termini",void 0,1,2)),t+=this.getMenuSep(),t+=this.getRadio("mn6_addlabel","mn6_labelColor","Change Label Color",void 0,1,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelNo","Remove",!0,1,2),t+="
      ",t+="",t+=this.getMenuText("labelscalewrap","Label Scale",void 0,1,1),t+="
        ";for(let e=1;e<=4;++e){let s=2*e;t+=this.getRadio("mn6_labelscale","mn6_labelscale0"+s,"0."+s,void 0,1,2)}for(let e=2;e<=10;++e){let s=(e/2).toFixed(1);t+=2==e?this.getRadio("mn6_labelscale","mn6_labelscale"+e+"0",s,!0,1,2):this.getRadio("mn6_labelscale","mn6_labelscale"+e+"0",s,void 0,1,2)}if(t+="
      ",t+="",t+=this.getMenuSep(),void 0===e.cfg.cid){t+=this.getMenuText("mn6_chemicalbindingwrap","Chem. Binding",void 0,void 0,1),t+="
        ",t+=this.getRadio("mn6_chemicalbinding","mn6_chemicalbindingshow","Show",void 0,void 0,2),t+=this.getRadio("mn6_chemicalbinding","mn6_chemicalbindinghide","Hide",!0,void 0,2),t+="
      ",t+="",t+=this.getMenuText("mn6_ssbondswrap","Disulfide Bonds",void 0,1,1),t+="
        ",t+=this.getRadio("mn6_ssbonds","mn6_ssbondsYes","Show",!0,1,2),t+=this.getRadio("mn6_ssbonds","mn6_ssbondsExport","Export Pairs",void 0,void 0,2),t+=this.getRadio("mn6_ssbonds","mn6_ssbondsNo","Hide",void 0,1,2),t+="
      ",t+="",t+=this.getMenuText("mn6_clbondswrap","Cross-Linkages",void 0,void 0,1),t+="
        ",t+=this.getRadio("mn6_clbonds","mn6_clbondsYes","Show",!0,void 0,2),t+=this.getRadio("mn6_clbonds","mn6_clbondsExport","Export Pairs",void 0,void 0,2),t+=this.getRadio("mn6_clbonds","mn6_clbondsNo","Hide",void 0,void 0,2),t+="
      ",t+="";let s=void 0!==e.cfg.mmtfid||void 0!==e.cfg.pdbid||void 0!==e.cfg.opmid||void 0!==e.cfg.mmcifid||void 0!==e.cfg.mmdbid||void 0!==e.cfg.mmdbafid||void 0!==e.cfg.gi||void 0!==e.cfg.blast_rep_id;s&&(t+=this.getMenuText("assemblyWrapper","Assembly",void 0,1,1),t+="
        ",e.cfg.bu?(t+=this.getRadio("mn6_assembly","mn6_assemblyYes","Biological Assembly",!0,1,2),t+=this.getRadio("mn6_assembly","mn6_assemblyNo","Asymmetric Unit",void 0,1,2)):(t+=this.getRadio("mn6_assembly","mn6_assemblyYes","Biological Assembly",void 0,1,2),t+=this.getRadio("mn6_assembly","mn6_assemblyNo","Asymmetric Unit",!0,1,2)),t+="
      ",t+=""),t+=this.getMenuText("mn6_symmetrywrap","Symmetry",void 0,void 0,1),t+="
        ",s&&(t+=this.getLink("mn6_symmetry","from PDB(precalculated) "+e.htmlCls.wifiStr,void 0,2)),t+=this.getLink("mn6_symd","from SymD(Dynamic) "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn6_clear_sym","Clear SymD Symmetry",void 0,2),t+=this.getLink("mn6_axes_only","Show Axes Only",void 0,2),t+="
      ",t+="",t+=this.getMenuText("mn6_igrefwrap","Ref. Number",void 0,void 0,1),t+="
        ",t+=this.getLink("mn6_igrefYes","Show Ig for Selection",void 0,2),t+=this.getLink("mn6_igrefTpl","Ig w/ Specified Template",void 0,2),t+=this.getLink("mn6_alignrefTpl","Align w/ Specified Template",void 0,2),t+=this.getLink("mn6_igrefNo","Reset Ig Ref. Number",void 0,2),t+=this.getMenuSep(),t+=this.getLink("mn6_customref","Custom Ref. Number",void 0,2),t+="
      ",t+="",t+=this.getMenuSep()}return t+=this.getLink("mn6_yournote","Window Title",void 0,1),void 0!==e.cfg.cid?(t+=this.getMenuText("mn1_linkwrap","Links",void 0,void 0,1),t+="
        ",t+=this.getLink("mn1_link_structure","Compound Summary "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_link_vast","Similar Compounds "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_link_bind","Structures Bound "+e.htmlCls.wifiStr,void 0,2),t+="
      ",t+=""):(t+=this.getMenuText("mn1_linkwrap","Links",void 0,void 0,1),t+="
        ",t+=this.getLink("mn1_link_structure","Structure Summary "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_link_vast","Similar Structures "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_link_pubmed","Literature "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_link_protein","Protein "+e.htmlCls.wifiStr,void 0,2),t+="
      ",t+=""),t+="

      • ",t+="
    ",t}setMenu6(){let e=this.icn3dui;if(e.bNode)return"";let t="";return t+="
    ",t+="",t+="

    Help

    ",t+="
    ",t+=this.setMenu6_base(),t+="
    ",t+="    ",t+="
    ",t}setMenu6_base(){let e=this.icn3dui;if(e.bNode)return"";let t="";return t+="
      ",t+=this.getMenuUrl("abouticn3d",e.htmlCls.baseUrl+"icn3d/icn3d.html#about","About iCn3D "+e.REVISION+"",1,1),t+=this.getMenuUrl("gallery",e.htmlCls.baseUrl+"icn3d/icn3d.html#gallery","Live Gallery "+e.htmlCls.wifiStr,1,1),t+=this.getMenuUrl("video",e.htmlCls.baseUrl+"icn3d/icn3d.html#videos","Videos & Tutorials",1,1),t+=this.getMenuText("mn6_faq","FAQ",void 0,1,1),t+="
        ",t+=this.getMenuUrl("faq_viewstru",e.htmlCls.baseUrl+"icn3d/icn3d.html#viewstru","View structure",1,2),t+=this.getMenuUrl("faq_tfstru",e.htmlCls.baseUrl+"icn3d/icn3d.html#tfstru","Transform Structure",1,2),t+=this.getMenuUrl("faq_selsubset",e.htmlCls.baseUrl+"icn3d/icn3d.html#selsubset","Select Subsets",1,2),t+=this.getMenuUrl("faq_stylecolor",e.htmlCls.baseUrl+"icn3d/icn3d.html#changestylecolor","Change Style/Color",1,2),t+=this.getMenuUrl("faq_savework",e.htmlCls.baseUrl+"icn3d/icn3d.html#saveview","Save Work",1,2),t+=this.getMenuUrl("faq_showanno",e.htmlCls.baseUrl+"icn3d/icn3d.html#showanno","Show Annotations",1,2),t+=this.getMenuUrl("faq_exportanno",e.htmlCls.baseUrl+"icn3d/icn3d.html#exportanno","Export Annotations",1,2),t+=this.getMenuUrl("faq_interanal",e.htmlCls.baseUrl+"icn3d/icn3d.html#interanalysis","Interaction Analysis",1,2),t+=this.getMenuUrl("faq_mutanal",e.htmlCls.baseUrl+"icn3d/icn3d.html#mutationanalysis","Mutation Analysis",1,2),t+=this.getMenuUrl("faq_elecpot",e.htmlCls.baseUrl+"icn3d/icn3d.html#elecpot","Electrostatic Pot.",1,2),t+=this.getMenuUrl("faq_simipdb",e.htmlCls.baseUrl+"icn3d/icn3d.html#simivast","Similar PDB",1,2),t+=this.getMenuUrl("faq_simialphapdb",e.htmlCls.baseUrl+"icn3d/icn3d.html#simifoldseek","Similar AlphaFold/PDB",1,2),t+=this.getMenuUrl("faq_alnstru",e.htmlCls.baseUrl+"icn3d/icn3d.html#alignmul","Align Multiple Structures",1,2),t+=this.getMenuUrl("faq_batchanal",e.htmlCls.baseUrl+"icn3d/icn3d.html#batchanalysis","Batch Analysis",1,2),t+=this.getMenuUrl("faq_batchanal",e.htmlCls.baseUrl+"icn3d/icn3d.html#igrefnum","Assign Ig Ref. Numbers",1,2),t+=this.getMenuUrl("faq_embedicn3d",e.htmlCls.baseUrl+"icn3d/icn3d.html#embedicn3d","Embed iCn3D",1,2),t+="
      ",t+="",t+=this.getMenuUrl("citing",e.htmlCls.baseUrl+"icn3d/icn3d.html#citing","Citing iCn3D",void 0,1),t+=this.getMenuText("mn6_source","Source Code",void 0,1,1),t+="
        ",t+=this.getMenuUrl("github","https://github.com/ncbi/icn3d","GitHub (browser) "+e.htmlCls.wifiStr,1,2),t+=this.getMenuUrl("npm","https://www.npmjs.com/package/icn3d","npm (Node.js) "+e.htmlCls.wifiStr,1,2),t+=this.getMenuUrl("notebook","https://pypi.org/project/icn3dpy","Jupyter Notebook "+e.htmlCls.wifiStr,1,2),t+="
      ",t+="",t+=this.getMenuText("mn6_develop","Develop",void 0,void 0,1),t+="
        ",t+=this.getMenuUrl("dev_embedicn3d2",e.htmlCls.baseUrl+"icn3d/icn3d.html#HowToUse","Embed iCn3D",void 0,2),t+=this.getMenuUrl("dev_urlpara",e.htmlCls.baseUrl+"icn3d/icn3d.html#parameters","URL Parameters",void 0,2),t+=this.getMenuUrl("dev_command",e.htmlCls.baseUrl+"icn3d/icn3d.html#commands","Commands",void 0,2),t+=this.getMenuUrl("dev_datastru",e.htmlCls.baseUrl+"icn3d/icn3d.html#datastructure","Data Structure",void 0,2),t+=this.getMenuUrl("dev_classstru",e.htmlCls.baseUrl+"icn3d/icn3d.html#classstructure","Class Structure",void 0,2),t+=this.getMenuUrl("dev_addclass",e.htmlCls.baseUrl+"icn3d/icn3d.html#addclass","Add New Classes",void 0,2),t+=this.getMenuUrl("dev_modfunc",e.htmlCls.baseUrl+"icn3d/icn3d.html#modifyfunction","Modify Functions",void 0,2),t+=this.getMenuUrl("dev_restful",e.htmlCls.baseUrl+"icn3d/icn3d.html#restfulapi","RESTful APIs",void 0,2),t+=this.getMenuUrl("dev_contributor",e.htmlCls.baseUrl+"icn3d/icn3d.html#contributors","iCn3D Contributors",void 0,2),t+="
      ",t+="",t+=this.getMenuUrl("helpdoc",e.htmlCls.baseUrl+"icn3d/docs/icn3d_help.html","Help Doc "+e.htmlCls.wifiStr,1,1),t+=this.getMenuSep(),t+=this.getMenuText("mn6_tfhint","Transform Hints",void 0,1,1),t+="
        ",t+=this.getMenuText("mn6_rotate","Rotate",void 0,1,2),t+="
          ",t+="
        • Left Mouse (Click & Drag)
          • ",t+="
        • Key l: Left
          • ",t+="
        • Key j: Right
          • ",t+="
        • Key i: Up
          • ",t+="
        • Key m: Down
          • ",t+="
        • Shift + Key l: Left 90°
          • ",t+="
        • Shift + Key j: Right 90°
          • ",t+="
        • Shift + Key i: Up 90°
          • ",t+="
        • Shift + Key m: Down 90°
          • ",t+="
        ",t+="",t+=this.getMenuText("mn6_zoom","Zoom",void 0,1,2),t+="
          ",t+="
        • Middle Mouse
          (Pinch & Spread)
          • ",t+="
        • Key z: Zoom in
          • ",t+="
        • Key x: Zoom out
          • ",t+="
        ",t+="",t+=this.getMenuText("mn6_translate","Translate",void 0,1,2),t+="
          ",t+="
        • Right Mouse
          (Two Finger Click & Drag)
          • ",t+="
        ",t+="",t+="
      ",t+="",t+=this.getMenuUrl("selhints",e.htmlCls.baseUrl+"icn3d/icn3d.html#selsubset","Selection Hints",void 0,1),t+=this.getMenuUrl("helpdesk","https://support.nlm.nih.gov/support/create-case/","Write to Help Desk",1,1),t+="

      • ",t+="
    ",t}hideMenu(){let e=this.icn3dui;e.bNode||(void 0!==$("#"+e.pre+"mnlist")[0]&&($("#"+e.pre+"mnlist")[0].style.display="none"),void 0!==$("#"+e.pre+"mnLogSection")[0]&&($("#"+e.pre+"mnLogSection")[0].style.display="none"),void 0!==$("#"+e.pre+"cmdlog")[0]&&($("#"+e.pre+"cmdlog")[0].style.display="none"),$("#"+e.pre+"title")[0].style.margin="10px 0 0 10px")}showMenu(){let e=this.icn3dui;e.bNode||(void 0!==$("#"+e.pre+"mnlist")[0]&&($("#"+e.pre+"mnlist")[0].style.display="block"),void 0!==$("#"+e.pre+"mnLogSection")[0]&&($("#"+e.pre+"mnLogSection")[0].style.display="block"),void 0!==$("#"+e.pre+"cmdlog")[0]&&($("#"+e.pre+"cmdlog")[0].style.display="block"))}}class c{constructor(e){this.icn3dui=e}openDlg(e,t){let s=this.icn3dui;s.icn3d,s.bNode||(e=s.pre+e,s.cfg.notebook?this.openDlgNotebook(e,t):this.openDlgRegular(e,t),s.htmlCls.themecolor||(s.htmlCls.themecolor="blue"),s.htmlCls.setMenuCls.setTheme(s.htmlCls.themecolor))}addSaveButton(e){let t=this.icn3dui;t.icn3d,t.bNode||void 0!==this.dialogHashSave&&this.dialogHashSave.hasOwnProperty(e)||($("#"+e).parent().children(".ui-dialog-titlebar").append("
    "),void 0===this.dialogHashSave&&(this.dialogHashSave={}),this.dialogHashSave[e]=1)}addHideButton(e){let t=this.icn3dui;t.icn3d,t.bNode||void 0!==this.dialogHashHide&&this.dialogHashHide.hasOwnProperty(e)||($("#"+e).parent().children(".ui-dialog-titlebar").append("
    "),void 0===this.dialogHashHide&&(this.dialogHashHide={}),this.dialogHashHide[e]=1)}getDialogStatus(){let e=this.icn3dui;if(e.icn3d,e.bNode)return;let t={},s={},i=$("#"+e.pre+"dl_selectannotations").hasClass("ui-dialog-content"),n=$("#"+e.pre+"dl_graph").hasClass("ui-dialog-content"),l=$("#"+e.pre+"dl_linegraph").hasClass("ui-dialog-content"),r=$("#"+e.pre+"dl_scatterplot").hasClass("ui-dialog-content"),o=$("#"+e.pre+"dl_contactmap").hasClass("ui-dialog-content"),a=$("#"+e.pre+"dl_alignerrormap").hasClass("ui-dialog-content"),d=$("#"+e.pre+"dl_interactionsorted").hasClass("ui-dialog-content"),c=$("#"+e.pre+"dl_alignment").hasClass("ui-dialog-content"),h=$("#"+e.pre+"dl_2ddgm").hasClass("ui-dialog-content"),p=$("#"+e.pre+"dl_2dctn").hasClass("ui-dialog-content"),m=$("#"+e.pre+"dl_definedsets").hasClass("ui-dialog-content");return t.bSelectannotationsInit2=!1,t.bGraph2=!1,t.bLineGraph2=!1,t.bScatterplot2=!1,t.bTable2=!1,t.bAlignmentInit2=!1,t.bTwoddgmInit2=!1,t.bTwodctnInit2=!1,t.bSetsInit2=!1,s.dl_selectannotations="bSelectannotationsInit2",s.dl_graph="bGraph2",s.dl_linegraph="bLineGraph2",s.dl_scatterplot="bScatterplot2",s.dl_contactmap="bContactmap2",s.dl_alignerrormap="bAlignerrormap2",s.dl_interactionsorted="bTable2",s.dl_alignment="bAlignmentInit2",s.dl_2ddgm="bTwoddgmInit2",s.dl_2dctn="bTwodctnInit2",s.dl_definedsets="bSetsInit2",i&&(t.bSelectannotationsInit2=$("#"+e.pre+"dl_selectannotations").dialog("isOpen")),n&&(t.bGraph2=$("#"+e.pre+"dl_graph").dialog("isOpen")),l&&(t.bLineGraph2=$("#"+e.pre+"dl_linegraph").dialog("isOpen")),r&&(t.bScatterplot2=$("#"+e.pre+"dl_scatterplot").dialog("isOpen")),o&&(t.bContactmap2=$("#"+e.pre+"dl_contactmap").dialog("isOpen")),a&&(t.bAlignerror2=$("#"+e.pre+"dl_alignerrormap").dialog("isOpen")),d&&(t.bTable2=$("#"+e.pre+"dl_interactionsorted").dialog("isOpen")),c&&(t.bAlignmentInit2=$("#"+e.pre+"dl_alignment").dialog("isOpen")),h&&(t.bTwoddgmInit2=$("#"+e.pre+"dl_2ddgm").dialog("isOpen")),p&&(t.bTwodctnInit2=$("#"+e.pre+"dl_2dctn").dialog("isOpen")),m&&(t.bSetsInit2=$("#"+e.pre+"dl_definedsets").dialog("isOpen")),{status:t,id2flag:s}}openDlgHalfWindow(e,t,s,i){let n=this.icn3dui,l=n.icn3d;if(n.bNode)return;let r=this,o=n.htmlCls.width2d+20;l.resizeCanvasCls.resizeCanvas(n.htmlCls.WIDTH-s,n.htmlCls.HEIGHT,i);let a,d=n.htmlCls.HEIGHT,c=s;a=!n.cfg.showmenu||n.utilsCls.isMobile()||n.cfg.mobilemenu?{my:"left top",at:"right top",of:"#"+n.pre+"viewer",collision:"none"}:{my:"left top",at:"right top+40",of:"#"+n.pre+"viewer",collision:"none"},n.cfg.resize=!1,window.dialog=$("#"+e).dialog({autoOpen:!0,title:t,height:d,width:c,modal:!1,position:a,close:function(t){let s=r.getDialogStatus(),i=s.status,a=s.id2flag,d=!1;for(let t in a){let s=e===n.pre+t;for(let e in i)i.hasOwnProperty(e)||(s=s&&!i[e]);d=d||s}if(d)if(i.bTwoddgmInit2||i.bTwodctnInit2||i.bSetsInit2){let e=n.utilsCls.isMobile()?n.htmlCls.WIDTH:n.htmlCls.WIDTH-o;l.resizeCanvasCls.resizeCanvas(e,n.htmlCls.HEIGHT,!0),i.bTwoddgmInit2&&r.openDlg2Ddgm(n.pre+"dl_2ddgm",void 0,i.bSetsInit2),i.bTwodctnInit2&&r.openDlg2Ddgm(n.pre+"dl_2dctn",void 0,i.bSetsInit2),i.bSetsInit2&&r.openDlg2Ddgm(n.pre+"dl_definedsets")}else l.resizeCanvasCls.resizeCanvas(n.htmlCls.WIDTH,n.htmlCls.HEIGHT,!0)},resize:function(t){if(e==n.pre+"dl_selectannotations")l.annotationCls.hideFixedTitle();else if(e==n.pre+"dl_graph"){let t=$("#"+e).width(),s=$("#"+e).height();d3.select("#"+n.svgid).attr("width",t).attr("height",s)}else if(e==n.pre+"dl_linegraph"||e==n.pre+"dl_scatterplot"||e==n.pre+"dl_contactmap"||e==n.pre+"dl_alignerrormap"){let t=status.bTwoddgmInit2||status.bSetsInit2?(n.htmlCls.WIDTH-o)/2:n.htmlCls.WIDTH/2,s=$("#"+e).width()/t;if(e==n.pre+"dl_linegraph"){let e=l.linegraphWidth*s;$("#"+n.linegraphid).attr("width",e)}else if(e==n.pre+"dl_scatterplot"){let e=l.scatterplotWidth*s;$("#"+n.scatterplotid).attr("width",e)}else if(e==n.pre+"dl_contactmap"){let e=l.contactmapWidth*s;$("#"+n.contactmapid).attr("width",e)}else if(e==n.pre+"dl_alignerrormap"){let e=l.alignerrormapWidth*s;$("#"+n.alignerrormapid).attr("width",e)}}}}),this.addSaveButton(e),this.addHideButton(e)}openDlg2Ddgm(e,t,s){let i=this.icn3dui,n=i.icn3d;if(i.bNode)return;let l,r,o=this,a=i.htmlCls.width2d+20;e===i.pre+"dl_definedsets"?(l="right top",r="Select sets"):e!==i.pre+"dl_2ddgm"&&e!==i.pre+"dl_2dctn"||(l=s?"right top+240":"right top",r=e===i.pre+"dl_2ddgm"?"2D Diagram":"2D Cartoon");let d={my:"left top+"+i.htmlCls.MENU_HEIGHT,at:l,of:"#"+i.pre+"viewer",collision:"none"};window.dialog=$("#"+e).dialog({autoOpen:!0,title:r,height:"auto",width:a,modal:!1,position:d,close:function(e){let t=o.getDialogStatus().status;t.bSelectannotationsInit2||t.bGraph2||t.bLineGraph2||t.bScatterplot2||t.bTable2||t.bAlignmentInit2||n.resizeCanvasCls.resizeCanvas(i.htmlCls.WIDTH,i.htmlCls.HEIGHT,!0)},resize:function(t,s){e==i.pre+"dl_2dctn"&&(n.resizeRatioX=s.size.width/i.htmlCls.width2d,n.resizeRatioY=s.size.height/(i.htmlCls.width2d+70))},resizeStop:function(e,t){n.resizeRatioX=t.size.width/i.htmlCls.width2d,n.resizeRatioY=t.size.height/(i.htmlCls.width2d+70)}}),this.addSaveButton(e),this.addHideButton(e)}openDlgRegular(e,t){let s=this.icn3dui,i=s.icn3d;if(s.bNode)return;let n=400,l=150,r=s.htmlCls.width2d+20,o=this.getDialogStatus().status;if(e===s.pre+"dl_selectannotations"||e===s.pre+"dl_graph"||e===s.pre+"dl_linegraph"||e===s.pre+"dl_scatterplot"||e===s.pre+"dl_contactmap"||e===s.pre+"dl_alignerrormap"||e===s.pre+"dl_interactionsorted"||e===s.pre+"dl_alignment"){let a=.5*s.htmlCls.WIDTH-.5*r;if(s.htmlCls.WIDTH>=s.htmlCls.HEIGHT)this.openDlgHalfWindow(e,t,a,!0),(o.bTwoddgmInit2||o.bTwodctnInit2||o.bSetsInit2)&&(i.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH-a-r,s.htmlCls.HEIGHT,!0),o.bTwoddgmInit2&&this.openDlg2Ddgm(s.pre+"dl_2ddgm",void 0,o.bSetsInit2),o.bTwodctnInit2&&this.openDlg2Ddgm(s.pre+"dl_2dctn",void 0,o.bSetsInit2),o.bSetsInit2&&this.openDlg2Ddgm(s.pre+"dl_definedsets"));else{i.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH,.5*s.htmlCls.HEIGHT,!0),l=.5*s.htmlCls.HEIGHT,n=s.htmlCls.WIDTH;let a={my:"left top",at:"left bottom+32",of:"#"+s.pre+"canvas",collision:"none"};window.dialog=$("#"+e).dialog({autoOpen:!0,title:t,height:l,width:n,modal:!1,position:a,close:function(t){if(!((e!==s.pre+"dl_selectannotations"||o.bAlignmentInit2||o.bGraph2||o.bTable2||o.bLineGraph2||o.bScatterplot2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_graph"||o.bSelectannotationsInit2||o.bAlignmentInit2||o.bTable2||o.bLineGraph2||o.bScatterplot2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_alignment"||o.bSelectannotationsInit2||o.bGraph2||o.bTable2||o.bLineGraph2||o.bScatterplot2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_interactionsorted"||o.bSelectannotationsInit2||o.bGraph2||o.bAlignmentInit2||o.bLineGraph2||o.bScatterplot2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_linegraph"||o.bSelectannotationsInit2||o.bGraph2||o.bAlignmentInit2||o.bTable2||o.bScatterplot2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_scatterplot"||o.bSelectannotationsInit2||o.bGraph2||o.bAlignmentInit2||o.bTable2||o.bLineGraph2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_contactmap"||o.bSelectannotationsInit2||o.bGraph2||o.bAlignmentInit2||o.bTable2||o.bLineGraph2||o.bScatterplot2||o.bAlignerrormap2)&&(e!==s.pre+"dl_alignerrormap"||o.bSelectannotationsInit2||o.bGraph2||o.bAlignmentInit2||o.bTable2||o.bLineGraph2||o.bScatterplot2||o.bContactmap2)))if(o.bTwoddgmInit2||o.bTwodctnInit2||o.bSetsInit2){let e=s.utilsCls.isMobile()?s.htmlCls.WIDTH:s.htmlCls.WIDTH-r;i.resizeCanvasCls.resizeCanvas(e,s.htmlCls.HEIGHT,!0),o.bTwoddgmInit2&&thisClass.openDlg2Ddgm(s.pre+"dl_2ddgm",void 0,o.bSetsInit2),o.bTwodctnInit2&&thisClass.openDlg2Ddgm(s.pre+"dl_2dctn",void 0,o.bSetsInit2),o.bSetsInit2&&thisClass.openDlg2Ddgm(s.pre+"dl_definedsets")}else i.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH,s.htmlCls.HEIGHT,!0)},resize:function(t){if(e==s.pre+"dl_selectannotations")i.annotationCls.hideFixedTitle();else if(e==s.pre+"dl_graph"){let t=$("#"+e).width(),i=$("#"+e).height();d3.select("#"+s.svgid).attr("width",t).attr("height",i)}else if(e==s.pre+"dl_linegraph"||e==s.pre+"dl_scatterplot"||e==s.pre+"dl_contactmap"||e==s.pre+"dl_alignerrormap"){let t=o.bTwoddgmInit2||o.bSetsInit2?(s.htmlCls.WIDTH-r)/2:s.htmlCls.WIDTH/2,n=$("#"+e).width()/t;if(e==s.pre+"dl_linegraph"){let e=i.linegraphWidth*n;$("#"+s.linegraphid).attr("width",e)}else if(e==s.pre+"dl_scatterplot"){let e=i.scatterplotWidth*n;$("#"+s.scatterplotid).attr("width",e)}else if(e==s.pre+"dl_contactmap"){let e=i.contactmapWidth*n;$("#"+s.contactmapid).attr("width",e)}else if(e==s.pre+"dl_alignerrormap"){let e=i.alignerrormapWidth*n;$("#"+s.alignerrormapid).attr("width",e)}}}}),this.addSaveButton(e),this.addHideButton(e)}}else if(e===s.pre+"dl_2ddgm"||e===s.pre+"dl_2dctn"){let t=0;if(s.htmlCls.WIDTH>=s.htmlCls.HEIGHT)(o.bSelectannotationsInit2||o.bGraph2||o.bLineGraph2||o.bScatterplot2||o.bTable2||o.bAlignmentInit2)&&(t=.5*s.htmlCls.WIDTH-.5*r),i.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH-t-r,s.htmlCls.HEIGHT,!0),this.openDlg2Ddgm(e,void 0,o.bSetsInit2);else{let t=s.utilsCls.isMobile()?s.htmlCls.WIDTH:s.htmlCls.WIDTH-r;i.resizeCanvasCls.resizeCanvas(t,.5*s.htmlCls.HEIGHT,!0),this.openDlg2Ddgm(e,.5*s.htmlCls.HEIGHT),this.openDlg2Ddgm(e,.5*s.htmlCls.HEIGHT,o.bSetsInit2)}}else{let a;if(l="auto",n="auto",e===s.pre+"dl_addtrack"?n="50%":e===s.pre+"dl_menupref"&&(n=600,l=500),e===s.pre+"dl_definedsets"){let t=0;if(s.htmlCls.WIDTH>=s.htmlCls.HEIGHT)(o.bSelectannotationsInit2||o.bGraph2||o.bLineGraph2||o.bScatterplot2||o.bTable2||o.bAlignmentInit2)&&(t=.5*s.htmlCls.WIDTH-.5*r),i.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH-t-r,s.htmlCls.HEIGHT,!0),this.openDlg2Ddgm(e),o.bTwoddgmInit2&&this.openDlg2Ddgm(s.pre+"dl_2ddgm",void 0,!0),o.bTwodctnInit2&&this.openDlg2Ddgm(s.pre+"dl_2dctn",void 0,!0);else{let t=s.utilsCls.isMobile()?s.htmlCls.WIDTH:s.htmlCls.WIDTH-r;i.resizeCanvasCls.resizeCanvas(t,.5*s.htmlCls.HEIGHT,!0),this.openDlg2Ddgm(e,.5*s.htmlCls.HEIGHT),o.bTwoddgmInit2&&this.openDlg2Ddgm(s.pre+"dl_2ddgm",.5*s.htmlCls.HEIGHT,!0),o.bTwodctnInit2&&this.openDlg2Ddgm(s.pre+"dl_2dctn",.5*s.htmlCls.HEIGHT,!0)}}else s.utilsCls.isMobile()?a={my:"left top",at:"left bottom-50",of:"#"+s.pre+"canvas",collision:"none"}:e===s.pre+"dl_allinteraction"||e===s.pre+"dl_buriedarea"?(a={my:"right top",at:"right top+50",of:"#"+i.divid,collision:"none"},n=700,l=500):a=e===s.pre+"dl_rmsd"||e===s.pre+"dl_legend"?{my:"left bottom",at:"left+20 bottom-20",of:"#"+s.pre+"canvas",collision:"none"}:e===s.pre+"dl_symd"?{my:"left top",at:"right-200 bottom-200",of:"#"+s.pre+"canvas",collision:"none"}:s.cfg.align?{my:"left top",at:"left top+90",of:"#"+s.pre+"canvas",collision:"none"}:e===s.pre+"dl_mmdbafid"?{my:"left top",at:"left top+130",of:"#"+s.pre+"canvas",collision:"none"}:{my:"left top",at:"left top+50",of:"#"+s.pre+"canvas",collision:"none"},window.dialog=$("#"+e).dialog({autoOpen:!0,title:t,height:l,width:n,modal:!1,position:a}),this.addSaveButton(e),this.addHideButton(e)}$(".ui-dialog .ui-button span").removeClass("ui-icon-closethick").addClass("ui-icon-close")}openDlgNotebook(e,t){let s=this.icn3dui,i=s.icn3d;if(s.bNode)return;let n=400,l=150,r=s.htmlCls.width2d+20;e===s.pre+"dl_selectannotations"||e===s.pre+"dl_graph"||e===s.pre+"dl_linegraph"||e===s.pre+"dl_scatterplot"||e===s.pre+"dl_contactmap"||e===s.pre+"dl_alignerrormap"||e===s.pre+"dl_interactionsorted"||e===s.pre+"dl_alignment"?($("#"+e).show(),$("#"+e+"_nb").show(),$("#"+e+"_title").html(t),l=.5*s.htmlCls.HEIGHT,n=s.htmlCls.WIDTH,$("#"+e).width(n),$("#"+e).height(l),$("#"+e).resize((function(t){let n=s.htmlCls.WIDTH/2,l=$("#"+e).width()/n;if(e==s.pre+"dl_selectannotations")i.annotationCls.hideFixedTitle();else if(e==s.pre+"dl_graph"){let t=$("#"+e).width(),i=$("#"+e).height();d3.select("#"+s.svgid).attr("width",t).attr("height",i)}else if(e==s.pre+"dl_linegraph"){let e=i.linegraphWidth*l;$("#"+s.linegraphid).attr("width",e)}else if(e==s.pre+"dl_scatterplot"){let e=i.scatterplotWidth*l;$("#"+s.scatterplotid).attr("width",e)}else if(e==s.pre+"dl_contactmap"){let e=i.contactmapWidth*l;$("#"+s.contactmapid).attr("width",e)}else if(e==s.pre+"dl_alignerrormap"){let e=i.alignerrormapWidth*l;$("#"+s.alignerrormapid).attr("width",e)}}))):(i.bRender&&($("#"+e).show(),$("#"+e+"_nb").show(),$("#"+e+"_title").html(t)),l="auto",n="auto",e===s.pre+"dl_addtrack"?n="50%":e===s.pre+"dl_2ddgm"||e===s.pre+"dl_2dctn"||e===s.pre+"dl_definedsets"?n=r:e!==s.pre+"dl_allinteraction"&&e!==s.pre+"dl_buriedarea"||(n=700,l=500),$("#"+e).width(n),$("#"+e).height(l))}}class h{constructor(e){this.icn3dui=e}setCustomDialogs(){let e=this.icn3dui;if(e.icn3d,e.bNode)return"";return""}getHtmlAlignResidueByResidue(e,t,s){let i=this.icn3dui;i.icn3d;let n="";return n+="All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

    ",n+="Chain IDs: "+i.htmlCls.inputTextStr+"id='"+i.pre+e+"' value='P69905,P01942,1HHO_A' size=50>

    ",n+='Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.

    ",n+=i.htmlCls.buttonStr+s+"'>Align Residue by Residue
    ",n}addNotebookTitle(e,t,s){let i=this.icn3dui;i.icn3d;let n='';return s&&(n+='
    '),n}setDialogs(){let e=this.icn3dui,t=e.icn3d;if(e.bNode)return"";let s="";e.htmlCls.optionStr="";for(let l=0,r=t[n].length;l"+r+", Strands: "+s[r]+""}i+=""}return i}getAnnoHeader(){let e=this.icn3dui;e.icn3d;let t="";t+="
    Annotations: 
    ",t+="
    ";let s="",t+=i+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_cdd' checked>Conserved Domains"+e.htmlCls.space2+"",t+=s+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_clinvar'>ClinVar"+e.htmlCls.space2+"",t+=s+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_binding'>Functional Sites"+e.htmlCls.space2+"",t+="",t+=s+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_custom'>Custom"+e.htmlCls.space2+"",t+=i+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_3dd'>3D Domains"+e.htmlCls.space2+"",t+=s+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_snp'>SNPs"+e.htmlCls.space2+"",t+=s+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_ptm'>PTM (UniProt)"+e.htmlCls.space2+"",t+="",t+="",t+=s+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_ssbond'>Disulfide Bonds"+e.htmlCls.space2+"",t+=s+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_interact'>Interactions"+e.htmlCls.space2+"",t+=s+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_crosslink'>Cross-Linkages"+e.htmlCls.space2+"",t+=s+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_transmem'>Transmembrane"+e.htmlCls.space2+"",t+="",t+="",t+=s+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_ig'>Ig Domains"+e.htmlCls.space2+"",t+="",t+="
    ",i="";return t+=s+e.htmlCls.inputCheckStr+"id='"+e.pre+"anno_all'>All"+e.htmlCls.space2+"
    ",t}}class p{constructor(e){this.icn3dui=e}setLogCmd(e,t,s){var i=this.icn3dui;i.icn3d,i.htmlCls.clickMenuCls.setLogCmd(e,t,s)}fullScreenChange(){let e=this.icn3dui,t=e.icn3d,s=this;e.bNode||document.fullscreenElement||document.webkitFullscreenElement||document.mozFullscreenElement||document.msFullscreenElement||(s.setLogCmd("exit full screen",!1),t.bFullscreen=!1,e.utilsCls.setViewerWidthHeight(e,!0),t.applyCenterCls.setWidthHeight(e.htmlCls.WIDTH,e.htmlCls.HEIGHT),t.drawCls.draw())}convertUniProtInChains(e){this.icn3dui.icn3d;let t=e.split(","),s="";for(let e=0,i=t.length;e0&&(i.hAtoms=i.definedSetsCls.getAtomsFromNameArray(l)),s.cfg.aligntool=e;let r="vast"==e?"structure align":"tmalign";if(r+=t?" msa":"",l.length>0?n.setLogCmd("realign on "+r+" | "+l,!0):n.setLogCmd("realign on "+r,!0),t){if(0==l.length){l=[];let e={};for(let t in i.chains){let s=i.firstAtomObjCls.getFirstAtomObj(i.chains[t]);e.hasOwnProperty(s.structure)||!i.proteins.hasOwnProperty(s.serial)&&!i.nucleotides.hasOwnProperty(s.serial)||(l.push(t),e[s.structure]=1)}}await i.realignParserCls.realignOnStructAlignMsa(l)}else await i.realignParserCls.realignOnStructAlign()}async readFile(e,t,s,i,n){let l=this.icn3dui.icn3d,r=this,o=t[s],a=e?"append":"load";a+=n?" mmcif file ":" pdb file ";let d=new FileReader;d.onload=async function(d){let c=d.target.result;r.setLogCmd(a+o.name,!1),e?(l.resetConfig(),l.bResetAnno=!0,l.bResetSets=!0):l.init(),l.bInputfile=!0,l.InputfileType=n?"mmcif":"pdb",l.InputfileData=l.InputfileData?l.InputfileData+"\nENDMDL\n"+c:c,i=s>0?i+"\nENDMDL\n"+c:c,Object.keys(t).length==s+1?(e&&(l.hAtoms={},l.dAtoms={}),n?await l.mmcifParserCls.loadMultipleMmcifData(i,void 0,e):await l.pdbParserCls.loadPdbData(i,void 0,void 0,e)):await r.readFile(e,t,s+1,i,n),e&&(l.bSetChainsAdvancedMenu&&l.definedSetsCls.showSets(),l.bResetAnno=!0,l.bAnnoShown&&(await l.showAnnoCls.showAnnotations(),l.annotationCls.resetAnnoTabAll()))},"object"==typeof o&&d.readAsText(o)}async loadPdbFile(e,t,s){let i=this.icn3dui,n=i.icn3d;n.bInitial=!0,i.cfg.notebook||dialog.dialog("close"),i.cfg.notebook?n.resizeCanvasCls.closeDialogs():$(".ui-dialog-content").dialog("close");let l=$("#"+i.pre+t)[0].files;l[0]?(i.htmlCls.setHtmlCls.fileSupport(),n.molTitle="",n.dataStrAll="",await this.readFile(e,l,0,"",s)):alert("Please select a file before clicking 'Load'")}saveHtml(e){let t=this.icn3dui.icn3d,s="";s+='\n',s+='\n',s+=$("#"+e).html();let i=e.split("_"),n=i.length>2?i[2]:e,l=Object.keys(t.structures)[0];Object.keys(t.structures).length>1&&(l+="-"+Object.keys(t.structures)[1]),t.saveFileCls.saveFile(l+"-"+n+".html","html",encodeURIComponent(s))}setPredefinedMenu(e){let t=this.icn3dui,s=t.icn3d;if(Object.keys(s.chains).length<2)return void alert("At least two chains are required for alignment...");t.htmlCls.clickMenuCls.SetChainsAdvancedMenu();let i=s.definedSetsCls.setAtomMenu(["protein"]);$("#"+t.pre+e).length&&$("#"+t.pre+e).html(i),$("#"+t.pre+e).resizable()}async launchMmdb(e,t,s,i){let n=this.icn3dui,l=n.icn3d,r=this;n.cfg.notebook||dialog.dialog("close");let o=t?1:0;if(!(e=e.replace(/,/g," ").replace(/\s+/g,",").trim()))return void alert("Please enter a list of PDB IDs or AlphaFold UniProt IDs...");let a=e.split(",");if(i)if(l.structures||1!=a.length||4!=a[0].length&&isNaN(a[0])){n.cfg.mmdbafid=e,n.cfg.bu=o,l.bMmdbafid=!0,l.inputid=l.inputid?l.inputid+n.cfg.mmdbafid:n.cfg.mmdbafid,1==n.cfg.bu?l.loadCmd="load mmdbaf1 "+n.cfg.mmdbafid:l.loadCmd="load mmdbaf0 "+n.cfg.mmdbafid,n.htmlCls.clickMenuCls.setLogCmd(l.loadCmd,!0);let t=!!(l.structures&&Object.keys(l.structures).length>0);await l.chainalignParserCls.downloadMmdbAf(n.cfg.mmdbafid),t&&(l.bSetChainsAdvancedMenu&&l.definedSetsCls.showSets(),l.bAnnoShown&&(await l.showAnnoCls.showAnnotations(),l.annotationCls.resetAnnoTabAll()))}else{r.setLogCmd("load mmdb"+o+" "+e,!1);let t=l.structures&&Object.keys(l.structures).length>0?"_blank":"_self";window.open(s+"?mmdbid="+e+"&bu="+o,t)}else if(1!=a.length||4!=a[0].length&&isNaN(a[0])){r.setLogCmd("load mmdbaf"+o+" "+e,!1);let t=l.structures&&Object.keys(l.structures).length>0?"_blank":"_self";window.open(s+"?mmdbafid="+e+"&bu="+o,t)}else{r.setLogCmd("load mmdb"+o+" "+e,!1);let t=l.structures&&Object.keys(l.structures).length>0?"_blank":"_self";window.open(s+"?mmdbid="+e+"&bu="+o,t)}}allEventFunctions(){let e=this.icn3dui,t=e.icn3d,s=this;if(e.bNode)return;let i=document.URL,n=i.indexOf("?");i=-1==n?i:i.substr(0,n),"https://www.ncbi.nlm.nih.gov/Structure/vast/icn3d/"==i&&(i="https://www.ncbi.nlm.nih.gov/Structure/icn3d/"),t.definedSetsCls.clickCustomAtoms(),t.definedSetsCls.clickCommand_apply(),t.definedSetsCls.clickModeswitch(),t.selectionCls.clickShow_selected(),t.selectionCls.clickHide_selected(),t.diagram2dCls.click2Ddgm(),t.cartoon2dCls.click2Dcartoon(),t.addTrackCls.clickAddTrackButton(),t.resizeCanvasCls.windowResize(),t.annotationCls.setTabs(),t.resid2specCls.switchHighlightLevel(),e.utilsCls.isMobile()?(t.hlSeqCls.selectSequenceMobile(),t.hlSeqCls.selectChainMobile()):t.hlSeqCls.selectSequenceNonMobile(),e.htmlCls.clickMenuCls.clickMenu1(),e.htmlCls.clickMenuCls.clickMenu2(),e.htmlCls.clickMenuCls.clickMenu3(),e.htmlCls.clickMenuCls.clickMenu4(),e.htmlCls.clickMenuCls.clickMenu5(),e.htmlCls.clickMenuCls.clickMenu6(),e.myEventCls.onIds(["#"+e.pre+"back","#"+e.pre+"mn6_back"],"click",(async function(t){let i=e.icn3d;t.preventDefault(),s.setLogCmd("back",!1),await i.resizeCanvasCls.back()})),e.myEventCls.onIds(["#"+e.pre+"forward","#"+e.pre+"mn6_forward"],"click",(async function(t){let i=e.icn3d;t.preventDefault(),s.setLogCmd("forward",!1),await i.resizeCanvasCls.forward()})),e.myEventCls.onIds(["#"+e.pre+"fullscreen","#"+e.pre+"mn6_fullscreen"],"click",(function(t){let i=e.icn3d;t.preventDefault(),s.setLogCmd("enter full 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t=$("#"+e.pre+"colorcustom").val();l.set("#"+t).enter()}));let r=new CP(document.querySelector("#"+e.pre+"labelcolorall"));r.on("change",(function(e){this.target.value=e})),e.myEventCls.onIds("#"+e.pre+"labelcolorall","input",(function(){let t=$("#"+e.pre+"labelcolorall").val();r.set("#"+t).enter()})),e.myEventCls.onIds("#"+e.pre+"labelcolorall","keyup",(function(){let t=$("#"+e.pre+"labelcolorall").val();r.set("#"+t).enter()})),e.myEventCls.onIds("#"+e.pre+"labelcolorall","paste",(function(){let t=$("#"+e.pre+"labelcolorall").val();r.set("#"+t).enter()})),e.myEventCls.onIds("#"+e.pre+"labelcolorall","cut",(function(){let t=$("#"+e.pre+"labelcolorall").val();r.set("#"+t).enter()})),e.myEventCls.onIds("#"+e.pre+"applypick_stabilizer_rm","click",(function(t){let i=e.icn3d;if(t.preventDefault(),e.cfg.notebook||dialog.dialog("close"),void 0===i.pAtom||void 0===i.pAtom2)alert("Please pick another atom");else{i.pickpair=!1,s.setLogCmd("remove one stabilizer | "+i.pAtom.serial+" 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i=e.icn3d;t.preventDefault(),e.cfg.notebook||dialog.dialog("close"),i.bMeasureDistance=!1;let n=$("#"+e.pre+"atomsCustomDist").val(),l=$("#"+e.pre+"atomsCustomDist2").val();i.analysisCls.measureDistTwoSets(n,l),s.setLogCmd("dist | "+l+" "+n,!0)})),$(document).on("click",".icn3d-distance",(function(t){let i=e.icn3d;t.preventDefault(),i.bMeasureDistance=!1,i.distPnts=[],i.labels.distance=[],i.lines.distance=[];let n=$(this).attr("sets").split("|"),l=[n[0]],r=[n[1]];i.analysisCls.measureDistTwoSets(l,r),s.setLogCmd("dist | "+r+" "+l,!0)})),e.myEventCls.onIds("#"+e.pre+"applydisttable","click",(function(t){let i=e.icn3d;t.preventDefault(),e.cfg.notebook||dialog.dialog("close"),i.bMeasureDistance=!1;let n=$("#"+e.pre+"atomsCustomDistTable").val(),l=$("#"+e.pre+"atomsCustomDistTable2").val();i.analysisCls.measureDistManySets(n,l),e.htmlCls.dialogCls.openDlg("dl_disttable","Distance among the sets"),s.setLogCmd("disttable | "+l+" 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h,p=void 0===t||t;p&&(o.hAtoms={});let m,u,g=0,f=0;for(let t=0,l=e.length;t0?m:l,p&&(o.hAtoms=r.hashUtilsCls.unionHash(o.hAtoms,o.alnChains[l]));let C=[],b="",y=void 0!==o.alnChainsSeq[l]?o.alnChainsSeq[l].length:0;y>d&&(d=y);let v,_,w=u.indexOf("_"),S=u.substr(0,w),A=u.substr(w+1);for(let e=0,t=y;e=0;--e)if("-"!=o.alnChainsSeq[l][e].resn){_=o.alnChainsSeq[l][e].resi;break}b+=""+v+"",h=!(void 0===e||!c.hasOwnProperty(u));for(let e=0,t=y;e"}""!==a?-1!=o.alnChainsSeq[l][e].resi?b+=""+o.alnChainsSeq[l][e].resn+"":b+=""+o.alnChainsSeq[l][e].resn+"":b+=""+o.alnChainsSeq[l][e].resn+""}b+=""+_+"";let x=e.length,k=void 0!==o.alnChainsAnno[l]?o.alnChainsAnno[l].length:0;for(let t=0,s=k;t";for(let e=0,i=o.alnChainsAnno[l][t].length;e ':' ';else if("E"==i)if(void 0!==o.alnChainsSeq[s][e]){let i=s+"_"+o.alnChainsSeq[s][e].resi;if(o.residues.hasOwnProperty(i)){o.firstAtomObjCls.getFirstCalphaAtomObj(o.residues[i]).ssend?C[t]+=' ':C[t]+=' '}else C[t]+=' '}else C[t]+=' ';else C[t]+="c"==i?' ':"o"==i?' ':"";else C[t]+=""+i+""}C[t]+=""}let O=l,R=void 0!==o.pdbid_chain2title?o.pdbid_chain2title[u]:"";for(let e=k-1;e>=0;--e){let t=o.alnChainsAnTtl[l][e][0];"SS"==t&&(t=""),a+="
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    "+C[e]+"
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    '+O+'
    '+b+"
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  • "+t+"
    • "}getMenuText(e,t,s,i,n){let l=this.icn3dui;l.icn3d,l.htmlCls.allMenus[e]=t,n&&(l.htmlCls.allMenusSel[e]=n),i&&(l.htmlCls.simpleMenus[e]=1);let r="icn3d-menupd"==s?" style='padding-left:1.5em!important;'":"";return"
  • "+t+""}getMenuUrl(e,t,s,i,n){let l=this.icn3dui;return l.icn3d,l.htmlCls.allMenus[e]=s,n&&(l.htmlCls.allMenusSel[e]=n),i&&(l.htmlCls.simpleMenus[e]=1),"
  • "+s+"
    • "}getMenuSep(){return this.icn3dui.icn3d,"
  • -
    • "}getLinkWrapper(e,t,s,i,n,l){let r=this.icn3dui;r.icn3d,r.htmlCls.allMenus[e]=t,n&&(r.htmlCls.allMenusSel[e]=n),i&&(r.htmlCls.simpleMenus[e]=1);let o=l?' style="display:none"':"";return"
  • "+t+"
    • "}getLinkWrapper2(e,t,s,i,n){let l=this.icn3dui;return l.icn3d,l.htmlCls.allMenus[e]=t,n&&(l.htmlCls.allMenusSel[e]=n),i&&(l.htmlCls.simpleMenus[e]=1),"
  • "+t+""}getRadio(e,t,s,i,n,l){let r=this.icn3dui;r.icn3d,r.htmlCls.allMenus[t]=s,l&&(r.htmlCls.allMenusSel[t]=l),n&&(r.htmlCls.simpleMenus[t]=1);let o=i?" checked":"";return"
    • "}getRadioColor(e,t,s,i,n,l,r){let o=this.icn3dui;o.icn3d,o.htmlCls.allMenus[t]=s,r&&(o.htmlCls.allMenusSel[t]=r),l&&(o.htmlCls.simpleMenus[t]=1);let a=n?" checked":"";return"
    • "}setAdvanced(e){let t=this.icn3dui;t.icn3d;let s=void 0===e?"":e,i=t.cfg.notebook?"icn3d-hidden":"",n=t.htmlCls.divStr+"dl_advanced"+s+"' class='"+i+"'>";return n+="",n+="",n+="
    ",n+="",n+="",n+="",n+="
    Select:"+t.htmlCls.inputTextStr+"id='"+t.pre+"command"+s+"' placeholder='$[structures].[chains]:[residues]@[atoms]' size='60'>
    Name:"+t.htmlCls.inputTextStr+"id='"+t.pre+"command_name"+s+"' placeholder='my_selection' size='60'>
    "+t.htmlCls.space3+t.htmlCls.buttonStr+"command_apply"+s+"'>Save Selection to Defined Sets
    ",n+='Specification Tips:

    ',n+=t.htmlCls.divStr+"specguide"+s+"' style='display:none; width:500px' class='icn3d-box'>",n+='Specification: In the selection "$1HHO,4N7N.A,B,C:5-10,LV,3AlaVal,chemicals@CA,C,C*":',n+='
    • "$1HHO,4N7N" uses "$" to indicate structure selection.
      ',n+='
    • ".A,B,C" uses "." to indicate chain selection.
      ',n+='
    • ":5-10,LV,3LeuVal,chemicals" uses the colon ":" to indicate residue selection. Residue selection could be residue number(5-10), one-letter IUPAC residue name abbreviations(LV), three-letter residue names(AlaVal, "3" indicates each residue name has three letters), or predefined names: "proteins", "nucleotides", "chemicals", "ions", and "water". IUPAC abbreviations can be written either as a contiguous string(e.g., ":LV"), in order to find all instances of that sequence in the structure, or they can be separated by commas(e.g., ":L,V") to select all residues of a given type in the structure(in the latter case, select all Leucine and Valine in the structure).
      ',n+='
    • "@CA,C,C*" uses "@" to indicate atom name selection. "C*" selects any atom names starting with "C".
      ',n+='
    • Partial definition is allowed, e.g., ":1-10" selects all residue IDs 1-10 in all chains.
      ',n+='
    • Different selections can be unioned(with "or", default), intersected(with "and"), or negated(with "not"). For example, ":1-10 or :K" selects all residues 1-10 and all Lys residues. ":1-10 and :K" selects all Lys residues in the range of residue number 1-10. ":1-10 or not :K" selects all residues 1-10, which are not Lys residues.
      ',n+='
    • The wild card character "X" or "x" can be used to represent any character.',n+="
    ",n+="Set Operation:",n+='
    • Users can select multiple sets in the menu "Select > Defined Sets".
      ',n+='
    • Different sets can be unioned(with "or", default), intersected(with "and"), or negated(with "not"). For example, if the "Defined Sets" menu has four sets ":1-10", ":11-20", ":5-15", and ":7-8", the command "saved atoms :1-10 or :11-20 and :5-15 not :7-8" unions all residues 1-10 and 11-20 to get the residues 1-20, then intersects with the residues 5-15 to get the residues 5-15, then exclude the residues 7-8 to get the final residues 5-6 and 9-15.
    ',n+="Full commands in url or command window:",n+="
    • Select without saving the set: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C*
      ",n+="
    • Select and save: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C* | name my_name
    ",n+="",n+="
    ",n+="",n}getOptionHtml(e,t){let s=this.icn3dui;s.icn3d;let i="";for(let n=0,l=e.length;n"+l+"":s.htmlCls.optionStr+"'"+l+"'>"+l+""}return i}setColorHints(){let e=this.icn3dui;e.icn3d;let t="";return t+=e.htmlCls.divNowrapStr+'Green: H-Bonds; ',t+='Cyan: Salt Bridge/Ionic; ',t+='Grey: contacts',t+=e.htmlCls.divNowrapStr+'Magenta: Halogen Bonds; ',t+='Red: π-Cation; ',t+='Blue: π-Stacking',t}setThicknessHtml(e){let t=this.icn3dui,s=t.icn3d,i="",n="3dprint"==e?"1":"0.1",l="3dprint"==e?"1.2":"0.3",r="3dprint"==e?"0.8":"0.4",o="3dprint"==e?"0.8":"0.4",a="3dprint"==e?"1":"0.4",d="3dprint"==e?"0.6":"0.3",c="3dprint"==e?"1":"0.2",h="3dprint"==e?"2":"1.3",p="3dprint"==e?"1.4":"0.8",m=40,u=.8,g=.4,f=.2,C=0,b=1,y=0;if("style"==e){if(""!=this.getCookie("shininess")&&(m=parseFloat(this.getCookie("shininess"))),""!=this.getCookie("light1")&&(u=parseFloat(this.getCookie("light1")),g=parseFloat(this.getCookie("light2")),f=parseFloat(this.getCookie("light3"))),""!=this.getCookie("lineRadius")){n=parseFloat(this.getCookie("lineRadius")),l=parseFloat(this.getCookie("coilWidth")),r=parseFloat(this.getCookie("cylinderRadius"));let e=this.getCookie("crosslinkRadius");o=isNaN(e)?s.crosslinkRadius:parseFloat(e),a=parseFloat(this.getCookie("traceRadius")),d=parseFloat(this.getCookie("dotSphereScale")),c=parseFloat(this.getCookie("ribbonthickness")),h=parseFloat(this.getCookie("helixSheetWidth")),p=parseFloat(this.getCookie("nucleicAcidWidth"))}""!=this.getCookie("glycan")&&(C=parseFloat(this.getCookie("glycan"))),""!=this.getCookie("membrane")&&(b=parseFloat(this.getCookie("membrane"))),""!=this.getCookie("cmdwindow")&&(y=parseFloat(this.getCookie("cmdwindow"))),i+="Note: The following parameters will be saved in cache. You just need to set them once.

    ",i+="1. Shininess: "+t.htmlCls.inputTextStr+"id='"+t.pre+"shininess' value='"+m+"' size=4>"+t.htmlCls.space3+"(for the shininess of the 3D objects, default 40)

    ",i+="2. Three directional lights:
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    ",i+="Fill Light: "+t.htmlCls.inputTextStr+"id='"+t.pre+"light2' value='"+g+"' size=4>"+t.htmlCls.space3+"(for the light strength of the fill light, default 0.4)
    ",i+="Back Light: "+t.htmlCls.inputTextStr+"id='"+t.pre+"light3' value='"+f+"' size=4>"+t.htmlCls.space3+"(for the light strength of the back light, default 0.2)

    ",i+="3. Thickness:
    "}return i+="Line Radius: "+t.htmlCls.inputTextStr+"id='"+t.pre+"linerad_"+e+"' value='"+n+"' size=4>"+t.htmlCls.space3+"(for stabilizers, hydrogen bonds, distance lines, default 0.1)
    ",i+="Coil Radius: "+t.htmlCls.inputTextStr+"id='"+t.pre+"coilrad_"+e+"' value='"+l+"' size=4>"+t.htmlCls.space3+"(for coils, default 0.3)
    ",i+="Stick Radius: "+t.htmlCls.inputTextStr+"id='"+t.pre+"stickrad_"+e+"' value='"+r+"' size=4>"+t.htmlCls.space3+"(for sticks, default 0.4)
    ",i+="Cross-Linkage Radius: "+t.htmlCls.inputTextStr+"id='"+t.pre+"crosslinkrad_"+e+"' value='"+o+"' size=4>"+t.htmlCls.space3+"(for cross-linkages, default 0.4)
    ",i+="Trace Radius: "+t.htmlCls.inputTextStr+"id='"+t.pre+"tracerad_"+e+"' value='"+a+"' size=4>"+t.htmlCls.space3+"(for C alpha trace, O3' trace, default 0.4)
    ",i+="Ribbon Thickness: "+t.htmlCls.inputTextStr+"id='"+t.pre+"ribbonthick_"+e+"' value='"+c+"' size=4>"+t.htmlCls.space3+"(for helix and sheet ribbons, nucleotide ribbons, default 0.2)
    ",i+="Protein Ribbon Width: "+t.htmlCls.inputTextStr+"id='"+t.pre+"prtribbonwidth_"+e+"' value='"+h+"' size=4>"+t.htmlCls.space3+"(for helix and sheet ribbons, default 1.3)
    ",i+="Nucleotide Ribbon Width: "+t.htmlCls.inputTextStr+"id='"+t.pre+"nucleotideribbonwidth_"+e+"' value='"+p+"' size=4>"+t.htmlCls.space3+"(for nucleotide ribbons, default 0.8)
    ",i+="Ball Scale: "+t.htmlCls.inputTextStr+"id='"+t.pre+"ballscale_"+e+"' value='"+d+"' size=4>"+t.htmlCls.space3+"(for styles 'Ball and Stick' and 'Dot', default 0.3)
    ","style"==e&&(i+="
    4. Show Glycan Cartoon: "+t.htmlCls.inputTextStr+"id='"+t.pre+"glycan' value='"+C+"' size=4>"+t.htmlCls.space3+"(0: hide, 1: show, default 0)
    ",i+="
    5. Show Membrane: "+t.htmlCls.inputTextStr+"id='"+t.pre+"membrane' value='"+b+"' size=4>"+t.htmlCls.space3+"(0: hide, 1: show, default 1)
    ",i+="
    6. Enlarge Command Window: "+t.htmlCls.inputTextStr+"id='"+t.pre+"cmdwindow' value='"+y+"' size=4>"+t.htmlCls.space3+"(0: Regular, 1: Large, default 0)

    "),i+=t.htmlCls.spanNowrapStr+""+t.htmlCls.buttonStr+"apply_thickness_"+e+"'>Apply   ",i+=t.htmlCls.spanNowrapStr+""+t.htmlCls.buttonStr+"reset_thickness_"+e+"'>Reset",i}getCookie(e){let t=e+"=",s=decodeURIComponent(document.cookie).split(";");for(let e=0;e":(n+='
    ',n+="
    Selection: Name: "+s.htmlCls.inputTextStr+"id='"+s.pre+"seq_command_name"+e+"' value='seq_"+l+"' size='5'> "+s.htmlCls.space2+"

    ",n+=s.htmlCls.divStr+"seqguide"+e+"' style='display:none; white-space:normal;' class='icn3d-box'>"),n+=this.getSelectionHints();return n+="Residue labeling: standard residue with coordinates: UPPER case letter; nonstandard residue with coordinates: the first UPPER case letter plus a period except that water residue uses the letter 'O'; residue missing coordinates: lower case letter."+(s.utilsCls.isMac()&&!s.utilsCls.isMobile()?"

    Turn on scroll bar: System preferences -> General -> show scroll bars -> check Always":"")+"
    ",n}setAlignSequenceGuide(e,t){let s=this.icn3dui,i=s.icn3d,n="";let l=i&&i.defNames2Atoms?Object.keys(i.defNames2Atoms).length:1;n+='
    ',n+="
    Selection: Name: "+s.htmlCls.inputTextStr+"id='"+s.pre+"alignseq_command_name' value='alseq_"+l+"' size='10'> "+s.htmlCls.space2+"

    ",n+=s.htmlCls.divStr+"alignseqguide' style='display:none; white-space:normal;' class='icn3d-box'>",n+=this.getSelectionHints();return n+="Residue labeling: aligned residue with coordinates: UPPER case letter; non-aligned residue with coordinates: lower case letter which can be highlighted; residue missing coordinates: lower case letter which can NOT be highlighted."+(s.utilsCls.isMac()&&!s.utilsCls.isMobile()?"

    Turn on scroll bar: System preferences -> General -> show scroll bars -> check Always":"")+"
    ",n}getSelectionHints(){let e=this.icn3dui;e.icn3d;let t="";if(e.utilsCls.isMobile())t+='Select Aligned Sequences: touch to select, touch again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.
    ';else{t+='Select on 1D sequences: drag to select, drag again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.

    ',t+="Select on 2D interaction diagram: click on the nodes or lines. The nodes are chains and can be united with the Ctrl key. The lines are interactions and can NOT be united. Each click on the lines selects half of the lines, i.e., select the interacting residues in one of the two chains.

    ",t+="Select on 3D structures: "+(e.utilsCls.isMobile()?"use finger to pick":'hold "Alt" and use mouse to pick')+', click the second time to deselect, hold "Ctrl" to union selection, hold "Shift" to select a range, press the up/down arrow to switch among atom/residue/strand/chain/structure, click "Save Selection" to save the current selection.

    ',t+='Save the current selection(either on 3D structure, 2D interactions, or 1D sequence): open the menu "Select -> Save Selection", specify the name and description for the selection, and click "Save".

    '}return t}addGsizeSalt(e){let t=this.icn3dui;t.icn3d;let s="";s+="Grid Size: ",s+="Salt Concentration: M
    ",s}getFootHtml(e,t){let s=this.icn3dui;s.icn3d;let i="
    ";return"delphi"==e?s.cfg.cid?i+="Note: Partial charges(MMFF94) are from PubChem Compound SDF files.

    ":(i+="Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation.",i+='

    ',i+=s.htmlCls.divStr+t+"' style='display:none;'>",i+="
    The hydrogens and partial charges of proteins and nucleotides are added using DelPhiPKa with the Amber charge and size files. The hydrogens of ligands are added using Open Babel. The partial charges of ligands are calculated using Antechamber with the Gasteiger charge method. All partial charges are calculated at pH 7.

    ",i+='Lipids are treated as ligands. Please use "HETATM" instead of "ATOM " for each lipid atom in your PDB file. Each phosphate in lipids is assigned with a charge of -1. You can download PQR and modify it, or prepare your PQR file using other tools. Then load the PQR file at the menu "Analysis > Load PQR/Potential".

    ',i+="
    "):(i+="Note: Always load a PDB file before loading a PQR or DelPhi potential file.",i+='

    ',i+=s.htmlCls.divStr+t+"' style='display:none;'>",i+='The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file. ',"url"==e&&(i+="The PQR or potential file can be accessed in a URL if it is located in the same host as iCn3D."),i+="

    ",i+=""),i+="",i}getPotentialHtml(e,t){let s=this.icn3dui;s.icn3d;let i,n,l,r,o,a="";r="Equipotential Map",o="Surface with Potential","delphi"==e?n="delphi":"local"==e?(i="pqr",n="phi",l="cube"):"url"==e&&(i="pqrurl",n="phiurl",l="cubeurl"),a+=s.htmlCls.divStr+"dl_"+n+"' class='"+t+"'>",a+=s.htmlCls.setDialogCls.addNotebookTitle("dl_"+n,"DelPhi Potential"),a+=s.htmlCls.divStr+"dl_"+n+"_tabs' style='border:0px;'>",a+="",a+=s.htmlCls.divStr+n+"tab1'>","delphi"==e&&(a+=this.addGsizeSalt(n+"1")+"
    "),a+="Potential contour at: kT/e(25.6mV at 298K)

    ","delphi"==e?(a+=s.htmlCls.buttonStr+"reload_"+n+"file' style='margin-top: 6px;'>Equipotential Map",a+=s.htmlCls.buttonStr+n+"mapNo' style='margin-left:30px;'>Remove Map
    "):"local"==e?(a+=s.htmlCls.divStr+n+"tab1_tabs' style='border:0px;'>",a+="",d=""+s.htmlCls.buttonStr+n+"mapNo'>Remove Map",a+=s.htmlCls.divStr+n+"tab1_"+i+"'>",a+=this.addGsizeSalt(i)+"
    ",a+="PQR File: "+s.htmlCls.inputFileStr+"id='"+s.pre+i+"file'>

    "+s.htmlCls.buttonStr+"reload_"+i+"file' style='margin-top: 6px;'>Equipotential Map"+d,a+=s.htmlCls.divStr+n+"tab1_"+n+"'>",a+="Phi File: "+s.htmlCls.inputFileStr+"id='"+s.pre+n+"file'>

    "+s.htmlCls.buttonStr+"reload_"+n+"file' style='margin-top: 6px;'>Equipotential Map"+d,a+=s.htmlCls.divStr+n+"tab1_"+l+"'>",a+="Cube File: "+s.htmlCls.inputFileStr+"id='"+s.pre+l+"file'>

    "+s.htmlCls.buttonStr+"reload_"+l+"file' style='margin-top: 6px;'>Equipotential Map"+d,a+=""):"url"==e&&(a+=s.htmlCls.divStr+n+"tab1_tabs' style='border:0px;'>",a+="",d=""+s.htmlCls.buttonStr+n+"mapNo'>Remove Map",a+=s.htmlCls.divStr+n+"tab1_"+i+"2'>",a+=this.addGsizeSalt(i)+"
    ",a+="PQR URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+i+"file'>

    "+s.htmlCls.buttonStr+"reload_"+i+"file' style='margin-top: 6px;'>Equipotential Map"+d,a+=s.htmlCls.divStr+n+"tab1_"+n+"2'>",a+="Phi URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+n+"file'>

    "+s.htmlCls.buttonStr+"reload_"+n+"file' style='margin-top: 6px;'>Equipotential Map"+d,a+=s.htmlCls.divStr+n+"tab1_"+l+"2'>",a+="Cube URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+l+"file'>

    "+s.htmlCls.buttonStr+"reload_"+l+"file' style='margin-top: 6px;'>Equipotential Map"+d,a+=""),a+="
    "+this.getFootHtml(e,n+"tab1_foot"),a+="",a+=s.htmlCls.divStr+n+"tab2'>","delphi"==e&&(a+=this.addGsizeSalt(n+"2")+"
    "),a+="Surface with max potential at: kT/e(25.6mV at 298K)

    ",a+="Surface: ",a+="Opacity: ",a+="Wireframe:
    ",a+="
    ","delphi"==e?(a+=s.htmlCls.buttonStr+"reload_"+n+"file2' style='margin-top: 6px;'>Surface with Potential",a+=s.htmlCls.buttonStr+n+"mapNo2' style='margin-left:30px;'>Remove Surface
    "):"local"==e?(a+=s.htmlCls.divStr+n+"tab2_tabs' style='border:0px;'>",a+="",d=""+s.htmlCls.buttonStr+n+"mapNo2'>Remove Surface",a+=s.htmlCls.divStr+n+"tab2_"+i+"'>",a+=this.addGsizeSalt(i+"2")+"
    ",a+="PQR File: "+s.htmlCls.inputFileStr+"id='"+s.pre+i+"file2'>

    "+s.htmlCls.buttonStr+"reload_"+i+"file2' style='margin-top: 6px;'>Surface with Potential"+d,a+=s.htmlCls.divStr+n+"tab2_"+n+"'>",a+="Phi File: "+s.htmlCls.inputFileStr+"id='"+s.pre+n+"file2'>

    "+s.htmlCls.buttonStr+"reload_"+n+"file2' style='margin-top: 6px;'>Surface with Potential"+d,a+=s.htmlCls.divStr+n+"tab2_"+l+"'>",a+="Cube File: "+s.htmlCls.inputFileStr+"id='"+s.pre+l+"file2'>

    "+s.htmlCls.buttonStr+"reload_"+l+"file2' style='margin-top: 6px;'>Surface with Potential"+d,a+=""):"url"==e&&(a+=s.htmlCls.divStr+n+"tab2_tabs' style='border:0px;'>",a+="",d=""+s.htmlCls.buttonStr+n+"mapNo2'>Remove Surface",a+=s.htmlCls.divStr+n+"tab2_"+i+"2'>",a+=this.addGsizeSalt(i+"2")+"
    ",a+="PQR URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+i+"file2'>

    "+s.htmlCls.buttonStr+"reload_"+i+"file2' style='margin-top: 6px;'>Surface with Potential"+d,a+=s.htmlCls.divStr+n+"tab2_"+n+"2'>",a+="Phi URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+n+"file2'>

    "+s.htmlCls.buttonStr+"reload_"+n+"file2' style='margin-top: 6px;'>Surface with Potential"+d,a+=s.htmlCls.divStr+n+"tab2_"+l+"2'>",a+="Cube URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+l+"file2'>

    "+s.htmlCls.buttonStr+"reload_"+l+"file2' style='margin-top: 6px;'>Surface with Potential"+d,a+=""),a+="
    "+this.getFootHtml(e,n+"tab2_foot"),a+="",a+="",a+="",a}async exportPqr(e){let t=this.icn3dui,s=t.icn3d,i={},n={},l=t.hashUtilsCls.intHash(s.dAtoms,s.hAtoms);for(let e in l)s.atoms[e],s.ions.hasOwnProperty(e)?i[e]=1:n[e]=1;let r=e?"pdb":"pqr";if(t.cfg.cid){let l="",o=!e;l+=s.saveFileCls.getAtomPDB(n,o)+s.saveFileCls.getAtomPDB(i,o);let a=Object.keys(t.utilsCls.getHlStructures()).join(",");s.saveFileCls.saveFile(a+"_icn3d."+r,"text",[l])}else{if(t.utilsCls.isCalphaPhosOnly(t.hashUtilsCls.hash2Atoms(n,s.atoms)))return void alert("The potential will not be shown because the side chains are missing in the structure...");let l="",o=!0;l+=s.saveFileCls.getAtomPDB(n,void 0,void 0,void 0,void 0,void 0,o),l+=s.saveFileCls.getAtomPDB(i,!0,void 0,!0);let a=t.htmlCls.baseUrl+"delphi/delphi.cgi",d={pdb2pqr:l,pdbid:t.cfg.cid?t.cfg.cid:Object.keys(s.structures).toString()},c=await t.getAjaxPostPromise(a,d,!0,void 0,void 0,!0,"text");if(e){let e=c.split("\n"),s="";for(let i=0,n=e.length;i Save File > iCn3D PNG Image"...');else if(-1!=l){let t=e.substr(l+n.length);s.htmlCls.clickMenuCls.setLogCmd("load iCn3D PNG image "+$("#"+s.pre+"pngimage").val(),!1),window.open(t,"_self")}else if(-1!=o){let n="Start of data file======\n",l=e.indexOf(n);i.bInputfile=-1!=l,i.bInputPNGWithData=i.bInputfile;let a,d=t?t.replace(/;/g,"\n"):"";if(i.bInputfile){let t=e.indexOf("End of data file======\n"),s=e.substr(l+n.length,t-l-n.length);i.InputfileData=i.InputfileData?i.InputfileData+"\nENDMDL\n"+s:s;let c="Start of type file======\n",h=e.indexOf(c),p=e.indexOf("End of type file======\n"),m=e.substr(h+c.length,p-h-c.length-1);i.InputfileType=m;let u=e.indexOf("End of state file======\n");a=e.substr(o+r.length,u-o-r.length),a=decodeURIComponent(a+"\n"+d),"pdb"===m?(await i.pdbParserCls.loadPdbData(s),i.commands=[],i.optsHistory=[]):("mol2"===m?await i.mol2ParserCls.loadMol2Data(s):"sdf"===m?await i.sdfParserCls.loadSdfData(s):"xyz"===m?await i.xyzParserCls.loadXyzData(s):"mmcif"===m&&await i.mmcifParserCls.loadMmcifData(s),i.commands=[],i.optsHistory=[])}else{let t=e.indexOf("End of state file======\n");a=e.substr(o+r.length,t-o-r.length),a=decodeURIComponent(a+"\n"+d),i.commands=[],i.optsHistory=[]}await i.loadScriptCls.loadScript(a,!0),s.htmlCls.clickMenuCls.setLogCmd("load iCn3D PNG image "+$("#"+s.pre+"pngimage").val(),!1)}}fileSupport(){window.File&&window.FileReader&&window.FileList&&window.Blob||alert("The File APIs are not fully supported in this browser.")}getLinkColor(){let e="";return e+=", linkmap: {\n",e+='3: {"type": "peptidebond", "c":""},\n',e+='4: {"type": "ssbond", "c":"FFA500"},\n',e+='5: {"type": "ionic", "c":"0FF"},\n',e+='6: {"type": "ionicInside", "c":"FFF"},\n',e+='11: {"type": "contact", "c":"888"},\n',e+='12: {"type": "contactInside", "c":"FFF"},\n',e+='13: {"type": "hbond", "c":"0F0"},\n',e+='14: {"type": "hbondInside", "c":"FFF"},\n',e+='15: {"type": "clbond", "c":"006400"},\n',e+='17: {"type": "halogen", "c":"F0F"},\n',e+='18: {"type": "halogenInside", "c":"FFF"},\n',e+='19: {"type": "pication", "c":"F00"},\n',e+='20: {"type": "picationInside", "c":"FFF"},\n',e+='21: {"type": "pistacking", "c":"00F"},\n',e+='22: {"type": "pistackingInside", "c":"FFF"}\n',e+="}}\n",', linkmap: {\n3: {"type": "peptidebond", "c":""},\n4: {"type": "ssbond", "c":"FFA500"},\n5: {"type": "ionic", "c":"0FF"},\n6: {"type": "ionicInside", "c":"FFF"},\n11: {"type": "contact", "c":"888"},\n12: {"type": "contactInside", "c":"FFF"},\n13: {"type": "hbond", "c":"0F0"},\n14: {"type": "hbondInside", "c":"FFF"},\n15: {"type": "clbond", "c":"006400"},\n17: {"type": "halogen", "c":"F0F"},\n18: {"type": "halogenInside", "c":"FFF"},\n19: {"type": "pication", "c":"F00"},\n20: {"type": "picationInside", "c":"FFF"},\n21: {"type": "pistacking", "c":"00F"},\n22: {"type": "pistackingInside", "c":"FFF"}\n}}\n'}setCookieForThickness(){let e=this.icn3dui,t=e.icn3d;if(!e.bNode){let e=3650;this.setCookie("lineRadius",t.lineRadius,e),this.setCookie("coilWidth",t.coilWidth,e),this.setCookie("cylinderRadius",t.cylinderRadius,e),this.setCookie("crosslinkRadius",t.crosslinkRadius,e),this.setCookie("traceRadius",t.traceRadius,e),this.setCookie("dotSphereScale",t.dotSphereScale,e),this.setCookie("ribbonthickness",t.ribbonthickness,e),this.setCookie("helixSheetWidth",t.helixSheetWidth,e),this.setCookie("nucleicAcidWidth",t.nucleicAcidWidth,e)}}setLineThickness(e,t){let s=this.icn3dui,i=s.icn3d;if(i.bSetThickness=!0,"style"==e&&(t&&($("#"+s.pre+"shininess").val("40"),$("#"+s.pre+"light1").val("0.8"),$("#"+s.pre+"light2").val("0.4"),$("#"+s.pre+"light3").val("0.2"),$("#"+s.pre+"glycan").val("0"),$("#"+s.pre+"membrane").val("1"),$("#"+s.pre+"cmdwindow").val("0")),i.shininess=parseFloat($("#"+s.pre+"shininess").val()),i.light1=parseFloat($("#"+s.pre+"light1").val()),i.light2=parseFloat($("#"+s.pre+"light2").val()),i.light3=parseFloat($("#"+s.pre+"light3").val()),i.bGlycansCartoon=parseInt($("#"+s.pre+"glycan").val()),i.bMembrane=parseInt($("#"+s.pre+"membrane").val()),i.bCmdWindow=parseInt($("#"+s.pre+"cmdwindow").val())),t&&($("#"+s.pre+"linerad_"+e).val(.1),$("#"+s.pre+"coilrad_"+e).val(.3),$("#"+s.pre+"stickrad_"+e).val(.4),$("#"+s.pre+"crosslinkrad_"+e).val(.4),$("#"+s.pre+"tracerad_"+e).val(.4),$("#"+s.pre+"ballscale_"+e).val(.3),$("#"+s.pre+"ribbonthick_"+e).val(.2),$("#"+s.pre+"prtribbonwidth_"+e).val(1.3),$("#"+s.pre+"nucleotideribbonwidth_"+e).val(.8)),i.lineRadius=parseFloat($("#"+s.pre+"linerad_"+e).val()),i.coilWidth=parseFloat($("#"+s.pre+"coilrad_"+e).val()),i.cylinderRadius=parseFloat($("#"+s.pre+"stickrad_"+e).val()),i.crosslinkRadius=parseFloat($("#"+s.pre+"crosslinkrad_"+e).val()),i.traceRadius=parseFloat($("#"+s.pre+"tracerad_"+e).val()),i.dotSphereScale=parseFloat($("#"+s.pre+"ballscale_"+e).val()),i.ribbonthickness=parseFloat($("#"+s.pre+"ribbonthick_"+e).val()),i.helixSheetWidth=parseFloat($("#"+s.pre+"prtribbonwidth_"+e).val()),i.nucleicAcidWidth=parseFloat($("#"+s.pre+"nucleotideribbonwidth_"+e).val()),!s.bNode){let e=3650;this.setCookie("shininess",i.shininess,e),this.setCookie("light1",i.light1,e),this.setCookie("light2",i.light2,e),this.setCookie("light3",i.light3,e),this.setCookie("glycan",i.bGlycansCartoon,e),this.setCookie("membrane",i.bMembrane,e),this.setCookie("cmdwindow",i.bCmdWindow,e)}if(this.setCookieForThickness(),e=t){let e="reset thickness";s.htmlCls.clickMenuCls.setLogCmd(e,!0),i.bSetThickness=!1,i.threeDPrintCls.resetAfter3Dprint()}else s.htmlCls.clickMenuCls.setLogCmd("set thickness | linerad "+i.lineRadius+" | coilrad "+i.coilWidth+" | stickrad "+i.cylinderRadius+" | crosslinkrad "+i.crosslinkRadius+" | tracerad "+i.traceRadius+" | ribbonthick "+i.ribbonthickness+" | proteinwidth "+i.helixSheetWidth+" | nucleotidewidth "+i.nucleicAcidWidth+" | ballscale "+i.dotSphereScale,!0),s.htmlCls.clickMenuCls.setLogCmd("set glycan "+i.bGlycansCartoon,!0),s.htmlCls.clickMenuCls.setLogCmd("set membrane "+i.bMembrane,!0),s.htmlCls.clickMenuCls.setLogCmd("set cmdwindow "+i.bCmdWindow,!0);i.drawCls.draw()}setCookie(e,t,s){let i=new Date;i.setTime(i.getTime()+24*s*60*60*1e3);let n="expires="+i.toUTCString();document.cookie=e+"="+t+";"+n+";path=/"}updateSurfPara(e){let t=this.icn3dui,s=t.icn3d;s.phisurftype=$("#"+t.pre+e+"surftype").val(),s.phisurfop=$("#"+t.pre+e+"surfop").val(),s.phisurfwf=$("#"+t.pre+e+"surfwf").val()}exportPdb(){let e=this.icn3dui,t=e.icn3d,s="",i=e.hashUtilsCls.intHash(t.dAtoms,t.hAtoms);if(s+=t.saveFileCls.getAtomPDB(i),!e.bNode){let i=Object.keys(e.utilsCls.getHlStructures()).join(",");t.saveFileCls.saveFile(i+"_icn3d.pdb","text",[s])}return s}exportSecondary(){let e=this.icn3dui,t=e.icn3d,s="",i=e.hashUtilsCls.intHash(t.dAtoms,t.hAtoms);if(s+=t.saveFileCls.getSecondary(i),!e.bNode){let i=Object.keys(e.utilsCls.getHlStructures()).join(",");t.saveFileCls.saveFile(i+"_icn3d_ss.txt","text",[s])}return s}}class g{constructor(e){let t=e;this.icn3dui=e,this.cfg=this.icn3dui.cfg,this.opts={},this.opts.background="black",this.allMenus={},this.allMenusSel={},this.simpleMenus={},this.shownMenus={},this.WIDTH=400,this.HEIGHT=400,this.RESIDUE_WIDTH=10,t.utilsCls.isMobile()||this.cfg.mobilemenu?this.MENU_HEIGHT=0:this.MENU_HEIGHT=40,this.LOG_HEIGHT=65,this.MENU_WIDTH=750,this.LESSWIDTH=20,this.LESSWIDTH_RESIZE=20,this.LESSHEIGHT=20,this.width2d=200,this.CMD_HEIGHT=.8*this.LOG_HEIGHT,this.EXTRAHEIGHT=this.MENU_HEIGHT+this.CMD_HEIGHT,null!=this.cfg.showmenu&&0==this.cfg.showmenu&&(this.EXTRAHEIGHT-=this.MENU_HEIGHT),null!=this.cfg.showcommand&&0==this.cfg.showcommand&&(this.EXTRAHEIGHT-=this.CMD_HEIGHT),this.GREY8="#AAAAAA",this.GREYB="#CCCCCC",this.GREYC="#DDDDDD",this.GREYD="#EEEEEE",this.ORANGE="#FFA500",this.themecolor="blue",this.defaultValue=1,this.ssValue=3,this.coilValue=3,this.contactValue=11,this.contactInsideValue=12,this.hbondValue=13,this.hbondInsideValue=14,this.ssbondValue=4,this.ionicValue=5,this.ionicInsideValue=6,this.clbondValue=15,this.halogenValue=17,this.halogenInsideValue=18,this.picationValue=19,this.picationInsideValue=20,this.pistackingValue=21,this.pistackingInsideValue=22,this.contactColor="888",this.contactInsideColor="FFF",this.hbondColor="0F0",this.hbondInsideColor="FFF",this.ssbondColor="FFA500",this.ionicColor="0FF",this.ionicInsideColor="FFF",this.clbondColor="006400",this.halogenColor="F0F",this.halogenInsideColor="FFF",this.picationColor="F00",this.picationInsideColor="FFF",this.pistackingColor="00F",this.pistackingInsideColor="FFF",this.hideedges=1,this.force=4,this.simulation=void 0,this.baseUrl=window&&window.location&&"structure.ncbi.nlm.nih.gov"==window.location.hostname?"https://structure.ncbi.nlm.nih.gov/Structure/":"https://www.ncbi.nlm.nih.gov/Structure/",this.tmalignUrl=this.baseUrl+"tmalign/tmalign.cgi",this.divStr="
    ",this.spanNowrapStr="",this.inputTextStr="=2.0 are supported.")));const a=new pe(o,{path:t||this.resourcePath||"",crossOrigin:this.crossOrigin,requestHeader:this.requestHeader,manager:this.manager,ktx2Loader:this.ktx2Loader,meshoptDecoder:this.meshoptDecoder});a.fileLoader.setRequestHeader(this.requestHeader);for(let e=0;e=0&&void 0===r[t]&&console.warn('THREE.GLTFLoader: Unknown extension "'+t+'".')}}a.setExtensions(l),a.setPlugins(r),a.parse(s,i)}parseAsync(e,t){const s=this;return new Promise((function(i,n){s.parse(e,t,i,n)}))}}function C(){let e={};return{get:function(t){return e[t]},add:function(t,s){e[t]=s},remove:function(t){delete e[t]},removeAll:function(){e={}}}}const b={KHR_BINARY_GLTF:"KHR_binary_glTF",KHR_DRACO_MESH_COMPRESSION:"KHR_draco_mesh_compression",KHR_LIGHTS_PUNCTUAL:"KHR_lights_punctual",KHR_MATERIALS_CLEARCOAT:"KHR_materials_clearcoat",KHR_MATERIALS_IOR:"KHR_materials_ior",KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS:"KHR_materials_pbrSpecularGlossiness",KHR_MATERIALS_SHEEN:"KHR_materials_sheen",KHR_MATERIALS_SPECULAR:"KHR_materials_specular",KHR_MATERIALS_TRANSMISSION:"KHR_materials_transmission",KHR_MATERIALS_UNLIT:"KHR_materials_unlit",KHR_MATERIALS_VOLUME:"KHR_materials_volume",KHR_TEXTURE_BASISU:"KHR_texture_basisu",KHR_TEXTURE_TRANSFORM:"KHR_texture_transform",KHR_MESH_QUANTIZATION:"KHR_mesh_quantization",EXT_TEXTURE_WEBP:"EXT_texture_webp",EXT_MESHOPT_COMPRESSION:"EXT_meshopt_compression"};class y{constructor(e){this.parser=e,this.name=b.KHR_LIGHTS_PUNCTUAL,this.cache={refs:{},uses:{}}}_markDefs(){const e=this.parser,t=this.parser.json.nodes||[];for(let s=0,i=t.length;s=0)throw new Error("THREE.GLTFLoader: setKTX2Loader must be called before loading KTX2 textures");return null}return t.loadTextureImage(e,n.source,l)}}class R{constructor(e){this.parser=e,this.name=b.EXT_TEXTURE_WEBP,this.isSupported=null}loadTexture(e){const t=this.name,s=this.parser,i=s.json,n=i.textures[e];if(!n.extensions||!n.extensions[t])return null;const l=n.extensions[t],r=i.images[l.source];let o=s.textureLoader;if(r.uri){const e=s.options.manager.getHandler(r.uri);null!==e&&(o=e)}return this.detectSupport().then((function(n){if(n)return s.loadTextureImage(e,l.source,o);if(i.extensionsRequired&&i.extensionsRequired.indexOf(t)>=0)throw new Error("THREE.GLTFLoader: WebP required by asset but unsupported.");return s.loadTexture(e)}))}detectSupport(){return this.isSupported||(this.isSupported=new Promise((function(e){const t=new Image;t.src="data:image/webp;base64,UklGRiIAAABXRUJQVlA4IBYAAAAwAQCdASoBAAEADsD+JaQAA3AAAAAA",t.onload=t.onerror=function(){e(1===t.height)}}))),this.isSupported}}class I{constructor(e){this.name=b.EXT_MESHOPT_COMPRESSION,this.parser=e}loadBufferView(e){const t=this.parser.json,s=t.bufferViews[e];if(s.extensions&&s.extensions[this.name]){const e=s.extensions[this.name],i=this.parser.getDependency("buffer",e.buffer),n=this.parser.options.meshoptDecoder;if(!n||!n.supported){if(t.extensionsRequired&&t.extensionsRequired.indexOf(this.name)>=0)throw new Error("THREE.GLTFLoader: setMeshoptDecoder must be called before loading compressed files");return null}return Promise.all([i,n.ready]).then((function(t){const s=e.byteOffset||0,i=e.byteLength||0,l=e.count,r=e.byteStride,o=new ArrayBuffer(l*r),a=new Uint8Array(t[0],s,i);return n.decodeGltfBuffer(new Uint8Array(o),l,r,a,e.mode,e.filter),o}))}return null}}const E="glTF",T=1313821514,D=5130562;class P{constructor(e){this.name=b.KHR_BINARY_GLTF,this.content=null,this.body=null;const t=new DataView(e,0,12);if(this.header={magic:THREE.LoaderUtils.decodeText(new Uint8Array(e.slice(0,4))),version:t.getUint32(4,!0),length:t.getUint32(8,!0)},this.header.magic!==E)throw new Error("THREE.GLTFLoader: Unsupported glTF-Binary header.");if(this.header.version<2)throw new Error("THREE.GLTFLoader: Legacy binary file detected.");const s=this.header.length-12,i=new DataView(e,12);let n=0;for(;n",t).replace("#include ",s).replace("#include ",i).replace("#include ",n).replace("#include ",l)},Object.defineProperties(this,{specular:{get:function(){return r.specular.value},set:function(e){r.specular.value=e}},specularMap:{get:function(){return r.specularMap.value},set:function(e){r.specularMap.value=e,e?this.defines.USE_SPECULARMAP="":delete this.defines.USE_SPECULARMAP}},glossiness:{get:function(){return r.glossiness.value},set:function(e){r.glossiness.value=e}},glossinessMap:{get:function(){return r.glossinessMap.value},set:function(e){r.glossinessMap.value=e,e?(this.defines.USE_GLOSSINESSMAP="",this.defines.USE_UV=""):(delete this.defines.USE_GLOSSINESSMAP,delete this.defines.USE_UV)}}}),delete this.metalness,delete this.roughness,delete this.metalnessMap,delete this.roughnessMap,this.setValues(e)}copy(e){return super.copy(e),this.specularMap=e.specularMap,this.specular.copy(e.specular),this.glossinessMap=e.glossinessMap,this.glossiness=e.glossiness,delete this.metalness,delete this.roughness,delete this.metalnessMap,delete this.roughnessMap,this}}class L{constructor(){this.name=b.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS,this.specularGlossinessParams=["color","map","lightMap","lightMapIntensity","aoMap","aoMapIntensity","emissive","emissiveIntensity","emissiveMap","bumpMap","bumpScale","normalMap","normalMapType","displacementMap","displacementScale","displacementBias","specularMap","specular","glossinessMap","glossiness","alphaMap","envMap","envMapIntensity"]}getMaterialType(){return H}extendParams(e,t,s){const i=t.extensions[this.name];e.color=new Color(1,1,1),e.opacity=1;const n=[];if(Array.isArray(i.diffuseFactor)){const t=i.diffuseFactor;e.color.fromArray(t),e.opacity=t[3]}if(void 0!==i.diffuseTexture&&n.push(s.assignTexture(e,"map",i.diffuseTexture,sRGBEncoding)),e.emissive=new Color(0,0,0),e.glossiness=void 0!==i.glossinessFactor?i.glossinessFactor:1,e.specular=new Color(1,1,1),Array.isArray(i.specularFactor)&&e.specular.fromArray(i.specularFactor),void 0!==i.specularGlossinessTexture){const t=i.specularGlossinessTexture;n.push(s.assignTexture(e,"glossinessMap",t)),n.push(s.assignTexture(e,"specularMap",t,sRGBEncoding))}return Promise.all(n)}createMaterial(e){const t=new H(e);return t.fog=!0,t.color=e.color,t.map=void 0===e.map?null:e.map,t.lightMap=null,t.lightMapIntensity=1,t.aoMap=void 0===e.aoMap?null:e.aoMap,t.aoMapIntensity=1,t.emissive=e.emissive,t.emissiveIntensity=1,t.emissiveMap=void 0===e.emissiveMap?null:e.emissiveMap,t.bumpMap=void 0===e.bumpMap?null:e.bumpMap,t.bumpScale=1,t.normalMap=void 0===e.normalMap?null:e.normalMap,t.normalMapType=TangentSpaceNormalMap,e.normalScale&&(t.normalScale=e.normalScale),t.displacementMap=null,t.displacementScale=1,t.displacementBias=0,t.specularMap=void 0===e.specularMap?null:e.specularMap,t.specular=e.specular,t.glossinessMap=void 0===e.glossinessMap?null:e.glossinessMap,t.glossiness=e.glossiness,t.alphaMap=null,t.envMap=void 0===e.envMap?null:e.envMap,t.envMapIntensity=1,t}}class N{constructor(){this.name=b.KHR_MESH_QUANTIZATION}}class q extends THREE.Interpolant{constructor(e,t,s,i){super(e,t,s,i)}copySampleValue_(e){const t=this.resultBuffer,s=this.sampleValues,i=this.valueSize,n=e*i*3+i;for(let e=0;e!==i;e++)t[e]=s[n+e];return t}}q.prototype.beforeStart_=q.prototype.copySampleValue_,q.prototype.afterEnd_=q.prototype.copySampleValue_,q.prototype.interpolate_=function(e,t,s,i){const n=this.resultBuffer,l=this.sampleValues,r=this.valueSize,o=2*r,a=3*r,d=i-t,c=(s-t)/d,h=c*c,p=h*c,m=e*a,u=m-a,g=-2*p+3*h,f=p-h,C=1-g,b=f-h+c;for(let e=0;e!==r;e++){const t=l[u+e+r],s=l[u+e+o]*d,i=l[m+e+r],a=l[m+e]*d;n[e]=C*t+b*s+g*i+f*a}return n};const U=new THREE.Quaternion;class B extends q{interpolate_(e,t,s,i){const n=super.interpolate_(e,t,s,i);return U.fromArray(n).normalize().toArray(n),n}}const j=0,z=1,G=2,V=3,W=4,Y=5,X=6,K={5120:Int8Array,5121:Uint8Array,5122:Int16Array,5123:Uint16Array,5125:Uint32Array,5126:Float32Array},J={9728:THREE.NearestFilter,9729:THREE.LinearFilter,9984:THREE.NearestMipmapNearestFilter,9985:THREE.LinearMipmapNearestFilter,9986:THREE.NearestMipmapLinearFilter,9987:THREE.LinearMipmapLinearFilter},Z={33071:THREE.ClampToEdgeWrapping,33648:THREE.MirroredRepeatWrapping,10497:THREE.RepeatWrapping},Q={SCALAR:1,VEC2:2,VEC3:3,VEC4:4,MAT2:4,MAT3:9,MAT4:16},ee={POSITION:"position",NORMAL:"normal",TANGENT:"tangent",TEXCOORD_0:"uv",TEXCOORD_1:"uv2",COLOR_0:"color",WEIGHTS_0:"skinWeight",JOINTS_0:"skinIndex"},te={scale:"scale",translation:"position",rotation:"quaternion",weights:"morphTargetInfluences"},se={CUBICSPLINE:void 0,LINEAR:THREE.InterpolateLinear,STEP:THREE.InterpolateDiscrete},ie="OPAQUE",ne="MASK",le="BLEND";function re(e,t,s){for(const i in s.extensions)void 0===e[i]&&(t.userData.gltfExtensions=t.userData.gltfExtensions||{},t.userData.gltfExtensions[i]=s.extensions[i])}function oe(e,t){void 0!==t.extras&&("object"==typeof t.extras?Object.assign(e.userData,t.extras):console.warn("THREE.GLTFLoader: Ignoring primitive type .extras, "+t.extras))}function ae(e,t){if(e.updateMorphTargets(),void 0!==t.weights)for(let s=0,i=t.weights.length;s{const s=this.associations.get(e);null!=s&&this.associations.set(t,s);for(const[s,i]of e.children.entries())n(i,t.children[s])};return n(s,i),i.name+="_instance_"+e.uses[t]++,i}_invokeOne(e){const t=Object.values(this.plugins);t.push(this);for(let s=0;s=2&&m.setY(t,c[e*l+1]),l>=3&&m.setZ(t,c[e*l+2]),l>=4&&m.setW(t,c[e*l+3]),l>=5)throw new Error("THREE.GLTFLoader: Unsupported itemSize in sparse BufferAttribute.")}}return m}))}loadTexture(e){const t=this.json,s=this.options,i=t.textures[e].source,n=t.images[i];let l=this.textureLoader;if(n.uri){const e=s.manager.getHandler(n.uri);null!==e&&(l=e)}return this.loadTextureImage(e,i,l)}loadTextureImage(e,t,s){const i=this,n=this.json,l=n.textures[e],r=n.images[t],o=(r.uri||r.bufferView)+":"+l.sampler;if(this.textureCache[o])return this.textureCache[o];const a=this.loadImageSource(t,s).then((function(t){t.flipY=!1,l.name&&(t.name=l.name);const s=(n.samplers||{})[l.sampler]||{};return t.magFilter=J[s.magFilter]||LinearFilter,t.minFilter=J[s.minFilter]||LinearMipmapLinearFilter,t.wrapS=Z[s.wrapS]||RepeatWrapping,t.wrapT=Z[s.wrapT]||RepeatWrapping,i.associations.set(t,{textures:e}),t})).catch((function(){return null}));return this.textureCache[o]=a,a}loadImageSource(e,t){const s=this,i=this.json,n=this.options;if(void 0!==this.sourceCache[e])return this.sourceCache[e].then((e=>e.clone()));const l=i.images[e],r=self.URL||self.webkitURL;let o=l.uri||"",a=!1;if(void 0!==l.bufferView)o=s.getDependency("bufferView",l.bufferView).then((function(e){a=!0;const t=new Blob([e],{type:l.mimeType});return o=r.createObjectURL(t),o}));else if(void 0===l.uri)throw new Error("THREE.GLTFLoader: Image "+e+" is missing URI and bufferView");const d=Promise.resolve(o).then((function(e){return new Promise((function(s,i){let l=s;!0===t.isImageBitmapLoader&&(l=function(e){const t=new Texture(e);t.needsUpdate=!0,s(t)}),t.load(THREE.LoaderUtils.resolveURL(e,n.path),l,void 0,i)}))})).then((function(e){var t;return!0===a&&r.revokeObjectURL(o),e.userData.mimeType=l.mimeType||((t=l.uri).search(/\.jpe?g($|\?)/i)>0||0===t.search(/^data\:image\/jpeg/)?"image/jpeg":t.search(/\.webp($|\?)/i)>0||0===t.search(/^data\:image\/webp/)?"image/webp":"image/png"),e})).catch((function(e){throw console.error("THREE.GLTFLoader: Couldn't load texture",o),e}));return this.sourceCache[e]=d,d}assignTexture(e,t,s,i){const n=this;return this.getDependency("texture",s.index).then((function(l){if(void 0===s.texCoord||0==s.texCoord||"aoMap"===t&&1==s.texCoord||console.warn("THREE.GLTFLoader: Custom UV set "+s.texCoord+" for texture "+t+" not yet supported."),n.extensions[b.KHR_TEXTURE_TRANSFORM]){const e=void 0!==s.extensions?s.extensions[b.KHR_TEXTURE_TRANSFORM]:void 0;if(e){const t=n.associations.get(l);l=n.extensions[b.KHR_TEXTURE_TRANSFORM].extendTexture(l,e),n.associations.set(l,t)}}return void 0!==i&&(l.encoding=i),e[t]=l,l}))}assignFinalMaterial(e){const t=e.geometry;let s=e.material;const i=void 0===t.attributes.tangent,n=void 0!==t.attributes.color,l=void 0===t.attributes.normal;if(e.isPoints){const e="PointsMaterial:"+s.uuid;let t=this.cache.get(e);t||(t=new PointsMaterial,Material.prototype.copy.call(t,s),t.color.copy(s.color),t.map=s.map,t.sizeAttenuation=!1,this.cache.add(e,t)),s=t}else if(e.isLine){const e="LineBasicMaterial:"+s.uuid;let t=this.cache.get(e);t||(t=new LineBasicMaterial,Material.prototype.copy.call(t,s),t.color.copy(s.color),this.cache.add(e,t)),s=t}if(i||n||l){let e="ClonedMaterial:"+s.uuid+":";s.isGLTFSpecularGlossinessMaterial&&(e+="specular-glossiness:"),i&&(e+="derivative-tangents:"),n&&(e+="vertex-colors:"),l&&(e+="flat-shading:");let t=this.cache.get(e);t||(t=s.clone(),n&&(t.vertexColors=!0),l&&(t.flatShading=!0),i&&(t.normalScale&&(t.normalScale.y*=-1),t.clearcoatNormalScale&&(t.clearcoatNormalScale.y*=-1)),this.cache.add(e,t),this.associations.set(t,this.associations.get(s))),s=t}s.aoMap&&void 0===t.attributes.uv2&&void 0!==t.attributes.uv&&t.setAttribute("uv2",t.attributes.uv),e.material=s}getMaterialType(){return MeshStandardMaterial}loadMaterial(e){const t=this,s=this.json,i=this.extensions,n=s.materials[e];let l;const r={},o=n.extensions||{},a=[];if(o[b.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS]){const e=i[b.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS];l=e.getMaterialType(),a.push(e.extendParams(r,n,t))}else if(o[b.KHR_MATERIALS_UNLIT]){const e=i[b.KHR_MATERIALS_UNLIT];l=e.getMaterialType(),a.push(e.extendParams(r,n,t))}else{const s=n.pbrMetallicRoughness||{};if(r.color=new Color(1,1,1),r.opacity=1,Array.isArray(s.baseColorFactor)){const e=s.baseColorFactor;r.color.fromArray(e),r.opacity=e[3]}void 0!==s.baseColorTexture&&a.push(t.assignTexture(r,"map",s.baseColorTexture,sRGBEncoding)),r.metalness=void 0!==s.metallicFactor?s.metallicFactor:1,r.roughness=void 0!==s.roughnessFactor?s.roughnessFactor:1,void 0!==s.metallicRoughnessTexture&&(a.push(t.assignTexture(r,"metalnessMap",s.metallicRoughnessTexture)),a.push(t.assignTexture(r,"roughnessMap",s.metallicRoughnessTexture))),l=this._invokeOne((function(t){return t.getMaterialType&&t.getMaterialType(e)})),a.push(Promise.all(this._invokeAll((function(t){return t.extendMaterialParams&&t.extendMaterialParams(e,r)}))))}!0===n.doubleSided&&(r.side=DoubleSide);const d=n.alphaMode||ie;if(d===le?(r.transparent=!0,r.depthWrite=!1):(r.transparent=!1,d===ne&&(r.alphaTest=void 0!==n.alphaCutoff?n.alphaCutoff:.5)),void 0!==n.normalTexture&&l!==MeshBasicMaterial&&(a.push(t.assignTexture(r,"normalMap",n.normalTexture)),r.normalScale=new Vector2(1,1),void 0!==n.normalTexture.scale)){const e=n.normalTexture.scale;r.normalScale.set(e,e)}return void 0!==n.occlusionTexture&&l!==MeshBasicMaterial&&(a.push(t.assignTexture(r,"aoMap",n.occlusionTexture)),void 0!==n.occlusionTexture.strength&&(r.aoMapIntensity=n.occlusionTexture.strength)),void 0!==n.emissiveFactor&&l!==MeshBasicMaterial&&(r.emissive=(new Color).fromArray(n.emissiveFactor)),void 0!==n.emissiveTexture&&l!==MeshBasicMaterial&&a.push(t.assignTexture(r,"emissiveMap",n.emissiveTexture,sRGBEncoding)),Promise.all(a).then((function(){let s;return s=l===H?i[b.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS].createMaterial(r):new l(r),n.name&&(s.name=n.name),oe(s,n),t.associations.set(s,{materials:e}),n.extensions&&re(i,s,n),s}))}createUniqueName(e){const t=PropertyBinding.sanitizeNodeName(e||"");let s=t;for(let e=1;this.nodeNamesUsed[s];++e)s=t+"_"+e;return this.nodeNamesUsed[s]=!0,s}loadGeometries(e){const t=this,s=this.extensions,i=this.primitiveCache;function n(e){return s[b.KHR_DRACO_MESH_COMPRESSION].decodePrimitive(e,t).then((function(s){return ue(s,e,t)}))}const l=[];for(let s=0,r=e.length;s0&&ae(h,n),h.name=t.createUniqueName(n.name||"mesh_"+e),oe(h,n),c.extensions&&re(i,h,c),t.assignFinalMaterial(h),a.push(h)}for(let s=0,i=a.length;s1?new Group:1===t.length?t[0]:new Object3D,r!==t[0])for(let e=0,s=t.length;e{const t=new Map;for(const[e,s]of n.associations)(e instanceof Material||e instanceof Texture)&&t.set(e,s);return e.traverse((e=>{const s=n.associations.get(e);null!=s&&t.set(e,s)})),t})(l),l}))}}function me(e,t,s,i){const n=s.nodes[e];return i.getDependency("node",e).then((function(e){if(void 0===n.skin)return e;let t;return i.getDependency("skin",n.skin).then((function(e){t=e;const s=[];for(let e=0,n=t.joints.length;e{const s=n[e];return s&&(l={profileId:e,profilePath:`${t}/${s.path}`,deprecated:!!s.deprecated}),!!l})),!l){if(!s)throw new Error("No matching profile name found");const e=n[s];if(!e)throw new Error(`No matching profile name found and default profile "${s}" missing.`);l={profileId:s,profilePath:`${t}/${e.path}`,deprecated:!!e.deprecated}}const r=await Ce(l.profilePath);let o;if(i){let t;if(t="any"===e.handedness?r.layouts[Object.keys(r.layouts)[0]]:r.layouts[e.handedness],!t)throw new Error(`No matching handedness, ${e.handedness}, in profile ${l.profileId}`);t.assetPath&&(o=l.profilePath.replace("profile.json",t.assetPath))}return{profile:r,assetPath:o}}const ye={xAxis:0,yAxis:0,button:0,state:fe.ComponentState.DEFAULT};class ve{constructor(e){this.componentProperty=e.componentProperty,this.states=e.states,this.valueNodeName=e.valueNodeName,this.valueNodeProperty=e.valueNodeProperty,this.valueNodeProperty===fe.VisualResponseProperty.TRANSFORM&&(this.minNodeName=e.minNodeName,this.maxNodeName=e.maxNodeName),this.value=0,this.updateFromComponent(ye)}updateFromComponent({xAxis:e,yAxis:t,button:s,state:i}){const{normalizedXAxis:n,normalizedYAxis:l}=function(e=0,t=0){let s=e,i=t;if(Math.sqrt(e*e+t*t)>1){const n=Math.atan2(t,e);s=Math.cos(n),i=Math.sin(n)}return{normalizedXAxis:.5*s+.5,normalizedYAxis:.5*i+.5}}(e,t);switch(this.componentProperty){case fe.ComponentProperty.X_AXIS:this.value=this.states.includes(i)?n:.5;break;case fe.ComponentProperty.Y_AXIS:this.value=this.states.includes(i)?l:.5;break;case fe.ComponentProperty.BUTTON:this.value=this.states.includes(i)?s:0;break;case fe.ComponentProperty.STATE:this.valueNodeProperty===fe.VisualResponseProperty.VISIBILITY?this.value=this.states.includes(i):this.value=this.states.includes(i)?1:0;break;default:throw new Error(`Unexpected visualResponse componentProperty ${this.componentProperty}`)}}}class _e{constructor(e,t){if(!(e&&t&&t.visualResponses&&t.gamepadIndices&&0!==Object.keys(t.gamepadIndices).length))throw new Error("Invalid arguments supplied");this.id=e,this.type=t.type,this.rootNodeName=t.rootNodeName,this.touchPointNodeName=t.touchPointNodeName,this.visualResponses={},Object.keys(t.visualResponses).forEach((e=>{const s=new ve(t.visualResponses[e]);this.visualResponses[e]=s})),this.gamepadIndices=Object.assign({},t.gamepadIndices),this.values={state:fe.ComponentState.DEFAULT,button:void 0!==this.gamepadIndices.button?0:void 0,xAxis:void 0!==this.gamepadIndices.xAxis?0:void 0,yAxis:void 0!==this.gamepadIndices.yAxis?0:void 0}}get data(){return{id:this.id,...this.values}}updateFromGamepad(e){if(this.values.state=fe.ComponentState.DEFAULT,void 0!==this.gamepadIndices.button&&e.buttons.length>this.gamepadIndices.button){const t=e.buttons[this.gamepadIndices.button];this.values.button=t.value,this.values.button=this.values.button<0?0:this.values.button,this.values.button=this.values.button>1?1:this.values.button,t.pressed||1===this.values.button?this.values.state=fe.ComponentState.PRESSED:(t.touched||this.values.button>fe.ButtonTouchThreshold)&&(this.values.state=fe.ComponentState.TOUCHED)}void 0!==this.gamepadIndices.xAxis&&e.axes.length>this.gamepadIndices.xAxis&&(this.values.xAxis=e.axes[this.gamepadIndices.xAxis],this.values.xAxis=this.values.xAxis<-1?-1:this.values.xAxis,this.values.xAxis=this.values.xAxis>1?1:this.values.xAxis,this.values.state===fe.ComponentState.DEFAULT&&Math.abs(this.values.xAxis)>fe.AxisTouchThreshold&&(this.values.state=fe.ComponentState.TOUCHED)),void 0!==this.gamepadIndices.yAxis&&e.axes.length>this.gamepadIndices.yAxis&&(this.values.yAxis=e.axes[this.gamepadIndices.yAxis],this.values.yAxis=this.values.yAxis<-1?-1:this.values.yAxis,this.values.yAxis=this.values.yAxis>1?1:this.values.yAxis,this.values.state===fe.ComponentState.DEFAULT&&Math.abs(this.values.yAxis)>fe.AxisTouchThreshold&&(this.values.state=fe.ComponentState.TOUCHED)),Object.values(this.visualResponses).forEach((e=>{e.updateFromComponent(this.values)}))}}class we{constructor(e,t,s){if(!e)throw new Error("No xrInputSource supplied");if(!t)throw new Error("No profile supplied");this.xrInputSource=e,this.assetUrl=s,this.id=t.profileId,this.layoutDescription=t.layouts[e.handedness],this.components={},Object.keys(this.layoutDescription.components).forEach((e=>{const t=this.layoutDescription.components[e];this.components[e]=new _e(e,t)})),this.updateFromGamepad()}get gripSpace(){return this.xrInputSource.gripSpace}get targetRaySpace(){return this.xrInputSource.targetRaySpace}get data(){const e=[];return Object.values(this.components).forEach((t=>{e.push(t.data)})),e}updateFromGamepad(){Object.values(this.components).forEach((e=>{e.updateFromGamepad(this.xrInputSource.gamepad)}))}}class Se extends THREE.Object3D{constructor(){super(),this.motionController=null,this.envMap=null}setEnvironmentMap(e){return this.envMap==e||(this.envMap=e,this.traverse((e=>{e.isMesh&&(e.material.envMap=this.envMap,e.material.needsUpdate=!0)}))),this}updateMatrixWorld(e){super.updateMatrixWorld(e),this.motionController&&(this.motionController.updateFromGamepad(),Object.values(this.motionController.components).forEach((e=>{Object.values(e.visualResponses).forEach((e=>{const{valueNode:t,minNode:s,maxNode:i,value:n,valueNodeProperty:l}=e;t&&(l===fe.VisualResponseProperty.VISIBILITY?t.visible=n:l===fe.VisualResponseProperty.TRANSFORM&&(t.quaternion.slerpQuaternions(s.quaternion,i.quaternion,n),t.position.lerpVectors(s.position,i.position,n)))}))})))}}function Ae(e,t){!function(e,t){Object.values(e.components).forEach((e=>{const{type:s,touchPointNodeName:i,visualResponses:n}=e;if(s===fe.ComponentType.TOUCHPAD)if(e.touchPointNode=t.getObjectByName(i),e.touchPointNode){const t=new SphereGeometry(.001),s=new MeshBasicMaterial({color:255}),i=new Mesh(t,s);e.touchPointNode.add(i)}else console.warn(`Could not find touch dot, ${e.touchPointNodeName}, in touchpad component ${e.id}`);Object.values(n).forEach((e=>{const{valueNodeName:s,minNodeName:i,maxNodeName:n,valueNodeProperty:l}=e;if(l===fe.VisualResponseProperty.TRANSFORM){if(e.minNode=t.getObjectByName(i),e.maxNode=t.getObjectByName(n),!e.minNode)return void console.warn(`Could not find ${i} in the model`);if(!e.maxNode)return void console.warn(`Could not find ${n} in the model`)}e.valueNode=t.getObjectByName(s),e.valueNode||console.warn(`Could not find ${s} in the model`)}))}))}(e.motionController,t),e.envMap&&t.traverse((t=>{t.isMesh&&(t.material.envMap=e.envMap,t.material.needsUpdate=!0)})),e.add(t)}class xe{constructor(e=null){this.gltfLoader=e,this.path="https://cdn.jsdelivr.net/npm/@webxr-input-profiles/assets@1.0/dist/profiles",this._assetCache={},this.gltfLoader||(this.gltfLoader=new f)}createControllerModel(e){const t=new Se;let s=null;return e.addEventListener("connected",(e=>{const i=e.data;"tracked-pointer"===i.targetRayMode&&i.gamepad&&be(i,this.path,"generic-trigger").then((({profile:e,assetPath:n})=>{t.motionController=new we(i,e,n);const l=this._assetCache[t.motionController.assetUrl];if(l)s=l.scene.clone(),Ae(t,s);else{if(!this.gltfLoader)throw new Error("GLTFLoader not set.");this.gltfLoader.setPath(""),this.gltfLoader.load(t.motionController.assetUrl,(e=>{this._assetCache[t.motionController.assetUrl]=e,s=e.scene.clone(),Ae(t,s)}),null,(()=>{throw new Error(`Asset ${t.motionController.assetUrl} missing or malformed.`)}))}})).catch((e=>{console.warn(e)}))})),e.addEventListener("disconnected",(()=>{t.motionController=null,t.remove(s),s=null})),t}}class ke extends THREE.EventDispatcher{constructor(e){if(super(),void 0===e)return void console.error("ControllerGestures must be passed a renderer");const t=new THREE.Clock;this.controller1=e.xr.getController(0),this.controller1.userData.gestures={index:0},this.controller1.userData.selectPressed=!1,this.controller1.addEventListener("selectstart",i),this.controller1.addEventListener("selectend",n),this.controller2=e.xr.getController(1),this.controller2.userData.gestures={index:1},this.controller2.userData.selectPressed=!1,this.controller2.addEventListener("selectstart",i),this.controller2.addEventListener("selectend",n),this.doubleClickLimit=.2,this.pressMinimum=.4,this.right=new THREE.Vector3(1,0,0),this.up=new THREE.Vector3(0,1,0),this.type="unknown",this.prevTap="none",this.clock=t;const s=this;function i(){const e=this.userData.gestures;e.startPosition=void 0,e.startTime=t.getElapsedTime(),-1==s.type.indexOf("tap")&&(e.taps=0),s.type="unknown",this.userData.selectPressed=!0}function n(){const e=this.userData.gestures;e.endTime=t.getElapsedTime();e.endTime-e.startTime.05&&(e.startPosition=this.controller1.position.clone())),this.controller2.userData.selectPressed&&void 0===t.startPosition&&(i=s-t.startTime,i>.05&&(t.startPosition=this.controller2.position.clone())),!this.controller1.userData.selectPressed&&"tap"===this.type&&(i=this.clock.getElapsedTime()-e.endTime,i>this.doubleClickLimit)){switch(e.taps){case 1:self.prevTap="tap";break;case 2:this.dispatchEvent({type:"doubletap",position:this.controller1.position,matrixWorld:this.controller1.matrixWorld}),self.prevTap="doubletap"}this.type="unknown",e.taps=0}if("unknown"===this.type&&this.touch)"doubletap"==self.prevTap?(this.type="pinch",this.startDistance=this.controller1.position.distanceTo(this.controller2.position),this.dispatchEvent({type:"pinch",delta:new THREE.Vector3(0,0,0),scale:1,initialise:!0})):(this.type="pan",this.startPosition=this.controller1.position.clone(),this.dispatchEvent({type:"pan",delta:new THREE.Vector3(0,0,0),initialise:!0}));else if(("pinch"===this.type||"pan"===this.type)&&"doubletap"==self.prevTap&&this.controller2.position){const e=this.controller1.position.distanceTo(this.controller2.position)/this.startDistance,t=this.controller1.position.clone().sub(this.startPosition);this.dispatchEvent({type:"pinch",delta:t,scale:e})}}}class Oe{constructor(e,t){this.config=void 0===t?{panelSize:{width:1,height:1},width:512,height:512,opacity:.7,body:{fontFamily:"Arial",fontSize:30,padding:2,backgroundColor:"#000",fontColor:"#fff",borderRadius:6}}:t,void 0===this.config.width&&(this.config.width=512),void 0===this.config.height&&(this.config.height=512),void 0===this.config.body&&(this.config.body={fontFamily:"Arial",size:30,padding:2,backgroundColor:"#000",fontColor:"#fff",borderRadius:6});const s=this.config.body;void 0===s.borderRadius&&(s.borderRadius=6),void 0===s.fontFamily&&(s.fontFamily="Arial"),void 0===s.padding&&(s.padding=2),void 0===s.fontSize&&(s.fontSize=30),void 0===s.backgroundColor&&(s.backgroundColor="#000"),void 0===s.fontColor&&(s.fontColor="#fff"),Object.entries(this.config).forEach((([e,t])=>{if(!("object"!=typeof t||"panelSize"===e||t instanceof THREE.WebGLRenderer||t instanceof THREE.Scene)){const e=void 0!==t.position?t.position:{x:0,y:0};void 0!==e.left&&void 0===e.x&&(e.x=e.left),void 0!==e.top&&void 0===e.y&&(e.y=e.top);const s=void 0!==t.width?t.width:this.config.width,i=void 0!==t.height?t.height:this.config.height;void 0!==e.right&&void 0===e.x&&(e.x=this.config.width-e.right-s),void 0!==e.bottom&&void 0===e.y&&(e.y=this.config.height-e.bottom-i),void 0===e.x&&(e.x=0),void 0===e.y&&(e.y=0),t.position=e,void 0===t.type&&(t.type="text")}}));const i=this.createOffscreenCanvas(this.config.width,this.config.height);this.context=i.getContext("2d"),this.context.save();const n=void 0!==this.config.opacity?this.config.opacity:.7,l=new THREE.MeshBasicMaterial({transparent:!0,opacity:n});this.panelSize=void 0!==this.config.panelSize?this.config.panelSize:{width:1,height:1};const r=new THREE.PlaneGeometry(this.panelSize.width,this.panelSize.height);this.mesh=new THREE.Mesh(r,l),this.texture=new THREE.CanvasTexture(i),this.mesh.material.map=this.texture,this.scene=this.config.scene;if(Object.values(this.config).filter((e=>"input-text"===e.type)).length>0){this.keyboard=new Re(this.panelSize.width,this.config.renderer);this.keyboard.mesh.position.set(0,-.3,.2),this.mesh.add(this.keyboard.mesh)}if(void 0===e)this.content={body:""},this.config.body.type="text";else{this.content=e;Object.values(t).filter((e=>"button"===e.type||"scroll"===e.overflow||"input-text"===e.type)).length>0&&(void 0===t||void 0===t.renderer?console.warn("CanvasUI: button, scroll or input-text in the config but no renderer"):(this.renderer=t.renderer,this.initControllers()))}this.selectedElements=[void 0,void 0],this.selectPressed=[!1,!1],this.scrollData=[void 0,void 0],this.intersects=[void 0,void 0],this.needsUpdate=!0,this.update()}getIntersectY(e){const t=this.config.height||512,s=this.intersects[e];return void 0===s||void 0===s.uv?0:(1-s.uv.y)*t}initControllers(){this.vec3=new THREE.Vector3,this.mat4=new THREE.Matrix4,this.raycaster=new THREE.Raycaster;const e=this;function t(t){const s=t.target===e.controller?0:1,i=e.selectedElements[s];if(void 0!==i)if("button"==i.type)e.select(s);else if("input-text"==i.type&&e.keyboard)if(e.keyboard.visible)e.keyboard.linkedUI=void 0,e.keyboard.linkedText=void 0,e.keyboard.linkedElement=void 0,e.keyboard.visible=!1;else{let t;e.keyboard.linkedUI=e,Object.entries(e.config).forEach((([e,s])=>{s==i&&(t=e)}));const s=(.5-(i.position.y+i.height+e.config.body.padding)/e.config.height)*e.panelSize.height,n=Math.max(e.panelSize.width,e.panelSize.height)/2;e.keyboard.position.set(0,-n/1.5-s,.1),e.keyboard.linkedText=e.content[t],e.keyboard.linkedName=t,e.keyboard.linkedElement=i,e.keyboard.visible=!0}}function s(t){const s=t.target===e.controller?0:1;if(e.selectPressed[s]=!0,void 0!==e.selectedElements[s]&&"scroll"==e.selectedElements[s].overflow){const t=e.selectedElements[s];e.scrollData[s]={scrollY:t.scrollY,rayY:e.getIntersectY(s)}}}function i(t){const s=t.target===e.controller?0:1;e.selectPressed[s]=!1,void 0!==e.selectedElements[s]&&"scroll"==e.selectedElements[s].overflow&&(e.scrollData[s]=void 0)}if(this.controller=this.renderer.xr.getController(0),this.controller.addEventListener("select",t),this.controller.addEventListener("selectstart",s),this.controller.addEventListener("selectend",i),this.controller1=this.renderer.xr.getController(1),this.controller1.addEventListener("select",t),this.controller1.addEventListener("selectstart",s),this.controller1.addEventListener("selectend",i),this.scene){const e=.015,t=new THREE.IcosahedronBufferGeometry(e),s=new THREE.MeshBasicMaterial({color:170}),i=new THREE.Mesh(t,s);i.visible=!1,this.scene.add(i);const n=new THREE.Mesh(t,s);n.visible=!1,this.scene.add(n),this.intersectMesh=[i,n]}}setClip(e){const t=this.context;if(t.restore(),t.save(),void 0!==e.clipPath){const s=new Path2D(e.clipPath);t.clip(s)}else{const s=void 0!==e.position?e.position:{x:0,y:0},i=e.borderRadius||0,n=e.width||this.config.width,l=e.height||this.config.height;if(t.beginPath(),0!==i){const e=Math.PI/2;t.moveTo(s.x+i,s.y),t.arc(s.x+i,s.y+i,i,e,2*e,!0),t.lineTo(s.x,s.y+l-i),t.arc(s.x+i,s.y+l-i,i,0,e,!0),t.lineTo(s.x+n-i,s.y+l),t.arc(s.x+n-i,s.y+l-i,i,3*e,4*e,!0),t.lineTo(s.x+n,s.y+i),t.arc(s.x+n-i,s.y+i,i,2*e,3*e,!0),t.closePath(),t.clip()}else t.rect(s.x,s.y,n,l),t.clip()}}setPosition(e,t,s){void 0!==this.mesh&&this.mesh.position.set(e,t,s)}setRotation(e,t,s){void 0!==this.mesh&&this.mesh.rotation.set(e,t,s)}updateElement(e,t){let s=this.content[e];void 0!==s?("object"==typeof s?s.content=t:s=t,this.content[e]=s,this.needsUpdate=!0):console.warn(`CanvasGUI.updateElement: No ${e} found`)}get panel(){return this.mesh}getElementAtLocation(e,t){const s=this,i=Object.entries(this.config).filter((([i,n])=>{if(!("object"!=typeof n||"panelSize"===i||"body"===i||n instanceof THREE.WebGLRenderer||n instanceof THREE.Scene)){const i=n.position,l=void 0!==n.width?n.width:s.config.width,r=void 0!==n.height?n.height:s.config.height;return e>=i.x&&e=i.y&&t0?(this.hover(t,s[0].uv),this.intersects[t]=s[0],this.scroll(t)):(this.hover(t),this.intersects[t]=void 0,this.scroll(t))}update(){if(void 0===this.mesh)return;if(this.controller&&this.handleController(this.controller,0),this.controller1&&this.handleController(this.controller1,1),this.keyboard&&this.keyboard.visible&&this.keyboard.update(),!this.needsUpdate)return;let e=this.context;e.clearRect(0,0,this.config.width,this.config.height);const t=this.config.body.backgroundColor?this.config.body.backgroundColor:"#000";!this.config.body.fontFamily||this.config.body.fontFamily;const s=this.config.body.fontColor?this.config.body.fontColor:"#fff";!this.config.body.fontSize||this.config.body.fontSize,this.setClip(this.config.body),e.fillStyle=t,e.fillRect(0,0,this.config.width,this.config.height);const i=this;Object.entries(this.content).forEach((([t,n])=>{const l=void 0!==i.config[t]?i.config[t]:i.config.body;if("none"!==(void 0!==l.display?l.display:"block")){const r=void 0!==l.position?l.position:{x:0,y:0},o=void 0!==l.width?l.width:i.config.width,a=void 0!==l.height?l.height:i.config.height;"button"!=l.type||n.toLowerCase().startsWith("")||(void 0===l.borderRadius&&(l.borderRadius=6),void 0===l.textAlign&&(l.textAlign="center")),i.setClip(l);const d=n.toLowerCase().startsWith(""),c=void 0!==i.selectedElements[0]&&this.selectedElements[0]===l||void 0!==i.selectedElements[1]&&this.selectedElements[1]===l;if(void 0!==l.backgroundColor&&(c&&"button"==l.type&&void 0!==l.hover?e.fillStyle=l.hover:e.fillStyle=l.backgroundColor,e.fillRect(r.x,r.y,o,a)),"text"==l.type||"button"==l.type||"input-text"==l.type){let h=!1;if(c?(d||"button"!=l.type?e.fillStyle=void 0!==l.hover?l.hover:void 0!==l.fontColor?l.fontColor:s:e.fillStyle=void 0!==l.fontColor?l.fontColor:s,h=void 0===l.hover):e.fillStyle=void 0!==l.fontColor?l.fontColor:s,d){const t=n.toUpperCase().substring(6,n.length-7);e.save(),e.translate(r.x,r.y);const s=new Path2D(t);e.fill(s),e.restore()}else i.wrapText(t,n);h&&(e.beginPath(),e.strokeStyle="#fff",e.lineWidth=2,e.rect(r.x,r.y,o,a),e.stroke())}else if("img"==l.type)if(void 0===l.img)this.loadImage(n).then((e=>{console.log(`w: ${e.width} | h: ${e.height}`),l.img=e,i.needsUpdate=!0,i.update()})).catch((e=>console.error(e)));else{const t=o/(l.img.width/l.img.height);e.drawImage(l.img,r.x,r.y,o,t)}}})),this.needsUpdate=!1,this.texture.needsUpdate=!0}loadImage(e){return new Promise(((t,s)=>{const i=new THREE.Image;i.addEventListener("load",(()=>t(i))),i.addEventListener("error",(e=>s(e))),i.src=e}))}createOffscreenCanvas(e,t){const s=document.createElement("canvas");return s.width=e,s.height=t,s}fillRoundedRect(e,t,s,i,n){const l=this.context;l.beginPath(),l.moveTo(e+n,t),l.lineTo(e+s-n,t),l.quadraticCurveTo(e+s,t,e+s,t+n),l.lineTo(e+s,t+i-n),l.quadraticCurveTo(e+s,t+i,e+s-n,t+i),l.lineTo(e+n,t+i),l.quadraticCurveTo(e,t+i,e,t+i-n),l.lineTo(e,t+n),l.quadraticCurveTo(e,t,e+n,t),l.closePath(),l.fill()}lookAt(e){void 0!==this.mesh&&(e instanceof Vector3?this.mesh.lookAt(e):console.error("CanvasUI lookAt called parameter not a THREE.Vector3"))}get visible(){return void 0!==this.mesh&&this.mesh.visible}set visible(e){this.mesh&&(this.mesh.visible=e)}get position(){if(void 0!==this.mesh)return this.mesh.position}set position(e){void 0!==this.mesh&&(e instanceof Vector3?this.mesh.position.copy(e):console.error("CanvasUI trying to set the mesh position using a parameter that is not a THREE.Vector3"))}get quaternion(){if(void 0!==this.mesh)return this.mesh.quaternion}set quaternion(e){void 0!==this.mesh&&(e instanceof QUaternion?this.mesh.quaternion.copy(e):console.error("CanvasUI trying to set the mesh quaternion using a parameter that is not a THREE.Quaternion"))}wrapText(e,t){const s=t.split(" ");let i="";const n=[],l=void 0!==this.config[e]?this.config[e]:this.config.body,r=void 0!==l.width?l.width:this.config.width,o=void 0!==l.height?l.height:this.config.height,a=void 0!==l.position?l.position:{x:0,y:0},d=void 0!==l.padding?l.padding:void 0!==this.config.body.padding?this.config.body.padding:10,c=void 0!==l.paddingTop?l.paddingTop:d,h=void 0!==l.paddingLeft?l.paddingLeft:d,p=void 0!==l.paddingBottom?l.paddingBottom:d,m=void 0!==l.paddingRight?l.paddingRight:d,u={x:a.x+h,y:a.y+c,width:r-h-m,height:o-c-p},g=void 0!==l.textAlign?l.textAlign:void 0!==this.config.body.textAlign?this.config.body.textAlign:"left",f=void 0!==l.fontSize?l.fontSize:void 0!==this.config.body.fontSize?this.config.body.fontSize:30,C=void 0!==l.fontFamily?l.fontFamily:void 0!==this.config.body.fontFamily?this.config.body.fontFamily:"Arial",b=f+(void 0!==l.leading?l.leading:void 0!==this.config.body.leading?this.config.body.leading:8),y=this.context;y.textAlign=g,y.font=`${f}px '${C}'`,s.forEach((function(e){let t=s.length>1?`${i}${e} `:e,l=y.measureText(t);if(l.width>u.width&&e.length>1)if(0==i.length&&l.width>u.width){for(;l.width>u.width;){let s=0;do{s++,t=e.substr(0,s),l=y.measureText(t)}while(l.widthu.height&&"scroll"===l.overflow){void 0===l.scrollY&&(l.scrollY=0);const e=void 0!==l.fontColor?l.fontColor:this.config.body.fontColor;y.fillStyle="#aaa",this.fillRoundedRect(a.x+r-12,a.y,12,o,6),y.fillStyle="#666";const t=u.height/v,s=t*o,i=-l.scrollY*t;this.fillRoundedRect(a.x+r-12,a.y+i,12,s,6),y.fillStyle=e,_=l.scrollY,l.minScrollY=u.height-v}let w,S=_+u.y+f/2;switch(g){case"center":w=u.x+u.width/2;break;case"right":w=u.x+u.width;break;default:w=u.x}n.forEach((e=>{S+b>0&&y.fillText(e,w,S),S+=b}))}}class Re{constructor(e,t,s="EN"){const i=this.getConfig(s);i.panelSize={width:e,height:.5*e},i.height=256,i.body={backgroundColor:"#555"},i.renderer=t;const n=this.getContent(s);this.keyboard=new Oe(n,i),this.keyboard.mesh.visible=!1,this.shift=!1}get mesh(){return this.keyboard.mesh}getConfig(e){const t={};let s=10;const i=39.2,n=49,l="#333",r="#000";let o=s,a=s;for(let e=0;e<10;e++){const d={type:"button",position:{x:a,y:o},width:i,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e)};t[`btn${e}`]=d,a+=49.2}o+=59,a=s;for(let e=0;e<10;e++){const d={type:"button",position:{x:a,y:o},width:i,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+10)};t[`btn${e+10}`]=d,a+=49.2}o+=59,a=s;for(let e=0;e<9;e++){const d=0==e||8==e?1.5*i+5:i,c={type:"button",position:{x:a,y:o},width:d,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+20)};t[`btn${e+20}`]=c,a+=d+s}o+=59,a=s;for(let e=0;e<5;e++){const d=0==e||4==e?88.4:2==e?186.8:i,c={type:"button",position:{x:a,y:o},width:d,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+30)};0==e&&(c.fontSize=20),t[`btn${e+30}`]=c,a+=d+s}return t}getContent(e,t=0){let s,i={};switch(this.language=e,this.keyboardIndex=t,t){case 0:s=["q","w","e","r","t","y","u","i","o","p","a","s","d","f","g","h","j","k","l","@","⇧","z","x","c","v","b","n","m","⇦","","?123",","," ",".","↲"];for(let e=0;e","_","`","~",":",";","⇦","","abc",","," ",".","↲"];for(let e=0;e=0;e--){let s=t.scene.children[e];t.scene.remove(s)}else t.scene=new THREE.Scene;if(void 0!==t.scene_ghost)for(let e=t.scene_ghost.children.length-1;e>=0;e--){let s=t.scene_ghost.children[e];t.scene_ghost.remove(s)}else t.scene_ghost=new THREE.Scene;if(""!=s.htmlCls.setHtmlCls.getCookie("shininess")){let e=parseFloat(s.htmlCls.setHtmlCls.getCookie("shininess"));t.shininess!=e&&s.htmlCls.clickMenuCls.setLogCmd("set shininess "+e,!0),t.shininess=e}if(!s.bNode&&""!=s.htmlCls.setHtmlCls.getCookie("light1")){let e=parseFloat(s.htmlCls.setHtmlCls.getCookie("light1")),i=parseFloat(s.htmlCls.setHtmlCls.getCookie("light2")),n=parseFloat(s.htmlCls.setHtmlCls.getCookie("light3"));t.light1==e&&t.light2==i&&t.light3==n||s.htmlCls.clickMenuCls.setLogCmd("set light | light1 "+e+" | light2 "+i+" | light3 "+n,!0),t.light1=e,t.light2=i,t.light3=n}t.directionalLight=new THREE.DirectionalLight(16777215,t.light1),t.directionalLight2=new THREE.DirectionalLight(16777215,t.light2),t.directionalLight3=new THREE.DirectionalLight(16777215,t.light3),t.cam_z>0?(t.directionalLight.position.set(-1,1,1),t.directionalLight2.position.set(1,1,1),t.directionalLight3.position.set(1,1,-1),t.lightPos=new THREE.Vector3(-1,1,1),t.lightPos2=new THREE.Vector3(1,1,1),t.lightPos3=new THREE.Vector3(1,1,-1)):(t.directionalLight.position.set(-1,1,-1),t.directionalLight2.position.set(1,1,-1),t.directionalLight3.position.set(1,1,1),t.lightPos=new THREE.Vector3(-1,1,-1),t.lightPos2=new THREE.Vector3(1,1,-1),t.lightPos3=new THREE.Vector3(1,1,1));let i=new THREE.AmbientLight(4210752);if(t.scene.add(t.directionalLight),t.scene.add(i),void 0!==t.mdl)for(let e=t.mdl.children.length-1;e>=0;e--){let s=t.mdl.children[e];s.geometry&&s.geometry.dispose(),s.material&&s.material.dispose(),t.mdl.remove(s)}if(void 0!==t.mdlImpostor){for(let e=t.mdlImpostor.children.length-1;e>=0;e--){let s=t.mdlImpostor.children[e];s.geometry&&s.geometry.dispose(),s.material&&s.material.dispose(),t.mdlImpostor.remove(s)}t.mdlImpostor.children.length=0}s.bNode||t.renderer.renderLists.dispose(),t.mdl=new THREE.Object3D,t.mdlImpostor=new THREE.Object3D,t.scene.add(t.mdl),t.scene.add(t.mdlImpostor),t.mdl_ghost=new THREE.Object3D,t.scene_ghost.add(t.mdl_ghost),t.objects=[],t.objects_ghost=[],t.raycaster=new THREE.Raycaster,t.projector=new THREE.Projector,t.mouse=new THREE.Vector2;let n=s.parasCls.backgroundColors[t.opts.background.toLowerCase()];s.bNode||("transparent"===t.opts.background.toLowerCase()?t.renderer.setClearColor(n,0):t.renderer.setClearColor(n,1)),t.perspectiveCamera=new THREE.PerspectiveCamera(20,t.container.whratio,.1,1e4),t.perspectiveCamera.position.set(0,0,t.cam_z),t.perspectiveCamera.lookAt(new THREE.Vector3(0,0,0)),t.orthographicCamera=new THREE.OrthographicCamera,t.orthographicCamera.position.set(0,0,t.cam_z),t.orthographicCamera.lookAt(new THREE.Vector3(0,0,0)),t.cams={perspective:t.perspectiveCamera,orthographic:t.orthographicCamera}}setVrAr(){let e=this.icn3d;e.icn3dui;let t=this;e.bSetVrAr=!0,e.bVr?(e.canvasUI=this.createUI(),e.raycasterVR=new THREE.Raycaster,e.workingMatrix=new THREE.Matrix4,e.workingVector=new THREE.Vector3,e.origin=new THREE.Vector3,e.dolly=new THREE.Object3D,e.dolly.position.z=5,e.dolly.add(e.cam),e.scene.add(e.dolly),e.dollyId=e.dolly.id,e.dummyCam=new THREE.Object3D,e.cam.add(e.dummyCam),e.clock=new THREE.Clock,e.controllers=this.getControllers(),e.controllers.forEach((s=>{s.addEventListener("connected",(function(e){try{const s={},i="https://cdn.jsdelivr.net/npm/@webxr-input-profiles/assets@1.0/dist/profiles",n="generic-trigger";be(e.data,i,n).then((({profile:i,assetPath:n})=>{s.name=i.profileId,s.targetRayMode=e.data.targetRayMode,Object.entries(i.layouts).forEach((([e,t])=>{const i={};Object.values(t.components).forEach((e=>{i[e.rootNodeName]=e.gamepadIndices})),s[e]=i})),t.updateControllers(s)}))}catch(e){}})),s.addEventListener("disconnected",(function(){this.remove(this.children[0]),e.controllers.forEach((e=>{}))}))}))):e.bAr&&(e.gestures=new ke(e.renderer),e.scene.add(e.gestures.controller1),e.scene.add(e.gestures.controller2),e.gestures.addEventListener("doubletap",(e=>{t.positionCenter()})),e.gestures.addEventListener("pinch",(s=>{if(void 0!==s.initialise)t.startPosition=e.mdl.position.clone(),t.startScale=e.mdl.scale.clone();else{let i=1;const n=t.startScale.clone().multiplyScalar(s.scale*i);e.mdl.scale.copy(n)}})))}positionCenter(){let e=this.icn3d;e.icn3dui;const t=e.gestures.controller1;e.mdl.position.set(-.06,0,-.6).applyMatrix4(t.matrixWorld),e.mdl.scale.copy(new THREE.Vector3(.005,.005,.005))}setVrArButtons(){let e=this.icn3d,t=e.icn3dui;e.bSetVrArButtons=!0,t.bNode||($("#"+t.pre+"VRButton").remove(),$("#"+t.pre+"viewer").get(0).appendChild(e.VRButtonCls.createButton(e.renderer)),$("#"+t.pre+"ARButton").remove(),$("#"+t.pre+"viewer").get(0).appendChild(e.ARButtonCls.createButton(e.renderer)))}updateControllers(e){this.icn3d.icn3dui,this.addEventForController(e,"right"),this.addEventForController(e,"left")}addEventForController(e,t){let s=this.icn3d;s.icn3dui;const i="right"==t?s.renderer.xr.getController(0):s.renderer.xr.getController(1),n="right"==t?e.right:e.left;if(i&&void 0!==n){let e=!1,t=!1;Object.keys(n).forEach((i=>{-1!=i.indexOf("trigger")&&(e=!0),-1!=i.indexOf("squeeze")&&(t=!0),-1==i.indexOf("thumbstick")&&-1==i.indexOf("touchpad")||(s.xAxisIndex=n[i].xAxis,s.yAxisIndex=n[i].yAxis)})),e&&(i.addEventListener("selectstart",(function(){this.userData.selectPressed=!0})),i.addEventListener("selectend",(function(){this.userData.selectPressed=!1,this.userData.selected=void 0}))),t&&(i.addEventListener("squeezestart",(function(){this.userData.squeezePressed=!0,s.cam.add(s.canvasUI.mesh)})),i.addEventListener("squeezeend",(function(){this.userData.squeezePressed=!1,s.cam.remove(s.canvasUI.mesh)})))}}createUI(){let e=this.icn3d,t=e.icn3dui,s=94,i=50,n=94,l=34,r=12,o="#1c94c4",a="#ccc",d="#fbcb09",c=20;const h={panelSize:{width:2,height:1.6},height:400,select:{type:"button",paddingTop:c,position:{top:6,left:6},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},residue:{type:"button",paddingTop:c,position:{top:62,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=2,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},secondarySelect:{type:"button",paddingTop:12,position:{top:118,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=3,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},chainSelect:{type:"button",paddingTop:c,position:{top:174,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=5,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},atom:{type:"button",paddingTop:c,position:{top:230,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=1,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},reset:{type:"button",paddingTop:c,position:{top:286,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.viewInterPairsCls.resetInteractionPairs(),e.selectionCls.resetAll(),e.cam.remove(e.canvasUI.mesh)}},togglehl:{type:"button",paddingTop:12,position:{top:342,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.hlUpdateCls.toggleHighlight(),e.cam.remove(e.canvasUI.mesh)}},style:{type:"button",paddingTop:c,position:{top:6,left:106},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},ribbon:{type:"button",paddingTop:c,position:{top:62,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","ribbon"),e.setOptionCls.setStyle("nucleotides","nucleotide cartoon"),e.cam.remove(e.canvasUI.mesh)}},schematic:{type:"button",paddingTop:c,position:{top:118,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","schematic"),e.setOptionCls.setStyle("nucleotides","schematic"),e.cam.remove(e.canvasUI.mesh)}},stick:{type:"button",paddingTop:c,position:{top:174,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","stick"),e.setOptionCls.setStyle("nucleotides","stick"),e.cam.remove(e.canvasUI.mesh)}},sphere:{type:"button",paddingTop:c,position:{top:230,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","sphere"),e.setOptionCls.setStyle("nucleotides","sphere"),e.cam.remove(e.canvasUI.mesh)}},surface:{type:"button",paddingTop:c,position:{top:286,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.opts.surface="molecular surface",e.applyMapCls.applySurfaceOptions(),e.cam.remove(e.canvasUI.mesh)}},surfaceTrn:{type:"button",paddingTop:12,position:{top:342,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.opts.surface="molecular surface",e.opts.opacity="0.2",e.applyMapCls.applySurfaceOptions(),e.cam.remove(e.canvasUI.mesh)}},color:{type:"button",paddingTop:c,position:{top:6,left:206},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},rainbow:{type:"button",paddingTop:c,position:{top:62,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","rainbow for chains"),e.cam.remove(e.canvasUI.mesh)}},atomColor:{type:"button",paddingTop:c,position:{top:118,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","atom"),e.cam.remove(e.canvasUI.mesh)}},chainColor:{type:"button",paddingTop:c,position:{top:174,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","chain"),e.cam.remove(e.canvasUI.mesh)}},secondaryColor:{type:"button",paddingTop:12,position:{top:230,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","secondary structure green"),e.cam.remove(e.canvasUI.mesh)}},charge:{type:"button",paddingTop:c,position:{top:342,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","charge"),e.cam.remove(e.canvasUI.mesh)}},AlphaFold:{type:"button",paddingTop:c,position:{top:286,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","confidence"),e.cam.remove(e.canvasUI.mesh)}},unicolor:{type:"button",paddingTop:c,position:{top:6,left:306},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},red:{type:"button",position:{top:i,left:300},width:n,height:l,fontColor:"red",hover:d,onSelect:function(){e.setOptionCls.setOption("color","red"),e.cam.remove(e.canvasUI.mesh)}},green:{type:"button",position:{top:78,left:300},width:n,height:l,fontColor:"green",hover:d,onSelect:function(){e.setOptionCls.setOption("color","green"),e.cam.remove(e.canvasUI.mesh)}},blue:{type:"button",position:{top:106,left:300},width:n,height:l,fontColor:"blue",hover:d,onSelect:function(){e.setOptionCls.setOption("color","blue"),e.cam.remove(e.canvasUI.mesh)}},blueviolet:{type:"button",position:{top:134,left:300},width:n,height:l,fontColor:"#8A2BE2",hover:d,onSelect:function(){e.setOptionCls.setOption("color","8A2BE2"),e.cam.remove(e.canvasUI.mesh)}},magenta:{type:"button",position:{top:162,left:300},width:n,height:l,fontColor:"magenta",hover:d,onSelect:function(){e.setOptionCls.setOption("color","magenta"),e.cam.remove(e.canvasUI.mesh)}},yellow:{type:"button",position:{top:190,left:300},width:n,height:l,fontColor:"yellow",hover:d,onSelect:function(){e.setOptionCls.setOption("color","yellow"),e.cam.remove(e.canvasUI.mesh)}},orange:{type:"button",position:{top:218,left:300},width:n,height:l,fontColor:"orange",hover:d,onSelect:function(){e.setOptionCls.setOption("color","FFA500"),e.cam.remove(e.canvasUI.mesh)}},cyan:{type:"button",position:{top:246,left:300},width:n,height:l,fontColor:"cyan",hover:d,onSelect:function(){e.setOptionCls.setOption("color","cyan"),e.cam.remove(e.canvasUI.mesh)}},gray:{type:"button",position:{top:274,left:300},width:n,height:l,fontColor:"gray",hover:d,onSelect:function(){e.setOptionCls.setOption("color","888888"),e.cam.remove(e.canvasUI.mesh)}},white:{type:"button",position:{top:302,left:300},width:n,height:l,fontColor:"white",hover:d,onSelect:function(){e.setOptionCls.setOption("color","white"),e.cam.remove(e.canvasUI.mesh)}},analysis:{type:"button",paddingTop:c,position:{top:6,left:406},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},distance:{type:"button",paddingTop:c,position:{top:62,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){try{e.bMeasureDistance=!0;let s=e.pickingCls.getPickedAtomList(e.pk,e.pAtom),i=e.pickingCls.getPickedAtomList(e.pk,e.pAtom2),n=e.applyCenterCls.centerAtoms(t.hashUtilsCls.hash2Atoms(s,e.atoms)).center,l=e.applyCenterCls.centerAtoms(t.hashUtilsCls.hash2Atoms(i,e.atoms)).center,r=0,o=0,a="#FFFF00",d=(n.x+l.x)/2,c=(n.y+l.y)/2,h=(n.z+l.z)/2,p=!0;e.analysisCls.addLine(n.x,n.y,n.z,l.x,l.y,l.z,a,p,"distance");let m=(parseInt(10*n.distanceTo(l))/10).toString()+" A";e.analysisCls.addLabel(m,d,c,h,r,a,o,"distance"),e.drawCls.draw(),e.cam.remove(e.canvasUI.mesh)}catch(e){}}},interaction:{type:"button",paddingTop:c,position:{top:118,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){try{e.viewInterPairsCls.viewInteractionPairs(["selected"],["non-selected"],!1,"3d",1,1,1,1,1,1),e.cam.remove(e.canvasUI.mesh)}catch(e){}}},delphi:{type:"button",paddingTop:c,position:{top:174,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:async function(){e.phisurftype=22,e.phisurfop=1,e.phisurfwf="no",await e.delphiCls.CalcPhi(65,.15,2,!0),e.cam.remove(e.canvasUI.mesh)}},removeLabel:{type:"button",paddingTop:c,position:{top:230,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){for(let t in e.labels)e.labels[t]=[];e.drawCls.draw(),e.cam.remove(e.canvasUI.mesh)}},renderer:e.renderer},p=new Oe({select:"Select",residue:"Residue",secondarySelect:"Secondary Structure",chainSelect:"Chain",atom:"Atom",reset:"Reset",togglehl:"Toggle Highlight",style:"Style",ribbon:"Ribbon",schematic:"Schematic",stick:"Stick",sphere:"Sphere",surface:"Surface",surfaceTrn:"Transparent Surface",color:"Color",rainbow:"Rainbow",atomColor:"Atom",chainColor:"Chain",secondaryColor:"Secondary Structure",AlphaFold:"AlphaFold",charge:"Charge",unicolor:"UniColor",red:"M 100 15 L 15 15 L 15 100 L 100 100 Z",green:"M 100 15 L 15 15 L 15 100 L 100 100 Z",blue:"M 100 15 L 15 15 L 15 100 L 100 100 Z",blueviolet:"M 100 15 L 15 15 L 15 100 L 100 100 Z",magenta:"M 100 15 L 15 15 L 15 100 L 100 100 Z",yellow:"M 100 15 L 15 15 L 15 100 L 100 100 Z",orange:"M 100 15 L 15 15 L 15 100 L 100 100 Z",cyan:"M 100 15 L 15 15 L 15 100 L 100 100 Z",gray:"M 100 15 L 15 15 L 15 100 L 100 100 Z",white:"M 100 15 L 15 15 L 15 100 L 100 100 Z",analysis:"Analysis",distance:"Distance",interaction:"Interaction",delphi:"DelPhi Potential",removeLabel:"Remove Label"},h);return p.mesh.position.set(0,0,-3),p}createUILog(){let e=this.icn3d;e.icn3dui;const t={panelSize:{width:2,height:2},height:512,info:{type:"text",overflow:"scroll",position:{top:6,left:6},width:506,height:506,backgroundColor:"#aaa",fontColor:"#000"},renderer:e.renderer},s=new Oe({info:"Debug info"},t);return s.mesh.position.set(0,-1,-2),s}getControllers(){let e=this.icn3d;e.icn3dui;const t=new xe,s=(new THREE.BufferGeometry).setFromPoints([new THREE.Vector3(0,0,0),new THREE.Vector3(0,0,-1)]),i=new THREE.Line(s);i.name="line",i.scale.z=50;const n=[];for(let s=0;s<=1;s++){const l=e.renderer.xr.getController(s);if(!l)continue;e.dolly.add(l),l.add(i.clone()),l.userData.selectPressed=!1,e.cam.add(l),n.push(l);const r=e.renderer.xr.getControllerGrip(s);r.add(t.createControllerModel(r)),e.scene.add(r)}return n}}class Ee{constructor(e){this.icn3d=e}setCamera(){let e=this.icn3d,t=e.icn3dui;if(e.bControlGl&&!t.bNode){window.cam=e.cams[e.opts.camera.toLowerCase()];let s=e.maxD;if(window.cam===e.perspectiveCamera){let i=void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>e.maxatomcnt;i?window.camMaxDFactor=1:void 0!==window.camMaxDFactorFog?window.camMaxDFactor=window.camMaxDFactorFog:window.camMaxDFactor=3,window.cam_z>0?window.cam.position.z=s*window.camMaxDFactor:window.cam.position.z=-s*window.camMaxDFactor,"yes"===e.opts.slab?i?window.cam.near=.1:void 0!==window.camMaxDFactorFog?window.cam.near=s*window.camMaxDFactorFog-10:window.cam.near=s*window.camMaxDFactor:window.cam.near=.1,window.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.TrackballControls(window.cam,void 0,e):t.bNode?e.controls=new THREE.TrackballControls(e.cam,document,e):e.controls=new THREE.TrackballControls(e.cam,document.getElementById(e.id),e)}else window.cam===e.orthographicCamera&&(void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>10*e.maxatomcnt?window.cam.right=e.maxD/2*1.5:window.cam.right=e.maxD/2*2.5,window.cam.left=-window.cam.right,window.cam.top=window.cam.right/e.container.whratio,window.cam.bottom=-window.cam.right/e.container.whratio,"yes"===e.opts.slab?window.cam.near=2*e.maxD:window.cam.near=0,window.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.OrthographicTrackballControls(window.cam,void 0,e):t.bNode?e.controls=new THREE.OrthographicTrackballControls(e.cam,document,e):e.controls=new THREE.OrthographicTrackballControls(e.cam,document.getElementById(e.id),e));window.cam.updateProjectionMatrix()}e.cam=e.cams[e.opts.camera.toLowerCase()];let s=e.maxD;if(e.cam===e.perspectiveCamera){let i=void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>e.maxatomcnt;i?e.camMaxDFactor=1:void 0!==e.camMaxDFactorFog?e.camMaxDFactor=e.camMaxDFactorFog:e.camMaxDFactor=3,e.cam_z>0?e.cam.position.z=s*e.camMaxDFactor:e.cam.position.z=-s*e.camMaxDFactor,"yes"===e.opts.slab?i?e.cam.near=.1:void 0!==e.camMaxDFactorFog?e.cam.near=s*e.camMaxDFactorFog-10:e.cam.near=s*e.camMaxDFactor:e.cam.near=.1,e.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.TrackballControls(e.cam,void 0,e):t.bNode?e.controls=new THREE.TrackballControls(e.cam,document,e):e.controls=new THREE.TrackballControls(e.cam,document.getElementById(e.id),e)}else e.cam===e.orthographicCamera&&(void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>10*e.maxatomcnt?e.cam.right=e.maxD/2*1.5:e.cam.right=e.maxD/2*2.5,e.cam.left=-e.cam.right,e.cam.top=e.cam.right/e.container.whratio,e.cam.bottom=-e.cam.right/e.container.whratio,"yes"===e.opts.slab?e.cam.near=2*e.maxD:e.cam.near=0,e.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.OrthographicTrackballControls(e.cam,void 0,e):t.bNode?e.controls=new THREE.OrthographicTrackballControls(e.cam,document,e):e.controls=new THREE.OrthographicTrackballControls(e.cam,document.getElementById(e.id),e));e.cam.updateProjectionMatrix()}}class Te{constructor(e){this.icn3d=e}setFog(e){let t=this.icn3d,s=t.icn3dui.parasCls.backgroundColors[t.opts.background.toLowerCase()];if(e){let e=t.applyCenterCls.centerAtoms(t.hAtoms);t.maxD=e.maxD,t.maxD<25&&(t.maxD=25)}let i=void 0!==t.biomtMatrices&&t.biomtMatrices.length*t.cnt>t.maxatomcnt;if("yes"===t.opts.fog)if("perspective"===t.opts.camera)if(i)t.scene.fog=void 0,t.bSetFog=!1;else{let e=t._zoomFactor>1?1*t._zoomFactor:t._zoomFactor;t.scene.fog=new THREE.Fog(s,2.5*t.maxD*e,4*t.maxD*e),t.bSetFog=!0,t.camMaxDFactorFog=3}else"orthographic"===t.opts.camera&&(t.scene.fog=void 0,t.bSetFog=!1);else t.scene.fog=void 0,t.bSetFog=!1}}class De{constructor(e){this.icn3d=e}createBox(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(o.bNode)return;void 0===t&&(t=.8),void 0===s&&(s=!1),void 0===i&&(i=.8),l?void 0===n&&(n=r.hColor):void 0===n&&(n=e.color);let a=s?t:(o.parasCls.vdwRadii[e.elem.toUpperCase()]||t)*(i||1);this.createBox_base(e.coord,a,n,l)}createBox_base(e,t,s,i,n,l,r){let o,a=this.icn3d;a.icn3dui.bNode||(void 0===r&&(r=l?.5:1),new THREE.BoxGeometry(1,1,1),o=new THREE.Mesh(a.boxGeometry,new THREE.MeshPhongMaterial({transparent:!0,opacity:r,specular:a.frac,shininess:a.shininess,emissive:a.emissive,color:s})),o.scale.x=o.scale.y=o.scale.z=t,o.position.copy(e),a.mdl.add(o),i?a.prevHighlightObjects.push(o):n?a.prevOtherMesh.push(o):a.objects.push(o))}createBoxRepresentation_P_CA(e,t,s){let i=this.icn3d;if(i.icn3dui.bNode)return;let n=this;i.reprSubCls.createRepresentationSub(e,(function(e){"CA"!==e.name&&"O3'"!==e.name&&"O3*"!==e.name||n.createBox(e,void 0,void 0,t,void 0,s)}))}}class Pe{constructor(e){this.icn3d=e}createBrick(e,t,s,i){let n=this.icn3d;if(n.icn3dui.bNode)return;let l=new THREE.CylinderGeometry(1,1,1,4,1),r=new THREE.Mesh(l,new THREE.MeshPhongMaterial({specular:n.frac,shininess:n.shininess,emissive:n.emissive,color:i}));r.position.copy(e).add(t).multiplyScalar(.5),r.matrixAutoUpdate=!1,r.lookAt(t.clone().sub(e)),r.updateMatrix(),r.matrix.multiply((new THREE.Matrix4).makeScale(s,s,e.distanceTo(t))).multiply((new THREE.Matrix4).makeRotationX(.5*Math.PI)),n.mdl.add(r)}}class Me{constructor(e){this.icn3d=e}createCurveSubArrow(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u){if(this.icn3d.icn3dui.bNode)return;let g=[],f=[];g.push(e),f.push(o),this.prepareStrand(g,f,t,s,i,void 0,n,l,r,a,d,!1,c,h,p,m,u),g=[],f=[]}createStripArrow(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u,g){if(this.icn3d.icn3dui.bNode)return;let f=[],C=[];f.push(e),f.push(t),C.push(o),C.push(a),this.prepareStrand(f,C,void 0,s,i,n,l,void 0,r,d,c,!0,h,p,m,u,g),f=[],C=[]}prepareStrand(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u,g,f){let C=this.icn3d,b=C.icn3dui;if(1===d.length)return;let y=i,v=!u,_=[];_.push(i[i.length-2]),_.push(i[i.length-1]),n=n||C.axisDIV;let w,S,A,x,k=2/(a-1),O={};for(let e=0,s=t.length;e1)if(void 0!==d){let i,n,l=[];for(let r=0,o=p.length;r0&&i.tubeCls.createTube(a,"CA",i.coilWidth,s),Object.keys(d).length>0&&i.strandCls.createStrand(d,void 0,void 0,!0,0,i.helixSheetWidth,!1,2*i.ribbonthickness,s)):(Object.keys(a).length>0&&i.tubeCls.createTube(a,"CA",i.coilWidth),Object.keys(d).length>0&&i.strandCls.createStrand(d,void 0,void 0,!0,0,i.helixSheetWidth,!1,2*i.ribbonthickness))}createCylinderCurve(e,t,s,i,n){let l=this.icn3d;if(l.icn3dui.bNode)return;let r,o,a,d,c,h,p=null;for(a in e)if(d=e[a],!d.het&&(c=d.structure+"_"+d.chain,h=d.structure+"_"+r,-1!=t.indexOf(d.name))){if(null!==p&&r===d.chain&&l.ParserUtilsCls.getResiNCBI(h,o)+1===l.ParserUtilsCls.getResiNCBI(c,d.resi)&&Math.abs(p.coord.x-d.coord.x)<8&&Math.abs(p.coord.y-d.coord.y)<8&&Math.abs(p.coord.z-d.coord.z)<8){let e=p.coord.clone().add(d.coord).multiplyScalar(.5);if(n)1===n&&(this.createCylinder(p.coord,e,s,p.color,n),this.createCylinder(e,d.coord,s,d.color,n),l.sphereCls.createSphere(d,s,!0,1,n));else if(i){let t=l.lineCls.createSingleLine(p.coord,e,p.color,!1);l.mdl.add(t),l.objects.push(t),t=l.lineCls.createSingleLine(e,d.coord,d.color,!1),l.mdl.add(t),l.objects.push(t)}else this.createCylinder(p.coord,e,s,p.color),this.createCylinder(e,d.coord,s,d.color),l.sphereCls.createSphere(d,s,!0,1,n)}p=d,r=d.chain,o=d.resi,l.sphereCls.createSphere(d,s,!0,1,n),2===n&&l.boxCls.createBox(d,void 0,void 0,void 0,void 0,n)}if(null!==p&&r===d.chain&&l.ParserUtilsCls.getResiNCBI(h,o)+1===l.ParserUtilsCls.getResiNCBI(c,d.resi)&&Math.abs(p.coord.x-d.coord.x)<8&&Math.abs(p.coord.y-d.coord.y)<8&&Math.abs(p.coord.z-d.coord.z)<8){let e=p.coord.add(d.coord).multiplyScalar(.5);if(n)1===n&&(this.createCylinder(p.coord,e,s,p.color,n),this.createCylinder(e,d.coord,s,d.color,n),l.sphereCls.createSphere(d,s,!0,1,n));else if(i){let t=l.lineCls.createSingleLine(p.coord,e,p.color,!1);l.mdl.add(t),l.objects.push(t),t=l.lineCls.createSingleLine(e,d.coord,d.color,!1),l.mdl.add(t),l.objects.push(t)}else this.createCylinder(p.coord,e,s,p.color),this.createCylinder(e,d.coord,s,d.color)}}}class Le{constructor(e){this.icn3d=e}createLineRepresentation(e,t){let s=this.icn3d;if(s.icn3dui.bNode)return;let i=new THREE.BufferGeometry,n=[],l=[],r=0,o=0;s.reprSubCls.createRepresentationSub(e,void 0,(function(e,t){if(e.color===t.color)n[r++]=e.coord.x,n[r++]=e.coord.y,n[r++]=e.coord.z,n[r++]=t.coord.x,n[r++]=t.coord.y,n[r++]=t.coord.z,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b;else{let s=e.coord.clone().add(t.coord).multiplyScalar(.5);n[r++]=e.coord.x,n[r++]=e.coord.y,n[r++]=e.coord.z,n[r++]=s.x,n[r++]=s.y,n[r++]=s.z,n[r++]=t.coord.x,n[r++]=t.coord.y,n[r++]=t.coord.z,n[r++]=s.x,n[r++]=s.y,n[r++]=s.z,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b}}));if(i.setAttribute("position",new THREE.BufferAttribute(new Float32Array(n),3)),i.setAttribute("color",new THREE.BufferAttribute(new Float32Array(l),3)),2!==t){let e;1===t||(e=new THREE.LineSegments(i,new THREE.LineBasicMaterial({linewidth:s.linewidth,vertexColors:!0})),s.mdl.add(e)),1===t?s.prevHighlightObjects.push(e):s.objects.push(e)}else 2===t&&s.boxCls.createBoxRepresentation_P_CA(e,.8,t)}createConnCalphSidechain(e,t){let s=this.icn3d;if(s.icn3dui.bNode)return;let i={};for(let s in e){let n=e[s];if(!n.het&&n.style2===t){i[n.structure+"_"+n.chain+"_"+n.resi]=1}}let n=[],l=[];for(let e in i){let t=s.firstAtomObjCls.getFirstAtomObjByName(s.residues[e],"CA");if(void 0!==t)for(let e=0,i=t.bonds.length;e=t.bonds.length&&e.bonds.length>1)s=e.serial,l=e.bonds[0],d=e.bonds[1];else{if(!(t.bonds.length>=e.bonds.length&&t.bonds.length>1))return void console.log("Double bond was not drawn due to the undefined cross plane");s=t.serial,l=t.bonds[0],d=t.bonds[1]}let i=r.atoms[s].coord.clone();i.sub(r.atoms[l].coord);let n=r.atoms[s].coord.clone();n.sub(r.atoms[d].coord),i.cross(n),0==parseInt(1e4*i.length())&&(i=new THREE.Vector3(.2,.3,.5)),c=t.coord.clone(),c.sub(e.coord),c.cross(i).normalize().multiplyScalar(.2*o),0==parseInt(1e4*c.length())&&(i=new THREE.Vector3(.5,.3,.2),c.cross(i).normalize().multiplyScalar(.2*o))}e.color===t.color?r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),t.coord.clone().add(c),a,e.color,n),r.cylinderCls.createCylinder(e.coord.clone().sub(c),t.coord.clone().sub(c),a,e.color,n)):r.bImpo?r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),t.coord.clone().add(c),a,e.color,n,t.color),r.cylinderCls.createCylinder(e.coord.clone().sub(c),t.coord.clone().sub(c),a,e.color,n,t.color)):r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),i.clone().add(c),a,e.color,n),r.cylinderCls.createCylinder(t.coord.clone().add(c),i.clone().add(c),a,t.color,n),r.cylinderCls.createCylinder(e.coord.clone().sub(c),i.clone().sub(c),a,e.color,n),r.cylinderCls.createCylinder(t.coord.clone().sub(c),i.clone().sub(c),a,t.color,n))}else if(r.aromaticbonds.hasOwnProperty(l)){let s,l,d;if(e.bonds.length>t.bonds.length&&e.bonds.length>1)s=e.serial,l=e.bonds[0],d=e.bonds[1];else{if(!(t.bonds.length>1))return;s=t.serial,l=t.bonds[0],d=t.bonds[1]}let c=r.atoms[s].coord.clone();c.sub(r.atoms[l].coord);let h=r.atoms[s].coord.clone();h.sub(r.atoms[d].coord),c.cross(h);let p=t.coord.clone();p.sub(e.coord),p.cross(c).normalize().multiplyScalar(.2*o);let m=0;for(let s=0,i=e.bondOrder.length;so+1?(s=k.clone(),i=d.atoms[$[$.length-1-o-1]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random()))):d.bCalphaOnly&&"CA"===p.name&&($.length>o+1?(s=k.clone(),i=d.atoms[$[$.length-1-o-1]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random())),s.normalize(),s.multiplyScalar(C),null!==I&&s.dot(I)<0&&s.negate(),I=s;for(let e=0,s=2/(t-1);e6||c&&Math.abs(S.y-c.y)>6||c&&Math.abs(S.z-c.z)>6;if((g!==p.chain||p.ssbegin||p.ssend||j||U==V&&"coil"!=p.ss)&&u[0].length>0){let c="CA",m=[],g=[];if(isNaN(d.atoms[P].resi))m=[];else{let e=d.atoms[P].structure+"_"+d.atoms[P].chain+"_"+(parseInt(d.atoms[P].resi)-1).toString(),t=d.firstAtomObjCls.getAtomCoordFromResi(e,c);m=void 0!==t?[t]:[]}if(!isNaN(d.atoms[P].resi)){let e=d.atoms[P].structure+"_"+d.atoms[P].chain+"_"+(parseInt(d.atoms[P].resi)+1).toString(),t=d.firstAtomObjCls.getAtomCoordFromResi(e,c);void 0!==t&&g.push(t);let s=d.atoms[P].structure+"_"+d.atoms[P].chain+"_"+(parseInt(d.atoms[P].resi)+2).toString(),i=d.firstAtomObjCls.getAtomCoordFromResi(s,c);void 0!==i&&g.push(i)}if(!j){1===a||2===a?w.push(d.hColor):w.push(R),C=p.ssend&&"sheet"===p.ss?0:"coil"===E&&p.ssbegin||T&&p.ssbegin||"coil"===p.ss?n:l;let s,i,o=4;"O"===p.name?(s=A.clone(),s.sub(S)):d.bCalphaOnly&&"CA"===p.name&&($.length>o?(s=S.clone(),i=d.atoms[$[$.length-1-o]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random())),s.normalize(),s.multiplyScalar(C),null!==I&&s.dot(I)<0&&s.negate(),I=s;for(let e=0,s=2/(t-1);e0){let e="CA",n=[],l=[];if(isNaN(d.atoms[P].resi))n=[];else{let t=d.atoms[P].structure+"_"+d.atoms[P].chain+"_"+(parseInt(d.atoms[P].resi)-1).toString();d.firstAtomObjCls.getAtomCoordFromResi(t,e)}for(let e=0;!i&&e0&&(o!==c.chain||Math.abs(c.coord.x-h.coord.x)>6||Math.abs(c.coord.y-h.coord.y)>6||Math.abs(c.coord.z-h.coord.z)>6||r.ParserUtilsCls.getResiNCBI(c.structure+"_"+o,a)+13||Math.abs(c.coord.y-h.coord.y)>3||Math.abs(c.coord.z-h.coord.z)>3))){if(2!==i){if(!isNaN(d.resi)&&!isNaN(h.resi)){let e=d.structure+"_"+d.chain+"_"+(parseInt(d.resi)-1).toString(),i=r.firstAtomObjCls.getAtomCoordFromResi(e,t);g=void 0!==i?[i]:[];let l=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+1).toString(),o=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+2).toString(),a=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+3).toString();if(r.residues.hasOwnProperty(l)){let e=r.firstAtomObjCls.getAtomFromResi(l,t);void 0!==e&&e.ssbegin&&(l=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+2).toString(),o=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+3).toString(),p.push(e.coord),n?u.push(this.getCustomtubesize(l)):u.push(this.getRadius(s,e)),m.push(e.color))}if(1==p.length&&r.residues.hasOwnProperty(l)){let e=r.firstAtomObjCls.getAtomFromResi(l,t);if(e){p.push(e.coord),m.push(e.color);let t=this.getRadius(s,c);u.push(t),l=o,o=a}}let C=r.firstAtomObjCls.getAtomCoordFromResi(l,t);void 0!==C&&f.push(C);let b=r.firstAtomObjCls.getAtomCoordFromResi(o,t);void 0!==b&&f.push(b)}b.push({pnts:p,colors:m,radii:u,prevone:g,nexttwo:f})}p=[],m=[],u=[],g=[],f=[],d=c,C=0}if(0==p.length&&!isNaN(c.resi)){let e=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)-1).toString();r.residues.hasOwnProperty(e)&&(h=r.firstAtomObjCls.getAtomFromResi(e,t),void 0!==h&&h.ssend&&(p.push(h.coord),n?u.push(this.getCustomtubesize(e)):u.push(this.getRadius(s,h)),m.push(h.color)))}let e;p.push(c.coord),e=n?this.getCustomtubesize(c.structure+"_"+c.chain+"_"+c.resi):this.getRadius(s,c),l||"coil"==c.ss||c.ssbegin||c.ssend||(e=0),u.push(e),m.push(c.color),1===C&&(m[m.length-2]=c.color),o=c.chain,a=c.resi;let y=1.2;2!==i||c.ssbegin||r.boxCls.createBox(c,void 0,void 0,y,void 0,i),++C,h=c}if(2!==i){if(g=[],void 0!==d&&!isNaN(d.resi)){let e=d.structure+"_"+d.chain+"_"+(parseInt(d.resi)-1).toString(),s=r.firstAtomObjCls.getAtomCoordFromResi(e,t);g=void 0!==s?[s]:[]}if(f=[],void 0!==c&&!isNaN(c.resi)){let e=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+1).toString(),i=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+2).toString(),n=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+3).toString();if(1==p.length&&r.residues.hasOwnProperty(e)){let l=r.firstAtomObjCls.getAtomFromResi(e,t);if(l){p.push(l.coord),m.push(l.color);let t=this.getRadius(s,c);u.push(t),e=i,i=n}}let l=r.firstAtomObjCls.getAtomCoordFromResi(e,t);void 0!==l&&f.push(l);let o=r.firstAtomObjCls.getAtomCoordFromResi(i,t);void 0!==o&&f.push(o)}b.push({pnts:p,colors:m,radii:u,prevone:g,nexttwo:f})}for(let e=0,t=b.length;e0&&(c=n);else if(g%1==0)n=s[g],n>0&&(c=n);else{let e=Math.floor(g),t=g-e;n=s[e]*(1-t)+s[e+1]*t,r||n<1*c&&(n=0)}e1?a.parasCls.thr(t[t.length-2]):a.parasCls.thr(t[e]),C[v++]=d.r,C[v++]=d.g,C[v++]=d.b}}let k,O=0;for(let e=0,t=S.length-1;er&&(l=r,e=1);for(let t=0;t0&&t.b<=100?.01*t.b:t.b>100?1:s.coilWidth),i}}class ze{constructor(e){this.icn3d=e}drawCartoonNucleicAcid(e,t,s,i){this.drawStrandNucleicAcid(e,2,t,!0,void 0,s,i)}drawStrandNucleicAcid(e,t,s,i,n,l,r){let o,a,d,c=this.icn3d;if(c.icn3dui.bNode)return;2===r&&(t=void 0,l=void 0),n=n||c.nucleicAcidWidth,s=s||c.axisDIV,t=t||c.nucleicAcidStrandDIV;let h=[];for(d=0;dy?y=b:b=y);let v=.8*C/y;if(g.width=b,g.height=y,f.clearRect(0,0,b,y),h)if(f.fillStyle="rgba("+n.r+","+n.g+","+n.b+","+n.a+")",f.strokeStyle="rgba("+l.r+","+l.g+","+l.b+","+l.a+")",f.lineWidth=r,p){let e=.4*b;this.circle(f,0,0,b,y,e)}else{let e=0;this.roundRect(f,0,0,b,y,e)}f.font="Bold "+a+"px "+o,f.textAlign="center",f.textBaseline="middle",f.fillStyle="rgba("+u.r+", "+u.g+", "+u.b+", 1.0)",f.strokeStyle="rgba("+u.r+", "+u.g+", "+u.b+", 1.0)",f.fillText(e,.5*b,.5*y);let _=new THREE.Texture(g);_.needsUpdate=!0;let w=new THREE.SpriteMaterial({map:_,depthTest:!1,depthWrite:!1});w.map.minFilter=THREE.LinearFilter;let S=new THREE.Sprite(w);return p?S.scale.set(.3*d,.3*d,1):S.scale.set(v*d,d,1),S.renderOrder=1,S}roundRect(e,t,s,i,n,l){e.beginPath(),e.moveTo(t+l,s),e.lineTo(t+i-l,s),e.quadraticCurveTo(t+i,s,t+i,s+l),e.lineTo(t+i,s+n-l),e.quadraticCurveTo(t+i,s+n,t+i-l,s+n),e.lineTo(t+l,s+n),e.quadraticCurveTo(t,s+n,t,s+n-l),e.lineTo(t,s+l),e.quadraticCurveTo(t,s,t+l,s),e.closePath(),e.fill(),e.stroke()}circle(e,t,s,i,n,l){e.beginPath(),e.arc(t+i/2,.9*(s+n/2),l,0,2*Math.PI,!0),e.closePath(),e.fill(),e.stroke()}}class Ve{constructor(e){this.icn3d=e,this.textSpriteCls=new Ge(e)}createLabelRepresentation(e){let t=this.icn3d;t.icn3dui;let s=t.oriMaxD/100;s<.4&&(s=.4);let i=3*s*t.labelScale;for(let s in e){let n=void 0!==e[s]?e[s]:[],l="black"!=t.opts.background?t.colorWhitebkgd:t.colorBlackbkgd;for(let e=0,r=n.length;e.99999)h.set(0,0,0,1);else if(e.y<-.99999)h.set(1,0,0,0);else{let t=new THREE.Vector3;t.set(e.z,0,-e.x).normalize();let s=Math.acos(e.y);h.setFromAxisAngle(t,s)}return c.applyQuaternion(h),c.scale.set(l,n,l),c.position.copy(t),c}setPc1Axes(){let e=this.icn3d,t=e.icn3dui;if(t.bNode)return;let s=t.hashUtilsCls.intHash(e.hAtoms,e.dAtoms),i=[],n=Object.keys(s).length<100;for(let t in s){let s=e.atoms[t],l=s.structure+"_"+s.chain+"_"+s.resi;(n||""!=l)&&i.push(s.coord.clone())}let l=t.rmsdSuprCls.getEigenForSelection(i,i.length),r=new THREE.Vector3(l.h1[0],l.h1[1],l.h1[2]);if(0==l.k&&e.bRender)return void alert("Can't determine the first principal component. Please select a subset and try it again.");let o=e.applyCenterCls.centerAtoms(s),a=o.maxD,d=o.center,c=d.clone().add(r.normalize().multiplyScalar(.4*a)),h=new THREE.Vector3(l.h2[0],l.h2[1],l.h2[2]),p=d.clone().add(h.normalize().multiplyScalar(.3*a)),m=new THREE.Vector3(l.h3[0],l.h3[1],l.h3[2]),u=d.clone().add(m.normalize().multiplyScalar(.3*a));this.buildAxes(void 0,d,c,p,u,!0);let g=[d,c,p,u];return e.axes.push(g),e.drawCls.draw(),g}}class Ye{constructor(e){this.icn3d=e}showGlycans(){let e=this.icn3d,t=e.icn3dui;if(t.bNode)return;let s={},i=e.dAtoms;for(let n in i){let i=e.atoms[n];i.het&&-1!=t.parasCls.glycanHash.hasOwnProperty(i.resn)&&(void 0===s[i.resn]&&(s[i.resn]={}),"Misc"!=i.chain&&(s[i.resn][i.structure+"_"+i.chain+"_"+i.resi]=1))}let n=Object.keys(s);for(let i=0,l=n.length;i>2))+i+((2&t)>>1))*c+n+(1&t)]&this.ISDONE)<=3&&(t.push(t[i]),i=t.length-1,t.push(t[n]),n=t.length-1,t.push(t[l]),l=t.length-1),s.push(i),s.push(n),s.push(l)}}},Xe.prototype.laplacianSmooth=function(e,t,s){let i,n,l,r,o,a=new Array(t.length);for(i=0,n=t.length;ithis.origextent[1][0])&&(!(tthis.origextent[1][1])&&!(sthis.origextent[1][2]))},Ke.prototype.getFacesAndVertices=function(){let e,t,s=this.verts;for(e=0,t=s.length;eh&&(h=this.pmaxy-this.pminy),this.pmaxz-this.pminz>h&&(h=this.pmaxz-this.pminz),this.scaleFactor=(c-1)/h,this.scaleFactor=this.defaultScaleFactor,this.defaultScaleFactor*h>this.threshbox&&(c=Math.floor(this.threshbox),this.scaleFactor=(this.threshbox-1)/h),this.bCalcArea&&(this.scaleFactor=this.defaultScaleFactor),this.pLength=Math.ceil(this.scaleFactor*(this.pmaxx-this.pminx))+1,this.pWidth=Math.ceil(this.scaleFactor*(this.pmaxy-this.pminy))+1,this.pHeight=Math.ceil(this.scaleFactor*(this.pmaxz-this.pminz))+1,this.boundingatom(t),this.cutRadius=this.probeRadius*this.scaleFactor,this.vpBits=new Uint8Array(this.pLength*this.pWidth*this.pHeight),this.vpDistance=new Float64Array(this.pLength*this.pWidth*this.pHeight),this.vpAtomID=new Int32Array(this.pLength*this.pWidth*this.pHeight),this.vpColor=[],this.vpPot=[]},Ke.prototype.boundingatom=function(e){let t,s,i,n,l=[];for(let r in this.vdwRadii){if(!this.vdwRadii.hasOwnProperty(r))continue;let o=this.vdwRadii[r];l[r]=e?(o+this.probeRadius)*this.scaleFactor+.5:o*this.scaleFactor+.5,i=l[r]*l[r],this.widxz[r]=Math.floor(l[r])+1,this.depty[r]=new Int32Array(this.widxz[r]*this.widxz[r]),n=0;for(let e=0;ei?this.depty[r][n]=-1:(s=Math.sqrt(i-t),this.depty[r][n]=Math.floor(s)),n++}},Ke.prototype.fillvoxels=function(e,t){let s,i,n,l;for(s=0,l=this.vpBits.length;sc&&(a=c),b>h&&(b=h),v>p&&(v=p);let _,w=g[o*m+d*u+y],S=g[a*m+d*u+y],A=g[o*m+b*u+y],x=g[o*m+d*u+v],k=g[a*m+b*u+y],O=g[o*m+b*u+v],R=g[a*m+d*u+v],I=g[a*m+b*u+v],E=r.x-o,T=r.y-d,D=r.z-y,P=((w*(1-E)+S*E)*(1-T)+(A*(1-E)+k*E)*T)*(1-D)+((x*(1-E)+R*E)*(1-T)+(O*(1-E)+I*E)*T)*D,M=s*f+i*C+n;this.vpPot[M]=P,P>this.isovalue&&(P=this.isovalue),P<-this.isovalue&&(P=-this.isovalue),P>0?(P/=1*this.isovalue,_=new THREE.Color(1-P,1-P,1)):(P/=-1*this.isovalue,_=new THREE.Color(1,1-P,1-P)),this.vpColor[M]=_}}for(s=0,l=this.vpBits.length;s=this.pLength||g>=this.pWidth||f>=this.pHeight)continue;let h=u*S+g*this.pHeight+f;if(this.vpBits[h]&this.INOUT){let p=t[this.vpAtomID[h]];p.serial!=e.serial&&(l=s+a-Math.floor(.5+this.scaleFactor*(p.x+this.ptranx)),r=i+d-Math.floor(.5+this.scaleFactor*(p.y+this.ptrany)),o=n+c-Math.floor(.5+this.scaleFactor*(p.z+this.ptranz)),a*a+d*d+c*c=this.pLength||p>=this.pWidth||m>=this.pHeight)continue;let u=h*S+p*this.pHeight+m;if(this.vpBits[u]&this.ISDONE){let h=t[this.vpAtomID[u]];h.serial!=e.serial&&(l=s+a-Math.floor(.5+this.scaleFactor*(h.x+this.ptranx)),r=i+d-Math.floor(.5+this.scaleFactor*(h.y+this.ptrany)),o=n+c-Math.floor(.5+this.scaleFactor*(h.z+this.ptranz)),a*a+d*d+c*c-1&&r-1&&a-1&&o=h)||(this.vpBits[n]|=this.ISBOUND))},Ke.prototype.fastoneshell=function(e,t){let s,i,n,l,r,o,a,d,c,h,p,m,u=[];if(0===e.length)return u;let g={ix:-1,iy:-1,iz:-1},f=this.pWidth*this.pHeight;for(a=0,c=e.length;a-1&&g.iy-1&&g.iz-1&&(m=g.ix*f+this.pHeight*g.iy+g.iz,this.vpBits[m]&this.INOUT&&!(this.vpBits[m]&this.ISDONE)?(t.set(g.ix,g.iy,n+this.nb[d][2],p),l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,this.vpDistance[m]=h,this.vpBits[m]|=this.ISDONE,this.vpBits[m]|=this.ISBOUND,u.push({ix:g.ix,iy:g.iy,iz:g.iz})):this.vpBits[m]&this.INOUT&&this.vpBits[m]&this.ISDONE&&(l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,h-1&&g.iy-1&&g.iz-1&&(m=g.ix*f+this.pHeight*g.iy+g.iz,this.vpBits[m]&this.INOUT&&!(this.vpBits[m]&this.ISDONE)?(t.set(g.ix,g.iy,n+this.nb[d][2],p),l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,this.vpDistance[m]=h,this.vpBits[m]|=this.ISDONE,this.vpBits[m]|=this.ISBOUND,u.push({ix:g.ix,iy:g.iy,iz:g.iz})):this.vpBits[m]&this.INOUT&&this.vpBits[m]&this.ISDONE&&(l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,h-1&&g.iy-1&&g.iz-1&&(m=g.ix*f+this.pHeight*g.iy+g.iz,this.vpBits[m]&this.INOUT&&!(this.vpBits[m]&this.ISDONE)?(t.set(g.ix,g.iy,n+this.nb[d][2],p),l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,this.vpDistance[m]=h,this.vpBits[m]|=this.ISDONE,this.vpBits[m]|=this.ISBOUND,u.push({ix:g.ix,iy:g.iy,iz:g.iz})):this.vpBits[m]&this.INOUT&&this.vpBits[m]&this.ISDONE&&(l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,hm&&(m=this.pmaxy-this.pminy),this.pmaxz-this.pminz>m&&(m=this.pmaxz-this.pminz),this.scaleFactor=1,this.pLength=Math.floor(.5+this.scaleFactor*(this.pmaxx-this.pminx))+1,this.pWidth=Math.floor(.5+this.scaleFactor*(this.pmaxy-this.pminy))+1,this.pHeight=Math.floor(.5+this.scaleFactor*(this.pmaxz-this.pminz))+1,this.cutRadius=this.probeRadius*this.scaleFactor,this.vpBits=new Uint8Array(this.pLength*this.pWidth*this.pHeight),this.ccp4&&(this.vpGridTrans=new Array(this.pLength*this.pWidth*this.pHeight)),this.vpAtomID=new Uint8Array(this.pLength*this.pWidth*this.pHeight)},Je.prototype.transformMemPro=function(e,t,s,i){let n=e.clone();n.sub(s);let l=n.x*t[0]+n.y*t[1]+n.z*t[2]+i.x,r=n.x*t[3]+n.y*t[4]+n.z*t[5]+i.y,o=n.x*t[6]+n.y*t[7]+n.z*t[8]+i.z;return n.x=l,n.y=r,n.z=o,n},Je.prototype.fillvoxels=function(e,t){let s,i,n,l,r,o;for(s=0,l=this.vpBits.length;sthis.pLength&&(o=this.pLength),p>this.pWidth&&(p=this.pWidth),C>this.pHeight&&(C=this.pHeight);let b,y=l[r*a+h*d+f],v=l[o*a+h*d+f],_=l[r*a+p*d+f],w=l[r*a+h*d+C],S=l[o*a+p*d+f],A=l[r*a+p*d+C],x=l[o*a+h*d+C],k=l[o*a+p*d+C],O=n.x-r,R=n.y-h,I=n.z-f,E=((y*(1-O)+v*O)*(1-R)+(_*(1-O)+S*O)*R)*(1-I)+((w*(1-O)+x*O)*(1-R)+(A*(1-O)+k*O)*R)*I;E>this.isovalue&&(E=this.isovalue),E<-this.isovalue&&(E=-this.isovalue),E>0?(E/=1*this.isovalue,b=new THREE.Color(1-E,1-E,1)):(E/=-1*this.isovalue,b=new THREE.Color(1,1-E,1-E)),this.icn3d.atoms[t[s]].color=b,this.icn3d.atomPrevColors[t[s]]=b}}else{for(let p in t){let f,C=e[t[p]];if("DUM"!==C.resn){if(void 0!==this.rmsd_supr&&void 0!==this.rmsd_supr.rot){f=this.transformMemPro(C.coord,g,u,m).applyMatrix4(c)}else f=C.coord.clone().applyMatrix4(c);for(s=Math.floor(f.x)-this.maxdist,l=Math.ceil(f.x)+this.maxdist;s<=l;++s)if(!(s<0||s>this.header.xExtent*this.scaleFactor-1))for(i=Math.floor(f.y)-this.maxdist,r=Math.ceil(f.y)+this.maxdist;i<=r;++i)if(!(i<0||i>this.header.yExtent*this.scaleFactor-1))for(n=Math.floor(f.z)-this.maxdist,o=Math.ceil(f.z)+this.maxdist;n<=o;++n){if(n<0||n>this.header.zExtent*this.scaleFactor-1)continue;let e=s*a+i*d+n;h.push(e)}}}for(s=0,l=h.length;s=this.isovalue?1:0:"fofc"==this.type?(this.vpBits[e]=this.dataArray[e]>=this.isovalue||this.dataArray[e]<=-this.isovalue?1:0,this.vpAtomID[e]=this.dataArray[e]>=0?1:0):"em"==this.type&&(this.vpBits[e]=this.dataArray[e]>=this.isovalue?1:0)}}}else for(s=0;s=this.isovalue||this.dataArray[e]<=-this.isovalue?1:0,this.vpAtomID[t]=this.dataArray[e]>=0?1:0)}for(s=0,l=this.vpBits.length;s-1&&r-1&&a-1&&o1?"Structure":"",a=Object.keys(i).length>1?"Chain":"";n+=""+o+a+"ResidueNumberSASA (Å2)Percent OutIn/Out";for(let e in l.resid2area){let d=e.lastIndexOf("_"),c=e.substr(d+1),h=r.utilsCls.getIdArray(e.substr(0,d));o=Object.keys(s).length>1?""+h[0]+"":"",a=Object.keys(i).length>1?""+h[1]+"":"";let p="",m="";l.resid2area[e]=(l.resid2area[e]/t).toFixed(2),r.parasCls.residueArea.hasOwnProperty(c)&&(m=parseInt(l.resid2area[e]/r.parasCls.residueArea[c]*100),m>100&&(m=100),m>=50&&(p="out"),m<20&&(p="in")),n+=''+o+a+""+c+''+h[2]+''+l.resid2area[e]+''+m+"%"+p+""}return n+="",void(l.areahtml=n)}let p,m,u,g=c.vertices,f=c.faces,C=r.parasCls.thr("#00FFFF"),b=r.parasCls.thr("#00FF00"),y=r.parasCls.thr("#ff0000"),v=r.parasCls.thr("#00FFFF"),_=r.parasCls.thr("#0000FF"),w=r.parasCls.thr("#FF0000");11!=t&&12!=t&&13!=t&&14!=t||void 0===l.rmsd_supr||void 0===l.rmsd_supr.rot||(p=l.rmsd_supr.rot,m=l.rmsd_supr.trans1,u=l.rmsd_supr.trans2);let S=(11==t||12==t||13==t||14==t&&"delphi"!=l.loadPhiFrom)&&void 0!==l.rmsd_supr&&void 0!==l.rmsd_supr.rot;n=new THREE.BufferGeometry;let A,x=[],k=[],O=[],R=0;for(let e=0,s=g.length;e0?-parseInt(b.z):parseInt(b.z),y.onBeforeRender=function(e,t,s,i,n,o){let a,d=new THREE.Vector3(0,0,0),c=i.getAttribute("position").array;for(let e=0,t=c.length;e0?-parseInt(a.z):parseInt(a.z)},l.mdl.add(y),11==t||12==t?l.prevMaps.push(y):13==t?l.prevEmmaps.push(y):14==t?l.prevPhimaps.push(y):l.prevSurfaces.push(y)}}else{let e=new THREE.Mesh(n,new THREE.MeshPhongMaterial({specular:l.frac,shininess:20,emissive:l.emissive,vertexColors:!0,wireframe:s,opacity:i,transparent:!0,depthWrite:10==parseInt(10*i),side:THREE.DoubleSide}));e.renderOrder=-2,l.mdl.add(e),11==t||12==t?l.prevMaps.push(e):13==t?l.prevEmmaps.push(e):14==t?l.prevPhimaps.push(e):l.prevSurfaces.push(e)}c=null,g=null,f=null,n=null}transformMemPro(e,t,s,i,n){this.icn3d.icn3dui;let l=e.clone();l.sub(s),n&&console.log("sub coord: "+JSON.stringify(l));let r=l.x*t[0]+l.y*t[1]+l.z*t[2]+i.x,o=l.x*t[3]+l.y*t[4]+l.z*t[5]+i.y,a=l.x*t[6]+l.y*t[7]+l.z*t[8]+i.z;return l.x=r,l.y=o,l.z=a,n&&console.log("out coord: "+JSON.stringify(l)),l}SetupSurface(e){let t=this.icn3d;t.icn3dui;let s=e.threshbox,i=new Ke(t,s);i.initparm(e.extent,1!==e.type,e.bCalcArea,e.atomsToShow,e.header,e.data,e.matrix,e.isovalue,e.loadPhiFrom),i.fillvoxels(e.allatoms,e.extendedAtoms),i.buildboundary(),2===e.type&&(i.fastdistancemap(),i.boundingatom(!1),i.fillvoxelswaals(e.allatoms,e.extendedAtoms));let n=i.marchingcube();i.vpBits=null,i.vpDistance=null,i.vpAtomID=null;let l=i.getFacesAndVertices(e.atomsToShow);return l.area=n.area,l.serial2area=n.serial2area,l.scaleFactor=n.scaleFactor,i.faces=null,i.verts=null,l}SetupMap(e){let t=this.icn3d;if(t.icn3dui,!e.ccp4){let s,i=new Je(t);return i.initparm(e.header,e.data,e.matrix,e.isovalue,e.center,e.maxdist,e.pmin,e.pmax,e.water,e.type,e.rmsd_supr,e.loadPhiFrom,e.icn3d),i.fillvoxels(e.allatoms,e.extendedAtoms),e.header.bSurface||i.buildboundary(),e.header.bSurface||i.marchingcube(),i.vpBits=null,i.vpAtomID=null,e.header.bSurface||(s=i.getFacesAndVertices(e.allatoms,e.atomsToShow)),i.faces=null,i.verts=null,s}{let s,i=10,n=t.center?[t.center.x,t.center.y,t.center.z]:[0,0,0];if("2fofc"==e.type){s="2fofc";let l=t.ccp4ParserCls.extract_block(e.grid,e.unit_cell,i,n,s),r=t.ccp4ParserCls.marchingCubes(l.size,l.values,l.points,e.isovalue,"marching cubes");t.ccp4ParserCls.makeChickenWire(r,s),l=null,r=null}else if("fofc"==e.type){s="fofc_neg";let l=t.ccp4ParserCls.extract_block(e.grid,e.unit_cell,i,n,s),r=t.ccp4ParserCls.marchingCubes(l.size,l.values,l.points,e.isovalue,"marching cubes");t.ccp4ParserCls.makeChickenWire(r,s),s="fofc_pos",l=t.ccp4ParserCls.extract_block(e.grid,e.unit_cell,i,n,s),r=t.ccp4ParserCls.marchingCubes(l.size,l.values,l.points,e.isovalue,"marching cubes"),t.ccp4ParserCls.makeChickenWire(r,s),l=null,r=null}}}}class Qe{constructor(e){this.icn3d=e}applyCenterOptions(e){let t,s=this.icn3d;switch(s.icn3dui,void 0===e&&(e=s.opts),e.rotationcenter.toLowerCase()){case"molecule center":void 0!==s.center&&this.setRotationCenter(s.center);break;case"pick center":void 0!==s.pAtom&&this.setRotationCenter(s.pAtom.coord);break;case"display center":t=this.centerAtoms(s.dAtoms).center,this.setRotationCenter(t);break;case"highlight center":t=this.centerAtoms(s.hAtoms).center,this.setRotationCenter(t)}}setRotationCenter(e){this.icn3d.icn3dui,this.setCenter(e)}setCenter(e){let t=this.icn3d;t.icn3dui,t.mdl.position.set(0,0,0),t.mdlImpostor.position.set(0,0,0),t.mdl_ghost.position.set(0,0,0),t.mdl.position.sub(e),t.mdlImpostor.position.sub(e),t.mdl_ghost.position.sub(e)}centerSelection(e,t){let s=this.icn3d,i=s.icn3dui;if(s.opts.rotationcenter="highlight center",void 0===e&&(e=i.hashUtilsCls.hash2Atoms(s.hAtoms,s.atoms)),t||(s._zoomFactor=1,s.mouseChange=new THREE.Vector2(0,0),s.quaternion=new THREE.Quaternion(0,0,0,1)),Object.keys(e).length>1){let t=this.centerAtoms(e);s.center=t.center,this.setCenter(s.center),s.cameraCls.setCamera()}}centerAtoms(e){let t=this.icn3d;t.icn3dui;let s=new THREE.Vector3(9999,9999,9999),i=new THREE.Vector3(-9999,-9999,-9999),n=new THREE.Vector3;for(let l in e){let e=t.atoms[l].coord;n.add(e),s.min(e),i.max(e)}let l=t.ParserUtilsCls.getGeoCenter(s,i);return{center:l,maxD:t.ParserUtilsCls.getStructureSize(e,s,i,l),pmin:s,pmax:i}}setWidthHeight(e,t){let s=this.icn3d;s.icn3dui,void 0===s.scaleFactor&&(s.scaleFactor=1),s.renderer.setSize(e*s.scaleFactor,t*s.scaleFactor),s.renderer.domElement.style.width=e*s.scaleFactor+"px",s.renderer.domElement.style.height=t*s.scaleFactor+"px",s.renderer.domElement.width=e*s.scaleFactor,s.renderer.domElement.height=t*s.scaleFactor,s.container.whratio=e/t}}class et{constructor(e){this.icn3d=e}applyClbondsOptions(e){let t=this.icn3d,s=t.icn3dui;if(void 0===e&&(e=t.opts),t.bCalcCrossLink||(t.clbondpnts={},t.clbondResid2serial={},this.applyClbondsOptions_base("chemical"),this.applyClbondsOptions_base("all"),t.bCalcCrossLink=!0),"yes"===e.clbonds.toLowerCase()&&"nothing"!==e.chemicals){let e="#006400";if(s.parasCls.thr(25600),t.lines.clbond=[],t.residuesHashClbonds={},t.structures){let i=Object.keys(t.structures);for(let n=0,l=i.length;n1&&"sphere"!==a[Object.keys(a)[0]].style&&"dot"!==a[Object.keys(a)[0]].style){if(void 0===i.bCid||!i.bCid)for(let e in a){let t=a[e],n=1;i.boxCls.createBox(t,void 0,void 0,n,void 0,s)}}else for(let e in o){let l=i.firstAtomObjCls.getFirstCalphaAtomObj(i.residues[e]),r=l,o=r.structure+"_"+r.chain+"_"+(parseInt(r.resi)-1).toString(),a=r.structure+"_"+r.chain+"_"+(parseInt(r.resi)+1).toString();if("cylinder and plate"===r.style&&"helix"===r.ss)for(let t in i.residues[e]){let e=i.atoms[t],n=1;i.boxCls.createBox(e,void 0,void 0,n,void 0,s)}else if("ribbon"===r.style&&"coil"===r.ss||"strand"===r.style&&"coil"===r.ss||"o3 trace"===r.style||"schematic"===r.style||"c alpha trace"===r.style||"b factor tube"===r.style||"cylinder and plate"===r.style&&"helix"!==r.ss){if(void 0!==l&&void 0!==l.style2&&"nothing"!==l.style2)continue;let e=!1;if(!isNaN(r.resi)&&!e&&i.residues.hasOwnProperty(a)){let s=Object.keys(i.residues[a])[0],l=n.hashUtilsCls.hash2Atoms(i.residues[a],i.atoms)[s];if(r.style===l.style&&!l.ssbegin||l.ssbegin){let s=i.residues[a];if(t=n.hashUtilsCls.unionHash(t,s),e=!0,l.ssbegin)for(let e in s)i.atoms[e].notshow=!0}}if(!isNaN(r.resi)&&!e&&i.residues.hasOwnProperty(o)){let s=Object.keys(i.residues[o])[0],l=n.hashUtilsCls.hash2Atoms(i.residues[o],i.atoms)[s];r.style===l.style&&(t=n.hashUtilsCls.unionHash(t,i.residues[o]),e=!0)}}else if("ribbon"===r.style&&"coil"!==r.ss&&r.ssend||"strand"===r.style&&"coil"!==r.ss&&r.ssend){if(void 0!==l&&void 0!==l.style2&&"nothing"!==l.style2)continue;let e=!1;if(!isNaN(r.resi)&&!e&&i.residues.hasOwnProperty(a)){let s=Object.keys(i.residues[a])[0];n.hashUtilsCls.hash2Atoms(i.residues[a],i.atoms)[s],t=n.hashUtilsCls.unionHash(t,i.residues[a]),e=!0}}}a={}}if(i.bInitial){if(""!=n.htmlCls.setHtmlCls.getCookie("membrane")){let e=parseInt(n.htmlCls.setHtmlCls.getCookie("membrane"));i.bMembrane!=e&&n.htmlCls.clickMenuCls.setLogCmd("set membrane "+e,!0),i.bMembrane=isNaN(e)?0:parseInt(e)}i.bMembrane?i.selectionCls.toggleMembrane(!0):i.selectionCls.toggleMembrane(!1)}i.setStyleCls.setStyle2Atoms(t);let d=.5*i.cylinderRadius;void 0!==i.labels&&delete i.labels.schematic;for(let e in i.style2atoms){let t=i.style2atoms[e],l=n.hashUtilsCls.intHash(t,i.nucleotides),r=n.utilsCls.isCalphaPhosOnly(n.hashUtilsCls.hash2Atoms(l,i.atoms));if("ribbon"===e)i.strandCls.createStrand(n.hashUtilsCls.hash2Atoms(t,i.atoms),2,void 0,!0,void 0,void 0,!1,i.ribbonthickness,s);else if("strand"===e)i.strandCls.createStrand(n.hashUtilsCls.hash2Atoms(t,i.atoms),null,null,null,null,null,!1,void 0,s);else if("cylinder and plate"===e)i.cylinderCls.createCylinderHelix(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderHelixRadius,s);else if("nucleotide cartoon"===e)r?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["P"],i.traceRadius,!1,s):(i.cartoonNuclCls.drawCartoonNucleicAcid(n.hashUtilsCls.hash2Atoms(t,i.atoms),null,i.ribbonthickness,s),2!==s&&i.cartoonNuclCls.drawNucleicAcidStick(n.hashUtilsCls.hash2Atoms(t,i.atoms),s));else if("o3 trace"===e)r?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["P"],i.traceRadius,!1,s):i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["O3'","O3*"],i.traceRadius,!1,s);else if("schematic"===e){let e=i.firstAtomObjCls.getFirstAtomObj(t);if(i.chemicals.hasOwnProperty(e.serial)){i.residueLabelsCls.addNonCarbonAtomLabels(n.hashUtilsCls.hash2Atoms(t,i.atoms));let e=!0;i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),d,d,void 0,s,e)}else i.residueLabelsCls.addResidueLabels(n.hashUtilsCls.hash2Atoms(t,i.atoms),!0),r?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["P"],i.traceRadius,!1,s):i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["O3'","O3*"],i.traceRadius,!1,s),i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["CA"],i.traceRadius,!1,s)}else"c alpha trace"===e?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["CA"],i.traceRadius,!1,s):"b factor tube"===e?i.tubeCls.createTube(n.hashUtilsCls.hash2Atoms(t,i.atoms),"CA",null,s,!1,!0):"custom tube"===e?i.tubeCls.createTube(n.hashUtilsCls.hash2Atoms(t,i.atoms),"CA",null,s,!0,!0):"lines"===e||"lines2"===e?(1===s?i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.hlLineRadius,i.hlLineRadius,void 0,s):i.lineCls.createLineRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),s),i.lineCls.createConnCalphSidechain(n.hashUtilsCls.hash2Atoms(t,i.atoms),e)):"stick"===e||"stick2"===e?(i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderRadius,i.cylinderRadius,void 0,s,void 0),i.lineCls.createConnCalphSidechain(n.hashUtilsCls.hash2Atoms(t,i.atoms),e)):"backbone"===e?(t=this.selectMainChainSubset(t),i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderRadius,i.cylinderRadius,void 0,s,void 0)):"ball and stick"===e||"ball and stick2"===e?(i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderRadius,.5*i.cylinderRadius,i.dotSphereScale,s,void 0),i.lineCls.createConnCalphSidechain(n.hashUtilsCls.hash2Atoms(t,i.atoms),e)):"sphere"===e||"sphere2"===e?i.sphereCls.createSphereRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.sphereRadius,void 0,void 0,s):"dot"===e&&i.sphereCls.createSphereRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.sphereRadius,!1,i.dotSphereScale,s)}if(i.cnt>i.maxmaxatomcnt&&i.init_base(),void 0!==i.labels&&Object.keys(i.labels).length>0){i.labelCls.hideLabels();for(let e in i.labels)"schematic"!=e&&this.changeLabelColor(i.labels[e]);i.labelCls.createLabelRepresentation(i.labels)}}changeLabelColor(e){let t=this.icn3d;if(t.icn3dui,e)for(let s=0,i=e.length;s0){this.updateStabilizer();let e="#FFFFFF",s=t.stabilizerpnts;t.lines.stabilizer=[];for(let i=0,n=Math.floor(s.length/2);i0)for(let e=0,s=t.distPnts.length;e0&&t.applySymdCls.applySymd(),void 0!==t.prevOtherMesh)for(let e=0,s=t.prevOtherMesh.length;e0&&(e=s.hashUtilsCls.hash2Atoms(t.chemicals,t.atoms));let i=4;if(void 0!==e){let n=t.contactCls.getAtomsWithinAtom(t.atoms,e,i),l=3.5;t.opts.hbonds="yes",Object.keys(n).length>0&&t.hBondCls.calculateChemicalHbonds(e,n,parseFloat(l)),t.bSetFog||t.transformCls.zoominSelection(s.hashUtilsCls.unionHash(e,n))}}else"hide"===e.chemicalbinding&&(t.hBondCls.hideHbonds(),t.showInterCls.hideExtraBonds(),t.bSetFog||t.transformCls.zoominSelection(t.atoms))}updateStabilizer(){let e=this.icn3d;if(e.icn3dui,e.stabilizerpnts=[],void 0!==e.pairArray)for(let t=0,s=e.pairArray.length;t=0;i--){let r=t.ssbondpnts[e][2*i],o=t.ssbondpnts[e][2*i+1],a={};a.color=n,a.dashed=!1;let d=[],c=[],h=[],p=[],m=!1,u=!1;for(let e in t.residues[r])"SG"===t.atoms[e].name&&(h.push(t.atoms[e].coord),d.push(t.atoms[e].serial),m=!0);if(!m)for(let e in t.residues[r])if("CA"===t.atoms[e].name){h.push(t.atoms[e].coord),d.push(t.atoms[e].serial),m=!0,u=!0;break}m=!1;for(let e in t.residues[o])"SG"===t.atoms[e].name&&(p.push(t.atoms[e].coord),c.push(t.atoms[e].serial),m=!0);if(!m)for(let e in t.residues[o])if("CA"===t.atoms[e].name){p.push(t.atoms[e].coord),c.push(t.atoms[e].serial),m=!0,u=!0;break}let g=u?7:3,f=!1;for(let e=0,t=h.length;e1&&(l=!0)}if(t)if(l){let t=Object.keys(r)[0];e=i.chains[t]}else{0==Object.keys(i.hAtoms).length&&(i.hAtoms=n.hashUtilsCls.cloneHash(i.dAtoms));let t,s=parseInt(Object.keys(i.hAtoms).length/u),l=0;for(let n in i.hAtoms)if(e[n]=1,t=n,++l,l>s)break;let r=i.atoms[t].structure+"_"+i.atoms[t].chain+"_"+i.atoms[t].resi;e=n.hashUtilsCls.unionHash(e,i.residues[r])}else{let t=Object.keys(i.structures)[0]+"_"+g;if(i.chains.hasOwnProperty(t)||(t=Object.keys(i.structures)[0]+"_"+g.toLowerCase()),!i.chains.hasOwnProperty(t)){t=Object.keys(i.chains)[0];for(let e in i.chains){let s=Object.keys(i.chains[e])[0];if(i.proteins.hasOwnProperty(s)){t=e;break}}}e=i.chains[t]}let a=s.clone().add(h).multiplyScalar(.5),c=new THREE.Vector3,p=0,f=h.clone().sub(s).normalize(),C=new THREE.Vector3(0,0,1),b=new THREE.Quaternion;b.setFromUnitVectors(f,C);let y=-9999;for(let t in e){let e=i.atoms[t].coord.clone();c.add(e),e.sub(a).applyQuaternion(b);let s=e.x*e.x+e.y*e.y;s>y&&(y=s),++p}let v=i.ParserUtilsCls.getMassCenter(c,p),_=new THREE.Line3(s,h),w=new THREE.Vector3;_.closestPointToPoint(v,!0,w);let S,A,x,k,O=Math.sqrt(y),R=v.clone().sub(w).normalize().multiplyScalar(O),I=a.clone().add(s.clone().sub(a).multiplyScalar(.83)).add(R),E=a.clone().add(h.clone().sub(a).multiplyScalar(.83)).add(R),T=2*Math.PI/o;for(let e=0;et&&(i.sphereCls.createSphereBase(r,m,d,1,0),i.cylinderCls.createCylinder(e,r,d,m,0),i.cylinderCls.createCylinder(s,r,d,m,0),void 0!==n&&i.cylinderCls.createCylinder(c[n],r,d,m,0),n=l)}}else if("O"==r)for(let e=0,t=c.length;e0&&(e.mdl.remove(e.prevSurfaces[e.prevSurfaces.length-1]),e.prevSurfaces.slice(e.prevSurfaces.length-1,1))}removeMaps(){let e=this.icn3d;e.icn3dui;for(let t=0,s=e.prevMaps.length;t0&&(e.mdl.remove(e.prevMaps[e.prevMaps.length-1]),e.prevMaps.slice(e.prevMaps.length-1,1))}removeLastEmmap(){let e=this.icn3d;e.icn3dui,e.prevEmmaps.length>0&&(e.mdl.remove(e.prevEmmaps[e.prevEmmaps.length-1]),e.prevEmmaps.slice(e.prevEmmaps.length-1,1))}removeLastPhimap(){let e=this.icn3d;e.icn3dui,e.prevPhimaps.length>0&&(e.mdl.remove(e.prevPhimaps[e.prevPhimaps.length-1]),e.prevPhimaps.slice(e.prevPhimaps.length-1,1))}}class ot{constructor(e){this.icn3d=e}addResidueLabels(e,t,s,i,n){let l=this.icn3d,r=l.icn3dui;if(r.bNode)return;let o=r.hashUtilsCls.intHash(l.hAtoms,e);t?void 0===l.labels.schematic&&(l.labels.schematic=[]):void 0===l.labels.residue&&(l.labels.residue=[]);let a="";for(let e in o){let s=l.atoms[e],o={},d=s.structure+"_"+s.chain+"_"+s.resi;if(!s.het&&("CA"===s.name||"O3'"===s.name||"O3*"===s.name)||l.water.hasOwnProperty(s.serial)||l.ions.hasOwnProperty(s.serial)||l.chemicals.hasOwnProperty(s.serial)&&d!==a){if(o.position=s.coord,o.bSchematic=0,t&&(o.bSchematic=1),o.text=r.utilsCls.residueName2Abbr(s.resn),i)o.text+=s.resi;else if(n){let e=s.structure+"_"+s.chain+"_"+s.resi,t="";l.resid2refnum[e]&&(t=" "==l.resid2refnum[e].substr(0,1)?"":l.resid2refnum[e]),o.text=t}o.size=18,o.factor=.3;let e=s.color.getHexString().toUpperCase();o.color=i?"black"!=l.opts.background?l.colorWhitebkgd:l.colorBlackbkgd:n?"#00FFFF":"CCCCCC"===e||"C8C8C8"===e?"#888888":"#"+e,o.background="#FFFFFF",t?l.labels.schematic.push(o):l.labels.residue.push(o)}a=d}l.hlObjectsCls.removeHlObjects()}addIgLabels(e){let t=this.icn3d;if(t.icn3dui.bNode)return;t.labels.ig=[];let s=t.firstAtomObjCls.getChainsFromAtoms(e);for(let e in t.igLabel2Pos)if(s.hasOwnProperty(e))for(let s in t.igLabel2Pos[e]){let i={};i.position=t.igLabel2Pos[e][s],i.text=s,i.size=60,i.color="#00FFFF",t.labels.ig.push(i)}t.hlObjectsCls.removeHlObjects()}addNonCarbonAtomLabels(e){let t=this.icn3d,s=t.icn3dui;if(s.bNode)return;let i=s.hashUtilsCls.intHash(t.hAtoms,e);void 0===t.labels.schematic&&(t.labels.schematic=[]);for(let e in i){let s=t.atoms[e];if(!t.residues.hasOwnProperty(s.structure+"_"+s.chain+"_"+s.resi))continue;if("C"===s.elem)continue;let i={};i.position=s.coord,i.bSchematic=1,i.text=s.elem,i.size=18,i.color="black"!=t.opts.background?t.colorWhitebkgd:s.color.getHexString(),i.background="#FFFFFF",t.labels.schematic.push(i)}t.hlObjectsCls.removeHlObjects()}addAtomLabels(e,t){let s=this.icn3d,i=s.icn3dui;if(i.bNode)return;let n=i.hashUtilsCls.intHash(s.hAtoms,e);n=i.hashUtilsCls.intHash(s.dAtoms,n),void 0===s.labels.residue&&(s.labels.residue=[]);for(let e in n){let i=s.atoms[e],n={};n.position=i.coord,n.bSchematic=0,n.text=t?i.elem:i.name.padEnd(2," "),n.size=18,t&&(n.bSchematic=!0);let l=i.color.getHexString().toUpperCase();n.color="black"!=s.opts.background?s.colorWhitebkgd:s.colorBlackbkgd,t&&(n.color="CCCCCC"===l||"C8C8C8"===l?"#888888":"#"+l),n.background="#FFFFFF",s.labels.residue.push(n)}s.hlObjectsCls.removeHlObjects()}}class at{constructor(e){this.icn3d=e}onBeforeRender(e,t,s,i,n,l){let r=n.uniforms,o=[];if(r.objectId&&(r.objectId.value=SupportsReadPixelsFloat?this.id:this.id/255,o.push("objectId")),(r.modelViewMatrixInverse||r.modelViewMatrixInverseTranspose||r.modelViewProjectionMatrix||r.modelViewProjectionMatrixInverse)&&this.modelViewMatrix.multiplyMatrices(s.matrixWorldInverse,this.matrixWorld),r.modelViewMatrixInverse&&(r.modelViewMatrixInverse.value.copy(this.modelViewMatrix).invert(),o.push("modelViewMatrixInverse")),r.modelViewMatrixInverseTranspose&&(r.modelViewMatrixInverse?r.modelViewMatrixInverseTranspose.value.copy(r.modelViewMatrixInverse.value).transpose():r.modelViewMatrixInverseTranspose.value.copy(this.modelViewMatrix).invert().transpose(),o.push("modelViewMatrixInverseTranspose")),r.modelViewProjectionMatrix&&(s.updateProjectionMatrix(),r.modelViewProjectionMatrix.value.multiplyMatrices(s.projectionMatrix,this.modelViewMatrix),o.push("modelViewProjectionMatrix")),r.modelViewProjectionMatrixInverse){let e=new THREE.Matrix4;r.modelViewProjectionMatrix?(e.copy(r.modelViewProjectionMatrix.value),r.modelViewProjectionMatrixInverse.value.copy(e).invert()):(s.updateProjectionMatrix(),e.multiplyMatrices(s.projectionMatrix,this.modelViewMatrix),r.modelViewProjectionMatrixInverse.value.copy(e).invert()),o.push("modelViewProjectionMatrixInverse")}if(r.projectionMatrix&&(s.updateProjectionMatrix(),r.projectionMatrix.value.copy(s.projectionMatrix),o.push("projectionMatrix")),r.projectionMatrixInverse&&(s.updateProjectionMatrix(),r.projectionMatrixInverse.value.copy(s.projectionMatrix).invert(),o.push("projectionMatrixInverse")),o.length){let t=e.properties.get(n);if(t.program){let s=e.getContext(),i=t.program;s.useProgram(i.program);let n=i.getUniforms();o.forEach((function(e){n.setValue(s,e,r[e].value)}))}}}setParametersForShader(e){let t,s=this.icn3d,i=s.icn3dui.parasCls.backgroundColors[s.opts.background.toLowerCase()],n=2.5*s.maxD,l=4*s.maxD,r=void 0!==s.biomtMatrices&&s.biomtMatrices.length*s.cnt>s.maxatomcnt;"yes"===s.opts.slab?r?t=.1:void 0!==s.camMaxDFactorFog?(t=s.maxD*s.camMaxDFactorFog-10,n=2.5*s.maxD-t<0?0:2.5*s.maxD-t,l=4*s.maxD-t):t=s.maxD*s.camMaxDFactor:t=.1;let o=void 0!==e?e:1,a=s.shininess/100*.5;s.uniforms=THREE.UniformsUtils.merge([THREE.UniformsLib.common,{modelViewMatrix:{value:new THREE.Matrix4},modelViewMatrixInverse:{value:new THREE.Matrix4},modelViewMatrixInverseTranspose:{value:new THREE.Matrix4},modelViewProjectionMatrix:{value:new THREE.Matrix4},modelViewProjectionMatrixInverse:{value:new THREE.Matrix4},projectionMatrix:{value:new THREE.Matrix4},projectionMatrixInverse:{value:new THREE.Matrix4},diffuse:{type:"v3",value:[1,1,1]},emissive:{type:"v3",value:[.06,.06,.06]},roughness:{type:"f",value:.5},metalness:{type:"f",value:a},opacity:{type:"f",value:o},nearClip:{type:"f",value:t},ortho:{type:"f",value:0},shrink:{type:"f",value:.13},fogColor:{type:"v3",value:[i.r,i.g,i.b]},fogNear:{type:"f",value:n},fogFar:{type:"f",value:l},fogDensity:{type:"f",value:2}},THREE.UniformsLib.ambient,THREE.UniformsLib.lights]),s.defines={USE_COLOR:1,NEAR_CLIP:1,CAP:1},"yes"!==s.opts.fog||r||(s.defines.USE_FOG=1,"orthographic"===s.opts.camera&&(s.defines.FOG_EXP2=1)),s.bExtFragDepth&&(s.defines.USE_LOGDEPTHBUF_EXT=1)}drawImpostorShader(){this.icn3d.icn3dui.bNode||(this.setParametersForShader(),this.createImpostorShaderSphere("SphereImpostor"),this.createImpostorShaderCylinder("CylinderImpostor"))}getShader(e){this.icn3d.icn3dui;let t=$NGL_shaderTextHash[e];return t=t.replace(/#include\s+(\S+)/gim,(function(e,t){let s;return THREE.ShaderChunk.hasOwnProperty(t)&&(s=THREE.ShaderChunk[t]),s||""})),t}createImpostorShaderBase(e,t,s,i,n,l,r,o,a){let d=this.icn3d;d.icn3dui;let c=new THREE.ShaderMaterial({defines:d.defines,uniforms:d.uniforms,vertexShader:this.getShader(e+".vert"),fragmentShader:this.getShader(e+".frag"),depthTest:!0,depthWrite:!0,lights:!0});c.extensions.fragDepth=!0,"CylinderImpostor"==e?d.CylinderImpostorMaterial=c:"SphereImpostor"==e&&(d.SphereImpostorMaterial=c);let h,p,m=l*r,u=l*o,g=new(m>65535?Uint32Array:Uint16Array)(u);for(let e=0;e=0;t--){let s=a.children[t];s.onBeforeRender=e.impostorCls.onBeforeRender,s.frustumCulled=!1}l.add(a)}void 0!==e.mdl_ghost&&(a=e.mdl_ghost.clone(),this.applyMat(a,d),r.add(a));let c=e.center.clone();this.applyMat(c,d,!0),s.add(c),++t}e.mdl.add(n),e.mdlImpostor.add(l),e.mdl_ghost.add(r),void 0!==e.bSetInstancing&&e.bSetInstancing?(e.maxD=e.maxDAssembly,e.center=e.centerAssembly.clone(),e.applyCenterCls.setCenter(e.center),e.cameraCls.setCamera()):(e.maxD*=Math.sqrt(t),e.center=e.ParserUtilsCls.getMassCenter(s,t),e.maxDAssembly=e.maxD,e.centerAssembly=e.center.clone(),e.applyCenterCls.setCenter(e.center),e.cameraCls.setCamera()),e.bSetInstancing=!0}createInstancedGeometry(e){let t=this.icn3d,s=t.icn3dui,i=e.geometry,n=new THREE.InstancedBufferGeometry,l=[],r=[],o=[],a=[],d=[],c=[],h=[],p=[];if(t.bImpo&&"Cylinder"==e.type){t.instancedMaterial=this.getInstancedMaterial("CylinderInstancing");let e=s.hashUtilsCls.hashvalue2array(i.attributes.position1.array),r=s.hashUtilsCls.hashvalue2array(i.attributes.color.array),m=s.hashUtilsCls.hashvalue2array(i.attributes.position2.array),u=s.hashUtilsCls.hashvalue2array(i.attributes.color2.array),g=s.hashUtilsCls.hashvalue2array(i.index.array),f=s.hashUtilsCls.hashvalue2array(i.attributes.radius.array),C=s.hashUtilsCls.hashvalue2array(i.attributes.mapping.array);l=l.concat(e),o=o.concat(r),h=h.concat(m),p=p.concat(u),a=a.concat(g),d=d.concat(f),c=c.concat(C),n.setAttribute("position1",new THREE.BufferAttribute(new Float32Array(l),3)),n.setAttribute("color",new THREE.BufferAttribute(new Float32Array(o),3)),n.setAttribute("position2",new THREE.BufferAttribute(new Float32Array(h),3)),n.setAttribute("color2",new THREE.BufferAttribute(new Float32Array(p),3)),n.setAttribute("radius",new THREE.BufferAttribute(new Float32Array(d),1)),n.setAttribute("mapping",new THREE.BufferAttribute(new Float32Array(c),3)),n.setIndex(new THREE.BufferAttribute(new Uint32Array(a),1)),e=null,r=null,m=null,u=null,g=null,f=null,C=null}else if(t.bImpo&&"Sphere"==e.type){t.instancedMaterial=this.getInstancedMaterial("SphereInstancing");let e=s.hashUtilsCls.hashvalue2array(i.attributes.position.array),r=s.hashUtilsCls.hashvalue2array(i.attributes.color.array),h=s.hashUtilsCls.hashvalue2array(i.index.array),p=s.hashUtilsCls.hashvalue2array(i.attributes.radius.array),m=s.hashUtilsCls.hashvalue2array(i.attributes.mapping.array);l=l.concat(e),o=o.concat(r),a=a.concat(h),d=d.concat(p),c=c.concat(m),n.setAttribute("position",new THREE.BufferAttribute(new Float32Array(l),3)),n.setAttribute("color",new THREE.BufferAttribute(new Float32Array(o),3)),n.setAttribute("radius",new THREE.BufferAttribute(new Float32Array(d),1)),n.setAttribute("mapping",new THREE.BufferAttribute(new Float32Array(c),2)),n.setIndex(new THREE.BufferAttribute(new Uint32Array(a),1)),e=null,r=null,h=null,p=null,m=null}else{t.instancedMaterial=this.getInstancedMaterial("Instancing");let e=i.attributes.position?s.hashUtilsCls.hashvalue2array(i.attributes.position.array):[],d=i.attributes.normal?s.hashUtilsCls.hashvalue2array(i.attributes.normal.array):[],c=i.attributes.color?s.hashUtilsCls.hashvalue2array(i.attributes.color.array):[],h=i.index?s.hashUtilsCls.hashvalue2array(i.index.array):[];l=l.concat(e),r=r.concat(d),o=o.concat(c),a=a.concat(h);let p=[],m="CylinderGeometry"==i.type?1:0;for(let e=0,t=l.length/3;e0&&(e.dAtoms=t.hashUtilsCls.cloneHash(s)),e.bShowHighlight=!1}e.applyMapCls.removeSurfaces(),e.applyMapCls.applySurfaceOptions(),e.applyMapCls.removeMaps(),e.applyMapCls.applyMapOptions(),e.applyMapCls.removeEmmaps(),e.applyMapCls.applyEmmapOptions(),e.applyMapCls.removePhimaps(),e.applyMapCls.applyPhimapOptions(),e.applyMapCls.removeSurfaces(),e.applyMapCls.applyphisurfaceOptions(),e.axes=[],e.pc1&&e.axesCls.setPc1Axes(),e.opts.rotationcenter="highlight center",e.drawCls.draw(),e.bShowHighlight=!0}async alternateWrapper(){let e=this.icn3d;e.icn3dui,e.bAlternate=!0,await this.alternateStructures(),e.bAlternate=!1}}class ht{constructor(e){this.icn3d=e}draw(e){let t=this.icn3d,s=t.icn3dui;if(t.impostorCls.clearImpostors(),!t.bRender||t.hAtoms&&0!=Object.keys(t.hAtoms)||(t.hAtoms=s.hashUtilsCls.cloneHash(t.atoms)),t.sceneCls.rebuildScene(),t.bImpo&&t.impostorCls.drawImpostorShader(),t.setColorCls.applyPrevColor(),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1)if(t.bAssembly&&1==Object.keys(t.structures).length&&(void 0===s.cfg.mmdbid&&1==s.cfg.bu||void 0!==s.cfg.mmdbid&&1==s.cfg.bu&&Object.keys(t.atoms).length*t.biomtMatrices.length>t.maxatomcnt))t.instancingCls.drawSymmetryMates();else{let e=!0;t.applyCenterCls.centerSelection(void 0,e)}let i=void 0!==t.hAtoms?Object.keys(t.hAtoms).length:0;if(i>0&&i0){e.children[0].scale.z=t[0].distance,t[0].point.sub(r.mdl.position);let s=r.rayThreshold,i=r.rayCls.getAtomsFromPosition(t[0].point,s);for(;!i&&s<10;)s+=.5,i=r.rayCls.getAtomsFromPosition(t[0].point,s);i&&(r.pAtomNum%2==0?r.pAtom=i:r.pAtom2=i,++r.pAtomNum,this.showPickingVr(r.pk,i))}}}}catch(e){}}showPickingVr(e,t){let s=this.icn3d;s.icn3dui,e||(e=2),s.hAtoms=s.pickingCls.getPickedAtomList(e,t),2===e?s.residueLabelsCls.addResidueLabels(s.hAtoms,void 0,void 0,!0):1===e&&s.residueLabelsCls.addAtomLabels(s.hAtoms),s.setOptionCls.setStyle("proteins",t.style)}render_base(){let e=this.icn3d,t=e.icn3dui,s=this;if(t.bNode)return;let i=e.bControlGl&&!t.bNode?window.cam:e.cam;if(e.directionalLight){let t=new THREE.Quaternion;t.setFromUnitVectors(new THREE.Vector3(0,0,e.cam_z).normalize(),i.position.clone().normalize()),e.directionalLight.position.copy(e.lightPos.clone().applyQuaternion(t).normalize()),e.directionalLight2.position.copy(e.lightPos2.clone().applyQuaternion(t).normalize()),e.directionalLight3.position.copy(e.lightPos3.clone().applyQuaternion(t).normalize())}if(e.bVr||e.renderer.setPixelRatio(window.devicePixelRatio),e.bVr){let t=.04;if(e.controllers){let i=this.updateGamepadState();for(let n=0,l=e.controllers.length;n{const i=e.gamepad.axes;let r=parseInt(1e3*i[t]),o=parseInt(-1e3*i[s]);n.push(r),l.push(o)})),{xArray:n,yArray:l}}return{xArray:[0,0],yArray:[0,0]}}}class pt{constructor(e){this.icn3d=e}getAtomsWithinAtom(e,t,s,i,n,l,r){let o=this.icn3d;o.icn3dui;let a=this.getNeighboringAtoms(e,t,s,r);i&&(o.resid2Residhash={});let d={};for(let e in t){let c,h,p=o.atoms[e],m=p.structure+"_"+p.chain+"_"+p.resi;for(let e in o.residues[m])if(o.atoms[e]&&("CA"===o.atoms[e].name&&"C"===o.atoms[e].elem||"O3'"===o.atoms[e].name||"O3*"===o.atoms[e].name)){c=o.atoms[e];break}void 0===c&&(c=p),i&&(h=p.resn+" $"+p.structure+"."+p.chain+":"+p.resi,void 0===o.resid2Residhash[h]&&(o.resid2Residhash[h]={}));let u=p.structure+"_"+p.chain+"_"+p.resi;for(let e in a){let m=a[e];if(!o.crossstrucinter&&p.structure!=m.structure)continue;if(!r&&m.serial in t)continue;if(o.bOpm&&"DUM"===m.resn)continue;let g=m.coord.distanceTo(p.coord);if(go?r:o,d=Math.sqrt(a),c=(d+s)*(d+s),h={};for(let r in e){let e=n.atoms[r];!i&&t.hasOwnProperty(e.serial)||(this.bOpm&&"DUM"===e.resn||e.coord.xl[1][0]+s||e.coord.yl[1][1]+s||e.coord.zl[1][2]+s||(e.coord.x-l[2][0])*(e.coord.x-l[2][0])+(e.coord.y-l[2][1])*(e.coord.y-l[2][1])+(e.coord.z-l[2][2])*(e.coord.z-l[2][2])e.coord.x?n:e.coord.x,l=l>e.coord.y?l:e.coord.y,r=r>e.coord.z?r:e.coord.z}return[[t,s,i],[n,l,r],[o/c,a/c,d/c]]}hideContact(){let e=this.icn3d;e.icn3dui,e.opts.contact="no",void 0===e.lines&&(e.lines={}),e.lines.contact=[],e.contactpnts=[]}}class mt{constructor(e){this.icn3d=e}isHbondDonorAcceptor(e){let t=this.icn3d;if(t.icn3dui,"N"==e.name&&!e.het||"N"==e.elem&&"Arg"==e.resn||"N"==e.elem&&"Asn"==e.resn||"N"==e.elem&&"Gln"==e.resn||"N"==e.elem&&"Lys"==e.resn||"N"==e.elem&&"Trp"==e.resn)return"donor";if("O"==e.name&&!e.het||"S"==e.elem&&"Met"==e.resn||"O"==e.elem&&"Asn"==e.resn||"O"==e.elem&&"Asp"==e.resn||"O"==e.elem&&"Gln"==e.resn||"O"==e.elem&&"Glu"==e.resn)return"acceptor";if("S"==e.elem&&"Cys"==e.resn||"N"==e.elem&&"His"==e.resn||"O"==e.elem&&"Ser"==e.resn||"O"==e.elem&&"Thr"==e.resn||"O"==e.elem&&"Tyr"==e.resn)return"both";if("Pro"==e.resn)return"none";if("N"==e.elem){if("Asn"==e.resn||"Gln"==e.resn)return"both";let s=0,i=0;for(let i=0,n=e.bonds.length;i1?"ring":"donor":"none"}if("O"==e.elem&&1==e.bonds.length){if("Asn"==e.resn||"Gln"==e.resn)return"both";for(let s=0,i=e.bonds.length;s=2?"acceptor":"both"}if("O"==e.elem&&2==e.bonds.length){for(let s=0,i=e.bonds.length;s1);++t)"H"!=s.atoms[e.bonds[t]].elem&&(i=s.atoms[e.bonds[t]],l[r++].subVectors(s.atoms[e.bonds[t]].coord,e.coord));if(1===r)for(let t=0,n=i.bonds.length;t1);++t)"H"!=s.atoms[i.bonds[t]].elem&&s.atoms[i.bonds[t]].serial!=e.serial&&l[r++].subVectors(s.atoms[i.bonds[t]].coord,e.coord);if(2!==r)return;let o=l[0].cross(l[1]);return Math.abs(Math.PI/2-o.angleTo(n))}isValidHbond(e,t,s){let i=this.icn3d;i.icn3dui;let n,l,r=this.isHbondDonorAcceptor(e),o=this.isHbondDonorAcceptor(t),a=50*Math.PI/180,d=50*Math.PI/180,c=90*Math.PI/180,h=30*Math.PI/180;if("donor"==r&&("acceptor"==o||"both"==o||"ring"==o)||"acceptor"==o&&("donor"==r||"both"==r||"ring"==r))n=e,l=t;else if("acceptor"==r&&("donor"==o||"both"==o||"ring"==o)||"donor"==o&&("acceptor"==r||"both"==r||"ring"==r))l=e,n=t;else{if("both"!=r&&"ring"!=r||"both"!=o&&"ring"!=o)return!1;n=e,l=t,i.nucleotides.hasOwnProperty(e.serial)&&i.nucleotides.hasOwnProperty(t.serial)&&("ring"==r||"ring"==o)||(e.het||t.het)&&"ring"==r&&"ring"==o||(h=90*Math.PI/180)}let p=this.calcAngles(n,l),m=90*Math.PI/180;for(let e=0,t=p.length;ed)return!1;let u=this.calcPlaneAngle(n,l);if(void 0!==u&&u>h)return!1;let g=this.calcAngles(l,n),f=90*Math.PI/180;for(let e=0,t=g.length;ea)return!1;let C=this.calcPlaneAngle(l,n);return!(void 0!==C&&C>c)}calculateChemicalHbonds(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(0===Object.keys(e).length||0===Object.keys(t).length)return;r.resid2Residhash={};let a,d,c={},h=s*s;for(let t in e){let s=e[t],n=i?"LYS"===s.resn&&"N"===s.elem&&"N"!==s.name||"ARG"===s.resn&&("NH1"===s.name||"NH2"===s.name)||("GLU"===s.resn||"ASP"===s.resn)&&"O"===s.elem&&"O"!==s.name||s.het&&("N"===s.elem||"O"===s.elem||"S"===s.elem):"N"===s.elem||"O"===s.elem||"S"===s.elem&&(s.het||"Cys"===s.resn||"Met"===s.resn);n=r.bOpm?n&&"DUM"!==s.resn:n,n&&(a=s.structure+"_"+s.chain+"_"+s.resi,d=a+"_"+s.name,c[d]=s)}let p={},m={},u=.5,g=-27.888,f={};for(let e in t){let C=t[e],b=i?"LYS"===C.resn&&"N"===C.elem&&"N"!==C.name||"ARG"===C.resn&&("NH1"===C.name||"NH2"===C.name)||("GLU"===C.resn||"ASP"===C.resn)&&"O"===C.elem&&"O"!==C.name||C.het&&("N"===C.elem||"O"===C.elem||"S"===C.elem):"N"===C.elem||"O"===C.elem||"S"===C.elem&&(C.het||"Cys"===C.resn||"Met"===C.resn);if(b=r.bOpm?b&&"DUM"!==C.resn:b,b){a=C.structure+"_"+C.chain+"_"+C.resi,d=a+"_"+C.name;let e=C.resn+" $"+C.structure+"."+C.chain+":"+C.resi+"@"+C.name;void 0===r.resid2Residhash[e]&&(r.resid2Residhash[e]={});for(let t in c){if(i&&!(("LYS"!==C.resn&&"ARG"!==C.resn||"LYS"!==c[t].resn&&"ARG"!==c[t].resn)&&("GLU"!==C.resn&&"ASP"!==C.resn||"GLU"!==c[t].resn&&"ASP"!==c[t].resn)))continue;if(!r.crossstrucinter&&C.structure!=c[t].structure)continue;if(a==t.substr(0,t.lastIndexOf("_")))continue;let d=Math.abs(C.coord.x-c[t].coord.x);if(d>s)continue;let b=Math.abs(C.coord.y-c[t].coord.y);if(b>s)continue;let y=Math.abs(C.coord.z-c[t].coord.z);if(y>s)continue;let v=d*d+b*b+y*y;if(v>h)continue;if(!r.proteins.hasOwnProperty(C.serial)||!r.proteins.hasOwnProperty(c[t].serial)||"N"!==C.name&&"O"!==C.name||"O"!==c[t].name&&"N"!==c[t].name){if(!this.isValidHbond(C,c[t],s))continue}else{if(C.name===c[t].name)continue;if(C.structure==c[t].structure&&C.chain==c[t].chain&&Math.abs(C.resi-c[t].resi)<=1)continue;let e,i="N"===C.name?C:c[t],n="O"===C.name?C:c[t];if("Pro"===i.resn)continue;if(void 0===i.hcoord){if(!this.isValidHbond(C,c[t],s))continue}else{let s,l=i.hcoord,o=i.coord,a=n.structure+"_"+n.chain+"_"+n.resi;for(let e in r.residues[a])if("C"===r.atoms[e].name){s=r.atoms[e];break}if(!s)continue;let d=s.coord,h=n.coord,p=l.distanceTo(h),m=l.distanceTo(d),f=o.distanceTo(d),b=o.distanceTo(h);e=p2||f[c[t].serial]>2)continue;void 0===f[C.serial]?f[C.serial]=1:++f[C.serial],void 0===f[c[t].serial]?f[c[t].serial]=1:++f[c[t].serial],"graph"!==n&&(i?(r.saltbridgepnts.push({serial:C.serial,coord:C.coord}),r.saltbridgepnts.push({serial:c[t].serial,coord:c[t].coord})):(r.hbondpnts.push({serial:C.serial,coord:C.coord}),r.hbondpnts.push({serial:c[t].serial,coord:c[t].coord})));let _=c[t].structure+"_"+c[t].chain+"_"+c[t].resi;p=o.hashUtilsCls.unionHash(p,r.residues[a]),p=o.hashUtilsCls.unionHash(p,r.residues[_]),m[a]=1,m[_]=1;let w=c[t].resn+" $"+c[t].structure+"."+c[t].chain+":"+c[t].resi+"@"+c[t].name,S=a+"_"+C.resn+","+_+"_"+c[t].resn;void 0!==r.resids2interAll[S]&&void 0!==r.resids2interAll[S].ionic&&r.resids2interAll[S].ionic.hasOwnProperty(e+","+w)||(r.resid2Residhash[e][w]=v.toFixed(1),l||(void 0===r.resids2inter[S]&&(r.resids2inter[S]={}),void 0===r.resids2inter[S].hbond&&(r.resids2inter[S].hbond={}),r.resids2inter[S].hbond[e+","+w]=v.toFixed(1)),void 0===r.resids2interAll[S]&&(r.resids2interAll[S]={}),void 0===r.resids2interAll[S].hbond&&(r.resids2interAll[S].hbond={}),r.resids2interAll[S].hbond[e+","+w]=v.toFixed(1))}}}let C=Object.keys(m);if("graph"!==n)for(let e=0,t=C.length;en)return!1;let c=Math.abs(e.coord.y-t.coord.y);if(c>n)return!1;let h=Math.abs(e.coord.z-t.coord.z);if(h>n)return!1;let p=d*d+c*c+h*h;if(p>l)return!1;"graph"!==s&&("halogen"==i?(a.halogenpnts.push({serial:e.serial,coord:e.coord}),a.halogenpnts.push({serial:t.serial,coord:t.coord})):"pi-cation"==i?(a.picationpnts.push({serial:e.serial,coord:e.coord}),a.picationpnts.push({serial:t.serial,coord:t.coord})):"pi-stacking"==i&&(a.pistackingpnts.push({serial:e.serial,coord:e.coord}),a.pistackingpnts.push({serial:t.serial,coord:t.coord})));let m=t.resn+" $"+t.structure+"."+t.chain+":"+t.resi+"@"+t.name;a.resid2Residhash[r][m]=p.toFixed(1);let u=e.structure+"_"+e.chain+"_"+e.resi+"_"+e.resn+","+t.structure+"_"+t.chain+"_"+t.resi+"_"+t.resn;return o||(void 0===a.resids2inter[u]&&(a.resids2inter[u]={}),void 0===a.resids2inter[u][i]&&(a.resids2inter[u][i]={}),a.resids2inter[u][i][r+","+m]=p.toFixed(1)),void 0===a.resids2interAll[u]&&(a.resids2interAll[u]={}),void 0===a.resids2interAll[u][i]&&(a.resids2interAll[u][i]={}),a.resids2interAll[u][i][r+","+m]=p.toFixed(1),!0}getRingNormal(e){if(this.icn3d.icn3dui,e.length<3)return;let t=e[0].clone().sub(e[1]),s=e[1].clone().sub(e[2]);return t.cross(s).normalize()}getAromaticRings(e,t,s){let i=this.icn3d;i.icn3dui;let n=[],l=[],r=[],o=[];if("nucleotide"==s){let s=new THREE.Vector3,a=new THREE.Vector3;if("A"==e.trim().toUpperCase()||"DA"==e.trim().toUpperCase()||"G"==e.trim().toUpperCase()||"DG"==e.trim().toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"N1"==t.name||"C2"==t.name||"N3"==t.name||"C6"==t.name?(s.add(t.coord),r.push(t.coord)):"C4"==t.name||"C5"==t.name?(s.add(t.coord),a.add(t.coord),r.push(t.coord),o.push(t.coord)):"N7"!=t.name&&"C8"!=t.name&&"N9"!=t.name||(a.add(t.coord),o.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r))),5==o.length&&(a.multiplyScalar(.2),n.push(a),l.push(this.getRingNormal(o)))}else if("C"==e.trim().toUpperCase()||"DC"==e.trim().toUpperCase()||"T"==e.trim().toUpperCase()||"DT"==e.trim().toUpperCase()||"U"==e.trim().toUpperCase()||"DU"==e.trim().toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"N1"==t.name||"C2"==t.name||"N3"==t.name||"C6"==t.name?(s.add(t.coord),r.push(t.coord)):"C4"!=t.name&&"C5"!=t.name||(s.add(t.coord),r.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r)))}}else if("protein"==s){let s=new THREE.Vector3,a=new THREE.Vector3;if("PHE"==e.toUpperCase()||"TYR"==e.toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"CG"!=t.name&&"CD1"!=t.name&&"CE1"!=t.name&&"CZ"!=t.name&&"CE2"!=t.name&&"CD2"!=t.name||(s.add(t.coord),r.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r)))}else if("HIS"==e.toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"CG"!=t.name&&"ND1"!=t.name&&"CE1"!=t.name&&"NE2"!=t.name&&"CD2"!=t.name||(s.add(t.coord),r.push(t.coord))}5==r.length&&(s.multiplyScalar(.2),n.push(s),l.push(this.getRingNormal(r)))}else if("TRP"==e.toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"CZ2"==t.name||"CH2"==t.name||"CZ3"==t.name||"CE3"==t.name?(s.add(t.coord),r.push(t.coord)):"CD2"==t.name||"CE2"==t.name?(s.add(t.coord),a.add(t.coord),r.push(t.coord),o.push(t.coord)):"CG"!=t.name&&"CD1"!=t.name&&"NE1"!=t.name||(a.add(t.coord),o.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r))),5==o.length&&(a.multiplyScalar(.2),n.push(a),l.push(this.getRingNormal(o)))}}return{piPosArray:n,normalArray:l}}dfs_cycle(e,t,s){let i=this.icn3d;if(i.icn3dui,2==i.ring_color[e])return s;if(1==i.ring_color[e]){s++;let n=t;for(i.ring_mark[n]=s;n!=e;)n=i.ring_par[n],i.ring_mark[n]=s;return s}if(i.ring_par[e]=t,i.ring_color[e]=1,void 0!==i.atoms[e])for(let t=0,n=i.atoms[e].bonds.length;t=3&&o<=6&&a[0]&&a[1]&&a[2]&&a[3]){let i=a[0].clone().sub(a[1]).normalize(),r=a[1].clone().sub(a[2]).normalize(),d=a[2].clone().sub(a[3]).normalize(),c=i.cross(r).normalize(),h=c.dot(d);if(Math.abs(h)<.052){l.multiplyScalar(1/o);let i=t.atoms[n];s[e+"_pi"+n]={resn:i.resn,name:"pi"+n,coord:l,serial:i.serial,structure:i.structure,chain:i.chain,resi:i.resi,normal:c}}}}return s}hideHalogenPi(){let e=this.icn3d;e.icn3dui,e.opts.halogen="no",e.opts["pi-cation"]="no",e.opts["pi-stacking"]="no",void 0===e.lines&&(e.lines={}),e.lines.halogen=[],e.lines["pi-cation"]=[],e.lines["pi-stacking"]=[],e.halogenpnts=[],e.picationpnts=[],e.pistackingpnts=[]}}class gt{constructor(e){this.icn3d=e}calculateIonicInteractions(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(0===Object.keys(e).length||0===Object.keys(t).length)return;r.resid2Residhash={};let a,d,c={},h={},p=s*s;for(let t in e){let s=e[t];if("ARG"===s.resn&&"NH2"===s.name||"GLU"===s.resn&&"OE2"===s.name||"ASP"===s.resn&&"OD2"===s.name)continue;let i=("LYS"===s.resn||"HIS"===s.resn)&&"N"===s.elem&&"N"!==s.name||"ARG"===s.resn&&("NH1"===s.name||"NH2"===s.name)||s.het&&-1!==o.parasCls.cationsTrimArray.indexOf(s.elem)||s.het&&"N"===s.elem&&1==s.bonds.length,n=this.isAnion(s);i=r.bOpm?i&&"DUM"!==s.resn:i,n=r.bOpm?n&&"DUM"!==s.resn:n,(i||n)&&(a=s.structure+"_"+s.chain+"_"+s.resi,d=a+"_"+s.name,i&&(c[d]=s),n&&(h[d]=s))}let m={},u={};for(let e in t){let i=t[e];if("ARG"===i.resn&&"NH2"===i.name||"GLU"===i.resn&&"OE2"===i.name||"ASP"===i.resn&&"OD2"===i.name)continue;let g=("LYS"===i.resn||"HIS"===i.resn)&&"N"===i.elem&&"N"!==i.name||"ARG"===i.resn&&("NH1"===i.name||"NH2"===i.name)||i.het&&-1!==o.parasCls.cationsTrimArray.indexOf(i.elem),f=this.isAnion(i);if(g=r.bOpm?g&&"DUM"!==i.resn:g,f=r.bOpm?f&&"DUM"!==i.resn:f,g||f){a=i.structure+"_"+i.chain+"_"+i.resi,d=a+"_"+i.name;let e=i.resn+" $"+i.structure+"."+i.chain+":"+i.resi+"@"+i.name;void 0===r.resid2Residhash[e]&&(r.resid2Residhash[e]={});let t={};g?t=h:f&&(t=c);let C,b=i.structure+"_"+i.chain+"_"+i.resi;g&&"ARG"===i.resn&&"NH1"===i.name?C=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[b],"NH2"):f&&"GLU"===i.resn&&"OE1"===i.name?C=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[b],"OE2"):f&&"ASP"===i.resn&&"OD1"===i.name&&(C=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[b],"OD2"));let y=void 0===C?i.coord:i.coord.clone().add(C.coord).multiplyScalar(.5);for(let d in t){if(a==d.substr(0,d.lastIndexOf("_")))continue;if(!r.crossstrucinter&&i.structure!=t[d].structure)continue;let c,h=t[d].structure+"_"+t[d].chain+"_"+t[d].resi;f&&"ARG"===t[d].resn&&"NH1"===t[d].name?c=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[h],"NH2"):g&&"GLU"===t[d].resn&&"OE1"===t[d].name?c=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[h],"OE2"):g&&"ASP"===t[d].resn&&"OD1"===t[d].name&&(c=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[h],"OD2"));let C=void 0===c?t[d].coord:t[d].coord.clone().add(c.coord).multiplyScalar(.5),b=Math.abs(y.x-C.x);if(b>s)continue;let v=Math.abs(y.y-C.y);if(v>s)continue;let _=Math.abs(y.z-C.z);if(_>s)continue;let w=b*b+v*v+_*_;if(w>p)continue;"graph"!==n&&(r.saltbridgepnts.push({serial:i.serial,coord:y}),r.saltbridgepnts.push({serial:t[d].serial,coord:C}));let S=t[d].structure+"_"+t[d].chain+"_"+t[d].resi;m=o.hashUtilsCls.unionHash(m,r.residues[a]),m=o.hashUtilsCls.unionHash(m,r.residues[S]),u[a]=1,u[S]=1;let A=t[d].resn+" $"+t[d].structure+"."+t[d].chain+":"+t[d].resi+"@"+t[d].name;r.resid2Residhash[e][A]=w.toFixed(1);let x=a+"_"+i.resn+","+S+"_"+t[d].resn;l||(void 0===r.resids2inter[x]&&(r.resids2inter[x]={}),void 0===r.resids2inter[x].ionic&&(r.resids2inter[x].ionic={}),r.resids2inter[x].ionic[e+","+A]=w.toFixed(1)),void 0===r.resids2interAll[x]&&(r.resids2interAll[x]={}),void 0===r.resids2interAll[x].ionic&&(r.resids2interAll[x].ionic={}),r.resids2interAll[x].ionic[e+","+A]=w.toFixed(1)}}}let g=Object.keys(u);if("graph"!==n)for(let e=0,t=g.length;e1?1/(n-1):1;for(let n in e){let e=t.atoms[n];e.color=e.het?s.parasCls.atomColors[e.elem]||s.parasCls.defaultAtomColor:s.parasCls.thr().setHSL(3/4*(1-i++*l),1,.45),t.atomPrevColors[n]=e.color}}colorRainbow(e){let t=this.icn3d,s=t.icn3dui,i=0,n=0;e=s.hashUtilsCls.intHash(e,t.hAtoms);for(let s in e){t.atoms[s].het||++n}let l=n>1?1/(n-1):1;for(let n in e){let e=t.atoms[n];e.color=e.het?s.parasCls.atomColors[e.elem]||s.parasCls.defaultAtomColor:s.parasCls.thr().setHSL(3/4*i++*l,1,.45),t.atomPrevColors[n]=e.color}}setColorAcrossSets(e,t){let s=this.icn3d,i=s.icn3dui,n=0,l=e.length,r=l>1?1/(l-1):1;for(let l=0,o=e.length;l0)this.setMmdbChainColor();else{let e=-1,s="",l=n.parasCls.stdChainColors.length;for(let r in t){let t=i.atoms[r];t.chain!=s&&(++e,e%=l),t.het?(t.color=n.parasCls.atomColors[t.elem],i.atomPrevColors[r]=t.color):(t.color=n.parasCls.stdChainColors[e],Object.keys(i.chainsColor).length>0&&this.updateChainsColor(t),i.atomPrevColors[r]=t.color),s=t.chain}}break;case"domain":s=0,l=0;let m=Object.keys(i.tddomains);l=m.length,r=l>1?1/(l-1):1;for(let e=0,t=m.length;e1?1/(l-1):1;for(let e=0;e Defined Sets", and try it again.');break;case"secondary structure green":case"secondary structure":i.sheetcolor="green";for(let e in t){let t=i.atoms[e];t.color=t.het?n.parasCls.atomColors[t.elem]||n.parasCls.defaultAtomColor:n.parasCls.ssColors[t.ss]||n.parasCls.thr(16711935),i.atomPrevColors[e]=t.color}break;case"secondary structure yellow":i.sheetcolor="yellow";for(let e in t){let t=i.atoms[e];t.color=t.het?n.parasCls.atomColors[t.elem]||n.parasCls.defaultAtomColor:n.parasCls.ssColors2[t.ss]||n.parasCls.thr(16711935),i.atomPrevColors[e]=t.color}break;case"secondary structure spectrum":s=0,l=0;let u,g,f=[],C=-9999;for(let e in t){if(!i.proteins.hasOwnProperty(e))continue;let t=i.atoms[e];-9999==C&&(u=parseInt(e)),-9999!=C&&(t.ss!=g.ss||Math.abs(t.resi-g.resi)>1||t.ssbegin&&g.ssend)&&("coil"==g.ss||f.push([u,C]),u=e),C=parseInt(e),g=t}"coil"==g.ss||f.push([u,C]),l=f.length,r=l>1?1/(l-1):1;for(let e=0,t=f.length;e100&&(e=100);let r=(i.middB-e)*i.spanBinv1,o=(e-i.middB)*i.spanBinv2;e=90?t.color=n.parasCls.thr().setRGB(0,.325,.839):e>=70&&e<90?t.color=n.parasCls.thr().setRGB(.396,.572,.953):e>=50&&e<70?t.color=n.parasCls.thr().setRGB(1,.859,.075):e<50&&(t.color=n.parasCls.thr().setRGB(1,.49,.271))}i.atomPrevColors[e]=t.color}break;case"b factor":i.middB=50,i.spanBinv1=.02,i.spanBinv2=.02;for(let e in t){let t=i.atoms[e];if(void 0===t.b||isNaN(t.b)||0==parseInt(1e3*t.b))t.color=n.parasCls.thr().setRGB(0,1,0);else{let e=t.b;e>100&&(e=100),e=t.structure.substr(0,4)!=i.defaultPdbId&&t.structure.length>5?100-e:e;let s=(i.middB-e)*i.spanBinv1,l=(e-i.middB)*i.spanBinv2;t.color=et.b&&(o=t.b),a5?100-t.b:t.b,s=i.bfactorArray.indexOf(e)/b;t.color=s<.5?n.parasCls.thr().setRGB(2*s,2*s,1):n.parasCls.thr().setRGB(1,2*(1-s),2*(1-s))}i.atomPrevColors[e]=t.color}break;case"area":if(void 0===i.resid2area){let e=n.hashUtilsCls.cloneHash(i.hAtoms);i.hAtoms=n.hashUtilsCls.cloneHash(i.atoms),i.bCalcArea=!0,i.opts.surface="solvent accessible surface",i.applyMapCls.applySurfaceOptions(),i.bCalcArea=!1,i.hAtoms=n.hashUtilsCls.cloneHash(e)}let y=void 0!==i.midpercent?i.midpercent:35;i.spanBinv1=.02,i.spanBinv2=.02;for(let e in t){let t=i.atoms[e],s=t.structure+"_"+t.chain+"_"+t.resi+"_"+t.resn,l=n.parasCls.residueArea.hasOwnProperty(t.resn)?i.resid2area[s]/n.parasCls.residueArea[t.resn]*100:y;l>100&&(l=100);let r=(y-l)*i.spanBinv1,o=(l-y)*i.spanBinv2;t.color=l

    ";if("atom"==e){let e=["proteins","nucleotides","chemicals","ions","water"];for(let i=0,l=e.length;i[e,s.parasCls.hydrophobicValues[e]]));l.sort(((e,t)=>parseFloat(e[1])-parseFloat(t[1])));var r=l.map((e=>[e[0],Object.keys(o[e[0]])[0]]));n+="
    ","normalized hydrophobic"==e?(n+="Dark green (W, F, L, I, Y, M, V, C): Hydrophobic
    ",n+="Light green (P, T, S, A, Q, N, G): Polar
    ",n+="Grey: Charged, not hydrophobic

    "):(n+="Green (W, F, L, I, Y, M, V, C): Hydrophobic
    ",n+="Yellow (P, T, S, A, Q, N, G): Polar
    ",n+="Red: Negatively Charged
    ",n+="Blue: Positively Charged

    ");let a=0;for(let e of r)s.parasCls.residueAbbrev[e[0]]&&(n+="
    ",n+="
    ",n+=s.parasCls.residueAbbrev[e[0]]+"
    ",a%4==3&&(n+="
    "),++a);n+="
    "}else"b factor"==e?(n+="
    B factor quantitates the uncertainty for each atom. A high B factor reflects that the position is less certain.

    ",n+=s.htmlCls.clickMenuCls.setLegendHtml()):"confidence"==e?n+=s.htmlCls.clickMenuCls.setLegendHtml(!0):"exon"==e?(t.startColor="red",t.midColor="white",t.endColor="blue",t.startValue="Start",t.midValue="Middle",t.endValue="End",n+=s.htmlCls.clickMenuCls.setLegendHtml()):n="";n?($("#"+s.pre+"dl_legend_html").html(n),s.htmlCls.dialogCls.openDlg("dl_legend","Color Legend")):$("#"+s.pre+"dl_legend").hasClass("ui-dialog-content")&&$("#"+s.pre+"dl_legend").dialog("isOpen")&&$("#"+s.pre+"dl_legend").dialog("close")}getColorLegendForElem(e,t){let s=this.icn3d,i=s.icn3dui,n="",l={};for(let e in t){let t=s.atoms[e],i=void 0===t||void 0===t.color||"FFFFFF"===t.color.getHexString().toUpperCase()?"DDDDDD":t.color.getHexString();void 0===l[t.elem]&&(l[t.elem]={}),l[t.elem][i]=1}if(Object.keys(l).length>0){n+=""+e+"
    ";let t=Object.keys(l).sort();for(let e=0,s=t.length;e";for(let e in l[s])n+="
    ";n+=i.parasCls.atomnames[s.toUpperCase()]+"
    "}n+="
    "}return n}getRes2color(e,t){let s=this.icn3d,i=s.icn3dui,n={},l=s.firstAtomObjCls.getResiduesFromAtoms(e);for(let e in l){let l=s.residues[e],r=s.firstAtomObjCls.getFirstAtomObj(l),o=t?r.resn:i.parasCls.residueAbbrev[r.resn],a=void 0===r||void 0===r.color||"FFFFFF"===r.color.getHexString().toUpperCase()?"DDDDDD":r.color.getHexString();null!=o&&(void 0===n[o]&&(n[o]={}),n[o][a]=1)}return n}getColorLegendForResidue(e){this.icn3d.icn3dui;let t="",s=this.getRes2color(e);if(Object.keys(s).length>0){t+="
    ";let e=Object.keys(s).sort(),i="",n=0;for(let l=0,r=e.length;l";for(let e in s[o])r+="
    ";r+=o+"
    ",n%4==3&&(r+="
    "),-1!=o.indexOf("(")?(t+=r,++n):i+=r}i&&(t+="
    "+i),t+="
    "}return t}getColorLegendForCharge(e){let t=this.icn3d;t.icn3dui;let s="",i=t.firstAtomObjCls.getResiduesFromAtoms(e),n={};for(let e in i){let s=t.residues[e],i=t.firstAtomObjCls.getFirstAtomObj(s);"ARG"==i.resn||"LYS"==i.resn?n.Positive=1:"HIS"==i.resn?n["Partial-Positive"]=1:"ASP"==i.resn||"GLU"==i.resn||t.nucleotides[i.serial]?n.Negative=1:n.Neutral=1}const l={Positive:"0000ff","Partial-Positive":"8080ff",Negative:"ff0000",Neutral:"888888"};let r=["Positive","Partial-Positive","Negative","Neutral"];s+="
    ";for(let e=0,t=r.length;e",s+="
    ",s+=t,s+="
    ")}return s+="
    (Charges are at pH 7)",s+="
    ",s}getColorLegendForIgstrand(e){this.icn3d.icn3dui;let t="";const s={"A Strand":"9400D3","B Strand":"ba55d3","C Strand":"0000FF","C' Strand":"6495ED","C'' Strand":"006400","D Strand":"00FF00","E Strand":"FFD700","F Strand":"FF8C00","G Strand":"FF0000",Loop:"CCCCCC"};t+="
    ";for(let e in s){t+="",t+="
    ",t+=e,t+="
    "}return t+="
    ",t}getColorLegendForIgproto(e){this.icn3d.icn3dui;let t="";const s={"Protodomain 1":"","A Strand":"0000FF","B Strand":"006400","C Strand":"FFD700","C' Strand":"FF8C00","
    Linker":"","C'' Strand":"FF0000","
    Protodomain 2":"","D Strand":"0000FF","E Strand":"006400","F Strand":"FFD700","G Strand":"FF8C00","":"",Loop:"CCCCCC"};t+="
    A protodomain is a supersecondary structure
    that by its duplication, symmetry operations
    can generate a structural domain.

    ";for(let e in s){let i=s[e];t+="",i&&(t+="
    "),t+=e,t+="
    "}return t+="
    ",t}}class vt{constructor(e){this.icn3d=e}async showCddSiteAll(){let e=this.icn3d,t=e.icn3dui,s=this;e.chainid2pssmid={};let i=$.map(e.protein_chainid,(function(e){return e})),n=Object.keys(e.protein_chainid),l="https://www.ncbi.nlm.nih.gov/Structure/cdannots/cdannots.fcgi?fmt&frclive&live=lcl&queries="+i;if(1==Object.keys(e.structures).length&&!t.cfg.afid&&(t.cfg.mmtfid||t.cfg.pdbid||t.cfg.opmid||t.cfg.mmdbid||t.cfg.gi||t.cfg.uniprotid||t.cfg.blast_rep_id||t.cfg.cid||t.cfg.mmcifid)||2==Object.keys(e.structures).length&&t.cfg.align){let e={};try{t.bNode?e=await t.getAjaxPromise(l,"jsonp"):e.value=await t.getAjaxPromise(l,"jsonp"),s.parseCddData([e],n)}catch(e){return void s.getNoCdd(i)}}else{let i=[];for(let s=0,r=n.length;s',p=h,m=h,u=d.doms;n.bNode&&!i.resid2cdd[c]&&(i.resid2cdd[c]=[]);let g=l.setDomainFeature(u,c,"domain",h,p,m);i.chainid2pssmid[c]={pssmid2name:g.pssmid2name,pssmid2fromArray:g.pssmid2fromArray,pssmid2toArray:g.pssmid2toArray};let f=g.acc2domain;h=g.html+"",p=g.html2+"",m=g.html3+"",$("#"+i.pre+"dt_cdd_"+c).html(h),$("#"+i.pre+"ov_cdd_"+c).html(p),$("#"+i.pre+"tt_cdd_"+c).html(m),h='
    ',p=h,m=h;let C=d.motifs;n.bNode&&!i.resid2site[c]&&(i.resid2site[c]=[]),g=l.setDomainFeature(C,c,"feat",h,p,m,f),h=g.html,p=g.html2,m=g.html3;let b=a.data[e].sites,y=void 0!==b?b.length:0;for(let e=0;e17&&(s=s.substr(0,17)+"...");let l,r=b[e].title,o=[];for(let t=0,s=b[e].locs.length;t'+s+"
    ",u=''+t.toString()+" Res",g='';m+=d+u+"
    ",h+=d+u+g,p+=d+u+g;let f="site"+e.toString(),C=0,y=0,v=1;i.seqStartLen&&i.seqStartLen[c]&&(p+=i.showSeqCls.insertMulGapOverview(c,i.seqStartLen[c])),i.seqStartLen&&i.seqStartLen[c]&&(h+=i.showSeqCls.insertMulGap(i.seqStartLen[c],"-"));for(let t=0,s=i.giSeq[c].length;t1&&(l=s[0]+"..");let r=i.ParserUtilsCls.getResi(c,t);if(h+=''+s+"",n.bNode){let t={};t[c+"_"+r]="site: "+b[e].title,i.resid2site[c].push(t)}p+=i.showSeqCls.insertGapOverview(c,t);let o=n.cfg.blast_rep_id==c?Math.round(i.seqAnnWidth*t/(i.maxAnnoLength+i.nTotalGap)-C-y):Math.round(i.seqAnnWidth*t/i.maxAnnoLength-C-y);o>=0&&(p+='
     
    ',p+='
     
    ',C+=o,y+=v)}else h+="-";i.seqStartLen&&i.seqStartLen[c]&&(h+=i.showSeqCls.insertMulGap(i.seqEndLen[c],"-")),g=' '+t.toString()+" Residues",g+="    ",g+="
    ",h+=g,p+=g}h+="",p+="",m+="",$("#"+i.pre+"dt_site_"+c).html(h),$("#"+i.pre+"ov_site_"+c).html(p),$("#"+i.pre+"tt_site_"+c).html(m)}}for(let e in i.protein_chainid)r.hasOwnProperty(e)||($("#"+i.pre+"dt_cdd_"+e).html(""),$("#"+i.pre+"ov_cdd_"+e).html(""),$("#"+i.pre+"tt_cdd_"+e).html(""),$("#"+i.pre+"dt_site_"+e).html(""),$("#"+i.pre+"ov_site_"+e).html(""),$("#"+i.pre+"tt_site_"+e).html(""));i.showAnnoCls.enableHlSeq(),i.bAjaxCddSite=!0}getNoCdd(e){let t=this.icn3d;t.icn3dui,console.log("No CDD data were found for the protein "+e+"...");for(let e in t.protein_chainid)$("#"+t.pre+"dt_cdd_"+e).html(""),$("#"+t.pre+"ov_cdd_"+e).html(""),$("#"+t.pre+"tt_cdd_"+e).html(""),$("#"+t.pre+"dt_site_"+e).html(""),$("#"+t.pre+"ov_site_"+e).html(""),$("#"+t.pre+"tt_site_"+e).html("");t.showAnnoCls.enableHlSeq(),t.bAjaxCddSite=!0}setDomainFeature(e,t,s,i,n,l,r,o,a){let d,c,h,p=this.icn3d,m=p.icn3dui,u="domain"!=s&&"feat"!=s;"domain"==s&&(r={},d={},c={},h={}),void 0===e&&(e=[]);let g=e.length,f="domain"==s?14:19,C="domain"==s?100:120;e.sort((function(e,t){let i=e.locs,n="domain"==s||"ig"==s?i[0].segs:[i[0]],l=Math.round(n[0].from);return i=t.locs,n="domain"==s||"ig"==s?i[0].segs:[i[0]],l-Math.round(n[0].from)}));for(let b=0;bf&&(w=w.substr(0,f)+"...");let S=u?a[b]:s+": "+v;"domain"==s&&(d[g]=v);let A=e[b].locs;if(A)for(let e=0,r=A.length;e'+w+" ",I=''+u.toString()+" Res";l+=R+I+"
    ";let E='';i+=R+I+E,"domain"==s&&(n+='
    '),n+='
    '+w+"
    ",n+=I+E;let T=s+b.toString();p.seqStartLen&&p.seqStartLen[t]&&(i+=p.showSeqCls.insertMulGap(p.seqStartLen[t],"-"));for(let e=0,n=p.giSeq[t].length;e1&&(l=n[0]+"..");let r=p.ParserUtilsCls.getResi(t,e);if(i+=''+n+"",m.bNode){let e={};e[t+"_"+r]=S,"domain"==s?p.resid2cdd[t].push(e):p.resid2site[t].push(e)}}else i+="-";if(p.seqStartLen&&p.seqStartLen[t]&&(i+=p.showSeqCls.insertMulGap(p.seqEndLen[t],"-")),p.seqStartLen&&p.seqStartLen[t]&&(n+=p.showSeqCls.insertMulGapOverview(t,p.seqStartLen[t])),m.cfg.blast_rep_id!=t){let i;for(let l=0,d=r.length;l ',n+='
    '+v+"
    "}}else{let i=[],l=[];for(let e=0,t=r.length;e ',n+='
    '+v+"
    "}}E=' '+u.toString()+" Residues",E+="    ",E+="
    ",i+=E,n+=E,"domain"==s&&(n+='')}}return{html:i,html2:n,html3:l,acc2domain:r,pssmid2name:d,pssmid2fromArray:c,pssmid2toArray:h}}getColorFromPos(e,t,s){let i,n=this.icn3d;n.icn3dui;let l=e+"_"+n.ParserUtilsCls.getResi(e,t),r=n.firstAtomObjCls.getFirstAtomObj(n.residues[l]),o=r&&void 0!==r.color&&"FFFFFF"!==r.color.getHexString()?r.color.getHexString():"DDDDDD";return i=r&&void 0!==r.color?o:"CCCCCC",i}showAnnoType(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui,a='
    ',d=a,c=a;if(0==n.length)return $("#"+r.pre+"dt_"+s+"_"+e).html(""),$("#"+r.pre+"ov_"+s+"_"+e).html(""),void $("#"+r.pre+"tt_"+s+"_"+e).html("");let h=i;i.length>17&&(i=i.substr(0,17)+"...");let p=[];for(let e=0,t=n.length;e'+i+"
    ",f=''+m.toString()+" Res";c+=g+f+"
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    ',d+='
     
    ',y+=u,v+=1)}else a+="-"}r.seqStartLen&&r.seqStartLen[e]&&(a+=r.showSeqCls.insertMulGap(r.seqEndLen[e],"-")),C=' '+m.toString()+" Residues",C+="",C+="
    ",a+=C,d+=C,a+="",d+="",c+="",$("#"+r.pre+"dt_"+s+"_"+e).html(a),$("#"+r.pre+"ov_"+s+"_"+e).html(d),$("#"+r.pre+"tt_"+s+"_"+e).html(c)}setToolTip(){let e=this.icn3d;e.icn3dui,$("[id^="+e.pre+"snp]").add("[id^="+e.pre+"clinvar]").add("[id^="+e.pre+"ssbond]").add("[id^="+e.pre+"crosslink]").tooltip({content:function(){return $(this).prop("title")},show:null,close:function(e,t){t.tooltip.hover((function(){$(this).stop(!0).fadeTo(400,1)}),(function(){$(this).fadeOut("400",(function(){$(this).remove()}))}))}})}}class _t{constructor(e){this.icn3d=e}showInteraction(e,t){this.icn3d.icn3dui,this.showInteraction_base(e,t)}showInteraction_base(e,t){let s=this.icn3d,i=s.icn3dui;i.bNode&&(s.resid2contact||(s.resid2contact={}),s.resid2contact[e]||(s.resid2contact[e]=[])),void 0===s.chainname2residues&&(s.chainname2residues={});let n=Object.keys(s.chains),l=e,r=Math.round(l.indexOf("_"));if(s.firstAtomObjCls.getFirstCalphaAtomObj(s.chains[l]),void 0===s.chainname2residues[l]){s.chainname2residues[l]={};let t=n.length;if(t>100&&void 0===i.cfg.mmdbid&&void 0===i.cfg.gi&&void 0===i.cfg.blast_rep_id&&void 0===i.cfg.align&&void 0===i.cfg.chainalign)return $("#"+s.pre+"dt_interaction_"+e).html(""),void $("#"+s.pre+"ov_interaction_"+e).html("");for(let e=0;e4)continue;let o,a=s.firstAtomObjCls.getFirstCalphaAtomObj(s.chains[t]);s.chemicals.hasOwnProperty(a.serial)?o="chemical":s.nucleotides.hasOwnProperty(a.serial)?o="nucleotide":s.ions.hasOwnProperty(a.serial)?o="ion":s.proteins.hasOwnProperty(a.serial)?o="protein":s.water.hasOwnProperty(a.serial)&&(o="water");let d=s.contactCls.getAtomsWithinAtom(i.hashUtilsCls.hash2Atoms(s.chains[l],s.atoms),i.hashUtilsCls.hash2Atoms(s.chains[t],s.atoms),4);if(0==Object.keys(d).length)continue;let c={};for(let e in d){let t=s.atoms[e];c[t.structure+"_"+t.chain+"_"+t.resi]=1}let h=t.substr(t.indexOf("_")+1)+"("+o+")";s.chainname2residues[l][h]=Object.keys(c)}}let o='
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    ',b+=h,y+=v)}else o+="-"}s.seqStartLen&&s.seqStartLen[e]&&(o+=s.showSeqCls.insertMulGap(s.seqEndLen[e],"-")),f=' '+p.toString()+" Residues",f+="    ",f+="
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    ",o+=b,a+=b}o+="",a+="",d+="",$("#"+l.pre+"dt_domain_"+e).html(o),$("#"+l.pre+"ov_domain_"+e).html(a),$("#"+l.pre+"tt_domain_"+e).html(d)}}class kt{constructor(e){this.icn3d=e}async showSnp(e,t){this.icn3d.icn3dui,await this.showSnpClinvar(e,t,!0)}async showClinvar(e,t){this.icn3d.icn3dui,await this.showSnpClinvar(e,t,!1)}async showSnpClinvar(e,t,s){let i=this.icn3d.icn3dui,n=this,l=i.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?chainid="+t;try{let r=await i.getAjaxPromise(l,"jsonp"),o=r.snpgi,a=r.gi;if(s)await n.showSnpPart2(e,t,o);else{let s=o;[6137708,1942289,224510717,2624886,253723219,2554905,75765331,3660278,312207882,319443632,342350956,1827805,109157826,1065265,40889086,6730307,163931185,494469,163931091,60594093,55669745,18655489,17942684,6980537,166235465,6435586,4139398,4389047,364506122,78101667,262118402,20664221,2624640,158430173,494395,28948777,34810587,13399647,3660342,261278854,342350965,384482350,378792570,15988303,213424334,4558333,2098365,10835631,3318817,374074330,332639529,122919696,4389286,319443573,2781341,67464020,194709238,210061039,364506106,28949044,40889076,161172338,17943181,4557976,62738484,365813173,6137343,350610552,17942703,576308,223674070,15826518,1310997,93279697,4139395,255311799,157837067,361132363,357380836,146387678,383280379,1127268,299856826,13786789,1311054,46015217,3402130,381353319,30750059,218766885,340707375,27065817,355333104,2624634,62738384,241913553,304446010].includes(a)&&(s=a),await n.showClinvarPart2(e,t,s)}}catch(t){return void(s?n.processNoSnp(e):n.processNoClinvar(e))}}navClinVar(e){let t=this.icn3d;t.icn3dui;let s=this;t.currClin[e]=-1,$(document).on("click","#"+t.pre+e+"_prevclin",(function(t){let i=s.icn3d;t.stopImmediatePropagation();let n=void 0!==i.resi2disease_nonempty[e]?Object.keys(i.resi2disease_nonempty[e]).length:0;--i.currClin[e],i.currClin[e]<0&&(i.currClin[e]=n-1),s.showClinVarLabelOn3D(e)})),$(document).on("click","#"+t.pre+e+"_nextclin",(function(t){let i=s.icn3d;t.stopImmediatePropagation();let n=void 0!==i.resi2disease_nonempty[e]?Object.keys(i.resi2disease_nonempty[e]).length:0;++i.currClin[e],i.currClin[e]>n-1&&(i.currClin[e]=0),s.showClinVarLabelOn3D(e)}))}showClinVarLabelOn3D(e){let t,s,i=this.icn3d,n=i.icn3dui,l=Object.keys(i.resi2disease_nonempty[e]);t=e,s=t+"_"+(parseInt(l[i.currClin[e]])+i.baseResi[e]).toString();let r="",o=i.resi2disease_nonempty[e][l[i.currClin[e]]];for(let e=0,t=o.length;e0?o[0]:"N/A");let a=i.applyCenterCls.centerAtoms(n.hashUtilsCls.hash2Atoms(i.residues[s],i.atoms));r.length>30&&(r=r.substr(0,30)+"..."),i.selectionCls.removeSelection(),null==i.labels&&(i.labels={}),i.labels.clinvar=[];let d=i.LABELSIZE,c="black"!=i.opts.background?i.colorWhitebkgd:i.colorBlackbkgd;i.analysisCls.addLabel(r,a.center.x+1,a.center.y+1,a.center.z+1,d,c,void 0,"clinvar"),i.hAtoms={};for(let e in i.residues[s])i.hAtoms[e]=1;$("#clinvar_"+i.pre+s).addClass("icn3d-highlightSeq"),void 0===$("#"+i.pre+"modeswitch")[0]||$("#"+i.pre+"modeswitch")[0].checked||i.definedSetsCls.setMode("selection"),i.drawCls.draw()}getSnpLine(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u,g){let f=this.icn3d,C=f.icn3dui,b="",y=m?"clinvar":"snp",v=!1;for(let e in i){for(let t=0,s=i[e].length;t(from human)",i=" (based on human sequences and mapped to this structure by sequence similarity)"),b+=m?'
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    '+t+s+"
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l.processNoClinvar(e)}}async showSnpPart2(e,t,s){let i=this.icn3d,n=i.icn3dui,l=this;if(void 0!==s){let s=n.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?chainid_snp="+t;i.chainsGene[e]&&i.chainsGene[e].geneSymbol&&(s+="&gene="+i.chainsGene[e].geneSymbol);try{let i=await n.getAjaxPromise(s,"jsonp");if(i&&i.data&&i.data.length>0){let s=!0,n=!0;l.processSnpClinvar(i,e,t,s,n)}else l.processNoSnp(e)}catch(t){return void l.processNoSnp(e)}}else this.processNoSnp(e),console.log("No gi was found for the chain "+t+"...")}processNoClinvar(e){let t=this.icn3d;t.icn3dui,console.log("No ClinVar data were found for the protein "+e+"..."),$("#"+t.pre+"dt_clinvar_"+e).html(""),$("#"+t.pre+"ov_clinvar_"+e).html(""),t.showAnnoCls.enableHlSeq(),t.bAjaxClinvar=!0}processNoSnp(e){let t=this.icn3d;t.icn3dui,console.log("No SNP data were found for the protein "+e+"..."),$("#"+t.pre+"dt_snp_"+e).html(""),$("#"+t.pre+"ov_snp_"+e).html(""),t.showAnnoCls.enableHlSeq(),t.bAjaxSnp=!0}}class Ot{constructor(e){this.icn3d=e}showSsbond(e,t){let s=this.icn3d;s.icn3dui;let i=this;void 0===s.ssbondpnts?setTimeout((function(){i.showSsbond_base(e,t)}),1e3):this.showSsbond_base(e,t)}showSsbond_base(e,t){let s=this.icn3d;s.icn3dui.bNode&&(s.resid2ssbond||(s.resid2ssbond={}),s.resid2ssbond[e]||(s.resid2ssbond[e]=[]));let i=t,n={},l=i.substr(0,i.indexOf("_")),r=s.ssbondpnts[l];if(void 0===r)return $("#"+s.pre+"dt_ssbond_"+e).html(""),$("#"+s.pre+"ov_ssbond_"+e).html(""),void $("#"+s.pre+"tt_ssbond_"+e).html("");for(let e=0,t=r.length;e-s.halfBilayerSize){i[t.structure+"_"+t.chain+"_"+t.resi]=1}}let n=Object.keys(i);s.annoCddSiteCls.showAnnoType(e,t,"transmem","Transmembrane",n)}}class It{constructor(e){this.icn3d=e,this.init3ddomain()}init3ddomain(){this.icn3d.icn3dui,this.dcut=8,this.min_contacts=2,this.MAX_SSE=512,this.ctc_cnt=[];for(let e=0;e=this.curr_ratio+.01||f>this.split_ratio)return 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s=this.icn3d,i=s.icn3dui;$("#"+s.pre+"dl_definedsets").hasClass("ui-dialog-content")&&$("#"+s.pre+"dl_definedsets").dialog("isOpen")||(i.htmlCls.dialogCls.openDlg("dl_definedsets","Select sets"),$("#"+s.pre+"atomsCustom").resizable());let n={},l=!1,r=!0;if(s.hAtoms={},"igdomain"==t){let t=s.chain2igArray[e];if(t&&t.length>0)for(let 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t,s,i="",n=!1,l=-1;for(t=0,s=(e=e.replace(/undefined/g," ")).length;t20)return!1;if(void 0!==o.giSeq&&void 0!==o.giSeq[e]){let r=this.getFullText(s);return s=r.text,this.showNewTrack(e,t,s,void 0,void 0,i,n,l),!1}setTimeout((function(){a.checkGiSeq(e,t,s,i,n,l,r+1)}),100)}getFullText(e){this.icn3d.icn3dui;let t="",s=[],i=[],n=e.split(","),l=-1;for(let e=0,r=n.length;ep?t+=c.substr(0,p):t+=c;for(let e=0;ed&&(d=t.length,c=h),++h}o=n.htmlCls.baseUrl+"pwaln/pwaln.fcgi?from=msa";let p=e.split(","),m={};m[t]=0;for(let e=0,t=p.length;e0&&(g+=","+p.join(","));let f={targets:u,queries:g},C=await n.getAjaxPostPromise(o,f);if(!C.data)return void console.log("The protein accessions "+u+","+g+" can not be aligned...");let b=[];i.qt_start_end={};let y=[],v=[],_=Object.keys(C.targets)[0],w=C.targets[_].seqdata;p.splice(0,0,t);for(let e=0,s=p.length;eA&&(A=e)}let x=S,k=w.length-(A+1),O=[],R=[];for(let e=0,t=p.length;ea&&(a=t.length,d=c),++c}s.qt_start_end={};let m="genomeRes",u={};for(let e=0,i=h.length;ef&&(f=e)}for(let e=0,t=h.length;e0&&(d=h,o.targetGapHash[a+o.startposGiSeq]={from:a+o.startposGiSeq,to:d+m-1+o.startposGiSeq}),c=t[s],h=p,"-"!=t[s]?(++p,f=s,o.seqEndLen[e]=C-1-f,u||(g=s,o.seqStartLen[e]=g,u=!0)):++m;o.maxAnnoLength0&&(b+=" "),b+=e+"_"+o.targetGapHash[e].from+"_"+o.targetGapHash[e].to,++y;let v={};for(let a=0,d=i.length;a5?(l.uniprot2acc&&l.uniprot2acc[y]&&(y=l.uniprot2acc[y]),f=y):f=e,y.length>5){let e="";for(let t=0,s=l.chainsSeq.length;t"),d=a[1].indexOf("\n");n=a[1].substr(d+1).replace(/\n/g,"");for(let e=2,t=a.length;e0&&($("#"+e.pre+"anno_cdd")[0].checked?(this.setAnnoTabCdd(),t.htmlCls.clickMenuCls.setLogCmd("set annotation cdd",!0)):(this.hideAnnoTabCdd(),t.htmlCls.clickMenuCls.setLogCmd("hide annotation cdd",!0)))}showAnnoSelectedChains(){let e=this.icn3d,t=e.icn3dui,s={};for(let t in e.hAtoms){let i=e.atoms[t];s[i.structure+"_"+i.chain]=1}$("#"+e.pre+"dl_annotations > .icn3d-annotation").hide();for(let i in s){$("#"+e.pre+"anno_"+i).length&&$("#"+e.pre+"anno_"+i).show();let s=e.firstAtomObjCls.getFirstCalphaAtomObj(e.chains[i]);if(void 0!==s.resn){let i=t.utilsCls.residueName2Abbr(s.resn.substr(0,3));$("#"+e.pre+"anno_"+i).show()}}}showAnnoAllChains(){let e=this.icn3d;e.icn3dui,$("#"+e.pre+"dl_annotations > .icn3d-annotation").show()}setAnnoView(e){let t=this.icn3d;t.icn3dui.bNode||("detailed view"===e?(t.view="detailed view",$("#"+t.pre+"dl_anno_view_tabs").tabs("option","active",1)):(t.view="overview",$("#"+t.pre+"dl_anno_view_tabs").tabs("option","active",0)))}setAnnoDisplay(e,t){let s=this.icn3d;s.icn3dui;let i=["giseq","custom","site","ptm","snp","clinvar","cdd","domain","interaction","ssbond","crosslink","transmem","ig"];for(let n in i){let l=i[n];$("[id^="+s.pre+t+"_"+l+"]").attr("style",e)}}showFixedTitle(){this.icn3d.icn3dui;this.setAnnoDisplay("display:block;","tt")}hideFixedTitle(){this.icn3d.icn3dui;this.setAnnoDisplay("display:none!important;","tt")}setAnnoViewAndDisplay(e){let t=this.icn3d;if(t.icn3dui,"detailed view"===e){this.setAnnoView("detailed view");let e="display:block;";this.setAnnoDisplay(e,"dt"),$("#"+t.pre+"seqguide_wrapper").attr("style",e),e="display:none;",this.setAnnoDisplay(e,"ov")}else{this.setAnnoView("overview"),this.hideFixedTitle();let e="display:none;";this.setAnnoDisplay(e,"dt"),$("#"+t.pre+"seqguide_wrapper").attr("style",e),e="display:block;",this.setAnnoDisplay(e,"ov")}}async updateClinvar(){let e=this.icn3d;if(e.icn3dui,void 0===e.bClinvarShown||!e.bClinvarShown)for(let t in e.protein_chainid){let s=e.protein_chainid[t];await e.annoSnpClinVarCls.showClinvar(t,s)}e.bClinvarShown=!0}async updateSnp(){let e=this.icn3d;if(e.icn3dui,void 0===e.bSnpShown||!e.bSnpShown)for(let t in e.protein_chainid){let s=e.protein_chainid[t];await e.annoSnpClinVarCls.showSnp(t,s)}e.bSnpShown=!0}updateDomain(){let e=this.icn3d;e.icn3dui,void 0!==e.bDomainShown&&e.bDomainShown||e.annoDomainCls.showDomainAll(),e.bDomainShown=!0}updateInteraction(){let e=this.icn3d;if(e.icn3dui,void 0===e.bInteractionShown||!e.bInteractionShown)for(let t in e.interactChainbase){let s=e.interactChainbase[t];e.annoContactCls.showInteraction(t,s)}e.bInteractionShown=!0}async updatePTM(){let e=this.icn3d;if(e.icn3dui,void 0===e.bPTMShown||!e.bPTMShown)for(let t in e.PTMChainbase){let s=e.PTMChainbase[t];await e.annoPTMCls.showPTM(t,s,"ptm")}e.bPTMShown=!0}updateSsbond(){let e=this.icn3d;if(e.icn3dui,void 0===e.bSSbondShown||!e.bSSbondShown)for(let t in e.ssbondChainbase){let s=e.ssbondChainbase[t];e.annoSsbondCls.showSsbond(t,s)}e.bSSbondShown=!0}updateCrosslink(){let e=this.icn3d;if(e.icn3dui,void 0===e.bCrosslinkShown||!e.bCrosslinkShown)for(let t in e.crosslinkChainbase){let s=e.crosslinkChainbase[t];e.annoCrossLinkCls.showCrosslink(t,s)}e.bCrosslinkShown=!0}async updateTransmem(){let e=this.icn3d,t=e.icn3dui;if(void 0===e.bTranememShown||!e.bTranememShown)for(let s in e.protein_chainid){let i=e.protein_chainid[s];if(void 0!==t.cfg.opmid)e.annoTransMemCls.showTransmem(s,i);else if(e.bAfMem&&e.afmem_start_end){let t=e.afmem_start_end[0],n=e.afmem_start_end[1];await e.annoPTMCls.showPTM(s,i,"afmem",t,n)}else await e.annoPTMCls.showPTM(s,i,"transmem")}e.bTranememShown=!0}async updateIg(e,t){let s=this.icn3d,i=s.icn3dui;if(s.opts.color="ig strand",!e){s.hAtoms={};for(let e in s.protein_chainid)s.hAtoms=i.hashUtilsCls.unionHash(s.hAtoms,s.chains[e])}let n=s.firstAtomObjCls.getResiduesFromAtoms(s.hAtoms);for(let e in n)s.resid2refnum&&delete s.resid2refnum[e],s.residIgLoop&&delete s.residIgLoop[e],s.resid2domainid&&delete s.resid2domainid[e];s.bRunRefnumAgain=!0;let l=e?s.firstAtomObjCls.getChainsFromAtoms(s.hAtoms):s.protein_chainid;for(let e in l)await s.annoIgCls.showIg(e,t),s.bRunRefnumAgain=!1;s.bShowRefnum&&(s.hlUpdateCls.updateHlAll(),s.drawCls.draw())}}class Dt{constructor(e){this.icn3d=e}showAnnotations_part1(e){let t=this.icn3d,s=t.icn3dui;if(s.htmlCls.dialogCls.openDlg("dl_selectannotations","Sequences and Annotations"),(void 0===t.bAssemblyNote||!t.bAssemblyNote)&&void 0!==t.asuCnt){let e="
    Assembly Tips: Only the asymmetric unit is shown in the sequence window.
    Click \"Assembly\" in the menu \"View\" to switch between asymmetric unit and biological assembly("+t.asuCnt+" asymmetric unit).
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    ":"",a=e.chainsGene[s]&&e.chainsGene[s].geneId&&e.chainsGene[s].geneDesc?"(Gene: "+e.chainsGene[s].geneSymbol+")":"",d=s.substr(0,s.indexOf("_")),c=d.length>5?''+s+"":s,h="
    "+o+"Annotations of "+c+": "+r+""+a+"   "+this.addButton(s,"icn3d-addtrack","Add Track","Add a custom track",60,i)+"   ";h+=this.addButton(s,"icn3d-customcolor","Custom Color/Tube","Use a custom file to define the colors or tubes in 3D structure",110,i)+"   ",h+=this.addButton(s,"icn3d-helixsets","Helix Sets",'Define sets for each helix in this chain and add them to the menu of "Defined Sets"',60,i)+" "+this.addButton(s,"icn3d-sheetsets","Sheet Sets",'Define sets for each sheet in this chain and add them to the menu of "Defined Sets"',60,i)+" "+this.addButton(s,"icn3d-coilsets","Coil Sets",'Define sets for each coil in this chain and add them to the menu of "Defined Sets"',60,i),h+="   "+this.addButton(s,"icn3d-iganchorsets","Ig Anchor Set",'Define the set for all Ig anchors in this chain and add them to the menu of "Defined Sets"',80,i)+" "+this.addButton(s,"icn3d-igstrandsets","Ig Strand Sets",'Define sets for each Ig strand in this chain and add them to the menu of "Defined Sets"',80,i)+" "+this.addButton(s,"icn3d-igloopsets","Ig Loop Sets",'Define sets for each Ig loop in this chain and add them to the menu of "Defined Sets"',80,i)+" "+this.addButton(s,"icn3d-igdomainsets","Ig Domain Sets",'Define sets for each Ig domain in this chain and add them to the menu of "Defined Sets"',80,i),$("#"+e.pre+"dl_annotations").append(h);let p=["giseq","cdd","clinvar","snp","site","ptm","ssbond","crosslink","transmem","domain","custom","interaction","ig"];for(let t in p){let i=p[t];$("#"+e.pre+"anno_"+s).append(this.getAnDiv(s,i))}$("#"+e.pre+"anno_"+s).append("

    "),++n}if(t.bNode||e.annoCddSiteCls.setToolTip(),void 0!==e.chainid_seq)await this.processSeqData(e.chainid_seq);else try{let n=[],l=[];for(let e=0,t=i.length;e=6?l.push(i[e]):n.push(i[e])}if(n.length>0){let s=t.htmlCls.baseUrl+"/vastdyn/vastdyn.cgi?chainlist="+n;e.chainid_seq=await t.getAjaxPromise(s,"jsonp")}else e.chainid_seq={};for(let t=0,s=l.length;t40&&(r=r.substr(0,40)+"...");let o="";0==i&&("protein"==s?o="Proteins:

    ":"nucleotide"==s?o="Nucleotides:

    ":"chemical"==s&&(o="Chemicals/Ions/Water:

    ")),$("#"+n.pre+"dl_annotations").append("
    "+o+""+e+": "+r+"
    "),$("#"+n.pre+"anno_"+e).append(this.getAnDiv(e,"giseq")),$("#"+n.pre+"anno_"+e).append(this.getAnDiv(e,"interaction")),$("#"+n.pre+"anno_"+e).append("

    "),n.giSeq[e]=[];for(let t=0;tChemicals/Ions/Water:

    ":"",o=t[0].lastIndexOf("_"),a=t[0].substr(0,o),d=void 0!==l.cfg.mmdbid&&void 0!==n.chainid2sid?n.chainid2sid[a]:void 0;i=void 0!==d?""+e+" ":""+e+"",$("#"+n.pre+"dl_annotations").append("
    "+r+i+"
    "),$("#"+n.pre+"anno_"+e).append("
    "),$("#"+n.pre+"anno_"+e).append("

    ");let c='
    ';c+='
    Chem. '+e+"
    ",c+='Count: '+t.length+"",c+='';let h=c,p=c;for(let s=0,i=t.length;s3&&(l=i.substr(0,3)),s'+l+""}let m=l.htmlCls.GREY8,u=Math.round(n.seqAnnWidth*t.length/n.maxAnnoLength);u<1&&(u=1),p+='
     
    ',c="",c+="
    ",c+="
    ",h+=c,p+=c,$("#"+n.pre+"dt_giseq_"+e).html(h),$("#"+n.pre+"ov_giseq_"+e).html(p)}async processSeqData(e){let t=this.icn3d,s=t.icn3dui;for(let i in t.protein_chainid){let n=t.protein_chainid[i];if(e.hasOwnProperty(n)){let s=e[n];t.giSeq[i]=s;let l="";for(let e=0;e<10&&e14?"Query: "+o.substr(0,6)+"...":isNaN(s.cfg.query_id)?"Query: "+o:"Query: gi "+o;let a="cannot be aligned";t.queryStart="",t.queryEnd="",t.bRender&&alert("The sequence can NOT be aligned to the structure"),t.showSeqCls.showSeq(i,n,void 0,e,l,a,r)}else if(s.cfg.blast_rep_id==i&&(void 0!==t.seqStructAlignData||void 0!==t.seqStructAlignDataSmithwm)){let e,l,r,o,a,d=s.cfg.oriQuery_id?s.cfg.oriQuery_id:s.cfg.query_id;if(e=d.length>14?"Query: "+d.substr(0,6)+"...":isNaN(s.cfg.query_id)?"Query: "+d:"Query: gi "+d,void 0!==t.seqStructAlignData){let e,s,i=t.seqStructAlignData;if(void 0!==i.data){e=i.data[0].query;let t=Object.keys(i.data[0].targets);s=i.data[0].targets[t[0]],s=void 0!==s&&s.hsps.length>0?s.hsps[0]:void 0}if(void 0!==e&&void 0!==s){l=s.scores.e_value.toPrecision(2),l>1e-200&&(l=parseFloat(l).toExponential()),s.scores.bit_score;let t=Object.keys(i.targets);r=i.targets[t[0]].seqdata,o=e.seqdata,a=s.segs}}else{let e=t.seqStructAlignDataSmithwm;l=e.score,r=e.target.replace(/-/g,""),o=e.query.replace(/-/g,""),a=[];let s=-1,i=-1,n=!1,d={};for(let t=0,l=e.target.length;t0)if(i.orifrom-ni.from-l)for(let t=n+1;t
    "+i+"
    "}addButton(e,t,s,i,n,l){return this.icn3d.icn3dui,"
    "}addSnpButton(e,t,s,i,n,l){let r=this.icn3d;return r.icn3dui,"
    "}conservativeReplacement(e,t){let s=this.icn3d.icn3dui,i=-1!==s.parasCls.b62ResArray.indexOf(e)?s.parasCls.b62ResArray.indexOf(e):s.parasCls.b62ResArray.length-1,n=-1!==s.parasCls.b62ResArray.indexOf(t)?s.parasCls.b62ResArray.indexOf(t):s.parasCls.b62ResArray.length-1;return s.parasCls.b62Matrix[i][n]>0}getColorhexFromBlosum62(e,t){let s=this.icn3d.icn3dui,i="333333";if(!e||!t)return i;e=e.toUpperCase(),t=t.toUpperCase();let n=-1!==s.parasCls.b62ResArray.indexOf(e)?s.parasCls.b62ResArray.indexOf(e):s.parasCls.b62ResArray.length-1,l=-1!==s.parasCls.b62ResArray.indexOf(t)?s.parasCls.b62ResArray.indexOf(t):s.parasCls.b62ResArray.length-1,r=s.parasCls.b62Matrix[n][l];if(void 0===r)return"333333";if(r>0){let e=221-parseInt(r/11*221),t=e<10?"0"+e.toString(16):e.toString(16);i="DD"+t+t}else{let e=221-parseInt(-1*r/4*221),t=e<10?"0"+e.toString(16):e.toString(16);i=t+t+"DD"}return i}}class Pt{constructor(e){this.icn3d=e}getSeq(e){let t,s=this.icn3d,i=s.icn3dui;if(void 0===i.cfg.mmdbid&&void 0===i.cfg.gi&&void 0===i.cfg.blast_rep_id&&void 0===i.cfg.align&&void 0===i.cfg.chainalign&&void 0===i.cfg.mmdbafid){t=[];for(let i=0;i10){m='
    ';let t=o.firstAtomObjCls.getFirstCalphaAtomObj(o.chains[e]);void 0===a.cfg.mmdbid&&void 0===a.cfg.gi&&void 0===a.cfg.blast_rep_id&&void 0===a.cfg.align&&void 0===a.cfg.chainalign&&void 0===a.cfg.mmdbafid||void 0===t.resi_ori||t.resi_ori==t.resi||-1!=e.indexOf("Misc")?m+='
    ':m+='
    NCBI Residue Numbers
    ',m+='',f+=m+"
    ",u+=m+'';let s=0,i=0,n="";o.seqStartLen&&o.seqStartLen[e]&&(u+=this.insertMulGap(o.seqStartLen[e]," "));for(let t=0,l=d.length;t",l%10==0&&(u+=l);let r=e+"_"+l,a=l%10!=0&&l%10!=1&&l%10!=9;if(o.residues.hasOwnProperty(r)){let e=o.firstAtomObjCls.getFirstCalphaAtomObj(o.residues[r]);"H"==o.secondaries[r]&&e.ssbegin?(++s,n='H'+s+"",a&&(u+=n,n="")):"E"==o.secondaries[r]&&e.ssbegin?(++i,"green"==o.sheetcolor?n='S'+i+"":"yellow"==o.sheetcolor&&(n='S'+i+""),a&&(u+=n,n="")):e.ssend&&(n=""),""!=n&&a&&(u+=n,n="")}u+=""}o.seqStartLen&&o.seqStartLen[e]&&(u+=this.insertMulGap(o.seqEndLen[e]," ")),u+='',u+="",u+="
    ",u+="
    ",f+=""}m='
    ',m+='
    ',m+='',f+=m+"
    ",u+=m+'',o.seqStartLen&&o.seqStartLen[e]&&(u+=this.insertMulGap(o.seqStartLen[e],"-"));for(let t=0,s=d.length;t':'',u+=" ";else if("E"==o.secondaries[s]){o.firstAtomObjCls.getFirstCalphaAtomObj(o.residues[s]).ssend?"green"==o.sheetcolor?u+='':"yellow"==o.sheetcolor&&(u+=''):"green"==o.sheetcolor?u+='':"yellow"==o.sheetcolor&&(u+=''),u+=" "}else"c"==o.secondaries[s]?u+=' ':"o"==o.secondaries[s]&&(u+=' ');else u+="-"}o.seqStartLen&&o.seqStartLen[e]&&(u+=this.insertMulGap(o.seqEndLen[e],"-")),u+='',u+="",u+="
    ",u+="
    ",u+="",f+="",m=a.cfg.blast_rep_id===e?'
    ':'
    ';let C="Protein",b="Protein";void 0!==s&&("nucleotide"==s?(C="Nucl.",b="Nucleotide"):"chemical"==s&&(C="Chem.",b="Chemical")),m+='
    '+C+" "+e+"
    ",m+=''+(o.baseResi[e]+1).toString()+"",f+=m+"
    ";let y='';u+=m+y,g+=m+y;let v,_=0;o.seqStartLen&&o.seqStartLen[e]&&(u+=this.insertMulGap(o.seqStartLen[e],"-"));for(let t=0,s=d.length;t1&&(i=s[0]+".."),v=o.ParserUtilsCls.getResi(e,t),o.residues.hasOwnProperty(e+"_"+v)){let n="333333";if(a.cfg.blast_rep_id==e&&void 0!==o.fullpos2ConsTargetpos&&void 0!==o.fullpos2ConsTargetpos[t+_])n=o.fullpos2ConsTargetpos[t+_].color;else{let t=o.firstAtomObjCls.getFirstCalphaAtomObj(o.residues[e+"_"+v]),s=void 0===t.color||"FFFFFF"===t.color.getHexString().toUpperCase()||"FFF"===t.color.getHexString().toUpperCase()?"DDDDDD":t.color.getHexString();n=void 0!==t.color?s:"CCCCCC"}u+=''+i+""}else i=i.toLowerCase(),u+=''+i+""}o.seqStartLen&&o.seqStartLen[e]&&(u+=this.insertMulGap(o.seqEndLen[e],"-")),a.cfg.blast_rep_id==e&&(o.opts.color=o.blastAcxn?"confidence":"conservation",o.setColorCls.setColorByOptions(o.opts,o.atoms));let w=o.firstAtomObjCls.getFirstCalphaAtomObj(o.chains[e]),S=w.color?w.color.getHexString():"CCCCCC",A=Math.round(o.seqAnnWidth*d.length/(o.maxAnnoLength+o.nTotalGap));if(A<1&&(A=1),o.seqStartLen&&o.seqStartLen[e]&&(g+=this.insertMulGapOverview(e,o.seqStartLen[e])),a.cfg.blast_rep_id!=e)g+='";else{let t=[],s=[];t.push(0);for(let e=0,i=d.length;e';for(let i=0,n=t.length;i'+e+"
    ";g+="
    "}if(m=''+v+"",m+="",m+="
    ",u+=m,g+=m,a.cfg.blast_rep_id==e){if(void 0!==r&&""!==r){m='
    '+n+"
    ",m+='',f+=m+"
    ";let t='';u+=m+t,g+=m+t;let s=0,i=0,l=1;o.queryStart;for(let t=0,n=r.length;t-";else if(" "==n)u+=" ";else{let r=o.fullpos2ConsTargetpos[t].pos;if(o.residues.hasOwnProperty(e+"_"+r)){let s=o.fullpos2ConsTargetpos[t].color;u+=''+n+""}else n=n.toLowerCase(),u+=''+n+"";g+=this.insertGapOverview(e,t);let a=Math.round(o.seqAnnWidth*t/(o.maxAnnoLength+o.nTotalGap)-s-i);a>=0&&(g+='
     
    ',g+='
     
    ',s+=a,i+=l)}}m='',m+="",m+="
    ",u+=m,g+=m}m='
    '+i+"
    ",m+=''+o.queryStart+"",f+=m+"
    ";let t='';u+=m+t,g+=m+t;let s=o.queryStart;for(let t=0,i=l.length;t-":(void 0===o.fullpos2ConsTargetpos||void 0===o.fullpos2ConsTargetpos[t]||o.residues.hasOwnProperty(e+"_"+o.fullpos2ConsTargetpos[t].pos)||(i=i.toLowerCase()),u+=''+i+"",++s)}let a=o.firstAtomObjCls.getFirstCalphaAtomObj(o.chains[e]),d=void 0===a.color||"FFFFFF"===a.color.getHexString()?"DDDDDD":a.color.getHexString(),c=void 0!==a.color?d:"CCCCCC",h=[],p=[],C="-";for(let e=0,t=l.length;e ',g+='
    '+i+"
    "}m=''+o.queryEnd+"",m+="",m+="
    ",u+=m,g+=m}if(u+="",g+="",f+="",d.length>10){let t=o.firstAtomObjCls.getFirstCalphaAtomObj(o.chains[e]);if((void 0!==a.cfg.mmdbid||void 0!==a.cfg.gi||void 0!==a.cfg.blast_rep_id||void 0!==a.cfg.align||void 0!==a.cfg.chainalign||void 0!==a.cfg.mmdbafid)&&void 0!==t.resi_ori&&t.resi_ori!=t.resi&&-1==e.indexOf("Misc")){m='
    ',m+='
    ',m+='
    PDB Residue Numbers
    ',m+='',f+=m+"
    ",u+=m+'',o.seqStartLen&&o.seqStartLen[e]&&(u+=this.insertMulGap(o.seqStartLen[e],"-"));for(let t=0,s=d.length;t",e%10==0&&(u+=e+" "),u+=""}else u+=""}o.seqStartLen&&o.seqStartLen[e]&&(u+=this.insertMulGap(o.seqEndLen[e],"-")),u+='',u+="",u+="
    ",u+="
    ",u+="
    ",f+=""}if(o.bShowCustomRefnum&&o.chainsMapping.hasOwnProperty(e)){let t=!0,s=o.annoIgCls.showRefNum(d,e,void 0,t);u+=s.html,f+=s.html3}}o.bShowRefnum&&o.hlUpdateCls.updateHlAll(),$("#"+o.pre+"dt_giseq_"+e).html(u),$("#"+o.pre+"ov_giseq_"+e).html(g),$("#"+o.pre+"tt_giseq_"+e).html(f)}insertGap(e,t,s,i){let n=this.icn3d;n.icn3dui;let l="";return void 0!==n.targetGapHash&&n.targetGapHash.hasOwnProperty(t)&&(l+=this.insertMulGap(n.targetGapHash[t].to-n.targetGapHash[t].from+1,s,i)),l}insertMulGap(e,t,s){this.icn3d.icn3dui;let i="";for(let n=0;n"+t+"";return i}insertGapOverview(e,t){let s=this.icn3d;s.icn3dui;let i="";return void 0!==s.targetGapHash&&s.targetGapHash.hasOwnProperty(t)&&(i+=this.insertMulGapOverview(e,s.targetGapHash[t].to-s.targetGapHash[t].from+1)),i}insertMulGapOverview(e,t){let s=this.icn3d;s.icn3dui;let i="",n=s.seqAnnWidth*t/(s.maxAnnoLength+s.nTotalGap);return n=parseInt(n),i+='
     
    ',i}setAlternativeSeq(e,t){let s=this.icn3d;s.icn3dui;let i=s.chainsSeq[e];s.giSeq[e]=[];for(let t=0,n=i.length;t1&&s.htmlCls.clickMenuCls.setLogCmd("select sets "+e,!0)}else{let o={};if(void 0!==$(e).attr("domain")||void 0!==$(e).attr("feat")||void 0!==$(e).attr("3ddomain")||void 0!==$(e).attr("custom")||void 0!==$(e).attr("ig")){t.hlUpdateCls.hlSummaryDomain3ddomain(e);let a,d,c,h=$(e).attr("from").split(","),p=$(e).attr("to").split(",");r.substr(0,r.indexOf("_"));for(let s=0,i=h.length;s1&&s.htmlCls.clickMenuCls.setLogCmd("select sets "+c,!0)}}else{t.bCtrl||t.bShift?(t.currSelectedSets.push(i),t.selectionCls.selectAChain(r,i,!0,!0)):(t.currSelectedSets=[i],t.selectionCls.selectAChain(r,i,t.bAlignSeq)),t.bAlignSeq?s.htmlCls.clickMenuCls.setLogCmd("select alignChain "+r,!0):s.htmlCls.clickMenuCls.setLogCmd("select chain "+r,!0);let e=t.currSelectedSets.join(" or ");t.currSelectedSets.length>1&&s.htmlCls.clickMenuCls.setLogCmd("select sets "+e,!0)}else t.hlObjectsCls.removeHlObjects(),t.hlUpdateCls.removeHl2D(),$("#"+t.pre+"atomsCustom").val("")}}selectResidues(e,t){let s=this.icn3d,i=s.icn3dui;if(!i.bNode&&(!1!==s.bSelectResidue||s.bShift||s.bCtrl||s.selectionCls.removeSelection(),void 0!==e&&""!==e)){e=e.substr(e.indexOf("_")+1),s.bSelectResidue=!0,$(t).toggleClass("icn3d-highlightSeq");let n=e.substr(e.indexOf("_")+1);if(s.residues.hasOwnProperty(n))if($(t).hasClass("icn3d-highlightSeq")){for(let e in s.residues[n])s.hAtoms[e]=1;if(s.selectedResidues[n]=1,s.bAnnotations&&void 0!==$(t).attr("disease")){let e=$(t).attr("disease"),l=s.applyCenterCls.centerAtoms(i.hashUtilsCls.hash2Atoms(s.residues[n],s.atoms)),r=15;e.length>r&&(e=e.substr(0,r)+"...");let o=s.LABELSIZE,a=i.htmlCls.GREYD;s.analysisCls.addLabel(e,l.center.x,l.center.y,l.center.z,o,a,void 0,"custom")}}else{for(let e in s.residues[n])delete s.hAtoms[e];delete s.selectedResidues[n],s.hlObjectsCls.removeHlObjects()}}}}class Ft{constructor(e){this.icn3d=e}update2DdgmContent(){let e=this.icn3d,t=e.icn3dui,s="";void 0!==t.cfg.mmdbid||void 0!==t.cfg.gi?(s+=e.diagram2dCls.draw2Ddgm(e.interactionData,e.inputid,void 0,!0),s+=e.diagram2dCls.set2DdgmNote(),$("#"+e.pre+"dl_2ddgm_html").html(s)):e.mmdbidArray&&(void 0!==t.cfg.align||void 0!==t.cfg.chainalign||e.bRealign)&&(s+=e.diagram2dCls.draw2Ddgm(e.interactionData1,e.mmdbidArray[0].toUpperCase(),0,!0),void 0!==e.mmdbid_q&&e.mmdbid_q===e.mmdbid_t?s+=e.diagram2dCls.draw2Ddgm(e.interactionData2,e.mmdbidArray[0].toUpperCase(),1,!0):s+=e.diagram2dCls.draw2Ddgm(e.interactionData2,e.mmdbidArray[1].toUpperCase(),1,!0),s+=e.diagram2dCls.set2DdgmNote(!0),$("#"+e.pre+"dl_2ddgm_html").html(s))}changeSeqColor(e){let t=this.icn3d,s=t.icn3dui;for(let i=0,n=e.length;i0&&($("#"+t.pre+"dl_2ddgm svg line").attr("stroke","#000000"),$("#"+t.pre+"dl_2ddgm line").attr("stroke-width",1)),e||($("#"+t.pre+"dl_linegraph circle").attr("stroke","#000000"),$("#"+t.pre+"dl_linegraph circle").attr("stroke-width",1),$("#"+t.pre+"dl_scatterplot rect").attr("stroke","#000000"),$("#"+t.pre+"dl_scatterplot circle").attr("stroke","#000000"),$("#"+t.pre+"dl_scatterplot rect").attr("stroke-width",1),$("#"+t.pre+"dl_scatterplot circle").attr("stroke-width",1))}removeHlMenus(){let e=this.icn3d;e.icn3dui,$("#"+e.pre+"atomsCustom").val(""),$("#"+e.pre+"atomsCustom")[0].blur()}updateHlAll(e,t,s,i){let n=this.icn3d,l=n.icn3dui;n.prevHighlightAtoms=l.hashUtilsCls.cloneHash(n.hAtoms),this.updateHlObjects(i),void 0!==e?this.updateHlSeqInChain(e,s):this.updateHlSeq(void 0,void 0,s),this.updateHl2D(),(void 0===t||t)&&this.updateHlMenus(e)}updateHlObjects(e){let t=this.icn3d;t.icn3dui,t.hlObjectsCls.removeHlObjects(),(t.hAtoms&&t.atoms&&Object.keys(t.hAtoms).length0&&(e=s.defNames2Residues[i]);let t={};if(void 0!==s.defNames2Atoms[i]&&s.defNames2Atoms[i].length>0){for(let e=0,n=s.defNames2Atoms[i].length;e0&&(r=t.firstAtomObjCls.getFirstCalphaAtomObj(l))}let o=void 0!==r&&void 0!==r.color?"#"+r.color.getHexString():"#FFFFFF",a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] rect[class='icn3d-hlnode']"),d=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] rect[class='icn3d-basenode']");void 0!==a&&(t.diagram2dCls.highlightNode("rect",a,d,l),$(a).attr("fill",o)),a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] circle[class='icn3d-hlnode']"),d=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] circle[class='icn3d-basenode']"),void 0!==a&&(t.diagram2dCls.highlightNode("circle",a,d,l),$(a).attr("fill",o)),a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] ellipse[class='icn3d-hlnode']"),void 0!==a&&t.diagram2dCls.highlightNode("ellipse",a,void 0,l),a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] polygon[class='icn3d-hlnode']"),d=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] polygon[class='icn3d-basenode']"),void 0!==a&&(t.diagram2dCls.highlightNode("polygon",a,d,l),$(a).attr("fill",o))}if(void 0!==t.lineArray2d)for(let e=0,i=t.lineArray2d.length;e1){let e={},l=[],o=[],a=[],c=[],h=[],m=[],u=[],g=[],f=[],C=[],b=[],y=[],v={},_={},w={};for(let t=0,s=p.length;t4&&!isNaN(parseInt(e.substr(-4,4)))||t.length>4&&!isNaN(parseInt(t.substr(-4,4))),c=e+"_"+t+"_"+s.c,h=n.hashUtilsCls.cloneHash(s);h.source+=S+i.chainsMapping[r][d],h.target+=S+i.chainsMapping[o][C];let m=n.hashUtilsCls.cloneHash(s);m.source+=A+i.chainsMapping[r][d],m.target+=A+i.chainsMapping[o][C],v[c]!=p.length||!a&&0!=w[c]?b[f].push(m):u[f].push(h),g[f][s.source]=i.chainsMapping[r][d],g[f][s.target]=i.chainsMapping[o][C],y[f][s.source]=i.chainsMapping[r][d],y[f][s.target]=i.chainsMapping[o][C]}else{let e=n.hashUtilsCls.cloneHash(s);e.source+=i.chainsMapping[r]&&i.chainsMapping[r][d]?A+i.chainsMapping[r][d]:A+k,e.target+=i.chainsMapping[o]&&i.chainsMapping[o][C]?A+i.chainsMapping[o][C]:A+k,b[f].push(e),g[f][s.source]=i.chainsMapping[r]&&i.chainsMapping[r][d]?i.chainsMapping[r][d]:x,g[f][s.target]=i.chainsMapping[o]&&i.chainsMapping[o][C]?i.chainsMapping[o][C]:x,y[f][s.source]=i.chainsMapping[r]&&i.chainsMapping[r][d]?i.chainsMapping[r][d]:k,y[f][s.target]=i.chainsMapping[o]&&i.chainsMapping[o][C]?i.chainsMapping[o][C]:k}}}let O=[],R=[],I=0,E=[],T=1;for(let e=0,t=p.length;e0&&(T=1,t=i.getGraphCls.getNodeTopBottom(c[e],d,void 0,T,g[e]),h[e]=t.nodeArray1,m[e]=t.nodeArray2,d=n.hashUtilsCls.unionHash(d,t.name2node),T=2,t=i.getGraphCls.getNodeTopBottom(c[e],d,void 0,T,y[e]),f[e]=t.nodeArray1,C[e]=t.nodeArray2,d=n.hashUtilsCls.unionHash(d,t.name2node)),O[e]=l[e].length,R[e]=o[e].length,I=Math.max(I,R[e]),E.push(p[e])}let D,P,M,F,H,L=1,N=3*L,q=7*L,U=10,B=10,$=30,j=20;t?(M=(n.utilsCls.sumArray(O)+2*E.length)*(N+q)+4*B+2*$+j*E.length,P=(I+2)*(N+q)+2*U+$):(D=110+j,M=D*E.length,P=(I+2)*(N+q)+2*U,P+=20),Object.keys(i.chainsMapping).length>0&&(M*=3),t?(i.scatterplotWidth=2*P,H=i.scatterplotWidth,F=n.scatterplotid):(i.linegraphWidth=2*P,H=i.linegraphWidth,F=n.linegraphid),s=0==E.length?"No interactions found for each structure

    ":"2D integration graph for "+E.length+" structure(s) "+E+'. There are three sections: "Interactions", "Common interactions", and "Different interactions". Each section has '+E.length+" graphs.

    ",s+="";let z,G=0;T=0,z=this.drawGraphPerType(T,p,t,l,o,a,d,G,D,j,O,N,q,B),G=z.heightFinal,s+=z.html,Object.keys(i.chainsMapping).length>0&&(T=1,z=this.drawGraphPerType(T,p,t,h,m,u,d,G,D,j,O,N,q,B),G=z.heightFinal,s+=z.html,T=2,z=this.drawGraphPerType(T,p,t,f,C,b,d,G,D,j,O,N,q,B),G=z.heightFinal,s+=z.html),s+=""}else if(t){let e,t,l,c,h=p[0],m=o.length,u=a.length,g=1,f=3*g,C=7*g,b=30;t=(m+2)*(f+C)+2*10+b,e=(u+2)*(f+C)+2*10+b,i.scatterplotWidth=2*e,c=i.scatterplotWidth,l=n.scatterplotid,s=r.length>0?"":"No interactions found for these two sets

    ",s+="",s+=this.drawScatterplot_base(o,a,r,d,0),i.lineGraphStr+=i.getGraphCls.updateGraphJson(h,1,o,a,r),s+=""}else{let e=p[0],t=o.length,l=a.length,c=1,h=3*c,m=7*c,u=110,g=10,f=t>l?t*(h+m)+2*g:l*(h+m)+2*g;i.linegraphWidth=2*f,s=r.length>0?"":"No interactions found for these two sets

    ",s+="",s+=this.drawLineGraph_base(o,a,r,d,0),i.lineGraphStr+=i.getGraphCls.updateGraphJson(e,1,o,a,r),s+=""}return i.lineGraphStr+="}\n",i.scatterplotStr=i.lineGraphStr,t?$("#"+i.pre+"scatterplotDiv").html(s):$("#"+i.pre+"linegraphDiv").html(s),s}drawGraphPerType(e,t,s,i,n,l,r,o,a,d,c,h,p,m){let u=this.icn3d;u.icn3dui;let g,f,C="",b=2==t.length&&"2"==t[1].replace(t[0],"");0==e?(g="Interactions in ",f=""):1==e?(g="Common interactions in ",f="_common"):2==e&&(g="Different interactions in ",f="_diff");for(let y=0,v=t.length;y0&&(u.lineGraphStr+=", \n"):u.lineGraphStr+=", \n",u.lineGraphStr+=u.getGraphCls.updateGraphJson(t[y],y+f,i[y],n[y],l[y])}return{heightFinal:o,html:C}}getIdArrayFromNode(e){let t=this.icn3d.icn3dui,s=[];s.push(""),s.push("");let i=e.r.substr(4);return s=s.concat(t.utilsCls.getIdArray(i)),s}drawLineGraph_base(e,t,s,i,n,l,r){let o,a,d=this.icn3d,c=d.icn3dui,h="",p=e.length,m=t.length;p>m?(o=10,a=10*Math.abs(p-m)*.5+10):(a=10,o=10*Math.abs(p-m)*.5+10),l&&(h+=""+l+"");let u=30+n,g=80+n,f="",C={},b={};for(let t=0;t";let u=1==t.n?"Interaction":t.n+" interactions";t.n>1&&(h+=""+u+" of residue "+n.id+" with residue "+l.id+""),h+=""}return h+=f,h}drawScatterplot_base(e,t,s,i,n,l,r,o,a){let d=this.icn3d;d.icn3dui;let c="",h=e.length,p=t.length,m=l?3:7,u=(h+1)*(3+m)+30+40;r&&(c+=""+r+"");let g=n+u-(50+(3+m)),f=40+(3+m),C="",b={},y={};for(let t=0;t";else{h+="";let i=1==e.n?"Interaction":e.n+" interactions";e.n>1&&(h+=""+i+" of residue "+t.id+" with residue "+s.id+""),h+=l?"":"",h+=""}return h}copyStylesInline(e,t){this.icn3d.icn3dui;let s=["svg","g"];for(let i=0;i",b=e.id;return c.resid2refnum[p]&&(b+="=>"+c.resid2refnum[p]),C+=""+b+"",o?(C+="",C+=""+g+""):(C+="",C+=""+g+""),C+="",C}getNodeTopBottom(e,t,s,i,n){let l=this.icn3d.icn3dui,r=this,o=[],a=[],d={};for(let s in e){let e=t[s];if(e){if(1==i||2==i){if(e=l.hashUtilsCls.cloneHash(e),1==i){let t=n[s]?n[s]:"-";e.id+="=>"+t}else{let t=n[s]?n[s]:"--";e.id+="==>"+t}d[e.id]=e}"a"==e.s?o.push(e):"b"==e.s?a.push(e):"ab"==e.s&&(o.push(e),a.push(e))}}return o.sort((function(e,t){return r.compNode(e,t)})),a.sort((function(e,t){return r.compNode(e,t,s)})),{nodeArray1:o,nodeArray2:a,name2node:d}}updateGraphJson(e,t,s,i,n){let l=this.icn3d.icn3dui,r="";return r+='"structure'+t+'": {"id": "'+e+'", "nodes1":[',r+=l.utilsCls.getJSONFromArray(s),r+='], \n"nodes2":[',r+=l.utilsCls.getJSONFromArray(i),r+='], \n"links":[',r+=l.utilsCls.getJSONFromArray(n),r+="]}",r}updateGraphColor(){this.icn3d.icn3dui}handleForce(){let e=this.icn3d;0==e.icn3dui.htmlCls.force&&void 0!==e.simulation?(e.simulation.stop(),e.simulation.force("charge",null),e.simulation.force("x",null),e.simulation.force("y",null),e.simulation.force("r",null),e.simulation.force("link",null)):e.drawGraphCls.drawGraph(e.graphStr,e.pre+"dl_graph")}getNodesLinksForSet(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=[],o=[],a=0,d=l.htmlCls.coilValue,c="",h="",p=0,m={};for(let u in e){let e=n.atoms[u];if("DUM"!=e.chain&&(i||e.het||"CA"==e.name&&"C"==e.elem||"O3'"==e.name||"O3*"==e.name||"P"==e.name)){let i=e.structure+"_"+e.chain+"_"+e.resi;if(m.hasOwnProperty(i))continue;m[i]=1;let u=l.utilsCls.residueName2Abbr(e.resn)+e.resi;"chain"!=t&&"structure"!=t||(u+="."+e.chain),"structure"==t&&(u+="."+e.structure);let g="1_1_"+i,f=e.color?e.color.getHexString().toUpperCase():"000";r.push('{"id": "'+u+'", "r": "'+g+'", "s": "'+s+'", "x": '+e.coord.x.toFixed(0)+', "y": '+e.coord.y.toFixed(0)+', "c": "'+f+'"}'),a>0&&c==e.chain&&(n.resid2ncbi[e.resi]==n.resid2ncbi[p]+1||n.resid2ncbi[e.resi]==n.resid2ncbi[p])&&(o.push('{"source": "'+h+'", "target": "'+u+'", "v": '+d+', "c": "'+f+'"}'),e.ssbegin&&(d=l.htmlCls.ssValue),e.ssend&&(d=l.htmlCls.coilValue)),c=e.chain,h=u,p=e.resi,++a}}return{node:r,link:o}}getHbondLinksForSet(e,t){let s=this.icn3d,i=s.icn3dui,n={},l=parseFloat($("#"+s.pre+"hbondthreshold").val()),r=e,o=r;if(Object.keys(o).length>0&&Object.keys(r).length>0){let e=!1;s.hBondCls.calculateChemicalHbonds(i.hashUtilsCls.hash2Atoms(o,s.atoms),i.hashUtilsCls.hash2Atoms(r,s.atoms),parseFloat(l),e,"graph",!0),n=i.hashUtilsCls.cloneHash(s.resid2Residhash)}return this.getGraphLinks(n,n,i.htmlCls.hbondInsideColor,t,i.htmlCls.hbondInsideValue)}getIonicLinksForSet(e,t){let s=this.icn3d,i=s.icn3dui,n={},l=parseFloat($("#"+s.pre+"saltbridgethreshold").val()),r=e,o=r;if(Object.keys(o).length>0&&Object.keys(r).length>0){let e=!1;s.saltbridgeCls.calculateIonicInteractions(i.hashUtilsCls.hash2Atoms(o,s.atoms),i.hashUtilsCls.hash2Atoms(r,s.atoms),parseFloat(l),e,"graph",!0),n=i.hashUtilsCls.cloneHash(s.resid2Residhash)}return this.getGraphLinks(n,n,i.htmlCls.ionicInsideColor,t,i.htmlCls.ionicInsideValue)}getHalogenPiLinksForSet(e,t){let s,i=this.icn3d,n=i.icn3dui,l={},r=e,o=r,a="";return s=parseFloat($("#"+i.pre+"halogenthreshold").val()),Object.keys(o).length>0&&Object.keys(r).length>0&&(i.piHalogenCls.calculateHalogenPiInteractions(n.hashUtilsCls.hash2Atoms(r,i.atoms),n.hashUtilsCls.hash2Atoms(o,i.atoms),parseFloat(s),"graph","halogen",!0),l=n.hashUtilsCls.cloneHash(i.resid2Residhash)),a+=this.getGraphLinks(l,l,n.htmlCls.halogenInsideColor,t,n.htmlCls.halogenInsideValue),s=parseFloat($("#"+i.pre+"picationthreshold").val()),Object.keys(o).length>0&&Object.keys(r).length>0&&(i.piHalogenCls.calculateHalogenPiInteractions(n.hashUtilsCls.hash2Atoms(r,i.atoms),n.hashUtilsCls.hash2Atoms(o,i.atoms),parseFloat(s),"graph","pi-cation",!0),l=n.hashUtilsCls.cloneHash(i.resid2Residhash)),a+=this.getGraphLinks(l,l,n.htmlCls.picationInsideColor,t,n.htmlCls.picationInsideValue),s=parseFloat($("#"+i.pre+"pistackingthreshold").val()),Object.keys(o).length>0&&Object.keys(r).length>0&&(i.piHalogenCls.calculateHalogenPiInteractions(n.hashUtilsCls.hash2Atoms(r,i.atoms),n.hashUtilsCls.hash2Atoms(o,i.atoms),parseFloat(s),"graph","pi-stacking",!0),l=n.hashUtilsCls.cloneHash(i.resid2Residhash)),a+=this.getGraphLinks(l,l,n.htmlCls.pistackingInsideColor,t,n.htmlCls.pistackingInsideValue),a}getContactLinksForSet(e,t,s){let i=this.icn3d;i.icn3dui;let n=[],l="",r="",o={};for(let t in e){let e=i.atoms[t];e.ss==l&&e.chain==r||(Object.keys(o).length>0&&n.push(o),o={}),o[e.serial]=1,l=e.ss,r=e.chain}Object.keys(o).length>0&&n.push(o);let a=n.length,d="";for(let e=0;ed?s?-1:1:ah?1:c0&&Object.keys(a).length>0)){let t,s=c.hBondCls.calculateChemicalHbonds(h.hashUtilsCls.hash2Atoms(d,c.atoms),h.hashUtilsCls.hash2Atoms(a,c.atoms),parseFloat(e),n);n?(c.resid2ResidhashSaltbridge=h.hashUtilsCls.cloneHash(c.resid2Residhash),t="all atoms that have salt bridges with the selected atoms"):(c.resid2ResidhashHbond=h.hashUtilsCls.cloneHash(c.resid2Residhash),t="all atoms that are hydrogen-bonded with the selected atoms");let i={};for(let e in s){i[c.atoms[e].structure+"_"+c.atoms[e].chain+"_"+c.atoms[e].resi]=1}c.hAtoms={};for(let e in i)for(let t in c.residues[e])c.hAtoms[t]=1,c.atoms[t].style2="stick";let l=r+"_auto";c.selectionCls.addCustomSelection(Object.keys(i),l,t,o,!0),c.selectionCls.saveSelectionIfSelected(),c.drawCls.draw()}}showHydrogens(){let e=this.icn3d;if(void 0!==e.icn3dui.cfg.cid)for(let t in e.hAtoms){let s=e.atoms[t];if("H"!==s.elem.substr(0,1)){e.atoms[s.serial].bonds=e.atoms[s.serial].bonds2.concat(),e.atoms[s.serial].bondOrder=e.atoms[s.serial].bondOrder2.concat();for(let t=0,i=e.atoms[s.serial].bonds.length;t0){let i=e.atoms[t].bonds[0];e.atoms[i].bonds.push(s.serial),e.atoms[i].bondOrder&&e.atoms[i].bondOrder.push(1)}e.dAtoms[t]=1}} +//!!!ic.bShowHighlight = false; +}hideHydrogens(){let e=this.icn3d;e.icn3dui;for(let t in e.hAtoms){let s=e.atoms[t];if("H"===s.elem.substr(0,1)){if(e.atoms[s.serial].bonds.length>0){let t=e.atoms[s.serial].bonds[0],i=e.atoms[t].bonds?e.atoms[t].bonds.indexOf(s.serial):-1;-1!==i&&(e.atoms[t].bonds.splice(i,1),e.atoms[t].bondOrder&&e.atoms[t].bondOrder.splice(i,1))}delete e.dAtoms[s.serial],delete e.hAtoms[s.serial]}}}hideExtraBonds(){let e=this.icn3d;e.icn3dui;for(let t in e.atoms)e.atoms[t].style2="nothing";for(let t in e.sidec)e.hAtoms.hasOwnProperty(t)&&(e.atoms[t].style2=e.opts.sidec);for(let t in e.water)e.hAtoms.hasOwnProperty(t)&&(e.atoms[t].style=e.opts.water)}hideHbondsContacts(){let e=this.icn3d,t=e.icn3dui,s="set hbonds off";t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.hBondCls.hideHbonds(),s="set salt bridge off",t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.saltbridgeCls.hideSaltbridge(),s="set contact off",t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.contactCls.hideContact(),s="set halogen pi off",t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.piHalogenCls.hideHalogenPi(),this.hideExtraBonds()}showIonicInteractions(e,t,s,i,n,l){let r,o,a,d,c=this.icn3d,h=c.icn3dui;if(!i&&(r="saltbridge",o="salt bridge "+e+" | sets "+t+" "+s+" | "+i,c.opts.saltbridge="yes",a=c.definedSetsCls.getAtomsFromNameArray(t),d=c.definedSetsCls.getAtomsFromNameArray(s),c.firstAtomObjCls.getFirstAtomObj(a),Object.keys(d).length>0&&Object.keys(a).length>0)){let t,s=c.saltbridgeCls.calculateIonicInteractions(h.hashUtilsCls.hash2Atoms(d,c.atoms),h.hashUtilsCls.hash2Atoms(a,c.atoms),parseFloat(e),n);c.resid2ResidhashSaltbridge=h.hashUtilsCls.cloneHash(c.resid2Residhash),t="all atoms that have ionic interactions with the selected atoms";let i={};for(let e in s){i[c.atoms[e].structure+"_"+c.atoms[e].chain+"_"+c.atoms[e].resi]=1}c.hAtoms={};for(let e in i)for(let t in c.residues[e])c.hAtoms[t]=1,c.atoms[t].style2="stick",c.ions.hasOwnProperty(t)&&(c.atoms[t].style2="sphere");let l="saltbridge_auto";c.selectionCls.addCustomSelection(Object.keys(i),l,t,o,!0),c.selectionCls.saveSelectionIfSelected(),c.drawCls.draw()}}showHalogenPi(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(i)return;let a,d,c=l+" "+e+" | sets "+t+" "+s+" | "+i;if(r.opts[l]="yes",a=r.definedSetsCls.getAtomsFromNameArray(t),d=r.definedSetsCls.getAtomsFromNameArray(s),r.firstAtomObjCls.getFirstAtomObj(a),Object.keys(d).length>0&&Object.keys(a).length>0){let t,s=r.piHalogenCls.calculateHalogenPiInteractions(o.hashUtilsCls.hash2Atoms(a,r.atoms),o.hashUtilsCls.hash2Atoms(d,r.atoms),parseFloat(e),n,l);"halogen"==l?(r.resid2ResidhashHalogen=o.hashUtilsCls.cloneHash(r.resid2Residhash),t="all atoms that have halogen bonds with the selected atoms"):"pi-cation"==l?(r.resid2ResidhashPication=o.hashUtilsCls.cloneHash(r.resid2Residhash),t="all atoms that have pi-cation interactions with the selected atoms"):"pi-stacking"==l&&(r.resid2ResidhashPistacking=o.hashUtilsCls.cloneHash(r.resid2Residhash),t="all atoms that have pi-stacking with the selected atoms");let i={};for(let e in s){i[r.atoms[e].structure+"_"+r.atoms[e].chain+"_"+r.atoms[e].resi]=1}r.hAtoms={};for(let e in i)for(let t in r.residues[e])r.hAtoms[t]=1,r.atoms[t].style2="stick",r.ions.hasOwnProperty(t)&&(r.atoms[t].style2="sphere");let h=l+"_auto";r.selectionCls.addCustomSelection(Object.keys(i),h,t,c,!0),r.selectionCls.saveSelectionIfSelected(),r.drawCls.draw()}}showClbonds(){let e=this.icn3d,t=e.icn3dui;e.opts.clbonds="yes";let s=e.applyClbondsCls.applyClbondsOptions();for(let i in s)e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.residues[i]);if(Object.keys(s).length>0){let t="clbonds",i="all atoms that have cross-linkages";e.selectionCls.addCustomSelection(Object.keys(s),t,i,"cross linkage",!0),e.selectionCls.saveSelectionIfSelected(),e.drawCls.draw()}}showSsbonds(){let e=this.icn3d,t=e.icn3dui;e.opts.ssbonds="yes";let s={},i=Object.keys(e.structures);for(let n=0,l=i.length;n0){let t="ssbonds",i="all atoms that have disulfide bonds";e.selectionCls.addCustomSelection(Object.keys(s),t,i,"disulfide bonds",!0),e.selectionCls.saveSelectionIfSelected(),e.drawCls.draw()}}pickCustomSphere(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(i)return;let a,d,c="select zone cutoff "+e+" | sets "+t+" "+s+" | "+i;n&&(c="interactions "+e+" | sets "+t+" "+s+" | "+i,r.opts.contact="yes"),a=r.definedSetsCls.getAtomsFromNameArray(t),d=r.definedSetsCls.getAtomsFromNameArray(s);let h,p,m=this.pickCustomSphere_base(e,a,d,i,n,l,c,!0),u=Object.keys(m.residues);r.hAtoms={};for(let e=0,t=u.length;e1?"structure":v>1?"chain":"residue";let w=[];if(n&&w.push("hbonds"),l&&w.push("salt bridge"),r&&w.push("interactions"),o&&w.push("halogen"),a&&w.push("pi-cation"),d&&w.push("pi-stacking"),s||(p.resids2inter={},p.resids2interAll={}),l){let n=parseFloat($("#"+p.pre+"saltbridgethreshold").val());n&&!isNaN(n)||(n=p.tsIonic),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showIonicInteractions(n,e,t,s,!0,i)),g=m.hashUtilsCls.unionHash(g,p.hAtoms)}if(n){let n=parseFloat($("#"+p.pre+"hbondthreshold").val());n&&!isNaN(n)||(n=p.tsHbond),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHbonds(n,e,t,s,void 0,i)),g=m.hashUtilsCls.unionHash(g,p.hAtoms)}let S,A,x,k,O="";if(n&&(O+=this.exportHbondPairs(i,u)),l&&(O+=this.exportSaltbridgePairs(i,u)),o){let n=parseFloat($("#"+p.pre+"halogenthreshold").val());n&&!isNaN(n)||(n=p.tsHalogen),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHalogenPi(n,e,t,s,i,"halogen")),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportHalogenPiPairs(i,u,"halogen")}if(a){let n=parseFloat($("#"+p.pre+"picationthreshold").val());n&&!isNaN(n)||(n=p.tsPication),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHalogenPi(n,e,t,s,i,"pi-cation")),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportHalogenPiPairs(i,u,"pi-cation")}if(d){let n=parseFloat($("#"+p.pre+"pistackingthreshold").val());n&&!isNaN(n)||(n=p.tsPistacking),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHalogenPi(n,e,t,s,i,"pi-stacking")),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportHalogenPiPairs(i,u,"pi-stacking")}if(r){let n=C?c:parseFloat($("#"+p.pre+"contactthreshold").val());if(n&&!isNaN(n)||(n=p.tsContact),1!=e.length||1!=t.length||e[0]!=t[0])s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.pickCustomSphere(n,e,t,s,!0,i)),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportSpherePairs(!0,i,u);else{if(!s){let l={},o={};if(C){let e=!0,t=p.showInterCls.pickCustomSphere_base(n,b,y,s,!0,void 0,void 0,!0,e);l=m.hashUtilsCls.unionHash(l,t.residues);for(let e in t.resid2Residhash)o[e]=m.hashUtilsCls.unionHash(o[e],t.resid2Residhash[e])}else{let r=[],a="",d="",c={};for(let e in b){let t=p.atoms[e];t.ss==a&&t.chain==d||(Object.keys(c).length>0&&r.push(c),c={}),c[t.serial]=1,a=t.ss,d=t.chain}Object.keys(c).length>0&&r.push(c);let h=r.length,u="interactions "+n+" | sets "+e+" "+t+" | true";p.opts.contact="yes";for(let e=0;e
    ",T=p.resid2specCls.atoms2residues(Object.keys(b)),D=p.resid2specCls.atoms2residues(Object.keys(y)),P="select "+p.resid2specCls.residueids2spec(T),M="select "+p.resid2specCls.residueids2spec(D);E+="Set 1: "+e+'
    ',E+="Set 2: "+t+'

    ',E+='
    The interfaces are:
    ';let F=p.resid2specCls.atoms2residues(Object.keys(R)),H=p.resid2specCls.atoms2residues(Object.keys(I)),L="select "+p.resid2specCls.residueids2spec(F),N="select "+p.resid2specCls.residueids2spec(H);E+='interface_1
    ',E+='interface_2

    ',E+='
    Note: Each checkbox below selects the corresponding residue. You can click "Save Selection" in the "Select" menu to save the selection and click on "Highlight" button to clear the checkboxes.

    ';let q=E;if(("graph"==i||"linegraph"==i||"scatterplot"==i||C)&&(E=""),E+=O,"save1"==i||"save2"==i){E=q;let e="";"save1"==i?e="Set 1":"save2"==i&&(e="Set 2"),E+='

    Interactions Sorted on '+e+':
    ';let t=this.getAllInteractionTable(i);E+=t.html,h=t.bondCnt,$("#"+p.pre+"dl_interactionsorted_html").html(E),m.htmlCls.dialogCls.openDlg("dl_interactionsorted","Show sorted interactions")}else if("view"==i)$("#"+p.pre+"dl_allinteraction_html").html(E),m.htmlCls.dialogCls.openDlg("dl_allinteraction","Show interactions");else if("linegraph"==i){m.htmlCls.dialogCls.openDlg("dl_linegraph","Show interactions between two lines of residue nodes"),p.graphStr=p.getGraphCls.getGraphData(b,y,e,t,E,u),p.bLinegraph=!0;let s=p.lineGraphCls.drawLineGraph(p.graphStr);$("#"+p.pre+"linegraphDiv").html(s)}else if("scatterplot"==i){m.htmlCls.dialogCls.openDlg("dl_scatterplot","Show interactions as scatterplot"),p.graphStr=p.getGraphCls.getGraphData(b,y,e,t,E,u),p.bScatterplot=!0;let s=p.lineGraphCls.drawLineGraph(p.graphStr,!0);$("#"+p.pre+"scatterplotDiv").html(s)}else if(C){m.htmlCls.dialogCls.openDlg("dl_contactmap","Show contact map");let s=!0,i=p.getGraphCls.getGraphData(b,y,e,t,E,u,s);p.bContactMap=!0;let n=p.contactMapCls.drawContactMap(i);$("#"+p.pre+"contactmapDiv").html(n)}else if("graph"==i){if(p.graphStr=p.getGraphCls.getGraphData(b,y,e,t,E,u),p.bGraph=!0,Object.keys(y).length+Object.keys(b).length>Object.keys(p.dAtoms).length&&(p.graphStr=p.selectionCls.getGraphDataForDisplayed()),void 0===p.bD3){let e="./script/d3v4-force-all.min.js";await m.getAjaxPromise(e,"script"),p.bD3=!0}$("#"+m.svgid).empty(),m.htmlCls.dialogCls.openDlg("dl_graph","Force-directed graph"),p.drawGraphCls.drawGraph(p.graphStr,p.pre+"dl_graph")}return{interactionTypes:w.toString(),bondCnt:h}}clearInteractions(){let e=this.icn3d;e.icn3dui,e.lines.hbond=[],e.hbondpnts=[],e.lines.saltbridge=[],e.saltbridgepnts=[],e.lines.contact=[],e.contactpnts=[],e.lines.halogen=[],e.lines["pi-cation"]=[],e.lines["pi-stacking"]=[],e.halogenpnts=[],e.picationpnts=[],e.pistackingpnts=[]}resetInteractionPairs(){let e=this.icn3d;e.icn3dui,e.bHbondCalc=!1,e.showInterCls.hideHbondsContacts(),e.hlUpdateCls.clearHighlight(),e.resids2inter={},e.resids2interAll={}}async retrieveInteractionData(){let e=this.icn3d,t=e.icn3dui;if(!e.b2DShown)if(void 0!==t.cfg.align){let s=Object.keys(e.structures);if(2==t.cfg.atype){let t=!0;await e.alignParserCls.downloadAlignment(s[0]+","+s[1],t)}await e.ParserUtilsCls.set2DDiagramsForAlign(s[0].toUpperCase(),s[1].toUpperCase())}else void 0!==t.cfg.chainalign?(Object.keys(e.structures),await e.ParserUtilsCls.set2DDiagramsForChainalign(e.chainidArray)):e.ParserUtilsCls.download2Ddgm(e.inputid.toUpperCase())}getAllInteractionTable(e){let t=this.icn3d,s=t.icn3dui,i=[],n=Object.keys(t.resids2inter);("save1"==e||"save2"==e)&&n.sort((function(t,i){return s.utilsCls.compResid(t,i,e)}));let l,r,o="",a="",d="",c="",h="",p="",m="",u="",g="",f=0,C=0,b=0,y=0,v=0,_=0,w="";for(let s=0,S=n.length;s0&&l!=a&&(i.push({res1:a,res2:w,cntHbond:f,cntIonic:C,cntContact:b,cntHalegen:y,cntPication:v,cntPistacking:_}),o+=this.getInteractionPerResidue(d,c,h,p,m,u,g,f,C,b,y,v,_),c="",h="",p="",m="",u="",g="",f=0,C=0,b=0,y=0,v=0,_=0,w=""),x=t.resids2inter[S].hbond,k=this.getInteractionPairDetails(x,e,"hbond"),c+=k.html,f+=k.cnt,k.cnt>0&&(w+=r+":hbond_"+k.cnt+" "),x=t.resids2inter[S].ionic,k=this.getInteractionPairDetails(x,e,"ionic"),h+=k.html,C+=k.cnt,k.cnt>0&&(w+=r+":ionic_"+k.cnt+" "),x=t.resids2inter[S].contact,k=this.getContactPairDetails(x,e,"contact"),p+=k.html,b+=k.cnt,k.cnt>0&&(w+=r+":contact_"+k.cnt+" "),x=t.resids2inter[S].halogen,k=this.getInteractionPairDetails(x,e,"halogen"),m+=k.html,y+=k.cnt,k.cnt>0&&(w+=r+":halogen_"+k.cnt+" "),x=t.resids2inter[S]["pi-cation"],k=this.getInteractionPairDetails(x,e,"pi-cation"),u+=k.html,v+=k.cnt,k.cnt>0&&(w+=r+":pi-cation_"+k.cnt+" "),x=t.resids2inter[S]["pi-stacking"],k=this.getInteractionPairDetails(x,e,"pi-stacking"),g+=k.html,_+=k.cnt,k.cnt>0&&(w+=r+":pi-stacking_"+k.cnt+" "),a=l,d=O}i.push({res1:a,res2:w,cntHbond:f,cntIonic:C,cntContact:b,cntHalegen:y,cntPication:v,cntPistacking:_}),o+=this.getInteractionPerResidue(d,c,h,p,m,u,g,f,C,b,y,v,_);let S="";if(n.length>0){S+='
    ',S+="",S+="",S+="",S+="",S+="";let e='';S+=e,S+=e,S+='',S+=e,S+=e,S+=e,S+="",S+="",S+=o,S+="
    Residue# Hydrogen
    Bond    		# Salt Bridge
    /Ionic Interaction    		# Contact# Halogen
    Bond    		# π-Cation# π-StackingHydrogen Bond (backbone atoms: @CA, @N, @C, @O)Salt Bridge/Ionic InteractionContactHalogen Bondπ-Cationπ-Stacking
    Atom1Atom2Distance(Å)Highlight in 3D
    Atom1Atom2# ContactsMin Distance(Å)C-alpha Distance(Å)Highlight in 3D

    "}return{html:S,bondCnt:i}}getInteractionPerResidue(e,t,s,i,n,l,r,o,a,d,c,h,p){this.icn3d.icn3dui;let m="";m+=''+e[3]+e[2]+""+o+""+a+""+d+""+c+""+h+""+p+"";let u=[t,s,i,n,l,r];for(let e in u){m+=''+u[e]+"
    "}return m+="",m}getInteractionPairDetails(e,t,s){let i=this.icn3d;i.icn3dui;let n="",l=0,r='    ';if(void 0!==e)for(let a in e){let d=a.split(","),c="save1"==t?d[0]:d[1],h="save1"==t?d[1]:d[0],p=i.getGraphCls.convertLabel2Resid(c),m=i.firstAtomObjCls.getFirstAtomObj(i.residues[p]),u=m.color?m.color.getHexString():"",g=i.getGraphCls.convertLabel2Resid(h),f=i.firstAtomObjCls.getFirstAtomObj(i.residues[g]),C=f.color?f.color.getHexString():"",b=Math.sqrt(e[a]).toFixed(1);n+=' '+c+r+u+o+' '+h+r+C+o+''+b+"",n+='',n+="",++l}return{html:n,cnt:l}}getContactPairDetails(e,t){let s=this.icn3d;s.icn3dui;let i="",n=0,l='    ';if(void 0!==e)for(let o in e){let a=o.split(","),d="save1"==t?a[0]:a[1],c="save1"==t?a[1]:a[0],h=s.getGraphCls.convertLabel2Resid(d),p=s.firstAtomObjCls.getFirstAtomObj(s.residues[h]),m=p.color?p.color.getHexString():"",u=s.getGraphCls.convertLabel2Resid(c),g=s.firstAtomObjCls.getFirstAtomObj(s.residues[u]),f=g.color?g.color.getHexString():"",C=e[o].split("_"),b=C[0],y=C[1],v=C[2],_=C[3],w=C[4];i+=' '+d+"@"+v+l+m+r+' '+c+"@"+_+l+f+r+''+w+''+b+''+y+"",i+='',i+="",n+=parseInt(w)}return{html:i,cnt:n}}exportInteractions(){var e=this.icn3d,t=e.icn3dui;let s='

    Interacting residues:
    ';for(let t in e.chainname2residues)for(let i in e.chainname2residues[t]){let n=t.substr(0,t.indexOf("_"))+"_"+i.substr(0,i.indexOf(" "));s+=""}s+="
    Base Chain: ResiduesInteracting Chain
    "+t+": ",s+=e.resid2specCls.residueids2spec(e.chainname2residues[t][i]),s+=""+n+"

    ";let i=Object.keys(t.utilsCls.getHlStructures()).join(",");e.saveFileCls.saveFile(i+"_interactions.html","html",s)}exportSsbondPairs(){var e=this.icn3d,t=e.icn3dui;let s="",i=0;for(let t in e.structures){let n=e.ssbondpnts[t];if(void 0===n)break;for(let e=0,t=n.length;e"+n[e]+" Cys"+n[e+1]+" Cys",++i}}let n='

    '+i+" disulfide pairs:

    ";n+=s,n+="
    Residue ID 1Residue ID 2

    ";let l=Object.keys(t.utilsCls.getHlStructures()).join(",");e.saveFileCls.saveFile(l+"_disulfide_pairs.html","html",n)}exportClbondPairs(){var e=this.icn3d,t=e.icn3dui;let s="",i=0,n={};for(let t in e.structures){let l=e.clbondpnts[t];if(void 0===l)break;for(let t=0,r=l.length;t"+r+" "+t.resn+""+o+" "+n.resn+"",++i}n[r+"_"+o]=1,n[o+"_"+r]=1}}let l='

    '+i+" cross-linkage pairs:

    ";l+=s,l+="
    Residue ID 1Residue ID 2

    ";let r=Object.keys(t.utilsCls.getHlStructures()).join(",");e.saveFileCls.saveFile(r+"_crosslinkage_pairs.html","html",l)}exportHbondPairs(e,t){var s=this.icn3d,i=s.icn3dui;let n="",l=0,r='    ';for(let t in s.resid2ResidhashHbond){let i=s.getGraphCls.convertLabel2Resid(t),a=s.firstAtomObjCls.getFirstAtomObj(s.residues[i]),d=a.color?a.color.getHexString():"";for(let i in s.resid2ResidhashHbond[t]){let a=s.getGraphCls.convertLabel2Resid(i),c=s.firstAtomObjCls.getFirstAtomObj(s.residues[a]),h=c.color?c.color.getHexString():"",p=Math.sqrt(s.resid2ResidhashHbond[t][i]).toFixed(1);n+=' '+t+r+d+o+' '+i+r+h+o+''+p+"","view"==e&&(n+=''),n+="",++l}}let a='

    '+l+" hydrogen bond pairs (backbone atoms: @CA, @N, @C, @O):

    ";if(l>0&&(a+="
    ","view"==e&&(a+=''),a+="",a+=n,a+="
    Atom 1Atom 2Distance(Å)Highlight in 3D

    "),"graph"==e||"linegraph"==e||"scatterplot"==e){return s.getGraphCls.getGraphLinks(s.resid2ResidhashHbond,s.resid2ResidhashHbond,i.htmlCls.hbondColor,t,i.htmlCls.hbondValue)}return a}exportSaltbridgePairs(e,t){var s=this.icn3d,i=s.icn3dui;let n="",l=0,r='    ';for(let t in s.resid2ResidhashSaltbridge){let i=s.getGraphCls.convertLabel2Resid(t),a=s.firstAtomObjCls.getFirstAtomObj(s.residues[i]),d=a.color?a.color.getHexString():"";for(let i in s.resid2ResidhashSaltbridge[t]){let a=s.getGraphCls.convertLabel2Resid(i),c=s.firstAtomObjCls.getFirstAtomObj(s.residues[a]),h=c.color?c.color.getHexString():"",p=Math.sqrt(s.resid2ResidhashSaltbridge[t][i]).toFixed(1);n+=' '+t+r+d+o+' '+i+r+h+o+''+p+"","view"==e&&(n+=''),n+="",++l}}let a='

    '+l+" salt bridge/ionic interaction pairs:

    ";if(l>0&&(a+="
    ","view"==e&&(a+=''),a+="",a+=n,a+="
    Atom 1Atom 2Distance(Å)Highlight in 3D

    "),"graph"==e||"linegraph"==e||"scatterplot"==e){return s.getGraphCls.getGraphLinks(s.resid2ResidhashSaltbridge,s.resid2ResidhashSaltbridge,i.htmlCls.ionicColor,t,i.htmlCls.ionicValue)}return a}exportHalogenPiPairs(e,t,s){var i=this.icn3d,n=i.icn3dui;let l,r,o,a="",d=0,c='    ';"halogen"==s?(l=i.resid2ResidhashHalogen,r=n.htmlCls.halogenColor,o=n.htmlCls.halogenValue):"pi-cation"==s?(l=i.resid2ResidhashPication,r=n.htmlCls.picationColor,o=n.htmlCls.picationValue):"pi-stacking"==s&&(l=i.resid2ResidhashPistacking,r=n.htmlCls.pistackingColor,o=n.htmlCls.pistackingValue);for(let t in l){let n=i.getGraphCls.convertLabel2Resid(t),r=i.firstAtomObjCls.getFirstAtomObj(i.residues[n]),o=r.color?r.color.getHexString():"";for(let n in l[t]){let r=i.getGraphCls.convertLabel2Resid(n),p=i.firstAtomObjCls.getFirstAtomObj(i.residues[r]),m=p.color?p.color.getHexString():"",u=Math.sqrt(l[t][n]).toFixed(1);a+=' '+t+c+o+h+' '+n+c+m+h+''+u+"","view"==e&&(a+=''),a+="",++d}}let p='

    '+d+" "+s+" pairs:

    ";if(d>0&&(p+="
    ","view"==e&&(p+=''),p+="",p+=a,p+="
    Atom 1Atom 2Distance(Å)Highlight in 3D

    "),"graph"==e||"linegraph"==e||"scatterplot"==e){return i.getGraphCls.getGraphLinks(l,l,r,t,o)}return p}exportSpherePairs(e,t,s){var i=this.icn3d,n=i.icn3dui;let l="",r=0,o=e?i.resid2ResidhashInteractions:i.resid2ResidhashSphere,a='    ';for(let s in o){let n=i.getGraphCls.convertLabel2Resid(s),c=i.firstAtomObjCls.getFirstAtomObj(i.residues[n]),h=c.color?c.color.getHexString():"";for(let n in o[s]){let p=i.getGraphCls.convertLabel2Resid(n),m=i.firstAtomObjCls.getFirstAtomObj(i.residues[p]),u=m.color?m.color.getHexString():"",g=o[s][n].split("_"),f=g[0],C=g[1];c=g[2],m=g[3];let b=g[4];e?(l+=' '+s+"@"+c+a+h+d+' '+n+"@"+m+a+u+d+''+b+''+f+''+C+"","view"==t&&(l+=''),l+=""):l+=""+s+""+n+''+b+''+f+''+C+"",++r}}let c='

    '+r+" residue pairs in "+(e?"the contacts":"sphere")+":

    ";if(r>0&&(e?(c+='
    ',"view"==t&&(c+=''),c+=""):c+='
    Residue 1Residue 2Num ContactsMin Distance(Å)C-alpha Distance(Å)Highlight in 3D
    ',c+=l,c+="
    Residue 1Residue 2Num ContactsMin Distance(Å)C-alpha Distance(Å)

    "),"graph"==t||"linegraph"==t||"scatterplot"==t||"calpha"==t||"cbeta"==t||"heavyatoms"==t){return i.getGraphCls.getGraphLinks(o,o,n.htmlCls.contactColor,s,n.htmlCls.contactValue)}return c}}class Bt{constructor(e){this.icn3d=e}drawGraph(e,t){var s=this.icn3d,i=s.icn3dui;if(void 0===n)var n=d3;var l=JSON.parse(e),r=$("#"+t).width(),o=$("#"+t).height(),a=isNaN(r)?300:1*r,d=isNaN(o)?300:1*o,c=r,h=o,p=d3.select("#"+i.svgid).attr("width",r).attr("height",o).attr("viewBox","0,0,"+a+","+d);p.selectAll(".g-main").remove();var m=p.append("g").classed("g-main",!0),u=m.append("rect").attr("width",c).attr("height",h).style("fill","#FFF"),g=m.append("g"),f=n.zoom().on("zoom",(function(){g.attr("transform",n.event.transform)}));if(m.call(f),l.links){for(var C=[],b={},y=0,v=l.nodes.length;y0?n.structures[0]:n.defaultPdbId;p=10*(a.length+2)+20+30,h=10*(d.length+2)+20+30,t?(n.alignerrormapWidth=2*h,u=n.alignerrormapWidth,m=l.alignerrormapid):(n.contactmapWidth=2*h,u=n.contactmapWidth,m=l.contactmapid),i=o.length>0?"":"No interactions found for these two sets

    ",i+="";if(t){n.hex2id={};let e=29/s;n.hex2skip={};let t=1e3;for(let s=0;se&&(n.hex2skip[d]=c)}}if(i+=n.lineGraphCls.drawScatterplot_base(a,d,o,c,0,!0,void 0,void 0,t),g+=n.getGraphCls.updateGraphJson(f,1,a,d,o),i+="",g+="}\n",t){n.alignerrormapStr=g,$("#"+n.pre+"alignerrormapDiv").html(i);let e=$("#"+l.alignerrormapid+"_scale").val();$("#"+l.alignerrormapid).attr("width",(n.alignerrormapWidth*parseFloat(e)).toString()+"px")}else n.contactmapStr=g,$("#"+n.pre+"contactmapDiv").html(i);return i}}class jt{constructor(e){this.icn3d=e}async downloadAlignment(e,t){let s=this.icn3d,i=s.icn3dui,n=this;s.opts.proteins="c alpha trace";let l=e.split(","),r="ids="+e,o=i.htmlCls.baseUrl+"vastplus/vastplus.cgi?v=3&cmd=c&b=1&s=1&w3d&"+r;void 0!==i.cfg.inpara&&(o+=i.cfg.inpara),s.pdbid_chain2title={},void 0===s.chainids2resids&&(s.chainids2resids={});let a={},d="These two MMDB IDs "+l+' do not have 3D alignment data in the VAST+ database. You can try the VAST alignment by visiting the VAST+ page https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=[PDB ID] (e.g., uid=1KQ2), and clicking "Original VAST"',c=await i.getAjaxPromise(o,"jsonp",!0,d);if(a=c.seqalign,void 0===a)return alert(d),!1;s.pdbid_molid2chain={},s.chainsColor={};for(let e=0,t=2;e5){let t=!1,s=!0;d=await r.pdbParserCls.loadPdbData(e,n,!1,t,"target",h,s)}else{let t=!0;d=await r.mmdbParserCls.parseMmdbData(e,"target",i[0],0,h,t)}for(let e=0,s=t.length;e5){let s=!0,i=!0;c=await r.pdbParserCls.loadPdbData(t[e],l,!1,s,"query",h,i)}else{let s=!0;c=await r.mmdbParserCls.parseMmdbData(t[e],"query",i[e+1],e,h,s)}d=o.hashUtilsCls.unionHash(d,c)}if(o.cfg.resnum)await r.realignParserCls.realignChainOnSeqAlign(s,i);else if(o.cfg.resdef)await r.realignParserCls.realignChainOnSeqAlign(s,i,void 0,!0);else{await r.pdbParserCls.applyCommandDssp(!0);for(let e in r.pdbChainIndexHash){let t=r.pdbChainIndexHash[e].split("_");l=t[0],t[1],n=t[2],t[3],a.transformStructure(l,e-1,"query")}let e=[],t=[],c=[],h=o.htmlCls.baseUrl+"vastdyn/vastdyn.cgi",p=o.htmlCls.baseUrl+"tmalign/tmalign.cgi";for(let s in r.afChainIndexHash){let i=r.afChainIndexHash[s].split("_");l=i[0];let a=i[1];n=i[2];let d,m=i[3];if("tmalign"!=o.cfg.aligntool){let e={domains1:r.domain3dCls.getDomainJsonForAlign(r.chains[l+"_"+a]),domains2:r.domain3dCls.getDomainJsonForAlign(r.chains[n+"_"+m])};d=o.getAjaxPostPromise(h,e)}else{let e={pdb_query:r.saveFileCls.getAtomPDB(r.chains[l+"_"+a]),pdb_target:r.saveFileCls.getAtomPDB(r.chains[n+"_"+m])};d=o.getAjaxPostPromise(p,e)}e.push(d),t.push(s-1),c.push(l)}let m=Promise.allSettled(e),u=await m;await a.downloadChainalignmentPart2b(s,i,d,u,t,n,c)}}async downloadChainalignmentPart2b(e,t,s,i,n,l,r){let o=this.icn3d,a=o.icn3dui;for(let e=0,t=i.length;ec&&(c=l[t[0]],a=t[0]),l[t[1]]>c&&(c=l[t[1]],a=t[1])}let h={},p={},m={},u={};for(let e in r){let t,s,i=e.split("_"),n=r[e].split(","),l=n[2];a==i[0]?(t=i[0],s=i[1]):a==i[1]?(t=i[1],s=i[0]):(t=i[0],s=i[1]),m[t]=1,m.hasOwnProperty(s)||(m[s]=1,u[e]=r[e],d="target",this.transformStructure(t,l,d),d="query",this.transformStructure(s,l,d),h[n[0]]=1,h[n[1]]=1)}for(let e in u)if(void 0!==i.q_rotation){let t=u[e].split(","),s=[t[1],t[0],t[2]],l=i.setSeqAlignCls.setSeqAlignChain(void 0,void 0,s);p=n.hashUtilsCls.unionHash(p,l);let r=!1,o=n.htmlCls.alignSeqCls.getAlignSequencesAnnotations(Object.keys(i.alnChains),void 0,void 0,!1,void 0,r),a=$("#"+i.pre+"dl_sequence2").html();$("#"+i.pre+"dl_sequence2").html(a+o.sequencesHtml),$("#"+i.pre+"dl_sequence2").width(n.htmlCls.RESIDUE_WIDTH*o.maxSeqCnt+200)}i.dAtoms=n.hashUtilsCls.cloneHash(p),i.hAtoms=n.hashUtilsCls.cloneHash(p);let g="protein_aligned";i.selectionCls.saveSelection(g,g),i.opts.color="identity",i.setColorCls.setColorByOptions(i.opts,i.hAtoms),n.htmlCls.dialogCls.openDlg("dl_alignment","Select residues in aligned sequences"),i.drawCls.draw(),i.transformCls.zoominSelection(),i.hlUpdateCls.updateHlAll()}transformStructure(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=n.structures[e];for(let e=0,o=r.length;e2){let e=i.firstAtomObjCls.getResiduesFromAtoms(s),t="protein_aligned",n="protein aligned",l="select "+i.resid2specCls.residueids2spec(Object.keys(e));i.selectionCls.addCustomSelection(Object.keys(e),t,n,l,!0)}i.hlUpdateCls.updateHlAll(),n.htmlCls.dialogCls.openDlg("dl_alignment","Select residues in aligned sequences"),void 0!==n.cfg.rotate&&i.resizeCanvasCls.rotStruc(n.cfg.rotate,!0),i.html2ddgm="",n.cfg.show2d&&i.bFullUi&&(n.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions"),i.bFullUi&&(i.bChainAlign?await i.ParserUtilsCls.set2DDiagramsForChainalign(t):i.ParserUtilsCls.download2Ddgm(i.inputid.toUpperCase())))}addPostfixForChainids(e){this.icn3d.icn3dui;let t={};for(let s=0,i=e.length;s5?(d="https://alphafold.ebi.ac.uk/files/AF-"+i.mmdbid_t+"-F1-model_"+i.AFUniprotVersion+".pdb",a=n.getAjaxPromise(d,"text")):(d=n.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+n.cfg.bu+"&uid="+i.mmdbid_t,void 0!==n.cfg.inpara&&(d+=n.cfg.inpara),a=n.getAjaxPromise(d,"jsonp")),c.push(a),i.ParserUtilsCls.setYourNote(e.toUpperCase()+" in iCn3D"),i.pdbid_chain2title={},void 0===i.chainids2resids&&(i.chainids2resids={}),i.afChainIndexHash={},i.pdbChainIndexHash={};for(let e=1,t=l.length;e5?(t="https://alphafold.ebi.ac.uk/files/AF-"+i.mmdbid_q+"-F1-model_"+i.AFUniprotVersion+".pdb",s=n.getAjaxPromise(t,"text")):(t=n.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+n.cfg.bu+"&uid="+i.mmdbid_q,void 0!==n.cfg.inpara&&(t+=n.cfg.inpara),s=n.getAjaxPromise(t,"jsonp")),c.push(s)}for(let e=1,t=l.length;e0?r[e]+","+r[0]:void 0;if("tmalign"!=n.cfg.aligntool&&4==i.mmdbid_t.length&&4==i.mmdbid_q.length){let o;o=r.length>0?n.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?domainpairs="+l:n.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?chainpairs="+t;let a=n.getAjaxPromise(o,"jsonp");c.push(a),i.pdbChainIndexHash[e]=s+"_"+i.chain_q+"_"+i.mmdbid_t+"_"+i.chain_t}else i.afChainIndexHash[e]=i.mmdbid_q+"_"+i.chain_q+"_"+i.mmdbid_t+"_"+i.chain_t}}let h=Promise.allSettled(c),p=await h;await this.parseChainAlignData(p,l,i.mmdbid_t,i.chain_t)}async parseChainAlignData(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=e[0].value,o="HEADER "+s+"\n";isNaN(s)&&s.length>5&&(r=o+r),n.t_trans_add=[],n.q_trans_sub=[],"tmalign"==l.cfg.aligntool&&(n.q_trans_add=[]),n.q_rotation=[],n.qt_start_end=[],n.mmdbidArray=[],n.mmdbidArray.push(s);let a=[];for(let s=1,i=t.length;s5&&(i=o+i),void 0===i||-1!==JSON.stringify(i).indexOf("Oops there was a problem"))return void alert("The coordinate data can NOT be retrieved for the structure "+r+"...");n.mmdbidArray.push(r),a.push(i)}let d=0;for(let r=1,o=t.length;r";"tmalign"==o.cfg.aligntool&&(d+="TM-score: "+n+"

    ",r.tmscore=n),$("#"+r.pre+"dl_rmsd_html").html(d),o.cfg.bSidebyside||o.htmlCls.dialogCls.openDlg("dl_rmsd","RMSD of alignment"),a=!0}return a}async loadOpmDataForChainalign(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=this;if(l.cfg.resnum||l.cfg.resdef)n.bCommandLoad||n.init(),await this.downloadChainalignmentPart2(e,t,void 0,s);else{let o=l.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?mmdbids2opm="+i.join("','"),a=await l.getAjaxPromise(o,"jsonp");if(a&&a.mmdbid){let i=a.mmdbid;n.selectedPdbid=i;let o="https://opm-assets.storage.googleapis.com/pdb/"+i.toLowerCase()+".pdb",d=await l.getAjaxPromise(o,"text");n.bOpm=!0;let c=!0,h=n.loadPDBCls.loadPDB(d,i,n.bOpm,c);$("#"+n.pre+"selectplane_z1").val(n.halfBilayerSize),$("#"+n.pre+"selectplane_z2").val(-n.halfBilayerSize),$("#"+n.pre+"extra_mem_z").val(n.halfBilayerSize),$("#"+n.pre+"intra_mem_z").val(-n.halfBilayerSize),n.bCommandLoad||n.init(),await r.downloadChainalignmentPart2(e,t,h,s)}else n.bCommandLoad||n.init(),await r.downloadChainalignmentPart2(e,t,void 0,s)}}async downloadMmdbAf(e,t,s,i){let n=this.icn3d,l=n.icn3dui;n.structArray=n.structures?Object.keys(n.structures):[],0==n.structArray.length?n.init():(n.bResetAnno=!0,n.bResetSets=!0);let r=e.split(","),o=[];for(let e=0,t=r.length;e5)t="https://alphafold.ebi.ac.uk/files/AF-"+i+"-F1-model_"+n.AFUniprotVersion+".pdb",s=l.getAjaxPromise(t,"text");else{let e=i;5==i.length&&(e=i.substr(0,4)),t=l.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+l.cfg.bu+"&uid="+e,void 0!==l.cfg.inpara&&(t+=l.cfg.inpara),s=l.getAjaxPromise(t,"jsonp")}a.push(s)}n.ParserUtilsCls.setYourNote(n.structArray+" in iCn3D"),n.ParserUtilsCls.showLoading();let d=Promise.allSettled(a),c=await d;await this.parseMMdbAfData(c,o,t,s),void 0===s&&n.ParserUtilsCls.hideLoading()}async parseMMdbAfData(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=[];for(let s=0,i=t.length;s5&&(i=n+i),void 0===i||-1!==JSON.stringify(i).indexOf("Oops there was a problem"))return void alert("The coordinate data can NOT be retrieved for the structure "+t[s]+"...");r.push(i)}let o=!1;for(let e=0,i=t.length;e5){let s=!1;await n.pdbParserCls.loadPdbData(r[e],t[e],!1,l,i,o,s)}else{let s=!0,l=t[e];await n.mmdbParserCls.parseMmdbData(r[e],i,void 0,void 0,o,s,l)}}let a=Object.keys(n.structures);if(n.opts.color=a.length>1?"structure":a[0].length>5?"confidence":"chain",n.setColorCls.setColorByOptions(n.opts,{}),await n.ParserUtilsCls.renderStructure(),n.bAnnoShown&&(await n.showAnnoCls.showAnnotations(),n.annotationCls.resetAnnoTabAll()),void 0!==l.cfg.rotate&&n.resizeCanvasCls.rotStruc(l.cfg.rotate,!0),s&&l.cfg.matchedchains){let e=!0,t=!0;await n.realignParserCls.realignChainOnSeqAlign(void 0,n.chainidArray,e,t),$("#"+n.pre+"dl_annotations").html(""),n.bAnnoShown=!1,$("#"+l.pre+"dl_selectannotations").hasClass("ui-dialog-content")&&$("#"+n.pre+"dl_selectannotations").dialog("isOpen")&&$("#"+n.pre+"dl_selectannotations").dialog("close")}else if(void 0!==i){let e=Object.keys(n.structures);2==i&&(l.cfg.aligntool="tmalign"),await n.vastplusCls.vastplusAlign(e,i)}}}class Gt{constructor(e){this.icn3d=e}async dsn6Parser(e,t,s){this.icn3d.icn3dui;let i="https://edmaps.rcsb.org/maps/"+e.toLowerCase()+"_"+t+".dsn6";await this.dsn6ParserBase(i,t,s,"url",!0)}async dsn6ParserBase(e,t,s,i,n){let l=this.icn3d,r=l.icn3dui,o=this;if("2fofc"==t&&l.bAjax2fofc)l.mapData.sigma2=s,l.setOptionCls.setOption("map",t);else if("fofc"==t&&l.bAjaxfofc)l.mapData.sigma=s,l.setOptionCls.setOption("map",t);else{let a=await r.getXMLHttpRqstPromise(e,"GET","arraybuffer","rcsbEdmaps");s=o.loadDsn6Data(a,t,s,i,n),"2fofc"==t?l.bAjax2fofc=!0:"fofc"==t&&(l.bAjaxfofc=!0),l.setOptionCls.setOption("map",t)}return s}loadDsn6Data(e,t,s,i,n){let l,r,o=this.icn3d,a=o.icn3dui,d={},c=e.buffer&&e.buffer instanceof ArrayBuffer?e.buffer:e,h=new Int16Array(c),p=new Uint8Array(c),m=String.fromCharCode.apply(null,p.subarray(0,512));if(0==m.indexOf(":-)"))d.xStart=parseInt(m.substr(10,5)),d.yStart=parseInt(m.substr(15,5)),d.zStart=parseInt(m.substr(20,5)),d.xExtent=parseInt(m.substr(32,5)),d.yExtent=parseInt(m.substr(38,5)),d.zExtent=parseInt(m.substr(42,5)),d.xRate=parseInt(m.substr(52,5)),d.yRate=parseInt(m.substr(58,5)),d.zRate=parseInt(m.substr(62,5)),d.xlen=1*parseFloat(m.substr(73,10)),d.ylen=1*parseFloat(m.substr(83,10)),d.zlen=1*parseFloat(m.substr(93,10)),d.alpha=parseFloat(m.substr(103,10)),d.beta=parseFloat(m.substr(113,10)),d.gamma=parseFloat(m.substr(123,10)),l=parseFloat(m.substr(138,12))/100,r=parseInt(m.substr(155,8)),d.sigma=100*parseFloat(m.substr(170,12));else{if(100!==h[18])for(let e=0,t=h.length;e>8&255}d.xStart=h[0],d.yStart=h[1],d.zStart=h[2],d.xExtent=h[3],d.yExtent=h[4],d.zExtent=h[5],d.xRate=h[6],d.yRate=h[7],d.zRate=h[8];let e=1/h[17],t=1*e;d.xlen=h[9]*t,d.ylen=h[10]*t,d.zlen=h[11]*t,d.alpha=h[12]*e,d.beta=h[13]*e,d.gamma=h[14]*e,l=h[15]/h[18],r=h[16]}a.bNode||console.log("header: "+JSON.stringify(d));let u=new Float32Array(d.xExtent*d.yExtent*d.zExtent),g=512,f=Math.ceil(d.xExtent/8),C=Math.ceil(d.yExtent/8),b=Math.ceil(d.zExtent/8),y=-999;for(let e=0;ey&&(y=u[e]),++g}}}}return n||(s=this.setSigma(y,i,t,s)),"2fofc"==t?(o.mapData.header2=d,o.mapData.data2=u,o.mapData.matrix2=this.getMatrix(d),o.mapData.type2=t,o.mapData.sigma2=s):(o.mapData.header=d,o.mapData.data=u,o.mapData.matrix=this.getMatrix(d),o.mapData.type=t,o.mapData.sigma=s),s}setSigma(e,t,s,i){let n,l=this.icn3d.icn3dui;"file"==t?n="dsn6sigma"+s:"url"==t&&(n="dsn6sigmaurl"+s);return n&&($("#"+l.pre+n).val()?i=$("#"+l.pre+n).val():(i=(.2*e).toFixed(2),$("#"+l.pre+n).val(i))),i}getMatrix(e){this.icn3d.icn3dui;let t=e,s=[t.xlen,0,0],i=[t.ylen*Math.cos(Math.PI/180*t.gamma),t.ylen*Math.sin(Math.PI/180*t.gamma),0],n=[t.zlen*Math.cos(Math.PI/180*t.beta),t.zlen*(Math.cos(Math.PI/180*t.alpha)-Math.cos(Math.PI/180*t.gamma)*Math.cos(Math.PI/180*t.beta))/Math.sin(Math.PI/180*t.gamma),0];n[2]=Math.sqrt(t.zlen*t.zlen*Math.sin(Math.PI/180*t.beta)*Math.sin(Math.PI/180*t.beta)-n[1]*n[1]);let l=[[],s,i,n],r=[0,t.xRate,t.yRate,t.zRate],o=[0,1,2,3],a=new THREE.Matrix4;return a.set(l[o[1]][0]/r[o[1]],l[o[2]][0]/r[o[2]],l[o[3]][0]/r[o[3]],0,l[o[1]][1]/r[o[1]],l[o[2]][1]/r[o[2]],l[o[3]][1]/r[o[3]],0,l[o[1]][2]/r[o[1]],l[o[2]][2]/r[o[2]],l[o[3]][2]/r[o[3]],0,0,0,0,1),a.multiply((new THREE.Matrix4).makeTranslation(t.xStart,t.yStart,t.zStart)),a}loadDsn6File(e){var t=this.icn3d,s=t.icn3dui;let i=this,n=$("#"+t.pre+"dsn6file"+e)[0].files[0],l=$("#"+t.pre+"dsn6sigma"+e).val();if(n){s.utilsCls.checkFileAPI();let t=new FileReader;t.onload=function(t){let n=i.icn3d,r=t.target.result;l=i.loadDsn6Data(r,e,l,"file"),"2fofc"==e?n.bAjax2fofc=!0:"fofc"==e&&(n.bAjaxfofc=!0),n.setOptionCls.setOption("map",e),s.htmlCls.clickMenuCls.setLogCmd("load map file "+$("#"+n.pre+"dsn6file"+e).val()+" with sigma "+l,!1)},t.readAsArrayBuffer(n)}else alert("Please select a file before clicking 'Load'")}loadDsn6FileUrl(e){var t=this.icn3d,s=t.icn3dui;let i=$("#"+t.pre+"dsn6fileurl"+e).val(),n=$("#"+t.pre+"dsn6sigmaurl"+e).val();i?(n=this.dsn6ParserBase(i,e,n,"url"),s.htmlCls.clickMenuCls.setLogCmd("set map "+e+" sigma "+n+" file dsn6 | "+encodeURIComponent(i),!0)):alert("Please input the file URL before clicking 'Load'")}}class Vt{constructor(e){this.icn3d=e}async ccp4ParserBase(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=await l.getXMLHttpRqstPromise(e,"GET","arraybuffer","");return s=this.load_map_from_buffer(r,t,s,i,!0),n.setOptionCls.setOption("map",t),s}load_map_from_buffer(e,t,s,i,n){let l=this.icn3d;if(l.icn3dui,e.byteLength<1024)throw Error("File shorter than 1024 bytes.");const r=new Int32Array(e,0,256);if(542130509!==r[52])throw Error("not a CCP4 map");const o=[r[0],r[1],r[2]],a=r[3];let d;if(2===a)d=4;else{if(0!==a)throw Error("Only Mode 2 and Mode 0 of CCP4 map is supported.");d=1}const c=[r[4],r[5],r[6]],h=[r[7],r[8],r[9]],p=r[23];if(1024+p+d*o[0]*o[1]*o[2]!==e.byteLength)throw Error("ccp4 file too short or too long");const m=new Float32Array(e,0,e.byteLength/4),u=new Yt(h),g=new Wt(m[10],m[11],m[12],m[13],m[14],m[15]),f=[r[16],r[17],r[18]],C=f.indexOf(1),b=f.indexOf(2),y=f.indexOf(3),v=m[19],_=m[20];if(p%4!=0)throw Error("CCP4 map with NSYMBT not divisible by 4 is not supported.");let w;w=2===a?m:new Int8Array(e);let S=(1024+p)/d|0,A=1,x=0;0===a&&-128===r[39]&&127===r[40]&&(A=(_-v)/255,x=.5*(v+_+A));const k=[c[0]+o[0],c[1]+o[1],c[2]+o[2]];let O=[0,0,0],R=-999;for(O[2]=c[2];O[2]R&&(R=e),S++}return n||(s=l.dsn6ParserCls.setSigma(R,i,t,s)),"2fofc"==t?(l.mapData.ccp4=1,l.mapData.grid2=u,l.mapData.unit_cell2=g,l.mapData.type2=t,l.mapData.sigma2=s):(l.mapData.ccp4=1,l.mapData.grid=u,l.mapData.unit_cell=g,l.mapData.type=t,l.mapData.sigma=s),s}load_maps_from_mtz_buffer(e,t,s,i,n,l){let r=this.icn3d;r.icn3dui;let o="fofc"==t,a=e.calculate_map(o),d=e.cell;const c=new Wt(d.a,d.b,d.c,d.alpha,d.beta,d.gamma);let h=-999;for(let e=0,t=a.length;eh&&(h=a[e]);if(n||(s=r.dsn6ParserCls.setSigma(h,i,t,s)),l){r.mapData.ccp4=0;let i={xExtent:e.nx,yExtent:e.ny,zExtent:e.nz,mean:void 0,sigma:s,ccp4:1,xStart:0,yStart:0,zStart:0};i.xRate=e.nx,i.yRate=e.ny,i.zRate=e.nz,i.xlen=d.a,i.ylen=d.b,i.zlen=d.c,i.alpha=d.alpha,i.beta=d.beta,i.gamma=d.gamma,"2fofc"==t?(r.mapData.header2=i,r.mapData.data2=a,r.mapData.matrix2=r.dsn6ParserCls.getMatrix(i),r.mapData.type2=t,r.mapData.sigma2=s):(r.mapData.header=i,r.mapData.data=a,r.mapData.matrix=r.dsn6ParserCls.getMatrix(i),r.mapData.type=t,r.mapData.sigma=s)}else{const i=new Yt([e.nx,e.ny,e.nz]);i.values.set(a),"2fofc"==t?(r.mapData.ccp4=1,r.mapData.grid2=i,r.mapData.unit_cell2=c,r.mapData.type2=t,r.mapData.sigma2=s):(r.mapData.ccp4=1,r.mapData.grid=i,r.mapData.unit_cell=c,r.mapData.type=t,r.mapData.sigma=s)}return e.delete(),s}parse_symop(e){const t=e.toLowerCase().replace(/\s+/g,"").split(",");if(3!==t.length)throw Error("Unexpected symop: "+e);let s=[];for(let i=0;i<3;i++){const n=t[i].split(/(?=[+-])/);let l=[0,0,0,0];for(let t=0;t0;for(let s=a[0];s<=d[0];s++)for(let i=a[1];i<=d[1];i++)for(let r=a[2];r<=d[2];r++){let o=e.grid2frac(s,i,r),a=t.orthogonalize(o);h.push(a);let d=new THREE.Vector3(a[0],a[1],a[2]),c=l.rayCls.getAtomsFromPosition(d,1,l.hAtoms)||!m?e.get_grid_value(s,i,r):0;"fofc_pos"==n&&c<0&&(c=0),"fofc_neg"==n&&(c=c>0?0:-c),p.push(c)}return{size:c,values:p,points:h}}marchingCubes(e,t,s,i,n){this.icn3d.icn3dui;const l=new Int32Array([0,0,514,770,1030,1030,1540,1796,2052,2053,2566,2566,3082,3331,3592,3840,144,152,658,658,1174,1182,1684,1684,2196,2196,2710,2710,3226,3218,3729,3728,560,560,51,314,1590,1590,1076,1084,2612,2613,2103,2358,3642,3890,3121,3376,672,680,163,170,1702,1711,1444,1196,2724,2724,2470,2214,4010,3747,3233,3232,1120,1120,1634,1890,102,102,613,868,3172,3173,3686,3686,2154,2147,2665,2656,1264,1272,1778,1778,246,254,757,764,3316,3316,3830,3830,2298,2291,2809,2800,1616,1616,1107,1362,598,598,84,340,3668,3924,3159,3414,2650,2898,2137,2384,1984,1729,1474,1218,966,718,197,196,4036,3781,3526,3270,3018,2754,2241,2240,2240,2240,2754,3010,3270,3270,3780,4044,196,197,710,966,1218,1474,1729,1984,2384,2137,2898,2650,3414,3159,3668,3676,340,84,606,598,1362,1107,1624,1616,2800,2800,2291,2298,3830,3830,3316,3324,756,1013,255,502,1778,1779,1273,1520,2656,2665,2147,2154,3686,3687,3429,3180,868,613,358,102,1898,1635,1120,1120,3232,3232,3746,4002,2214,2214,2724,2980,1196,1444,1710,1958,170,163,680,672,3376,3121,3890,3642,2358,2103,2869,2612,1084,1076,1854,1590,314,51,825,560,3728,3728,3218,3226,2710,2710,2196,2204,1684,1685,1183,1174,658,914,152,144,3840,3592,3331,3082,2566,2574,2053,2052,1796,1540,1286,1030,770,514,0,0]),r="snapped MC"===n,o=[[],[],[1,9],[1,8,1,9],[2,10,10,1],[2,10,10,1],[9,2,2,10,10,9],[2,8,2,10,10,8,10,9],[11,2],[0,11,11,2],[1,9,11,2],[1,11,11,2,1,9,9,11],[3,10,10,1,11,10],[0,10,10,1,8,10,11,10],[3,9,11,9,11,10,10,9],[8,10,10,9,11,10],[4,7],[4,3,4,7],[1,9,4,7],[4,1,1,9,4,7,7,1],[2,10,10,1,4,7],[3,4,4,7,2,10,10,1],[9,2,2,10,10,9,4,7],[2,10,10,9,9,2,9,7,7,2,4,7],[4,7,11,2],[11,4,4,7,11,2,2,4],[1,9,4,7,11,2],[4,7,11,4,11,9,11,2,2,9,1,9],[3,10,10,1,11,10,4,7],[1,11,11,10,10,1,1,4,4,11,4,7],[4,7,0,11,11,9,11,10,10,9],[4,7,11,4,11,9,11,10,10,9],[9,5,5,4],[9,5,5,4],[0,5,5,4,1,5],[8,5,5,4,3,5,1,5],[2,10,10,1,9,5,5,4],[2,10,10,1,9,5,5,4],[5,2,2,10,10,5,5,4,4,2],[2,10,10,5,5,2,5,3,5,4,4,3],[9,5,5,4,11,2],[0,11,11,2,9,5,5,4],[0,5,5,4,1,5,11,2],[1,5,5,2,5,8,8,2,11,2,5,4],[10,3,11,10,10,1,9,5,5,4],[9,5,5,4,8,1,8,10,10,1,11,10],[5,4,0,5,0,11,11,5,11,10,10,5],[5,4,8,5,8,10,10,5,11,10],[9,7,5,7,9,5],[9,3,9,5,5,3,5,7],[0,7,1,7,1,5,5,7],[1,5,5,3,5,7],[9,7,9,5,5,7,10,1,2,10],[10,1,2,10,9,5,5,0,5,3,5,7],[2,8,2,5,5,8,5,7,10,5,2,10],[2,10,10,5,5,2,5,3,5,7],[7,9,9,5,5,7,11,2],[9,5,5,7,7,9,7,2,2,9,11,2],[11,2,1,8,1,7,1,5,5,7],[11,2,1,11,1,7,1,5,5,7],[9,5,5,8,5,7,10,1,3,10,11,10],[5,7,7,0,0,5,9,5,11,0,0,10,10,1,11,10],[11,10,10,0,0,11,10,5,5,0,0,7,5,7],[11,10,10,5,5,11,5,7],[10,6,6,5,5,10],[5,10,10,6,6,5],[1,9,5,10,10,6,6,5],[1,8,1,9,5,10,10,6,6,5],[1,6,6,5,5,1,2,6],[1,6,6,5,5,1,2,6],[9,6,6,5,5,9,0,6,2,6],[5,9,8,5,8,2,2,5,2,6,6,5],[11,2,10,6,6,5,5,10],[11,0,11,2,10,6,6,5,5,10],[1,9,11,2,5,10,10,6,6,5],[5,10,10,6,6,5,1,9,9,2,9,11,11,2],[6,3,11,6,6,5,5,3,5,1],[11,0,11,5,5,0,5,1,11,6,6,5],[11,6,6,3,6,0,6,5,5,0,5,9],[6,5,5,9,9,6,9,11,11,6],[5,10,10,6,6,5,4,7],[4,3,4,7,6,5,5,10,10,6],[1,9,5,10,10,6,6,5,4,7],[10,6,6,5,5,10,1,9,9,7,7,1,4,7],[6,1,2,6,6,5,5,1,4,7],[2,5,5,1,2,6,6,5,4,3,4,7],[4,7,0,5,5,9,0,6,6,5,2,6],[3,9,9,7,4,7,2,9,5,9,9,6,6,5,2,6],[11,2,4,7,10,6,6,5,5,10],[5,10,10,6,6,5,4,7,7,2,2,4,11,2],[1,9,4,7,11,2,5,10,10,6,6,5],[9,2,1,9,9,11,11,2,4,11,4,7,5,10,10,6,6,5],[4,7,11,5,5,3,5,1,11,6,6,5],[5,1,1,11,11,5,11,6,6,5,0,11,11,4,4,7],[0,5,5,9,0,6,6,5,3,6,11,6,4,7],[6,5,5,9,9,6,9,11,11,6,4,7,7,9],[10,4,9,10,6,4,10,6],[4,10,10,6,6,4,9,10],[10,0,1,10,10,6,6,0,6,4],[1,8,1,6,6,8,6,4,1,10,10,6],[1,4,9,1,2,4,2,6,6,4],[2,9,9,1,2,4,2,6,6,4],[2,4,2,6,6,4],[2,8,2,4,2,6,6,4],[10,4,9,10,10,6,6,4,11,2],[8,2,11,2,9,10,10,4,10,6,6,4],[11,2,1,6,6,0,6,4,1,10,10,6],[6,4,4,1,1,6,1,10,10,6,8,1,1,11,11,2],[9,6,6,4,9,3,3,6,9,1,11,6],[11,1,1,8,11,6,6,1,9,1,1,4,6,4],[11,6,6,3,6,0,6,4],[6,4,8,6,11,6],[7,10,10,6,6,7,8,10,9,10],[0,7,0,10,10,7,9,10,6,7,10,6],[10,6,6,7,7,10,1,10,7,1,8,1],[10,6,6,7,7,10,7,1,1,10],[2,6,6,1,6,8,8,1,9,1,6,7],[2,6,6,9,9,2,9,1,6,7,7,9,9,3],[0,7,0,6,6,7,2,6],[2,7,6,7,2,6],[11,2,10,6,6,8,8,10,9,10,6,7],[0,7,7,2,11,2,9,7,6,7,7,10,10,6,9,10],[1,8,1,7,1,10,10,7,6,7,10,6,11,2],[11,2,1,11,1,7,10,6,6,1,1,10,6,7],[9,6,6,8,6,7,9,1,1,6,11,6,6,3],[9,1,11,6,6,7],[0,7,0,6,6,7,11,0,11,6],[11,6,6,7],[7,6,6,11],[7,6,6,11],[1,9,7,6,6,11],[8,1,1,9,7,6,6,11],[10,1,2,10,6,11,7,6],[2,10,10,1,6,11,7,6],[2,9,2,10,10,9,6,11,7,6],[6,11,7,6,2,10,10,3,10,8,10,9],[7,2,6,2,7,6],[7,0,7,6,6,0,6,2],[2,7,7,6,6,2,1,9],[1,6,6,2,1,8,8,6,1,9,7,6],[10,7,7,6,6,10,10,1,1,7],[10,7,7,6,6,10,1,7,10,1,1,8],[7,0,7,10,10,0,10,9,6,10,7,6],[7,6,6,10,10,7,10,8,10,9],[6,8,4,6,6,11],[3,6,6,11,0,6,4,6],[8,6,6,11,4,6,1,9],[4,6,6,9,6,3,3,9,1,9,6,11],[6,8,4,6,6,11,2,10,10,1],[2,10,10,1,0,11,0,6,6,11,4,6],[4,11,4,6,6,11,2,9,2,10,10,9],[10,9,9,3,3,10,2,10,4,3,3,6,6,11,4,6],[8,2,4,2,4,6,6,2],[4,2,4,6,6,2],[1,9,3,4,4,2,4,6,6,2],[1,9,4,1,4,2,4,6,6,2],[8,1,8,6,6,1,4,6,6,10,10,1],[10,1,0,10,0,6,6,10,4,6],[4,6,6,3,3,4,6,10,10,3,3,9,10,9],[10,9,4,10,6,10,4,6],[9,5,5,4,7,6,6,11],[9,5,5,4,7,6,6,11],[5,0,1,5,5,4,7,6,6,11],[7,6,6,11,3,4,3,5,5,4,1,5],[9,5,5,4,10,1,2,10,7,6,6,11],[6,11,7,6,2,10,10,1,9,5,5,4],[7,6,6,11,5,4,4,10,10,5,4,2,2,10],[3,4,3,5,5,4,2,5,10,5,2,10,7,6,6,11],[7,2,7,6,6,2,5,4,9,5],[9,5,5,4,8,6,6,0,6,2,7,6],[3,6,6,2,7,6,1,5,5,0,5,4],[6,2,2,8,8,6,7,6,1,8,8,5,5,4,1,5],[9,5,5,4,10,1,1,6,6,10,1,7,7,6],[1,6,6,10,10,1,1,7,7,6,0,7,9,5,5,4],[0,10,10,4,10,5,5,4,3,10,6,10,10,7,7,6],[7,6,6,10,10,7,10,8,5,4,4,10,10,5],[6,9,9,5,5,6,6,11,11,9],[3,6,6,11,0,6,0,5,5,6,9,5],[0,11,0,5,5,11,1,5,5,6,6,11],[6,11,3,6,3,5,5,6,1,5],[2,10,10,1,9,5,5,11,11,9,5,6,6,11],[0,11,0,6,6,11,9,6,5,6,9,5,2,10,10,1],[8,5,5,11,5,6,6,11,0,5,10,5,5,2,2,10],[6,11,3,6,3,5,5,6,2,10,10,3,10,5],[5,8,9,5,5,2,2,8,5,6,6,2],[9,5,5,6,6,9,6,0,6,2],[1,5,5,8,8,1,5,6,6,8,8,2,6,2],[1,5,5,6,6,1,6,2],[3,6,6,1,6,10,10,1,8,6,5,6,6,9,9,5],[10,1,0,10,0,6,6,10,9,5,5,0,5,6],[5,6,6,10,10,5],[10,5,5,6,6,10],[11,5,5,10,10,11,7,5],[11,5,5,10,10,11,7,5],[5,11,7,5,5,10,10,11,1,9],[10,7,7,5,5,10,10,11,8,1,1,9],[11,1,2,11,7,1,7,5,5,1],[2,7,7,1,7,5,5,1,2,11],[9,7,7,5,5,9,9,2,2,7,2,11],[7,5,5,2,2,7,2,11,5,9,9,2,2,8],[2,5,5,10,10,2,3,5,7,5],[8,2,8,5,5,2,7,5,10,2,5,10],[1,9,5,10,10,3,3,5,7,5,10,2],[8,2,2,9,1,9,7,2,10,2,2,5,5,10,7,5],[3,5,5,1,7,5],[7,0,7,1,7,5,5,1],[3,9,3,5,5,9,7,5],[7,9,5,9,7,5],[5,8,4,5,5,10,10,8,10,11],[5,0,4,5,5,11,11,0,5,10,10,11],[1,9,4,10,10,8,10,11,4,5,5,10],[10,11,11,4,4,10,4,5,5,10,3,4,4,1,1,9],[2,5,5,1,2,8,8,5,2,11,4,5],[4,11,11,0,4,5,5,11,2,11,11,1,5,1],[2,5,5,0,5,9,2,11,11,5,4,5,5,8],[4,5,5,9,2,11],[2,5,5,10,10,2,3,5,3,4,4,5],[5,10,10,2,2,5,2,4,4,5],[3,10,10,2,3,5,5,10,8,5,4,5,1,9],[5,10,10,2,2,5,2,4,4,5,1,9,9,2],[4,5,5,8,5,3,5,1],[4,5,5,0,5,1],[4,5,5,8,5,3,0,5,5,9],[4,5,5,9],[4,11,7,4,9,11,9,10,10,11],[9,7,7,4,9,11,9,10,10,11],[1,10,10,11,11,1,11,4,4,1,7,4],[1,4,4,3,1,10,10,4,7,4,4,11,10,11],[4,11,7,4,9,11,9,2,2,11,9,1],[9,7,7,4,9,11,9,1,1,11,2,11],[7,4,4,11,4,2,2,11],[7,4,4,11,4,2,2,11,3,4],[2,9,9,10,10,2,2,7,7,9,7,4],[9,10,10,7,7,9,7,4,10,2,2,7,7,0],[7,10,10,3,10,2,7,4,4,10,1,10,10,0],[1,10,10,2,7,4],[9,1,1,4,1,7,7,4],[9,1,1,4,1,7,7,4,8,1],[3,4,7,4],[7,4],[9,10,10,8,10,11],[9,3,9,11,9,10,10,11],[1,10,10,0,10,8,10,11],[1,10,10,3,10,11],[2,11,11,1,11,9,9,1],[9,3,9,11,2,9,9,1,2,11],[2,11,11,0],[2,11],[8,2,8,10,10,2,9,10],[9,10,10,2,2,9],[8,2,8,10,10,2,1,8,1,10],[1,10,10,2],[8,1,9,1],[9,1],[],[]];let a=new Array(12);const d=this.calculateVertOffsets(e),c=[[0,1],[1,2],[2,3],[3,0],[4,5],[5,6],[6,7],[7,4],[0,4],[1,5],[2,6],[3,7]];let h=new Float32Array(8),p=[0,0,0],m=[p,p,p,p,p,p,p,p];const u=e[0],g=e[1],f=e[2];if(null==t||null==s)return;let C=[],b=[],y=0;for(let e=0;e.85?t=1:t<.15&&(t=0));const s=m[e[0]],n=m[e[1]];C.push(s[0]+(n[0]-s[0])*t,s[1]+(n[1]-s[1])*t,s[2]+(n[2]-s[2])*t),a[v]=y++}const A=o[w];for(v=0;v=0?s:s+t}grid2index(e,t,s){return e=this.modulo(e,this.dim[0]),t=this.modulo(t,this.dim[1]),s=this.modulo(s,this.dim[2]),this.dim[2]*(this.dim[1]*e+t)+s}grid2index_unchecked(e,t,s){return this.dim[2]*(this.dim[1]*e+t)+s}grid2frac(e,t,s){return[e/this.dim[0],t/this.dim[1],s/this.dim[2]]}frac2grid(e){return[0|Math.floor(e[0]*this.dim[0]),0|Math.floor(e[1]*this.dim[1]),0|Math.floor(e[2]*this.dim[2])]}set_grid_value(e,t,s,i){const n=this.grid2index(e,t,s);this.values[n]=i}get_grid_value(e,t,s){const i=this.grid2index(e,t,s);return this.values[i]}}class Xt{constructor(e){this.icn3d=e}async mtzParserBase(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui,a=await o.getXMLHttpRqstPromise(e,"GET","arraybuffer","");return s=await this.loadMtzFileBase(a,t,s,i,n,e,l),r.setOptionCls.setOption("map",t),s}loadMtzFile(e,t){var s=this.icn3d,i=s.icn3dui;let n=this,l=$("#"+s.pre+"dsn6file"+e)[0].files[0],r=$("#"+s.pre+"dsn6sigma"+e).val();if(l){i.utilsCls.checkFileAPI();let s=new FileReader;s.onload=async function(s){let l=n.icn3d;r=await n.loadMtzFileBase(s.target.result,e,r,"file",void 0,void 0,t),i.htmlCls.clickMenuCls.setLogCmd("load map file "+$("#"+l.pre+"dsn6file"+e).val()+" with sigma "+r,!1)},s.readAsArrayBuffer(l)}else alert("Please select a file before clicking 'Load'")}async loadMtzFileBase(e,t,s,i,n,l,r){var o=this.icn3d,a=o.icn3dui;if(void 0===o.bMtz){let e="./script/mtz.js";await a.getAjaxPromise(e,"script"),o.bMtz=!0}GemmiMtz().then((function(d){let c=d.readMtz(e);s=o.ccp4ParserCls.load_maps_from_mtz_buffer(c,t,s,i,n,r),o.setOptionCls.setOption("map",t);let h=r?"rcsbmtz":"mtz";return l&&a.htmlCls.clickMenuCls.setLogCmd("set map "+t+" sigma "+s+" file "+h+" | "+encodeURIComponent(l),!0),s}))}async loadMtzFileUrl(e,t){var s=this.icn3d;s.icn3dui;let i=$("#"+s.pre+"dsn6fileurl"+e).val(),n=$("#"+s.pre+"dsn6sigmaurl"+e).val();i?n=await this.mtzParserBase(i,e,n,"url",void 0,t):alert("Please input the file URL before clicking 'Load'")}}class Kt{constructor(e){this.icn3d=e}async downloadMmcif(e){let t=this.icn3d,s=t.icn3dui;t.ParserUtilsCls.setYourNote(e.toUpperCase()+"(MMCIF) in iCn3D");let i="https://files.rcsb.org/download/"+e+".cif",n=await s.getAjaxPromise(i,"text",!0);await t.opmParserCls.loadOpmData(n,e,void 0,"mmcif",void 0,!0)}async downloadMmcifSymmetry(e,t){let s=this.icn3d,i=s.icn3dui;try{let n="https://models.rcsb.org/"+e+".bcif",l=await i.getXMLHttpRqstPromise(n,"GET","arraybuffer","bcif"),r=!1,o=!0,a=s.bcifParserCls.getBcifJson(l,e,r,o),d=JSON.parse(a);if(void 0!==d.emd&&(s.emd=d.emd),void 0!==d.organism&&(s.organism=d.organism),s.bAssemblyUseAsu){for(let e=0,t=d.assembly.length;es.maxatomcnt&&(s.bAssembly=!0)}if("mmtfid"===t&&void 0!==d.missingseq){let t=0,n="";for(let l=0,r=d.missingseq.length;lt)&&(s.chainMissingResidueArray[c].push(h),t=a,n=o)}s.loadPDBCls.adjustSeq(s.chainMissingResidueArray)}}catch(e){return void(i.bNode||console.log("mmcifparser.cgi issues: "+e))}}async loadMmcifData(e,t){let s=this.icn3d;if(s.icn3dui,t||(t=e.mmcif),t||(t=s.defaultPdbId),void 0===e.atoms)return!1;s.init(),void 0!==e.emd&&(s.emd=e.emd),void 0!==e.organism&&(s.organism=e.organism),await s.opmParserCls.loadOpmData(e,t,void 0,"mmcif"),s.opmParserCls.modifyUIMapAssembly()}async loadMultipleMmcifData(e,t,s){let i=this.icn3d;i.icn3dui;i.loadCIFCls.loadCIF(e,t,!0,s),Object.keys(i.structures).length>1&&(i.opts.color="structure"),i.opmParserCls.modifyUIMapAssembly(),i.pdbParserCls.addSecondary(s)}}class Jt{constructor(e){this.icn3d=e}async downloadMmdb(e,t){let s,i=this.icn3d,n=i.icn3dui;try{if(s=await this.loadMmdbPrms(e,t),!s||s.error)return void this.getNoData(e,t)}catch(s){return void this.getNoData(e,t)}if(0!=Object.keys(s.atoms).length)if(n.utilsCls.isCalphaPhosOnly(s.atoms)||s.atomCount<=i.maxatomcnt)await this.parseMmdbData(s);else{let s;try{s=await this.loadMmdbPrms(e,t,!0)}catch(s){return void this.getNoData(e,t)}await this.parseMmdbData(s)}else{let e=s.pdbId;await i.bcifParserCls.downloadBcif(e)}}async downloadGi(e){let t=this.icn3d;t.icn3dui,t.bCid=void 0;await this.downloadMmdb(e,!0)}async downloadBlast_rep_id(e){let t=this.icn3d,s=t.icn3dui,i=e.split(",");s.cfg.query_id=i[0],s.cfg.blast_rep_id=i[1];let n=s.cfg.blast_rep_id.split("_")[0];4==n.length?await this.downloadMmdb(n):(t.blastAcxn=s.cfg.blast_rep_id.split(".")[0],await this.downloadRefseq(t.blastAcxn,!0))}async downloadRefseq(e,t){let s=this.icn3d,i=s.icn3dui,n=i.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?refseq2uniprot="+e;i.cfg.refseqid=e;let l=await i.getAjaxPromise(n,"jsonp",!1,"The protein accession "+e+" can not be mapped to AlphaFold UniProt ID...");if(!l||!l.uniprot)return void alert("The accession "+e+" can not be mapped to AlphaFold UniProt ID. It will be treated as a UniProt ID instead.");i.cfg.afid=l.uniprot,s.uniprot2acc||(s.uniprot2acc={}),s.uniprot2acc[l.uniprot]=e,t&&(i.cfg.blast_rep_id=i.cfg.afid+"_A");await s.pdbParserCls.downloadPdb(i.cfg.afid,!0)}async downloadProteinname(e){let t=this.icn3d,s=t.icn3dui;s.icn3d.bCid=void 0;let i=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?protein2acc="+e,n=(await s.getAjaxPromise(i,"jsonp")).acc;if(0==n.length)return void(s.bNode||alert("The protein/gene name "+e+" can not be mapped to RefSeq proteins..."));let l=[];for(let e=0,t=n.length;e=20231001||!i.cfg.date&&parseInt(i.utilsCls.getDateDigitStr())>=20231001)&&(h=h.replace(/_/g,"")),void 0===d[h]?d[h]=1:++d[h];let p=n+"_"+(1===d[h]?h:h+d[h].toString());r[e]=c,o[p]=e,a[e]=p,(void 0===t||i.cfg.mmdbafid)&&(s.chainsColor[p]=i.parasCls.thr(c));let m=void 0===l[e].geneId?"":l[e].geneId,u=void 0===l[e].geneSymbol?"":l[e].geneSymbol,g=void 0===l[e].geneDesc?"":l[e].geneDesc;s.chainsGene[p]={geneId:m,geneSymbol:u,geneDesc:g}}s.molid2chain=a,$("#"+s.pre+"accordion5").show()}loadMmdbPrms(e,t,s){let i,n=this.icn3d,l=n.icn3dui;return i=t?l.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+l.cfg.bu+"&simple=1&gi="+e:l.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+l.cfg.bu+"&simple=1&uid="+e,void 0!==l.cfg.blast_rep_id&&(i+="&bu=0"),void 0!==l.cfg.inpara&&(i+=l.cfg.inpara),s&&(i+="&complexity=2"),void 0===n.chainids2resids&&(n.chainids2resids={}),l.getAjaxPromise(i,"jsonp",!0)}}class Zt{constructor(e){this.icn3d=e,this.mElem2Radius={},this.mElem2Radius.H=.31,this.mElem2Radius.HE=.28,this.mElem2Radius.LI=1.28,this.mElem2Radius.BE=.96,this.mElem2Radius.B=.84,this.mElem2Radius.C=.76,this.mElem2Radius.N=.71,this.mElem2Radius.O=.66,this.mElem2Radius.F=.57,this.mElem2Radius.NE=.58,this.mElem2Radius.NA=1.66,this.mElem2Radius.MG=1.41,this.mElem2Radius.AL=1.21,this.mElem2Radius.SI=1.11,this.mElem2Radius.P=1.07,this.mElem2Radius.S=1.05,this.mElem2Radius.CL=1.02,this.mElem2Radius.AR=1.06,this.mElem2Radius.K=2.03,this.mElem2Radius.CA=1.76,this.mElem2Radius.SC=1.7,this.mElem2Radius.TI=1.6,this.mElem2Radius.V=1.53,this.mElem2Radius.CR=1.39,this.mElem2Radius.MN=1.39,this.mElem2Radius.FE=1.32,this.mElem2Radius.CO=1.26,this.mElem2Radius.NI=1.24,this.mElem2Radius.CU=1.32,this.mElem2Radius.ZN=1.22,this.mElem2Radius.GA=1.22,this.mElem2Radius.GE=1.2,this.mElem2Radius.AS=1.19,this.mElem2Radius.SE=1.2,this.mElem2Radius.BR=1.2,this.mElem2Radius.KR=1.16,this.mElem2Radius.RB=2.2,this.mElem2Radius.SR=1.95,this.mElem2Radius.Y=1.9,this.mElem2Radius.ZR=1.75,this.mElem2Radius.NB=1.64,this.mElem2Radius.MO=1.54,this.mElem2Radius.TC=1.47,this.mElem2Radius.RU=1.46,this.mElem2Radius.RH=1.42,this.mElem2Radius.PD=1.39,this.mElem2Radius.AG=1.45,this.mElem2Radius.CD=1.44,this.mElem2Radius.IN=1.42,this.mElem2Radius.SN=1.39,this.mElem2Radius.SB=1.39,this.mElem2Radius.TE=1.38,this.mElem2Radius.I=1.39,this.mElem2Radius.XE=1.4,this.mElem2Radius.CS=2.44,this.mElem2Radius.BA=2.15,this.mElem2Radius.LA=2.07,this.mElem2Radius.CE=2.04,this.mElem2Radius.PR=2.03,this.mElem2Radius.ND=2.01,this.mElem2Radius.PM=1.99,this.mElem2Radius.SM=1.98,this.mElem2Radius.EU=1.98,this.mElem2Radius.GD=1.96,this.mElem2Radius.TB=1.94,this.mElem2Radius.DY=1.92,this.mElem2Radius.HO=1.92,this.mElem2Radius.ER=1.89,this.mElem2Radius.TM=1.9,this.mElem2Radius.YB=1.87,this.mElem2Radius.LU=1.87,this.mElem2Radius.HF=1.75,this.mElem2Radius.TA=1.7,this.mElem2Radius.W=1.62,this.mElem2Radius.RE=1.51,this.mElem2Radius.OS=1.44,this.mElem2Radius.IR=1.41,this.mElem2Radius.PT=1.36,this.mElem2Radius.AU=1.36,this.mElem2Radius.HG=1.32,this.mElem2Radius.TL=1.45,this.mElem2Radius.PB=1.46,this.mElem2Radius.BI=1.48,this.mElem2Radius.PO=1.4,this.mElem2Radius.AT=1.5,this.mElem2Radius.RN=1.5,this.mElem2Radius.FR=2.6,this.mElem2Radius.RA=2.21,this.mElem2Radius.AC=2.15,this.mElem2Radius.TH=2.06,this.mElem2Radius.PA=2,this.mElem2Radius.U=1.96,this.mElem2Radius.NP=1.9,this.mElem2Radius.PU=1.87,this.mElem2Radius.AM=1.8,this.mElem2Radius.CM=1.69}async downloadBcif(e){let t=this.icn3d,s=t.icn3dui;t.ParserUtilsCls.setYourNote(e.toUpperCase()+"(BCIF) in iCn3D");let i="https://models.rcsb.org/"+e+".bcif",n=await s.getXMLHttpRqstPromise(i,"GET","arraybuffer","bcif");if(0==n.length)return void alert("This PDB structure is not found at RCSB...");await t.opmParserCls.loadOpmData(n,e,void 0,"bcif",void 0,!1)}getBcifJson(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r="",o="",a="",d="",c="",h="",p=s?CIFTools.Text.parse(e):CIFTools.Binary.parse(e);if(p.isError)return void alert("The Binary CIF data can NOT be parsed: "+p.toString());let m=p.result.dataBlocks[0];t||(m.getCategory("_entry")&&(t=m.getCategory("_entry").getColumn("id").getString(0)),""==t&&(t="stru")),m.getCategory("_citation")&&(o=m.getCategory("_citation").getColumn("pdbx_database_id_PubMed").getString(0)),m.getCategory("_struct")&&(a=m.getCategory("_struct").getColumn("title").getString(0),a=a.replace(/"/,"'")),m.getCategory("_struct_keywords")&&(d=m.getCategory("_struct_keywords").getColumn("pdbx_keywords").getString(0)),m.getCategory("_entity_src_gen")&&(h=m.getCategory("_entity_src_gen").getColumn("gene_src_common_name").getString(0));let u={},g={},f={};if(m.getCategory("_database_2")){let e=m.getCategory("_database_2"),t=e.rowCount;for(let s=0;sn.maxatomcnt),j=[];if(!i){_=P.getColumn("group_PDB"),w=P.getColumn("label_comp_id"),S=P.getColumn("type_symbol"),A=P.getColumn("label_atom_id"),x=P.getColumn("auth_asym_id"),k=P.getColumn("label_seq_id"),O=P.getColumn("auth_seq_id"),R=P.getColumn("label_alt_id"),I=P.getColumn("B_iso_or_equiv"),E=P.getColumn("Cartn_x"),T=P.getColumn("Cartn_y"),D=P.getColumn("Cartn_z"),j=P.getColumn("label_asym_id");let e={},t="";for(let s=0;s0&&(r=r.substr(0,r.length-2)),r+="], ",f.hasOwnProperty(M)){r+='"ss":"'+f[M]+'", '}else r+='"ss":"coil", ';u.hasOwnProperty(M)?r+='"ssbegin":1, ':r+='"ssbegin":0, ',g.hasOwnProperty(M)?r+='"ssend":1, ':r+='"ssend":0, ',r+='"mt":"'+s+'"',r+="}",r+=",\n",q=a+"_"+n,prevAutochain=p,++B}B>1&&(r=r.substr(0,r.length-2)),r+="]"}_=w=S=A=x=k=O=R=I=E=T=D=j=[];let z={};if(m.getCategory("_pdbx_poly_seq_scheme")){let e=m.getCategory("_pdbx_poly_seq_scheme"),t=e.getColumn("seq_id"),s=e.getColumn("pdb_seq_num"),i=e.getColumn("mon_id"),n=e.getColumn("pdb_strand_id"),l=e.rowCount,r="",o="";for(let e=0;e0){r+=', "disulfides":[';for(let e=0;eMOLECULE"==o){t.molTitle=s[e+1].trim();let l=s[e+2].trim().replace(/\s+/g," ").split(" ");i=l[0],n=l[1],e+=4}else"@ATOM"==o?(c=1,h=!0,++e):"@BOND"==o?(p=!0,h=!1,++e):"@SUBSTRUCTURE"==o&&(p=!1,++e);if(o=s[e].trim(),""!==o&&"#"!==o.substr(0,1)){if(h&&a1&&($("#"+e.pre+"assemblyWrapper").show(),e.asuCnt=e.biomtMatrices.length))}async parseAtomData(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;"mmcif"===i||"bcif"===i?(r.loadCIFCls.loadCIF(e,t,l),this.modifyUIMapAssembly(),r.setStyleCls.setAtomStyleByOptions(r.opts),r.setColorCls.setColorByOptions(r.opts,r.atoms),await r.ParserUtilsCls.renderStructure(),void 0!==o.cfg.rotate&&r.resizeCanvasCls.rotStruc(o.cfg.rotate,!0)):"pdb"===i?await r.pdbParserCls.loadPdbData(e,t):"align"===i&&(r.bOpm?await r.alignParserCls.downloadAlignmentPart2(t):void 0!==n?await this.loadOpmData(e,n,s,i):await r.alignParserCls.downloadAlignmentPart2(t))}}class ts{constructor(e){this.icn3d=e}async downloadPdb(e,t){let s,i=this.icn3d,n=i.icn3dui;t?(s="https://alphafold.ebi.ac.uk/files/AF-"+e+"-F1-model_"+i.AFUniprotVersion+".pdb",n.cfg.refseqid?i.ParserUtilsCls.setYourNote(n.cfg.refseqid.toUpperCase()+"(NCBI Protein Acc.) in iCn3D"):n.cfg.protein?i.ParserUtilsCls.setYourNote(n.cfg.protein+"(NCBI Protein/Gene) in iCn3D"):i.ParserUtilsCls.setYourNote(e.toUpperCase()+"(AlphaFold) in iCn3D")):(s="https://files.rcsb.org/download/"+e+".pdb",e=e.toUpperCase(),i.ParserUtilsCls.setYourNote(e+"(PDB) in iCn3D"));let l=await n.getAjaxPromise(s,"text",!0,"The ID "+e+" can not be found in the server "+s+"...");if(t){l="HEADER "+e+"\n"+l,await i.opmParserCls.parseAtomData(l,e,void 0,"pdb",void 0)}else await i.opmParserCls.loadOpmData(l,e,void 0,"pdb")}async downloadUrl(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=e.lastIndexOf("/");if(-1!=r){let t=e.lastIndexOf(".");n.filename=e.substr(r+1,t-r-1)}else{let t=e.lastIndexOf(".");n.filename=e.substr(0,t)}let o=await l.getAjaxPromise(e,"text",!0);if(n.InputfileData=n.InputfileData?n.InputfileData+"\nENDMDL\n"+o:o,n.InputfileType=t,n.hAtoms={},n.dAtoms={},n.resetConfig(),n.bResetAnno=!0,n.bResetSets=!0,"pdb"===t){let e=!0,t=i?i.replace(/_/g,"").substr(0,4):void 0;await this.loadPdbData(o,t,void 0,e)}else if("mmcif"===t){let e=!0;await n.opmParserCls.loadOpmData(o,void 0,void 0,"mmcif",void 0,e)}else if("mol2"===t)await n.mol2ParserCls.loadMol2Data(o);else if("sdf"===t)await n.sdfParserCls.loadSdfData(o);else if("xyz"===t)await n.xyzParserCls.loadXyzData(o);else if("mmcif"===t)await n.mmcifParserCls.loadMmcifData(o);else if("icn3dpng"===t)await l.htmlCls.setHtmlCls.loadPng(o,s);else if("pae"===t){l.htmlCls.dialogCls.openDlg("dl_alignerrormap","Show Predicted Aligned Error (PAE) map");let e=!0;n.contactMapCls.processAfErrorMap(JSON.parse(o),e)}n.bSetChainsAdvancedMenu&&n.definedSetsCls.showSets(),n.bResetAnno=!0,n.bAnnoShown&&(await n.showAnnoCls.showAnnotations(),n.annotationCls.resetAnnoTabAll())}async loadPdbData(e,t,s,i,n,l,r,o){let a=this.icn3d,d=a.icn3dui;if(!i&&(void 0===n||"target"===n)){let e=!!a.bCommandLoad;a.bStatefile||a.init(e)}let c=a.loadPDBCls.loadPDB(e,t,s,void 0,void 0,i,n,o);return void 0===d.cfg.opmid&&a.ParserUtilsCls.transformToOpmOri(t),void 0!==a.biomtMatrices&&a.biomtMatrices.length>1&&(d.bNode||$("#"+a.pre+"assemblyWrapper").show(),a.asuCnt=a.biomtMatrices.length),d.bNode||(void 0!==a.emd?($("#"+a.pre+"mapWrapper1").hide(),$("#"+a.pre+"mapWrapper2").hide(),$("#"+a.pre+"mapWrapper3").hide()):($("#"+a.pre+"emmapWrapper1").hide(),$("#"+a.pre+"emmapWrapper2").hide(),$("#"+a.pre+"emmapWrapper3").hide())),await this.addSecondary(i,r),c}async addSecondary(e,t){let s=this.icn3d,i=s.icn3dui,n=!1;s.bSecondaryStructure&&1==Object.keys(s.structures).length?n=!1:i.cfg.mmtfid||i.cfg.pdbid||i.cfg.opmid||i.cfg.mmdbid||i.cfg.gi||i.cfg.uniprotid||i.cfg.blast_rep_id||i.cfg.cid||i.cfg.mmcifid||i.cfg.align||i.cfg.chainalign||(n=!0),(!s.bSecondaryStructure||n)&&Object.keys(s.proteins).length>0&&!t?await this.applyCommandDssp(e):(await this.loadPdbDataRender(e),i.bNode||await s.ParserUtilsCls.checkMemProteinAndRotate())}async applyCommandDssp(e){let t=this.icn3d,s=t.icn3dui,i=s.utilsCls.isCalphaPhosOnly(s.hashUtilsCls.hash2Atoms(t.proteins,t.atoms));await t.dsspCls.applyDssp(i,e)}async loadPdbDataRender(e){let t=this.icn3d,s=t.icn3dui;void 0===s.cfg.align&&1==Object.keys(t.structures).length&&$("#"+t.pre+"alternateWrapper").hide(),(s.cfg.afid&&!t.bAfMem||t.bEsmfold)&&(t.opts.color="confidence"),t.setStyleCls.setAtomStyleByOptions(t.opts),t.setColorCls.setColorByOptions(t.opts,t.hAtoms),await t.ParserUtilsCls.renderStructure(),t.saveFileCls.showTitle(),void 0!==s.cfg.rotate&&t.resizeCanvasCls.rotStruc(s.cfg.rotate,!0),e&&!s.bNode&&t.definedSetsCls.setModeAndDisplay("all")}}class ss{constructor(e){this.icn3d=e}async downloadCid(e){let t=this.icn3d,s=t.icn3dui;t.ParserUtilsCls.setYourNote("PubChem CID "+e+" in iCn3D"),t.bCid=!0;let i="https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/"+t.inputid+"/cids/JSONP?cids_type=parent",n="https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/"+(await s.getAjaxPromise(i,"jsonp",!0,"Can not retrieve the parent CID...")).IdentifierList.CID[0]+"/record/SDF/?record_type=3d&response_type=display",l=await s.getAjaxPromise(n,"text",!0,"This CID may not have 3D structure..."),r=this.loadSdfAtomData(l,e);void 0===s.cfg.align&&1==Object.keys(t.structures).length&&$("#"+t.pre+"alternateWrapper").hide(),r?(t.setStyleCls.setAtomStyleByOptions(t.opts),t.setColorCls.setColorByOptions(t.opts,t.atoms),await t.ParserUtilsCls.renderStructure(),void 0!==s.cfg.rotate&&t.resizeCanvasCls.rotStruc(s.cfg.rotate,!0)):alert("The SDF of CID "+e+" has the wrong format...")}async loadSdfData(e){let t=this.icn3d,s=t.icn3dui,i=this.loadSdfAtomData(e);void 0===s.cfg.align&&1==Object.keys(t.structures).length&&$("#"+t.pre+"alternateWrapper").hide(),i?(t.setStyleCls.setAtomStyleByOptions(t.opts),t.setColorCls.setColorByOptions(t.opts,t.atoms),await t.ParserUtilsCls.renderStructure(),void 0!==s.cfg.rotate&&t.resizeCanvasCls.rotStruc(s.cfg.rotate,!0)):alert("The SDF file has the wrong format...")}loadSdfAtomData(e,t){let s=this.icn3d;s.icn3dui;let i=e.split(/\r?\n|\r/);if(i.length<4)return!1;s.init();let n=t||1,l="LIG",r=n,o=n+"_A",a=o+"_1",d=parseInt(i[3].substr(0,3));if(isNaN(d)||d<=0)return!1;let c=parseInt(i[3].substr(3,3)),h=4;if(i.lengthr||(Math.abs(t.coord.y-i.coord.y)>r||Math.abs(t.coord.z-i.coord.z)>r||l.utilsCls.hasCovalentBond(t,i)&&(n.atoms[o[e]].bonds.push(o[s]),n.atoms[o[s]].bonds.push(o[e])))}}}loadXyzAtomData(e){let t=this.icn3d;t.icn3dui;let s=e.split(/\r?\n|\r/);if(s.length<3)return!1;t.init();let i,n,l,r={},o=0,a=1;t.molTitle="";for(let e=0,d=s.length;e1&&(t.molTitle+="; "),t.molTitle+=s[e+1].trim(),e+=2),d=s[e].trim(),""===d)continue;let c=d.replace(/,/," ").replace(/\s+/g," ").split(" "),h=c[0],p=parseFloat(c[1]),m=parseFloat(c[2]),u=parseFloat(c[3]),g={het:!0,serial:a,name:h,resn:"LIG",structure:l,chain:"A",resi:1,coord:new THREE.Vector3(p,m,u),b:0,elem:h,bonds:[],ss:"coil",ssbegin:!1,ssend:!1,bondOrder:[]};t.atoms[a]=g,r[a]=1,++a}return this.setXyzAtomSeq(r,o,i,n),t.ParserUtilsCls.setMaxD(),t.saveFileCls.showTitle(),!0}}class ns{constructor(e){this.icn3d=e}realign(){let e=this.icn3d,t=e.icn3dui;e.selectionCls.saveSelectionPrep();let s="alseq_"+(Object.keys(e.defNames2Atoms).length+Object.keys(e.defNames2Residues).length+1);e.selectionCls.saveSelection(s,s),t.htmlCls.clickMenuCls.setLogCmd("realign",!0);let i={},n={};e.realignResid={};let l="";for(let s in e.hAtoms){let r=e.atoms[s],o=r.structure+"_"+r.chain;if(e.proteins.hasOwnProperty(s)&&"CA"==r.name||e.nucleotides.hasOwnProperty(s)&&("O3'"==r.name||"O3*"==r.name)){if(r.structure+"_"+r.resi==l)continue;i.hasOwnProperty(r.structure)||(i[r.structure]=[]),i[r.structure].push(r.coord.clone()),e.realignResid.hasOwnProperty(o)||(e.realignResid[o]=[]),e.realignResid[o].push({resid:o+"_"+r.resi,resn:t.utilsCls.residueName2Abbr(r.resn.substr(0,3)).substr(0,1)}),n[r.structure]=r.structure+"_"+r.chain,l=r.structure+"_"+r.resi}}let r=Object.keys(i),o=r[0],a=[];e.qt_start_end=[],a.push(n[o]);for(let t=1,s=r.length;t5){console.log("RMSD from VAST is larger than 5. Realign the chains with TM-align.");let e=Object.keys(d);e.length>0&&(l.hAtoms=l.definedSetsCls.getAtomsFromNameArray(e)),r.cfg.aligntool="tmalign",await l.realignParserCls.realignOnStructAlign()}else l.hAtoms=l.chainalignParserCls.setMsa(e),l.transformCls.zoominSelection(),await l.chainalignParserCls.downloadChainalignmentPart3(void 0,e,l.hAtoms)}async parseChainRealignData(e,t,s,i,n,l,r){let o=this.icn3d,a=o.icn3dui,d=s[0].substr(0,s[0].indexOf("_"));r||(d=d.toUpperCase());let c={};o.realignResid={},o.opts.color="grey",o.setColorCls.setColorByOptions(o.opts,o.dAtoms),o.qt_start_end=[];for(let t=0,h=e.length;t=6&&b.length>=6&&!a.cfg.command&&o.bRender&&alert("These sequences can not be aligned to each other")):o.bRender&&alert("Please do not align residues in the same structure")}if(r){o.hAtoms=o.chainalignParserCls.setMsa(s);let e="protein_aligned";if(o.selectionCls.saveSelection(e,e),o.bAfMem?(o.selectionCls.selectAll_base(),o.opts.chemicals="stick",o.opts.color="confidence",o.setColorCls.setColorByOptions(o.opts,o.atoms)):(o.transformCls.zoominSelection(),o.dAtoms=a.hashUtilsCls.cloneHash(o.hAtoms),o.opts.color="identity",o.setColorCls.setColorByOptions(o.opts,o.hAtoms)),o.drawCls.draw(),o.hlUpdateCls.updateHlAll(),o.bAfMem){let e=new THREE.Vector3(1,0,0),t=-.5*Math.PI;o.transformCls.setRotation(e,t)}}else o.hAtoms=o.chainalignParserCls.setMsa(s),o.transformCls.zoominSelection(),await o.chainalignParserCls.downloadChainalignmentPart3(t,s,o.hAtoms)}async realignOnSeqAlign(e){let t=this.icn3d;t.icn3dui;let s=t.firstAtomObjCls.getChainsFromAtoms(t.hAtoms),i=Object.keys(s),n=[],l="";for(let e=0,t=i.length;ei){n[e][o]=a;break}}}let l=[],r=[],o=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi",a=s.htmlCls.baseUrl+"tmalign/tmalign.cgi",d=Object.keys(n);e&&(d=d.reverse());for(let e=0,i=d.length;ei){n[r]=o;break}}let l=[],r=[],o=[],a=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi",d=s.htmlCls.baseUrl+"tmalign/tmalign.cgi",c=e[0],h=c.substr(0,c.indexOf("_")),p=t.domain3dCls.getDomainJsonForAlign(n[c]);for(let i=1,m=e.length;if&&(f=s)}}}return{data:n,min:g,max:f}}(e.getCategory("_volume_data_3d").getColumn("values"),o,n.sampleCount,l);return{name:n.name,spacegroup:function(e,t,s){let i=Math.PI/180*s[0],n=Math.PI/180*s[1],l=Math.PI/180*s[2],r=t[0],o=t[1],a=t[2],d=Math.cos(n),c=(Math.cos(i)-Math.cos(n)*Math.cos(l))/Math.sin(l),h=Math.sqrt(1-d*d-c*c);return{number:e,size:t,angles:s,basis:{x:[r,0,0],y:[Math.cos(l)*o,Math.sin(l)*o,0],z:[d*a,c*a,h*a]}}}(n.spacegroupNumber,n.cellSize,n.cellAngles),box:{origin:r(n.origin),dimensions:r(n.dimensions),sampleCount:o},data:a.data,valuesInfo:{min:a.min,max:a.max,mean:n.mean,sigma:n.sigma}}}BinaryParse(e){this.icn3d.icn3dui;let t=new Uint8Array(e),s=this.MessagePackParse({buffer:t,offset:0,dataView:new DataView(t.buffer)}),i=function(){function e(e){this.additionalData={},this.header=e.header,this.categoryList=e.categories.map((function(e){return new n(e)})),this.categoryMap=new Map;for(let e=0,t=this.categoryList;e=0;s--)t=c(t,e.encoding[s]);return t}function p(e){if(!e.data.data)return _UndefinedColumn;let t,s=h(e.data);return e.mask&&(t=h(e.mask)),s.buffer&&s.byteLength&&s.BYTES_PER_ELEMENT?t?new f(s,t):new g(s):t?new b(s,t):new C(s)}function m(e,t,s){let i=0,n=1;for(45===e.charCodeAt(t)&&(n=-1,t++);t9||s<0)return n*i|0;i=10*i+s|0}return n*i}function u(e,t,s){let i=1,n=0,l=0,r=1;for(45===e.charCodeAt(t)&&(i=-1,++t);t=0&&o<10)){if(-2===o){for(++t;t=0&&o<10))return 53===o||21===o?parseScientific(i*(n+l/r),e,t+1,s):i*(n+l/r);l=10*l+o,r*=10,++t}return i*(n+l/r)}if(53===o||21===o)return parseScientific(i*n,e,t+1,s);break}n=10*n+o,++t}return i*n}let g=function(){function e(e){this.data=e,this.isDefined=!0}return e.prototype.getString=function(e){return""+this.data[e]},e.prototype.getInteger=function(e){return 0|this.data[e]},e.prototype.getFloat=function(e){return 1*this.data[e]},e.prototype.stringEquals=function(e,t){return this.data[e]===u(t,0,t.length)},e.prototype.areValuesEqual=function(e,t){return this.data[e]===this.data[t]},e.prototype.getValuePresence=function(e){return 0},e}(),f=function(){function e(e,t){this.data=e,this.mask=t,this.isDefined=!0}return e.prototype.getString=function(e){return 0===this.mask[e]?""+this.data[e]:null},e.prototype.getInteger=function(e){return 0===this.mask[e]?this.data[e]:0},e.prototype.getFloat=function(e){return 0===this.mask[e]?this.data[e]:0},e.prototype.stringEquals=function(e,t){return 0===this.mask[e]?this.data[e]===u(t,0,t.length):null==t},e.prototype.areValuesEqual=function(e,t){return this.data[e]===this.data[t]},e.prototype.getValuePresence=function(e){return this.mask[e]},e}(),C=function(){function e(e){this.data=e,this.isDefined=!0}return e.prototype.getString=function(e){return this.data[e]},e.prototype.getInteger=function(e){let t=this.data[e];return m(t,0,t.length)},e.prototype.getFloat=function(e){let t=this.data[e];return u(t,0,t.length)},e.prototype.stringEquals=function(e,t){return this.data[e]===t},e.prototype.areValuesEqual=function(e,t){return this.data[e]===this.data[t]},e.prototype.getValuePresence=function(e){return 0},e}(),b=function(){function e(e,t){this.data=e,this.mask=t,this.isDefined=!0}return e.prototype.getString=function(e){return 0===this.mask[e]?this.data[e]:null},e.prototype.getInteger=function(e){if(0!==this.mask[e])return 0;let t=this.data[e];return m(t||"",0,(t||"").length)},e.prototype.getFloat=function(e){if(0!==this.mask[e])return 0;let t=this.data[e];return u(t||"",0,(t||"").length)},e.prototype.stringEquals=function(e,t){return this.data[e]===t},e.prototype.areValuesEqual=function(e,t){return this.data[e]===this.data[t]},e.prototype.getValuePresence=function(e){return this.mask[e]},e}(),y=function(){function e(e){this.dataBlocks=e.dataBlocks.map((function(e){return new i(e)}))}return e.prototype.toJSON=function(){return this.dataBlocks.map((function(e){return e.toJSON()}))},e}();return new y(s)}MessagePackParse(e){this.icn3d.icn3dui;let t=this;function s(e,s){let i={};for(let n=0;n0&&(i[i.length]=l.slice(0,a).join(""));return i.join("")}(e.buffer,e.offset,t);return e.offset+=t,s}let r=function(){let e=[];for(let t=0;t<1024;t++)e[t]=String.fromCharCode(t);return e}();let o,a,d=e.buffer[e.offset];if(0==(128&d))return e.offset++,d;if(128==(240&d))return a=15&d,e.offset++,s(e,a);if(144==(240&d))return a=15&d,e.offset++,n(e,a);if(160==(224&d))return a=31&d,e.offset++,l(e,a);if(224==(224&d))return o=e.dataView.getInt8(e.offset),e.offset++,o;switch(d){case 192:return e.offset++,null;case 194:return e.offset++,!1;case 195:return e.offset++,!0;case 196:return a=e.dataView.getUint8(e.offset+1),e.offset+=2,i(e,a);case 197:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,i(e,a);case 198:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,i(e,a);case 202:return o=e.dataView.getFloat32(e.offset+1),e.offset+=5,o;case 203:return o=e.dataView.getFloat64(e.offset+1),e.offset+=9,o;case 204:return o=e.buffer[e.offset+1],e.offset+=2,o;case 205:return o=e.dataView.getUint16(e.offset+1),e.offset+=3,o;case 206:return o=e.dataView.getUint32(e.offset+1),e.offset+=5,o;case 208:return o=e.dataView.getInt8(e.offset+1),e.offset+=2,o;case 209:return o=e.dataView.getInt16(e.offset+1),e.offset+=3,o;case 210:return o=e.dataView.getInt32(e.offset+1),e.offset+=5,o;case 217:return a=e.dataView.getUint8(e.offset+1),e.offset+=2,l(e,a);case 218:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,l(e,a);case 219:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,l(e,a);case 220:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,n(e,a);case 221:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,n(e,a);case 222:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,s(e,a);case 223:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,s(e,a)}}}class rs{constructor(e){this.icn3d=e}alignCoords(e,t,s,i,n,l,r,o){let a,d=this.icn3d,c=d.icn3dui,h=e.length=4&&(d.bAfMem?d.rmsd_suprTmp=c.rmsdSuprCls.getRmsdSuprCls(t,e,h):d.rmsd_suprTmp=c.rmsdSuprCls.getRmsdSuprCls(e,t,h),void 0!==d.rmsd_suprTmp.rot)){let e=d.rmsd_suprTmp.rot;null===e[0]&&alert("Please select more residues in each structure...");let t=d.rmsd_suprTmp.trans1,i=d.rmsd_suprTmp.trans2;if(a=d.rmsd_suprTmp.rmsd,a){c.htmlCls.clickMenuCls.setLogCmd("realignment RMSD: "+a.toPrecision(4),!1);let e="
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    ";d.bAfMem&&!c.cfg.chainalign&&(e+=c.utilsCls.getMemDesc()),$("#"+d.pre+"dl_rmsd_html").html(e),c.cfg.bSidebyside||c.htmlCls.dialogCls.openDlg("dl_rmsd","Realignment RMSD")}let r={};for(let n=0,l=d.structures[s].length;n"+s.diagram2dCls.set2DdgmNote(!0),$("#"+s.pre+"dl_2ddgm_html").html(s.html2ddgm),s.b2DShown=!0}async set2DDiagramsForChainalign(e){let t=this.icn3d.icn3dui,s=this;t.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions");let i=[];for(let s=0,n=e.length;s"+s.diagram2dCls.set2DdgmNote(!0),s.b2DShown=!0,$("#"+s.pre+"dl_2ddgm_html").html(s.html2ddgm),i.cfg.show2d&&i.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions")}download2Ddgm(e,t){this.set2DDiagrams(e)}set2DDiagrams(e){let t=this.icn3d;t.icn3dui.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions"),void 0!==t.b2DShown&&t.b2DShown||(t.html2ddgm="",t.diagram2dCls.draw2Ddgm(t.interactionData,e),t.html2ddgm+="
    "+t.diagram2dCls.set2DdgmNote(),$("#"+t.pre+"dl_2ddgm_html").html(t.html2ddgm)),t.b2DShown=!0}showLoading(){let e=this.icn3d;e.icn3dui,$("#"+e.pre+"wait")&&$("#"+e.pre+"wait").show(),$("#"+e.pre+"canvas")&&$("#"+e.pre+"canvas").hide(),$("#"+e.pre+"cmdlog")&&$("#"+e.pre+"cmdlog").hide()}hideLoading(){let e=this.icn3d;e.icn3dui,$("#"+e.pre+"wait")&&$("#"+e.pre+"wait").hide(),$("#"+e.pre+"canvas")&&$("#"+e.pre+"canvas").show(),$("#"+e.pre+"cmdlog")&&$("#"+e.pre+"cmdlog").show()}setYourNote(e){let t=this.icn3d,s=t.icn3dui;t.yournote=e,$("#"+t.pre+"yournote").val(t.yournote),s.cfg.shownote&&(document.title=t.yournote)}transformToOpmOri(e){let t=this.icn3d;if(t.icn3dui,void 0!==t.rmsd_supr&&void 0!==t.rmsd_supr.rot){let s=t.rmsd_supr.rot,i=t.rmsd_supr.trans1,n=t.rmsd_supr.trans2;t.rmsd_supr.rmsd;let l=0;for(let e in t.atoms){let r=t.atoms[e];r.coord=t.surfaceCls.transformMemPro(r.coord,s,i,n);let o=r.coord.x*r.coord.x+r.coord.y*r.coord.y;Math.abs(r.coord.z)<=25&&o>l&&(l=o)}this.addMemAtoms(t.halfBilayerSize,e,Math.sqrt(l)),t.bStopRotate=!0,t.bOpm=!0,$("#"+t.pre+"togglememli").show(),$("#"+t.pre+"adjustmemli").show(),$("#"+t.pre+"selectplaneli").show()}else t.bOpm=!1}transformToOpmOriForAlign(e,t,s){let i=this.icn3d,n=i.icn3dui;if(void 0!==t){let l=i.loadPDBCls.getChainCalpha(i.chains,i.atoms,s,e),r=1==Object.keys(l.chainresiCalphaHash).length||1==Object.keys(t.chainresiCalphaHash).length,o=[],a=[];for(let e in l.chainresiCalphaHash)if(t.chainresiCalphaHash.hasOwnProperty(e)){let s=l.chainresiCalphaHash[e],i=t.chainresiCalphaHash[e];if((s.length==i.length||r)&&(o=o.concat(s),a=a.concat(i)),o.length>500)break}let d=o.length=4)if(i.rmsd_supr=n.rmsdSuprCls.getRmsdSuprCls(o,a,d),void 0!==i.rmsd_supr.rot&&i.rmsd_supr.rmsd<.1){let s=i.rmsd_supr.rot,l=i.rmsd_supr.trans1,r=i.rmsd_supr.trans2,o=i.rmsd_supr.rmsd;n.htmlCls.clickMenuCls.setLogCmd("RMSD of alignment to OPM: "+o.toPrecision(4),!1);let a=0;for(let e in i.atoms){let t=i.atoms[e];t.coord=i.surfaceCls.transformMemPro(t.coord,s,l,r);let n=t.coord.x*t.coord.x+t.coord.y*t.coord.y;Math.abs(t.coord.z)<=25&&n>a&&(a=n)}i.center=t.center,i.oriCenter=i.center.clone(),this.addMemAtoms(i.halfBilayerSize,e,Math.sqrt(a)),i.bStopRotate=!0,i.bOpm=!0,$("#"+i.pre+"togglememli").show(),$("#"+i.pre+"adjustmemli").show(),$("#"+i.pre+"selectplaneli").show()}else i.bOpm=!1;else i.bOpm=!1}}addOneDumAtom(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui,a={het:!0,serial:++l,name:t,alt:void 0,resn:"DUM",structure:e,chain:"MEM",resi:1,coord:new THREE.Vector3(s,i,n),b:void 0,elem:t,bonds:[],ss:"",ssbegin:!1,ssend:!1,color:o.parasCls.atomColors[t]};return r.atoms[l]=a,r.chains[e+"_MEM"][l]=1,r.residues[e+"_MEM_1"][l]=1,r.chemicals[l]=1,r.dAtoms[l]=1,r.hAtoms[l]=1,l}addMemAtoms(e,t,s){let i=this.icn3d;if(i.icn3dui,!t)return;t=t?t.toUpperCase():i.defaultPdbId,i.structures[t].push(t+"_MEM"),i.chains[t+"_MEM"]={},i.residues[t+"_MEM_1"]={},i.chainsSeq[t+"_MEM"]=[{name:"DUM",resi:1}];let n=Object.keys(i.atoms).length;for(let e=0;e<1e3;++e)if(!i.atoms.hasOwnProperty(n+e)){n=n+e-1;break}for(let i=0;i<81;++i)for(let l=0;l<81;++l){let r=2*i-80,o=2*l-80;if(Math.sqrt(r*r+o*o)=2?$("#"+e.pre+"mn2_alternateWrap").show():$("#"+e.pre+"mn2_alternateWrap").hide(),setTimeout((async function(){if(e.bInitial){if(void 0!==t.cfg.align||void 0!==t.cfg.chainalign){let s=e.pre+"selection";if($("#"+s).show(),$("#"+s+"_expand").hide(),$("#"+s+"_shrink").show(),void 0!==t.cfg.align&&2!=t.cfg.atype){let s=!1,i=t.htmlCls.alignSeqCls.getAlignSequencesAnnotations(Object.keys(e.alnChains),void 0,void 0,s);$("#"+e.pre+"dl_sequence2").html(i.sequencesHtml),$("#"+e.pre+"dl_sequence2").width(t.htmlCls.RESIDUE_WIDTH*i.maxSeqCnt+200)}}if(t.cfg.showanno){let s="view annotations";t.htmlCls.clickMenuCls.setLogCmd(s,!0),await e.showAnnoCls.showAnnotations()}(t.cfg.closepopup||t.cfg.imageonly)&&e.resizeCanvasCls.closeDialogs()}else e.hlUpdateCls.updateHlAll();$("#"+e.pre+"atomsCustom").length>0&&$("#"+e.pre+"atomsCustom")[0].blur(),e.bInitial=!1,t.cfg.imageonly&&e.saveFileCls.saveFile(void 0,"png",void 0,!0)}),0)}processCommand(){let e=this.icn3d,t=e.icn3dui;if(1==Object.keys(e.structures).length){let s=Object.keys(e.structures)[0];t.cfg.command=t.cfg.command.replace(new RegExp("!","g"),s+"_")}}getMassCenter(e,t){return this.icn3d.icn3dui,e.multiplyScalar(1/t)}getGeoCenter(e,t){return this.icn3d.icn3dui,e.clone().add(t).multiplyScalar(.5)}getStructureSize(e,t,s,i){let n=this.icn3d;n.icn3dui;let l=0;for(let r in e){let e=n.atoms[r].coord;if(Math.round(t.x)==Math.round(e.x)||Math.round(t.y)==Math.round(e.y)||Math.round(t.z)==Math.round(e.z)||Math.round(s.x)==Math.round(e.x)||Math.round(s.y)==Math.round(e.y)||Math.round(s.z)==Math.round(e.z)){let t=2*e.distanceTo(i);t>l&&(l=t)}}return l}async checkMemProteinAndRotate(){let e=this.icn3d,t=e.icn3dui;if(!e.bCheckMemProtein){e.bCheckMemProtein=!0;let s=t.cfg.afid?t.cfg.afid:t.cfg.mmdbafid;if(await e.ParserUtilsCls.checkMemProtein(s),t.cfg.url&&-1!=t.cfg.url.indexOf("membranome")){let t=new THREE.Vector3(1,0,0),s=-.5*Math.PI;e.transformCls.setRotation(t,s)}}}async checkMemProtein(e){let t=this.icn3d,s=t.icn3dui;try{let i=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?afid2mem="+e,n=await s.getAjaxPromise(i,"jsonp");if(n&&n.pdbid){let e='This is a single-spanning (bitopic) transmembrane protein according to the Membranome database. Do you want to align the protein with the model from Membranome? If you click "OK", you can press the letter "a" to alternate the structures.';if(s.bNode)return;if("off"==s.cfg.afmem);else if("on"==s.cfg.afmem||confirm(e))try{let e="https://storage.googleapis.com/membranome-assets/pdb_files/proteins/"+n.pdbid+".pdb",i=await s.getAjaxPromise(e,"text");t.bAfMem=!0,s.bNode||$("#"+s.pre+"togglememli").show();let l=n.pdbid.substr(0,n.pdbid.indexOf("_")),r=!0,o=!0;await t.pdbParserCls.loadPdbData(i,l,r,o),o&&(t.bSetChainsAdvancedMenu&&t.definedSetsCls.showSets(),t.bAnnoShown&&(await t.showAnnoCls.showAnnotations(),t.annotationCls.resetAnnoTabAll()));let a=n.segment.replace(/ /gi,"").split("(")[0];t.afmem_start_end=a.split("-"),t.hAtoms={},t.dAtoms={};for(let e in t.atoms)t.atoms[e].structure!=l&&(t.hAtoms[e]=1),t.dAtoms[e]=1;for(let e=parseInt(t.afmem_start_end[0]);e<=parseInt(t.afmem_start_end[1]);++e)t.hAtoms=s.hashUtilsCls.unionHash(t.hAtoms,t.residues[l+"_A_"+e]);await t.realignParserCls.realignOnSeqAlign(l)}catch(e){return void console.log("Error in retrieving matched PDB from Membranome...")}}}catch(e){return void console.log("Error in finding matched PDB in Membranome...")}}getResi(e,t){let s=this.icn3d;s.icn3dui;let i=s.ncbi2resid[e+"_"+(t+1).toString()];return i?i.substr(i.lastIndexOf("_")+1):""}getResiNCBI(e,t){let s=this.icn3d;s.icn3dui;let i=s.resid2ncbi[e+"_"+t];return i?parseInt(i.substr(i.lastIndexOf("_")+1)):0}}class os{constructor(e){this.icn3d=e}loadAtomDataIn(e,t,s,i,n,l,r,o,a){let d=this.icn3d,c=d.icn3dui;d.pmin=new THREE.Vector3(9999,9999,9999),d.pmax=new THREE.Vector3(-9999,-9999,-9999),d.psum=new THREE.Vector3;let h=e.atoms,p=d.atoms?Object.keys(d.atoms).length:0,m={},u={};d.pmid=e.pubmedId,void 0===d.chainid2title&&(d.chainid2title={}),void 0===d.chainid2sid&&(d.chainid2sid={});let g={},f={};if("align"===s){d.pmid="",d.molTitle="",c.cfg.inpara&&-1!==c.cfg.inpara.indexOf("atype=1")?d.molTitle="Invariant Core Structure Alignment (VAST) of ":c.cfg.inpara&&-1!==c.cfg.inpara.indexOf("atype=2")?d.molTitle="Structure Alignment (TM-align) of ":d.molTitle="Structure Alignment (VAST) of ";let t=!1;for(let s=0,i=e.alignedStructures[0].length;s'+i.pdbId.toUpperCase()+"",void 0!==i.descr&&(d.pmid+=i.descr.pubmedid),0===s&&(d.molTitle+=" and ",void 0!==i.descr&&(d.pmid+="_")),t=!0}d.molTitle+=" from VAST+",t||(d.molTitle="")}else if(void 0!==e.descr&&(d.molTitle=e.descr.name),"mmdbid"===s){let s=isNaN(t)?t:e.pdbId,i={};void 0===d.alignmolid2color&&(d.alignmolid2color=[]);let n=1;for(let t in e.moleculeInfor){if(0===Object.keys(e.moleculeInfor[t]).length)continue;let l=e.moleculeInfor[t].chain.trim();(parseInt(c.cfg.date)>=20231001||!c.cfg.date&&parseInt(c.utilsCls.getDateDigitStr())>=20231001)&&(l=l.replace(/_/g,""));let r=s+"_"+l;i.hasOwnProperty(l)?(++i[l],r+=i[l]):i[l]=1,void 0!==d.mmdbid_q&&(d.mmdbid_q,d.mmdbid_t);let o=e.moleculeInfor[t].kind,a=e.moleculeInfor[t].color,h=e.moleculeInfor[t].sid;if(g[r]=o,f[r]=a,"protein"==o&&(d.organism=e.moleculeInfor[t].taxonomyName.toLowerCase()),void 0!==h&&(d.chainid2sid[r]=h),void 0===d.pdbid_chain2title&&(d.pdbid_chain2title={}),d.pdbid_chain2title[r]=e.moleculeInfor[t].name,l==r.substr(r.lastIndexOf("_"))){let e={};e[t]=n.toString(),d.alignmolid2color.push(e)}++n}}"mmdbid"===s&&(d.molTitleHash||(d.molTitleHash={}),d.molTitleHash[t]=d.molTitle);let C,b,y,v,_,w={},S="",A="",x="",k="",O="",R="",I=0,E=0,T="",D=!0,P=!1,M="",F=c.utilsCls.isCalphaPhosOnly(h),H=0,L={};for(let e in h){++p,w[e]=p;let i,n=h[e];n.serial=p,"mmdbid"===s||"mmcifid"===s?i=t:"align"===s&&(i=m[p]);let l=!1;if(void 0!==n.chain||"mmdbid"!==s&&"align"!==s)n.chain=""===n.chain?"Misc":n.chain;else if("mmdbid"===s)if(C=n.ids.m,void 0!==d.molid2chain[C]){let e=d.molid2chain[C].indexOf("_");n.chain=d.molid2chain[C].substr(e+1)}else{let e="Misc";("protein"===g[O]&&"nucleotide"===g[O]&&n.resi!=E||"protein"!==g[O]&&"nucleotide"!==g[O]&&(n.resn.substr(0,3)!=T.substr(0,3)||n.resi!=E||"solvent"===g[O]||"HOH"===n.resn))&&++H,n.resi_ori=n.resi,n.resi=H,l=!0,n.chain=e}else if("align"===s)if(C=n.ids.m,void 0!==d.pdbid_molid2chain[i+"_"+C])n.chain=d.pdbid_molid2chain[i+"_"+C];else{let e="Misc";("protein"===g[O]&&"nucleotide"===g[O]&&n.resi!=E||"protein"!==g[O]&&"nucleotide"!==g[O]&&(n.resn.substr(0,3)!=T.substr(0,3)||n.resi!=E||"solvent"===g[O]||"HOH"===n.resn))&&(++H,n.resi_ori=n.resi,n.resi=H,l=!0),n.chain=e}if(n.chain=n.chain.trim(),(parseInt(c.cfg.date)>=20231001||!c.cfg.date&&parseInt(c.utilsCls.getDateDigitStr())>=20231001)&&(n.chain=n.chain.replace(/_/g,"")),"mmdbid"!==s&&"align"!==s||(n.structure=i,"mmdbid"===s&&void 0!==d.mmdbid_q&&(d.mmdbid_q,d.mmdbid_t)),k=n.structure,O=k+"_"+n.chain,"mmdbid"===s||"align"===s){l||(n.resi_ori=n.resi,d.bUsePdbNum?n.resi=n.resi_ori:n.resi=n.ids.r);let e=n.resn.indexOf(" ");-1!==e&&0!=e&&(n.resn=n.resn.substr(0,e))}O!==A&&(I=0),n.resi!==I&&(O!==A?(y=void 0,_=void 0):(y=b,_=v)),n.coord="mmdbid"===s?new THREE.Vector3(n.coord[0],n.coord[1],n.coord[2]):new THREE.Vector3(n.coord.x,n.coord.y,n.coord.z);let r=c.utilsCls.residueName2Abbr(n.resn.substr(0,3));"mmdbid"!==s&&"align"!==s||!d.bFullUi||(void 0===d.mmdbMolidResid2mmdbChainResi&&(d.mmdbMolidResid2mmdbChainResi={}),d.mmdbMolidResid2mmdbChainResi[i+"_"+n.ids.m+"_"+n.ids.r]=i+"_"+n.chain+"_"+n.resi),d.pmin.min(n.coord),d.pmax.max(n.coord),d.psum.add(n.coord);let o="protein"===g[O],a="nucleotide"===g[O],u="solvent"===g[O],N="ligand"===g[O]||void 0!==g[O]&&-1!==g[O].indexOf("other")||void 0===g[O];if("Misc"!==n.chain&&"other"!==g[O]||"protein"===L[O]||"nucleotide"===L[O]||("CA"===n.name&&"C"===n.elem?L[O]="protein":"P"===n.name&&"P"===n.elem?L[O]="nucleotide":L[O]="chemical"),o||a?(o?(d.proteins[p]=1,"CA"===n.name&&(d.calphas[p]=1),"N"!==n.name&&"H"!==n.name&&"CA"!==n.name&&"HA"!==n.name&&"C"!==n.name&&"O"!==n.name&&(d.sidec[p]=1)):a&&(d.nucleotides[p]=1,("O3'"==n.name||"O3*"==n.name||F&&"P"==n.name)&&(d.nucleotidesO3[p]=1),-1===c.parasCls.nuclMainArray.indexOf(n.name)&&(d.ntbase[p]=1)),n.het=!1):u?(d.water[p]=1,n.het=!0):N&&("HOH"===n.resn||"O"===n.resn?d.water[p]=1:n.elem===n.resn?d.ions[p]=1:d.chemicals[p]=1,n.het=!0),"mmdbid"===s?n.het?n.color=c.parasCls.atomColors[n.elem]||c.parasCls.defaultAtomColor:n.color=void 0!==f[O]?c.parasCls.thr(f[O]):c.parasCls.chargeColors[n.resn]:void 0!==n.color&&(n.color=c.parasCls.thr(n.color))," "!==n.resn.charAt(0)&&" "===n.resn.charAt(1)&&(n.resn=n.resn.charAt(0)),n.het||"C"!==n.name||(b=p),n.het||"O"!==n.name||(v=p),!n.het&&"N"===n.name&&void 0!==y&&void 0!==_){let e=d.atoms[y].coord.distanceTo(d.atoms[_].coord),t=n.coord.x+(d.atoms[y].coord.x-d.atoms[_].coord.x)/e,s=n.coord.y+(d.atoms[y].coord.y-d.atoms[_].coord.y)/e,i=n.coord.z+(d.atoms[y].coord.z-d.atoms[_].coord.z)/e;n.hcoord=new THREE.Vector3(t,s,i)}"HOH"==n.resn&&(d.water[p]=1),d.atoms[p]=n,d.dAtoms[p]=1,d.hAtoms[p]=1;let q=n.structure+"_"+n.chain;void 0===d.chains[q]&&(d.chains[q]={}),d.chains[q][p]=1;let U=q+"_"+n.resi;void 0===d.residues[U]&&(d.residues[U]={}),d.residues[U][p]=1,R=O+"_"+n.resi,R!==x&&O!==A&&(D=!0,""!==S&&(void 0===d.structures[S]&&(d.structures[S]=[]),d.structures[S].push(A))),d.residueId2Name[U]=r;let B="-";if("helix"===n.ss?B="H":"sheet"===n.ss?B="E":n.het||a?B="o":(!n.het&&c.parasCls.residueColors.hasOwnProperty(n.resn.toUpperCase())||"coil"===n.ss)&&(B="c"),d.secondaries[n.structure+"_"+n.chain+"_"+n.resi]=B,(n.resi!=I||C!=M)&&d.bFullUi&&(void 0===d.chainsSeq[q]&&(d.chainsSeq[q]=[],D=!1),!isNaN(n.resi)&&null!==n.resi))if(D&&!P&&void 0!==d.chainsSeq[q][n.resi-1])d.chainsSeq[q][n.resi-1].name=r;else if(!D||!d.chainsSeq[q].hasOwnProperty(n.resi-1)){let e={};e.resi=n.resi,e.name=r,n.resi%10==0&&n.resi.toString(),d.chainsSeq[q].push(e),P=!0}I=n.resi,E=n.resi_ori,T=n.resn,S=k,A=O,x=R,M=C}for(let e in d.chemicals){let t=d.atoms[e];if("P"==t.elem&&t.bonds.length>=4)for(let e=t.bonds.length-1;e>=0;--e){"P"==d.atoms[t.bonds[e]].elem&&t.bonds.splice(e,1)}}for(let e in L)if(!(Object.keys(d.chains[e]).length<10)&&"chemical"!==L[e])for(let t in d.chains[e]){let s=d.atoms[t];delete d.chemicals[t],s.het=!1,"protein"===L[e]?(d.proteins[t]=1,"CA"===s.name&&(d.calphas[t]=1),"N"!==s.name&&"H"!==s.name&&"CA"!==s.name&&"HA"!==s.name&&"C"!==s.name&&"O"!==s.name&&(d.sidec[t]=1)):"nucleotide"===L[e]&&(d.nucleotides[t]=1,("O3'"==s.name||"O3*"==s.name||F&&"P"==s.name)&&(d.nucleotidesO3[t]=1),-1===c.parasCls.nuclMainArray.indexOf(s.name)&&(d.ntbase[t]=1))}if(void 0===d.structures[k]&&(d.structures[k]=[]),d.structures[k].push(O),d.bFullUi)if("mmdbid"===s||"mmcifid"===s)for(let i in e.sequences){let n=e.sequences[i],l=t+"_"+i;void 0!==d.mmdbid_q&&(d.mmdbid_q,d.mmdbid_t),d.ParserUtilsCls.getMissingResidues(n,s,l)}else if("align"===s)for(let e in d.chainid2seq){let t=d.chainid2seq[e];d.ParserUtilsCls.getMissingResidues(t,s,e)}if(d.loadPDBCls.setResidMapping(),"mmcifid"!==s)for(let e in h){let t=w[e],s=void 0===d.atoms[t].bonds?0:d.atoms[t].bonds.length;for(let e=0;ed.maxatomcnt||void 0!==d.biomtMatrices&&d.biomtMatrices.length*d.cnt>10*d.maxatomcnt)&&(d.opts.proteins="c alpha trace",d.opts.nucleotides="o3 trace"),d.center=d.ParserUtilsCls.getGeoCenter(d.pmin,d.pmax),d.maxD=d.ParserUtilsCls.getStructureSize(d.atoms,d.pmin,d.pmax,d.center),d.maxD<5&&(d.maxD=5),d.oriMaxD=d.maxD,("align"===s||o)&&(d.ssbondpnts={},d.loadPDBCls.setSsbond()),"mmdbid"===s&&1==Object.keys(d.structures).length){let t=e.disulfides;if(void 0!==t)for(let e=0,s=t.length;ep&&(p=e)),c[e]={resi:t,resn:i,aligned:n}}r=e[t][1];let u=r.moleculeId,g=s.pdbid_molid2chain[l+"_"+u],f=l+"_"+g;void 0===s.alnChainsAnTtl[d]&&(s.alnChainsAnTtl[d]=[]),void 0===s.alnChainsAnTtl[d][0]&&(s.alnChainsAnTtl[d][0]=[]),void 0===s.alnChainsAnTtl[d][1]&&(s.alnChainsAnTtl[d][1]=[]),void 0===s.alnChainsAnTtl[d][2]&&(s.alnChainsAnTtl[d][2]=[]),void 0===s.alnChainsAnTtl[d][3]&&(s.alnChainsAnTtl[d][3]=[]),void 0===s.alnChainsAnTtl[d][4]&&(s.alnChainsAnTtl[d][4]=[]),void 0===s.alnChainsAnTtl[d][5]&&(s.alnChainsAnTtl[d][5]=[]),void 0===s.alnChainsAnTtl[d][6]&&(s.alnChainsAnTtl[d][6]=[]),s.alnChainsAnTtl[d][0].push(f),s.alnChainsAnTtl[d][1].push(d),s.alnChainsAnTtl[d][2].push(""),s.alnChainsAnTtl[d][3].push(""),s.alnChainsAnTtl[d][4].push(f),s.alnChainsAnTtl[d][5].push(d),s.alnChainsAnTtl[d][6].push("");let C=1;s.chainsMapping[d]||(s.chainsMapping[d]={}),s.chainsMapping[f]||(s.chainsMapping[f]={});for(let e=h;e<=p;++e){let t,o,p,m=s.bUsePdbNum?s.ParserUtilsCls.getResi(f,r.sequence[e][0]-1):r.sequence[e][0],u="~"===r.sequence[e][2]?"-":r.sequence[e][2],b=r.sequence[e][3]?1:0,y=c[e].aligned+b;2===y?(c[e].resn===u?(t="#FF0000",p="icn3d-cons",s.consHash1[d+"_"+c[e].resi]=1,s.consHash2[f+"_"+m]=1):(t="#0000FF",p="icn3d-ncons",s.nconsHash1[d+"_"+c[e].resi]=1,s.nconsHash2[f+"_"+m]=1),s.chainsMapping[d][d+"_"+c[e].resi]=c[e].resn+c[e].resi,s.chainsMapping[f][f+"_"+m]=c[e].resn+c[e].resi,o="#"+s.showAnnoCls.getColorhexFromBlosum62(c[e].resn,u)):(t=i.htmlCls.GREY8,p="icn3d-nalign",s.nalignHash1[d+"_"+c[e].resi]=1,s.nalignHash2[f+"_"+m]=1),void 0===s.alnChainsSeq[d]&&(s.alnChainsSeq[d]=[]);let v={};v.mmdbid=n,v.chain=a,v.resi=c[e].resi,v.resn=""===v.resi||"icn3d-nalign"===p?c[e].resn.toLowerCase():c[e].resn,v.aligned=y,v.color=""===v.resi?i.htmlCls.GREYC:t,v.color2=""===v.resi?i.htmlCls.GREYC:o,v.class=p,s.alnChainsSeq[d].push(v),""!==c[e].resi&&(void 0===s.alnChains[d]&&(s.alnChains[d]={}),$.extend(s.alnChains[d],s.residues[d+"_"+c[e].resi])),void 0===s.alnChainsSeq[f]&&(s.alnChainsSeq[f]=[]),v={},v.mmdbid=l,v.chain=g,v.resi=m,v.resn=""===v.resi||"icn3d-nalign"===p?u.toLowerCase():u,v.aligned=y,v.color=""===v.resi?i.htmlCls.GREYC:t,v.color2=""===v.resi?i.htmlCls.GREYC:o,v.class=p,s.alnChainsSeq[f].push(v),""!==v.resi&&(void 0===s.alnChains[f]&&(s.alnChains[f]={}),$.extend(s.alnChains[f],s.residues[f+"_"+m])),void 0===s.alnChainsAnno[d]&&(s.alnChainsAnno[d]=[]),void 0===s.alnChainsAnno[d][0]&&(s.alnChainsAnno[d][0]=[]),void 0===s.alnChainsAnno[d][1]&&(s.alnChainsAnno[d][1]=[]),void 0===s.alnChainsAnno[d][2]&&(s.alnChainsAnno[d][2]=[]),void 0===s.alnChainsAnno[d][3]&&(s.alnChainsAnno[d][3]=[]),e===h&&(void 0===s.alnChainsAnno[d][4]&&(s.alnChainsAnno[d][4]=[]),void 0===s.alnChainsAnno[d][5]&&(s.alnChainsAnno[d][5]=[]),void 0===s.alnChainsAnno[d][6]&&(s.alnChainsAnno[d][6]=[]),s.alnChainsAnno[d][4].push(s.pdbid_chain2title[f]),s.alnChainsAnno[d][5].push(s.pdbid_chain2title[d]),s.alnChainsAnno[d][6].push(""));let _=d+"_"+c[e].resi,w=f+"_"+m,S=s.secondaries[_],A=s.secondaries[w];A?s.alnChainsAnno[d][0].push(A):s.alnChainsAnno[d][0].push("-"),S?s.alnChainsAnno[d][1].push(S):s.alnChainsAnno[d][1].push("-");let x=".";C%5==0&&(x="*"),C%10==0&&(x="|"),s.alnChainsAnno[d][2].push(x);let k="";C%10==0&&(k=C.toString()),s.alnChainsAnno[d][3].push(k),++C}}e={}}getPosFromResi(e,t){let s=this.icn3d;s.icn3dui;let i,n=s.resid2ncbi[e+"_"+t];if(n){i=n.substr(n.lastIndexOf("_")+1)-1}return i}getResnFromResi(e,t){let s=this.icn3d;s.icn3dui;let i=e+"_"+t,n=s.residueId2Name[i];return n||(n="?"),n}getResiAferAlign(e,t,s){let i,n=this.icn3d,l=n.icn3dui;return t&&"tmalign"==l.cfg.aligntool?i=s:(s>n.chainsSeq[e].length-1&&(console.log("Error: the position "+s+" exceeds the max index "+(n.chainsSeq[e].length-1)),s=n.chainsSeq[e].length-1),i=n.chainsSeq[e][s].resi),i}setSeqAlignChain(e,t,s){let i,n,l,r,o,a,d,c,h,p,m,u=this.icn3d,g=u.icn3dui,f={},C=!!s;if(C){if(o=s[1],a=s[0],t=s[2],d=o.indexOf("_"),c=a.indexOf("_"),i=o.substr(0,d).toUpperCase(),n=a.substr(0,c).toUpperCase(),l=o.substr(d+1),r=a.substr(d+1),i==n&&l==r){let e=u.chainsSeq[n+"_"+r].length;u.qt_start_end[t]={q_start:1,q_end:e,t_start:1,t_end:e}}}else{let d=s[0].indexOf("_"),c=e.indexOf("_");if(i=u.mmdbid_t,n=e.substr(0,c).toUpperCase(),l=s[0].substr(d+1),r=e.substr(c+1),i==n&&l==r){let e=u.chainsSeq[u.mmdbid_q+"_"+u.chain_q].length;u.qt_start_end[t]={q_start:1,q_end:e,t_start:1,t_end:e}}o=i+"_"+l,a=n+"_"+r,void 0!==n&&u.mmdbid_t}u.conservedName1=o+"_cons",u.nonConservedName1=o+"_ncons",u.notAlignedName1=o+"_nalign",u.conservedName2=a+"_cons",u.nonConservedName2=a+"_ncons",u.notAlignedName2=a+"_nalign",u.consHash1={},u.nconsHash1={},u.nalignHash1={},u.consHash2={},u.nconsHash2={},u.nalignHash2={},u.alnChains={},u.alnChainsSeq[o]=[],u.alnChains[o]={},u.alnChainsSeq[a]=[],u.alnChains[a]={},u.alnChainsAnno[o]=[],u.alnChainsAnTtl[o]=[],void 0===u.alnChainsAnTtl[o]&&(u.alnChainsAnTtl[o]=[]);for(let e=0;e<7;++e)void 0===u.alnChainsAnTtl[o][e]&&(u.alnChainsAnTtl[o][e]=[]);u.alnChainsAnTtl[o][0].push(a),u.alnChainsAnTtl[o][1].push(o),u.alnChainsAnTtl[o][2].push(""),u.alnChainsAnTtl[o][3].push(""),u.alnChainsAnTtl[o][4].push(a),u.alnChainsAnTtl[o][5].push(o),u.alnChainsAnTtl[o][6].push("");let b=0,y=0;if(void 0===u.qt_start_end[t])return;let v=1;u.chainsMapping[o]||(u.chainsMapping[o]={}),u.chainsMapping[a]||(u.chainsMapping[a]={});let _={},w={};for(let e=0,s=u.qt_start_end[t].length;e0){let e=v;for(let t=b+1,i=s;tc&&(c=t)}}}"tmalign"==n.cfg.aligntool&&(s=!0);let p=Object.keys(a);p.sort((function(e,t){return parseInt(e.split("_")[2])-parseInt(t.split("_")[2])}));let m=-999,u=0,g=0,f=[],C=0;for(let e=0,t=p.length;e0&&i.resid2ncbi[s]!=i.resid2ncbi[m]+1&&i.resid2ncbi[s]!=i.resid2ncbi[m]){g=m;for(let e=0,t=f.length;ec)continue;let p={},m=r.indexOf("_");p.mmdbid=r.substr(0,m),p.chain=r.substr(m+1),p.resi=t,p.resn=a[s]?i.chainsSeq[r][e].name.toUpperCase():i.chainsSeq[r][e].name.toLowerCase(),p.aligned=!!a[s],p.color=a[s]?"#FF0000":n.htmlCls.GREYC,p.color2=a[s]?"#FF0000":n.htmlCls.GREYC,p.class=a[s]?"icn3d-align":"icn3d-nalign",i.alnChainsSeq[r].push(p),a[s]&&($.extend(i.alnChains[r],i.residues[r+"_"+p.resi]),l=n.hashUtilsCls.unionHash(l,i.residues[r+"_"+p.resi]))}let b=[0];for(let i=0,r=t.length;in)for(let e=0,t=u-m;e=n)for(let e=0,s=t-n;en)for(let e=0,t=d-a;e=n)for(let t=0,s=e-n;t0?void 0!==n?p.alnChainsAnno[t][0].push(n):p.alnChainsAnno[t][0].push("-"):console.log("Error: ic.alnChainsAnno[chainid1] is undefined")}}}class ds{constructor(e){this.icn3d=e}getStructureId(e,t,s){let i=this.icn3d;i.icn3dui;let n=e;return(e==i.defaultPdbId||s||i.structures.hasOwnProperty(e))&&(n=1===t?e:e+t.toString()),n}loadPDB(e,t,s,i,n,l,r,o){let a,d,c=this.icn3d,h=c.icn3dui,p={},m=!1,u=e.split("\n"),g={},f={};c.atoms||(l=!1),n||l?(c.oriNStru=c.structures?Object.keys(c.structures).length:0,d=c.oriNStru+1,a=c.atoms?Object.keys(c.atoms).length:0):(c.init(),d=1,a=0);let C,b,y,v,_,w,S,A,x,k=[],O=[],R=[],I=[],E=[],T=[],D="",P="",M="",F={},H=t||c.defaultPdbId,L=H,N="",q=!1,U=!0;for(let e in u){let r=u[e],B=r.substr(0,6);if("HEADER"!==B||q||t)if("TITLE "===B){let e=r.substr(10).replace(/ALPHAFOLD MONOMER V2.0 PREDICTION FOR /gi,"");c.molTitle+=e.trim()+" ",o&&c.esmTitle&&(c.molTitle=c.esmTitle),c.molTitleHash||(c.molTitleHash={}),c.molTitleHash[L]=c.molTitle}else if("HELIX "===B){c.bSecondaryStructure=!0;let e=""==r.substr(18,2).trim()?"A":r.substr(18,2).trim(),t=parseInt(r.substr(21,4)),s=parseInt(r.substr(33,4));for(let i=t;i<=s;++i){let n=L+"_"+e+"_"+i;I.push(n),i===t&&E.push(n),i===s&&T.push(n)}}else if("SHEET "===B){void 0!==s&&s||(c.bSecondaryStructure=!0);let e=""==r.substr(20,2).trim()?"A":r.substr(20,2).trim(),t=parseInt(r.substr(22,4)),i=parseInt(r.substr(33,4));for(let s=t;s<=i;++s){let n=L+"_"+e+"_"+s;k.push(n),s===t&&O.push(n),s===i&&R.push(n)}}else if("HBOND "===B)void 0!==s&&s||(c.bSecondaryStructure=!0);else if("SSBOND"===B){c.bSsbondProvided=!0;let e=L+"_"+(" "==r.substr(15,1)?"A":r.substr(15,1))+"_"+r.substr(17,4).trim(),t=L+"_"+(" "==r.substr(29,1)?"A":r.substr(29,1))+"_"+r.substr(31,4).trim();void 0===c.ssbondpnts[L]&&(c.ssbondpnts[L]=[]),c.ssbondpnts[L].push(e),c.ssbondpnts[L].push(t)}else if("REMARK"===B){let e=parseInt(r.substr(7,3));if(-1!==r.indexOf("1/2 of bilayer thickness:"))c.halfBilayerSize=parseFloat(r.substr(r.indexOf(":")+1).trim());else if(210==e)"EXPERIMENT TYPE"==r.substr(11,32).trim()&&"NMR"==r.substr(45).trim()&&(m=!0);else if(350==e&&"BIOMT"==r.substr(13,5)){let e=parseInt(r[18])-1,t=parseInt(r.substr(21,2))-1;null==c.biomtMatrices[t]&&(c.biomtMatrices[t]=(new THREE.Matrix4).identity()),c.biomtMatrices[t].elements[e]=parseFloat(r.substr(24,9)),c.biomtMatrices[t].elements[e+4]=parseFloat(r.substr(34,9)),c.biomtMatrices[t].elements[e+8]=parseFloat(r.substr(44,9)),c.biomtMatrices[t].elements[e+12]=parseFloat(r.substr(54,14))}else if(465==e&&" "==r.substr(18,1)&&" "==r.substr(20,1)&&"S"!=r.substr(21,1)){let e=r.substr(15,3),t=r.substr(18,2).trim(),s=r.substr(21,5).trim(),i=H+"_"+t;void 0===c.chainMissingResidueArray[i]&&(c.chainMissingResidueArray[i]=[]);let n={};n.resi=s,n.name=h.utilsCls.residueName2Abbr(e).toLowerCase(),""!=N&&t==N&&t!=N||(c.chainMissingResidueArray[i].push(n),N=t)}else 900==e&&void 0===c.emd&&"RELATED DB: EMDB"==r.substr(34).trim()&&(c.emd=r.substr(23,11).trim())}else if("SOURCE"===B&&void 0===c.organism&&"ORGANISM_COMMON"==r.substr(11,15).trim())c.organism=r.substr(28).toLowerCase().trim(),c.organism=c.organism.substr(0,c.organism.length-1);else if("ENDMDL"===B)++d,H=c.defaultPdbId,L=this.getStructureId(H,d,n),m||(k=[],O=[],R=[],I=[],E=[],T=[]),q=!1;else if("JRNL "===B)"PMID"===r.substr(12,4)&&(c.pmid=r.substr(19).trim());else if("ATOM "===B||"HETATM"===B){A=r.substr(72,4).trim(),U?(L=this.getStructureId(H,d,n),U=!1):A!=x&&(++d,H=c.defaultPdbId,L=this.getStructureId(H,d,n),m||(k=[],O=[],R=[],I=[],E=[],T=[]),q=!1),x=A;let e=r.substr(16,1);++a,F[parseInt(r.substr(6,5))]=a;let t=r.substr(76,2).trim();""===t&&(t=r.substr(12,2).trim());let l=r.substr(12,4).trim(),u=r.substr(17,3),N=r.substr(20,2).trim();""===N&&(N="A");let $=r.substr(22,5).trim(),j=$;if(s&&"DUM"===u&&(t=l,N="MEM",j=1,$=1),i&&"DUM"===u)break;C=L+"_"+N,y=C+"_"+$,b=C+"_"+j;let z=parseFloat(r.substr(30,8)),G=parseFloat(r.substr(38,8)),V=parseFloat(r.substr(46,8)),W=new THREE.Vector3(z,G,V),Y=parseFloat(r.substr(60,8));o&&(Y*=100);let X={het:"H"===B[0],serial:a,name:l,alt:e,resn:u,structure:L,chain:N,resi:j,coord:W,b:Y,elem:t,bonds:[],ss:"coil",ssbegin:!1,ssend:!1};if(X.het||"C"!==X.name||(v=a),X.het||"O"!==X.name||(w=a),!X.het&&"N"===X.name&&void 0!==_&&void 0!==S){let e=c.atoms[_].coord.distanceTo(c.atoms[S].coord),t=X.coord.x+(c.atoms[_].coord.x-c.atoms[S].coord.x)/e,s=X.coord.y+(c.atoms[_].coord.y-c.atoms[S].coord.y)/e,i=X.coord.z+(c.atoms[_].coord.z-c.atoms[S].coord.z)/e;X.hcoord=new THREE.Vector3(t,s,i)}c.atoms[a]=X,c.dAtoms[a]=1,c.hAtoms[a]=1,p[a]=1,this.isSecondary(b,k,m)?(c.atoms[a].ss="sheet",this.isSecondary(b,O,m)&&(c.atoms[a].ssbegin=!0),this.isSecondary(b,R,m)&&(c.atoms[a].ssend=!0)):this.isSecondary(b,I,m)&&(c.atoms[a].ss="helix",this.isSecondary(b,E,m)&&(c.atoms[a].ssbegin=!0),this.isSecondary(b,T,m)&&(c.atoms[a].ssend=!0));let K="-";if(K="helix"===c.atoms[a].ss?"H":"sheet"===c.atoms[a].ss?"E":!c.atoms[a].het&&h.parasCls.residueColors.hasOwnProperty(c.atoms[a].resn.toUpperCase())?"c":"o",c.secondaries[b]=K,y!==M){let e=h.utilsCls.residueName2Abbr(u);if(c.residueId2Name[b]=e,1!==a&&""!==P&&(c.residues[P]=f),b!==P&&(f={}),C!==D){_=void 0,S=void 0,1!==a&&""!==D&&(void 0===c.chains[D]&&(c.chains[D]={}),c.chains[D]=h.hashUtilsCls.unionHash(c.chains[D],g)),g={},void 0===c.structures[L.toString()]&&(c.structures[L.toString()]=[]),c.structures[L.toString()].includes(C)||c.structures[L.toString()].push(C),void 0===c.chainsSeq[C]&&(c.chainsSeq[C]=[]);let t={};t.resi=j,t.name=e,c.chainsSeq[C].push(t)}else{_=v,S=w;let t={};t.resi=j,t.name=e,c.chainsSeq[C].push(t)}}g[a]=1,f[a]=1,D=C,P=b,M=y}else if("CONECT"===B){let e=parseInt(r.substr(6,5));for(let t=0;t<4;++t){let s=parseInt(r.substr([11,16,21,26][t],5));isNaN(s)||void 0!==c.atoms[F[e]]&&c.atoms[F[e]].bonds.push(F[s])}}else B.substr(0,3);else H=r.substr(62).trim(),""==H&&(H=l?c.defaultPdbId:c.inputid&&-1==c.inputid.indexOf("/")?c.inputid.substr(0,10):c.defaultPdbId),L=this.getStructureId(H,d,n),c.molTitle="",c.molTitleHash={},q=!0}c.residues[b]=f,void 0===c.chains[C]&&(c.chains[C]={}),c.chains[C]=h.hashUtilsCls.unionHash2Atoms(c.chains[C],g,c.atoms),this.adjustSeq(c.chainMissingResidueArray);let B=Object.keys(c.structures);for(let e=0,t=B.length;e=l?n:l,o=new Array(s+i),a=0,d=0,c=0,h=!1;for(;ar&&i>r&&(h=!0),s<=r&&i>r?s>i||h?(o[c]=t[d],d++):(o[c]=e[a],a++):s>r&&i<=r?s<=i||h?(o[c]=e[a],a++):(o[c]=t[d],d++):s<=i?(o[c]=e[a],a++):(o[c]=t[d],d++),c++}if(a4||Math.abs(l.y-r.y)>4||Math.abs(l.z-r.z)>4||(l.x-r.x)*(l.x-r.x)+(l.y-r.y)*(l.y-r.y)+(l.z-r.z)*(l.z-r.z)<16&&(void 0===t.ssbondpnts[e]&&(t.ssbondpnts[e]=[]),t.ssbondpnts[e].push(o),t.ssbondpnts[e].push(a)))}}}getChainCalpha(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r={};for(let o in e){if(void 0!==i){if(o.split("_")[0]!==i)continue}let a=Object.keys(e[o]),d=[],c=0,h=0;for(let e=0,i=a.length;e3?i.resn.trim().substr(0,3):i.resn.trim();if(!l.parasCls.chargeColors.hasOwnProperty(e))continue;s?i.resi_ori:i.resi,d.push(i.coord.clone()),++c,h=i.resi}}if(c>0){r[t[a[0]].chain]=d}}return{chainresiCalphaHash:r,center:n.center.clone()}}isSecondary(e,t,s,i){if(this.icn3d.icn3dui,i)return!1;if(s){let s=e.substr(e.indexOf("_")+1),i=!1;for(let e=0,n=t.length;er.maxatomcnt);T||(r.opts.proteins="c alpha trace",r.opts.nucleotides="o3 trace");let D,P=I.getColumn("group_PDB"),M=I.getColumn("label_comp_id"),F=I.getColumn("type_symbol"),H=I.getColumn("label_atom_id"),L=I.getColumn("auth_asym_id"),N=I.getColumn("label_seq_id"),q=I.getColumn("auth_seq_id"),U=I.getColumn("label_alt_id"),B=I.getColumn("B_iso_or_equiv"),$=I.getColumn("Cartn_x"),j=I.getColumn("Cartn_y"),z=I.getColumn("Cartn_z"),G=I.getColumn("label_asym_id"),V={},W="",Y={};for(let e=0;e0&&(X[r]=a,a=[]),a.push({resi:l,name:o.utilsCls.residueName2Abbr(d)}),r=c}X[r]=a,t=s=i=n=[]}this.setSeq(x,Y,X,V)}let R=Object.keys(r.structures);for(let e=0,t=R.length;e0&&(d=!0);for(let n=0,l=t.length;na&&(a=l),s.push(l)}o.push(s)}if(!d)return void(n.bRender&&alert("These structures can not be aligned..."));a<1e-6&&(a=1);for(let e=0,s=t.length;ep[e]=4&&(n.rmsd_suprTmp=l.rmsdSuprCls.getRmsdSuprCls(c,a,p),void 0!==n.rmsd_suprTmp.rot))){let e=n.rmsd_suprTmp.rot;if(null===e[0])continue;let i=n.rmsd_suprTmp.trans1,r=n.rmsd_suprTmp.trans2,a=n.rmsd_suprTmp.rmsd;if(aRealignment RMSD: "+a.toPrecision(4)+" Å

    "),l.cfg.bSidebyside||l.htmlCls.dialogCls.openDlg("dl_rmsd","Realignment RMSD"),n.q_rotation=[],n.q_trans_sub=[],n.t_trans_add=[],n.q_rotation.push({x1:e[0],y1:e[1],z1:e[2],x2:e[3],y2:e[4],z2:e[5],x3:e[6],y3:e[7],z3:e[8]}),n.q_trans_sub.push(i),n.t_trans_add.push({x:-r.x,y:-r.y,z:-r.z}),l.cfg.aligntool="vast";//!= 'tmalign'; +let c=0,h="query",p=o.substr(0,o.indexOf("_")),m=!0;n.chainalignParserCls.transformStructure(p,c,h,m);let u="";for(let e=0,i=s.length;e8)return s;let g=[];g[0]=n[0]*r[0]+n[1]*r[1]+n[2]*r[2],g[1]=n[3]*r[0]+n[4]*r[1]+n[5]*r[2],g[2]=n[6]*r[0]+n[7]*r[1]+n[8]*r[2],g[0]-=n[0]*a[0]+n[1]*a[1]+n[2]*a[2],g[1]-=n[3]*a[0]+n[4]*a[1]+n[5]*a[2],g[2]-=n[6]*a[0]+n[7]*a[1]+n[8]*a[2];let f=0;return f=c[0]*g[0],f+=c[1]*g[1],f+=c[2]*g[2],f/=p*m,f<.866?s:(g[0]=l[0]*r[0]+l[1]*r[1]+l[2]*r[2],g[1]=l[3]*r[0]+l[4]*r[1]+l[5]*r[2],g[2]=l[6]*r[0]+l[7]*r[1]+l[8]*r[2],g[0]-=l[0]*a[0]+l[1]*a[1]+l[2]*a[2],g[1]-=l[3]*a[0]+l[4]*a[1]+l[5]*a[2],g[2]-=l[6]*a[0]+l[7]*a[1]+l[8]*a[2],f=c[0]*g[0],f+=c[1]*g[1],f+=c[2]*g[2],f/=p*m,f<.866?s:(u=0,u+=Math.pow(e.q_rotation.x1-t.q_rotation.x1,2),u+=Math.pow(e.q_rotation.y1-t.q_rotation.y1,2),u+=Math.pow(e.q_rotation.z1-t.q_rotation.z1,2),u+=Math.pow(e.q_rotation.x2-t.q_rotation.x2,2),u+=Math.pow(e.q_rotation.y2-t.q_rotation.y2,2),u+=Math.pow(e.q_rotation.z2-t.q_rotation.z2,2),u+=Math.pow(e.q_rotation.x3-t.q_rotation.x3,2),u+=Math.pow(e.q_rotation.y3-t.q_rotation.y3,2),u+=Math.pow(e.q_rotation.z3-t.q_rotation.z3,2),Math.sqrt(u)))}GetRotMatrix(e,t,s){this.icn3d.icn3dui;let i=[];return i&&(i[0]=e.q_rotation.x1/t,i[1]=e.q_rotation.y1/t,i[2]=e.q_rotation.z1/t,i[3]=e.q_rotation.x2/t,i[4]=e.q_rotation.y2/t,i[5]=e.q_rotation.z2/t,i[6]=e.q_rotation.x3/t,i[7]=e.q_rotation.y3/t,i[8]=e.q_rotation.z3/t,2!=s?(i[9]=e.t_trans_add.x/t,i[10]=e.t_trans_add.y/t,i[11]=e.t_trans_add.z/t,i[12]=-e.q_trans_sub.x/t,i[13]=-e.q_trans_sub.y/t,i[14]=-e.q_trans_sub.z/t):(i[9]=-e.q_trans_add.x/t,i[10]=-e.q_trans_add.y/t,i[11]=-e.q_trans_add.z/t,i[12]=0,i[13]=0,i[14]=0)),i}cbu_dist(e,t,s){return er&&(s.push(e[n].leaves),i.push(e[n].dist));return{clusters:s,scores:i}}}class ps{constructor(e){this.icn3d=e}async applyCommand(e){let t=this.icn3d,s=t.icn3dui;t.bAddCommands=!1;let i=e.split("|||")[0].split("%7C%7C%7C")[0].replace(/\s+/g," ").trim(),n=i.toLowerCase();if("share link"==n)await t.shareLinkCls.shareLink();else if("export state file"==n);else if(0==n.indexOf("export canvas"))setTimeout((async function(){let e=n.substr(13).trim();t.scaleFactor=""===e?1:parseInt(e);let s=""!==e;await t.shareLinkCls.shareLink(!0,s)}),500);else if("export interactions"==n)t.viewInterPairsCls.exportInteractions();else if("export stl file"==n)setTimeout((function(){t.export3DCls.exportStlFile("")}),500);else if("export vrml file"==n)setTimeout((function(){t.export3DCls.exportVrmlFile("")}),500);else if("export stl stabilizer file"==n)setTimeout((function(){t.threeDPrintCls.hideStabilizer(),t.threeDPrintCls.resetAfter3Dprint(),t.threeDPrintCls.addStabilizer(),t.export3DCls.exportStlFile("_stab")}),500);else if("export vrml stabilizer file"==n)setTimeout((function(){t.threeDPrintCls.hideStabilizer(),t.threeDPrintCls.resetAfter3Dprint(),t.threeDPrintCls.addStabilizer(),t.export3DCls.exportVrmlFile("_stab")}),500);else if("export pdb"==n)s.htmlCls.setHtmlCls.exportPdb();else if("export pdb missing atoms"==n)await t.scapCls.exportPdbProfix(!1);else if("export pdb hydrogen"==n)await t.scapCls.exportPdbProfix(!0);else if(-1!=n.indexOf("export refnum ")){let e=n.substr(14);t.refnumCls.exportRefnum(e)}else if("export secondary structure"==n)s.htmlCls.setHtmlCls.exportSecondary();else if("select all"==n)t.selectionCls.selectAll();else if("show all"==n)t.selectionCls.showAll();else if("select complement"==n)t.resid2specCls.selectComplement();else if("set pk atom"==n)t.pk=1,t.opts.pk="atom";else if("set pk off"==n)t.pk=0,t.opts.pk="no",t.drawCls.draw(),t.hlObjectsCls.removeHlObjects();else if("set pk residue"==n)t.pk=2,t.opts.pk="residue";else if("set pk strand"==n)t.pk=3,t.opts.pk="strand";else if("set pk domain"==n)t.pk=4,t.opts.pk="domain";else if("set pk chain"==n)t.pk=5,t.opts.pk="chain";else if("set surface wireframe on"==n)t.opts.wireframe="yes",t.applyMapCls.applySurfaceOptions();else if("set surface wireframe off"==n)t.opts.wireframe="no",t.applyMapCls.applySurfaceOptions();else if("set map wireframe on"==n)t.opts.mapwireframe="yes",t.applyMapCls.applyMapOptions();else if("set map wireframe off"==n)t.opts.mapwireframe="no",t.applyMapCls.applyMapOptions();else if("set emmap wireframe on"==n)t.opts.emmapwireframe="yes",t.applyMapCls.applyEmmapOptions();else if("set emmap wireframe off"==n)t.opts.emmapwireframe="no",t.applyMapCls.applyEmmapOptions();else if("set surface neighbors on"==n)t.bConsiderNeighbors=!0,t.applyMapCls.applySurfaceOptions();else if("set surface neighbors off"==n)t.bConsiderNeighbors=!1,t.applyMapCls.applySurfaceOptions();else if("set axis on"==n)t.opts.axis="yes";else if("set pc1 axis"==n)t.pc1=!0,t.axesCls.setPc1Axes();else if("set axis off"==n)t.opts.axis="no",t.pc1=!1;else if("set fog on"==n)t.opts.fog="yes",t.fogCls.setFog(!0);else if("set fog off"==n)t.opts.fog="no",t.fogCls.setFog(!0);else if("set slab on"==n)t.opts.slab="yes";else if("set slab off"==n)t.opts.slab="no";else if("set assembly on"==n)t.bAssembly=!0;else if("set assembly off"==n)t.bAssembly=!1;else if("set chemicalbinding show"==n)t.setOptionCls.setOption("chemicalbinding","show");else if("set chemicalbinding hide"==n)t.setOptionCls.setOption("chemicalbinding","hide");else if("set hbonds off"==n)t.hBondCls.hideHbonds(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("set salt bridge off"==n)t.saltbridgeCls.hideSaltbridge(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("set contact off"==n)t.contactCls.hideContact(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("set halogen pi off"==n)t.piHalogenCls.hideHalogenPi(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("hydrogens"==n)t.showInterCls.showHydrogens(),t.drawCls.draw();else if("set hydrogens off"==n)t.showInterCls.hideHydrogens(),t.drawCls.draw();else if("close popup"==n)t.resizeCanvasCls.closeDialogs();else if("set stabilizer off"==n)t.threeDPrintCls.hideStabilizer(),t.drawCls.draw();else if("set disulfide bonds off"==n)t.opts.ssbonds="no",t.drawCls.draw();else if("set cross linkage off"==n)t.opts.clbonds="no",t.drawCls.draw();else if("set lines off"==n)t.labels.distance=[],t.lines.distance=[],t.drawCls.draw();else if("set labels off"==n){for(let e in t.labels)t.labels[e]=[];t.drawCls.draw()}else if("set mode all"==n)t.definedSetsCls.setModeAndDisplay("all");else if("set mode selection"==n)t.definedSetsCls.setModeAndDisplay("selection");else if("set view detailed view"==n)t.annotationCls.setAnnoViewAndDisplay("detailed view");else if("set view overview"==n)t.annotationCls.setAnnoViewAndDisplay("overview");else if("set annotation custom"==n)t.annotationCls.setAnnoTabCustom();else if("set annotation interaction"==n)t.annotationCls.setAnnoTabInteraction();else if("set annotation ptm"==n)await t.annotationCls.setAnnoTabPTM();else if("set annotation cdd"==n)t.annotationCls.setAnnoTabCdd();else if("set annotation site"==n)t.annotationCls.setAnnoTabSite();else if("set annotation ssbond"==n)t.annotationCls.setAnnoTabSsbond();else if("set annotation crosslink"==n)t.annotationCls.setAnnoTabCrosslink();else if("set annotation transmembrane"==n)await t.annotationCls.setAnnoTabTransmem();else if("set annotation ig"==n)t.bRunRefnumAgain=!0,await t.annotationCls.setAnnoTabIg(),t.bRunRefnumAgain=!1;else if("ig refnum on"==n)t.bRunRefnumAgain=!0,t.bAnnoShown||await t.showAnnoCls.showAnnotations(),await t.annotationCls.setAnnoTabIg(!0),t.bRunRefnumAgain=!1;else if("highlight level up"==n)t.resid2specCls.switchHighlightLevelUp();else if("highlight level down"==n)t.resid2specCls.switchHighlightLevelDown();else if(0==n.indexOf("hide annotation")){let e=n.lastIndexOf(" "),s=n.substr(e+1);"all"==s?t.annotationCls.hideAnnoTabAll():"custom"==s?t.annotationCls.hideAnnoTabCustom():"clinvar"==s?t.annotationCls.hideAnnoTabClinvar():"snp"==s?t.annotationCls.hideAnnoTabSnp():"cdd"==s?t.annotationCls.hideAnnoTabCdd():"3ddomain"==s?t.annotationCls.hideAnnoTab3ddomain():"site"==s?t.annotationCls.hideAnnoTabSite():"ptm"==s?t.annotationCls.hideAnnoTabPTM():"interaction"==s?t.annotationCls.hideAnnoTabInteraction():"ssbond"==s?t.annotationCls.hideAnnoTabSsbond():"crosslink"==s?t.annotationCls.hideAnnoTabCrosslink():"transmembrane"==s&&t.annotationCls.hideAnnoTabTransmem()}else if("add residue labels"==n)t.residueLabelsCls.addResidueLabels(t.hAtoms),t.drawCls.draw();else if("add residue number labels"==n)t.residueLabelsCls.addResidueLabels(t.hAtoms,void 0,void 0,!0),t.drawCls.draw();else if("add reference number labels"==n)t.residueLabelsCls.addResidueLabels(t.hAtoms,void 0,void 0,void 0,!0),t.drawCls.draw();else if("add ig labels"==n)t.residueLabelsCls.addIgLabels(t.hAtoms),t.drawCls.draw();else if("add atom labels"==n)t.residueLabelsCls.addAtomLabels(t.hAtoms),t.drawCls.draw();else if("add element labels"==n)t.residueLabelsCls.addAtomLabels(t.hAtoms,!0),t.drawCls.draw();else if("add chain labels"==n)t.analysisCls.addChainLabels(t.hAtoms),t.drawCls.draw();else if("add terminal labels"==n)t.analysisCls.addTerminiLabels(t.hAtoms),t.drawCls.draw();else if("rotate left"==n)t.bStopRotate=!1,t.ROT_DIR="left",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("left");else if("rotate right"==n)t.bStopRotate=!1,t.ROT_DIR="right",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("right");else if("rotate up"==n)t.bStopRotate=!1,t.ROT_DIR="up",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("up");else if("rotate down"==n)t.bStopRotate=!1,t.ROT_DIR="down",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("down");else if("rotate x"==n){let e=new THREE.Vector3(1,0,0),s=.5*Math.PI;t.transformCls.setRotation(e,s)}else if("rotate y"==n){let e=new THREE.Vector3(0,1,0),s=.5*Math.PI;t.transformCls.setRotation(e,s)}else if("rotate z"==n){let e=new THREE.Vector3(0,0,1),s=.5*Math.PI;t.transformCls.setRotation(e,s)}else if("reset"===n)t.selectionCls.resetAll();else if("reset orientation"===n)t.transformCls.resetOrientation(),t.drawCls.draw();else if("reset thickness"==n)t.threeDPrintCls.resetAfter3Dprint(),t.drawCls.draw();else if("clear selection"==n)t.hlObjectsCls.removeHlObjects(),t.hlUpdateCls.removeHl2D(),t.bSelectResidue=!1;else if("zoom selection"==n)t.transformCls.zoominSelection(),t.drawCls.draw();else if("center selection"==n)t.applyCenterCls.centerSelection(),t.drawCls.draw();else if("show selection"==n)t.selectionCls.showSelection();else if("hide selection"==n)t.selectionCls.hideSelection();else if("output selection"==n)t.threeDPrintCls.outputSelection();else if("toggle selection"==n)t.selectionCls.toggleSelection();else if("toggle highlight"==n)t.hlUpdateCls.toggleHighlight();else if("stabilizer"==n)t.threeDPrintCls.addStabilizer(),t.threeDPrintCls.prepareFor3Dprint();else if("disulfide bonds"==n)t.showInterCls.showSsbonds();else if("cross linkage"==n)t.showInterCls.showClbonds();else if("back"==n)await t.resizeCanvasCls.back();else if("forward"==n)await t.resizeCanvasCls.forward();else if("clear all"==n)t.selectionCls.selectAll();else if("defined sets"==n)t.definedSetsCls.showSets(),t.bDefinedSets=!0;else if("delete selected sets"==n)t.definedSetsCls.deleteSelectedSets();else if("view interactions"==n)void 0===s.cfg.mmdbid&&void 0===s.cfg.gi||t.ParserUtilsCls.set2DDiagrams(t.inputid);else if("show annotations all chains"==n)t.annotationCls.showAnnoAllChains();else if("save color"==n)t.setOptionCls.saveColor();else if("apply saved color"==n)t.setOptionCls.applySavedColor();else if("save style"==n)t.setOptionCls.saveStyle();else if("apply saved style"==n)t.setOptionCls.applySavedStyle();else if("select main chains"==n)t.selectionCls.selectMainChains();else if("select side chains"==n)t.selectionCls.selectSideChains();else if("select main side chains"==n)t.selectionCls.selectMainSideChains();else if("realign"==n)t.realignParserCls.realign();else if(-1!=n.indexOf("realign predefined ")){let e="realign predefined ",n=i.substr(e.length),l=n.indexOf(" "),r=n.substr(0,l).split(",");s.cfg.resdef=n.substr(l+1).replace(/:/gi,";"),await t.realignParserCls.realignChainOnSeqAlign(void 0,r,!0,!0)}else if("area"==n)t.analysisCls.calculateArea();else if("table inter count only"==n)$(".icn3d-border").hide();else if("table inter details"==n)$(".icn3d-border").show();else if("setoption map nothing"==n)t.setOptionCls.setOption("map","nothing");else if("setoption emmap nothing"==n)t.setOptionCls.setOption("emmap","nothing");else if("setoption phimap nothing"==n)t.setOptionCls.setOption("phimap","nothing");else if("setoption phisurface nothing"==n)t.setOptionCls.setOption("phisurface","nothing");else if("clear symd symmetry"==n)t.symdArray=[];else if("show axis"==n)t.bAxisOnly=!0;else if(0==i.indexOf("define helix sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineSecondary(e,"helix")}else if(0==i.indexOf("define sheet sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineSecondary(e,"sheet")}else if(0==i.indexOf("define coil sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineSecondary(e,"coil")}else if(0==i.indexOf("define iganchor sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineIgstrand(e,"iganchor")}else if(0==i.indexOf("define igstrand sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineIgstrand(e,"igstrand")}else if(0==i.indexOf("define igloop sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineIgstrand(e,"igloop")}else if(0==i.indexOf("select interaction")){let e=i.substr(i.lastIndexOf(" ")+1).split(",");if(null!==e){let s=e[0].split("_")[0];t.b2DShown||t.ParserUtilsCls.download2Ddgm(s.toUpperCase()),t.diagram2dCls.selectInteraction(e[0],e[1])}}else if(0==i.indexOf("select saved atoms")||0==i.indexOf("select sets")){i=i.replace(/aligned_protein/g,"protein_aligned"),t.bDefinedSets||(t.definedSetsCls.setPredefinedInMenu(),t.bDefinedSets=!0);let e=i.split(" | "),s=e[0].replace(/,/g," or "),n=19;0==i.indexOf("select sets")&&(n=12);let l=s.substr(n),r=l;2==e.length&&(r=e[1].substr(5)),t.definedSetsCls.selectCombinedSets(l,r)}else if(-1!==i.indexOf("select chain")){let e=i.substr(i.lastIndexOf(" ")+1).split(",");for(let s=0,i=e.length;s6?e[6].substr(e[6].lastIndexOf(" ")+1):0,d=e.length>7?e[7].substr(e[7].lastIndexOf(" ")+1):1;t.analysisCls.addLine(parseFloat(s[1]),parseFloat(s[3]),parseFloat(s[5]),parseFloat(i[1]),parseFloat(i[3]),parseFloat(i[5]),l,r,o,parseFloat(a),parseFloat(d)),t.drawCls.draw()}else if(0==n.indexOf("add sphere"))this.addShape(i,"sphere"),t.shapeCmdHash[i]=1;else if(0==n.indexOf("add cube"))this.addShape(i,"cube"),t.shapeCmdHash[i]=1;else if(0==n.indexOf("clear shape"))t.shapeCmdHash={};else if(0==n.indexOf("clear line between sets"))t.lines.cylinder=[];else if(0==i.indexOf("add label")){let e,n,l,r,o,a,d,c=i.split(" | "),h=c[0].substr("add label".length+1),p=!1;for(let t=1,s=c.length;t=5&&(e=l[4].substr(5)),l.length>=6&&(s=l[5].substr(6)),l.length>=7&&(n=l[6].substr(4)),$("#"+t.pre+"anno_custom")[0]&&($("#"+t.pre+"anno_custom")[0].checked=!0),$("[id^="+t.pre+"custom]").show(),"0"==s&&(s=void 0),t.addTrackCls.checkGiSeq(r,o,a,e,s,n,0)}else if(0==n.indexOf("remove one stabilizer")){let e=n.split(" | ")[1].split(" "),s=[];s.push(parseInt(e[0])),s.push(parseInt(e[1])),t.threeDPrintCls.removeOneStabilizer(s),t.drawCls.draw()}else if(0==n.indexOf("add one stabilizer")){let e=n.split(" | ")[1].split(" ");void 0===t.pairArray&&(t.pairArray=[]),t.pairArray.push(parseInt(e[0])),t.pairArray.push(parseInt(e[1])),t.drawCls.draw()}else if(0==n.indexOf("select planes z-axis")){let e=n.split(" ");if(5==e.length){let s=parseFloat(e[3]),i=parseFloat(e[4]);t.selectionCls.selectBtwPlanes(s,i)}}else if(0==n.indexOf("adjust membrane z-axis")){let e=n.split(" ");if(5==e.length){let s=parseFloat(e[3]),i=parseFloat(e[4]);t.selectionCls.adjustMembrane(s,i)}}else if(0==n.indexOf("toggle membrane"))t.selectionCls.toggleMembrane();else if(0==i.indexOf("calc buried surface")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(" ");if(2==s.length){let e=s[0].split(","),i=s[1].split(",");t.analysisCls.calcBuriedSurface(e,i)}}}else if(0==i.indexOf("dist ")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(" ");if(2==s.length){let e=s[0].split(","),i=s[1].split(",");t.analysisCls.measureDistTwoSets(e,i)}}}else if(0==i.indexOf("disttable")){let e=i.split(" | ");if(2==e.length){let i=e[1].split(" ");if(2==i.length){let e=i[0].split(","),n=i[1].split(",");t.analysisCls.measureDistManySets(e,n),s.htmlCls.dialogCls.openDlg("dl_disttable","Distance among the sets")}}}else if(0==i.indexOf("display interaction 3d")||0==i.indexOf("view interaction pairs")||0==i.indexOf("save1 interaction pairs")||0==i.indexOf("save2 interaction pairs")||0==i.indexOf("line graph interaction pairs")||0==i.indexOf("scatterplot interaction pairs")){let e=i.split(" | ");if(e.length>=3){let s=e[1].split(" ");if(2==s.length){let n,l,r=s[0].split(","),o=s[1].split(","),a=-1!==e[2].indexOf("hbonds"),d=-1!==e[2].indexOf("salt bridge"),c=-1!==e[2].indexOf("interactions"),h=-1!==e[2].indexOf("halogen"),p=-1!==e[2].indexOf("pi-cation"),m=-1!==e[2].indexOf("pi-stacking");if(e.length>=4&&(n="true"==e[3]),e.length>=5){let s=e[4].split(" ");s.length>=4&&($("#"+t.pre+"hbondthreshold").val(s[1]),$("#"+t.pre+"saltbridgethreshold").val(s[2]),$("#"+t.pre+"contactthreshold").val(s[3]),7==s.length&&($("#"+t.pre+"halogenthreshold").val(s[4]),$("#"+t.pre+"picationthreshold").val(s[5]),$("#"+t.pre+"pistackingthreshold").val(s[6])))}0==i.indexOf("display interaction 3d")?l="3d":0==i.indexOf("view interaction pairs")?l="view":0==i.indexOf("save1 interaction pairs")?l="save1":0==i.indexOf("save2 interaction pairs")?l="save2":0==i.indexOf("line graph interaction pairs")?l="linegraph":0==i.indexOf("scatterplot interaction pairs")&&(l="scatterplot"),await t.viewInterPairsCls.viewInteractionPairs(r,o,n,l,a,d,c,h,p,m)}}}else if(0==i.indexOf("export pairs")){let e=i.split(" | ");if(3==e.length){let i=e[1].split(" ");if(2==i.length){let n=i[0].split(","),l=i[1].split(","),r=e[2].split(" ")[1];t.showInterCls.pickCustomSphere(r,n,l,t.bSphereCalc),t.bSphereCalc=!0;let o=t.viewInterPairsCls.exportSpherePairs(),a=Object.keys(s.utilsCls.getHlStructures()).join(",");t.saveFileCls.saveFile(a+"_sphere_pairs.html","html",o)}}}else if(0==n.indexOf("graph label")){let e=n.lastIndexOf(" "),t=n.substr(e+1);$("#"+s.svgid+"_label").val(t),$("#"+s.svgid+" text").removeClass(),$("#"+s.svgid+" text").addClass(t)}else if(0==n.indexOf("cartoon label")){let e=n.lastIndexOf(" "),t=n.substr(e+1);$("#"+s.svgid_ct+"_label").val(t),$("#"+s.svgid_ct+" text").removeClass(),$("#"+s.svgid_ct+" text").addClass(t)}else if(0==n.indexOf("line graph scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.linegraphid+"_scale").val(i),$("#"+s.linegraphid).attr("width",(t.linegraphWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("scatterplot scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.scatterplotid+"_scale").val(i),$("#"+s.scatterplotid).attr("width",(t.scatterplotWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("contactmap scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.contactmapid+"_scale").val(i),$("#"+s.contactmapid).attr("width",(t.contactmapWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("alignerrormap scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.alignerrormapid+"_scale").val(i),$("#"+s.alignerrormapid).attr("width",(t.alignerrormapWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("graph force")){let e=n.lastIndexOf(" ");s.htmlCls.force=parseInt(n.substr(e+1)),$("#"+s.svgid+"_force").val(s.htmlCls.force),t.getGraphCls.handleForce()}else if(0==n.indexOf("hide edges")){let e=n.lastIndexOf(" ");s.htmlCls.hideedges=parseInt(n.substr(e+1)),$("#"+s.svgid+"_hideedges").val(s.htmlCls.hideedges),s.htmlCls.hideedges?(s.htmlCls.contactInsideColor="FFF",s.htmlCls.hbondInsideColor="FFF",s.htmlCls.ionicInsideColor="FFF"):(s.htmlCls.contactInsideColor="DDD",s.htmlCls.hbondInsideColor="AFA",s.htmlCls.ionicInsideColor="8FF"),void 0!==t.graphStr&&t.bRender&&s.htmlCls.force&&t.drawGraphCls.drawGraph(t.graphStr,t.pre+"dl_graph")}else if(0==n.indexOf("reset interaction pairs"))t.viewInterPairsCls.resetInteractionPairs();else if(0==n.indexOf("side by side")){let e=n.split(" | ")[1],t="_blank";window.open(e,t)}else if(0==i.indexOf("your note")){let e=i.split(" | ");t.yournote=e[1],$("#"+t.pre+"yournote").val(t.yournote),s.cfg.shownote&&(document.title=t.yournote)}else if(0==n.indexOf("cross structure interaction"))t.crossstrucinter=parseInt(n.substr(n.lastIndexOf(" ")+1)),$("#"+t.pre+"crossstrucinter").val(t.crossstrucinter);else if("replay on"==n)await t.resizeCanvasCls.replayon();else if("replay off"==n)await t.resizeCanvasCls.replayoff();else if(0==n.indexOf("contact map")){let e=n.split(" | ");if(3===e.length){let s=parseFloat(e[1].split(" ")[1]),i=e[2].split(" ")[1];await t.contactMapCls.contactMap(s,i)}}else if(0==n.indexOf("pickatom")){let e=parseInt(n.substr(n.lastIndexOf(" ")+1));t.pAtom=t.atoms[e],t.pickingCls.showPicking(t.pAtom)}else if(0==i.indexOf("set color spectrum")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!0;t.setColorCls.setColorAcrossSets(s,i)}}else if(0==i.indexOf("set residues color spectrum")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!0;t.setColorCls.setColorBySets(s,i)}}else if(0==i.indexOf("set color rainbow")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!1;t.setColorCls.setColorAcrossSets(s,i)}}else if(0==i.indexOf("set residues color rainbow")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!1;t.setColorCls.setColorBySets(s,i)}}else if(0==i.indexOf("color")){let e=i.split(" | "),n=e[0].substr(e[0].indexOf(" ")+1);if(t.opts.color=n,"residue custom"==n&&2==e.length){t.customResidueColors=JSON.parse(e[1]);for(let e in t.customResidueColors)t.customResidueColors[e.toUpperCase()]=s.parasCls.thr("#"+t.customResidueColors[e])}else if("align custom"==n&&3==e.length){let s=e[1],i=e[2].split(", ");t.queryresi2score={},t.queryresi2score[s]={};for(let e=0,n=i.length;e=4?this.setQueryresi2score(e):"area"==n&&2==e.length&&(t.midpercent=e[1],$("#"+t.pre+"midpercent").val(t.midpercent));t.setColorCls.setColorByOptions(t.opts,t.hAtoms),t.hlUpdateCls.updateHlAll()}else if(0==i.indexOf("remove legend"))$("#"+s.pre+"legend").hide();else if(0==i.indexOf("custom tube")){let e=i.split(" | ");this.setQueryresi2score(e),t.setOptionCls.setStyle("proteins","custom tube")}else if(0==n.indexOf("style")){let e=n.substr(n.indexOf(" ")+1),s=e.substr(0,e.indexOf(" ")),i=e.substr(e.indexOf(" ")+1);t.setOptionCls.setStyle(s,i)}else if(0==n.indexOf("window")){let e=n.substr(n.indexOf(" ")+1);setTimeout((function(){"aligned sequences"==e?s.htmlCls.dialogCls.openDlg("dl_alignment","Select residues in aligned sequences"):"interaction table"==e?s.htmlCls.dialogCls.openDlg("dl_allinteraction","Show interactions"):"interaction graph"==e?s.htmlCls.dialogCls.openDlg("dl_linegraph","Show interactions between two lines of residue nodes"):"interaction scatterplot"==e?s.htmlCls.dialogCls.openDlg("dl_scatterplot","Show interactions as scatterplot"):"force-directed graph"==e&&s.htmlCls.dialogCls.openDlg("dl_graph","Force-directed graph")}),1e3)}else if(0==n.indexOf("set theme")){let e=n.substr(n.lastIndexOf(" ")+1);s.htmlCls.setMenuCls.setTheme(e)}else if(0==n.indexOf("set double color")){let e=n.substr(n.lastIndexOf(" ")+1);"on"==e?(t.bDoublecolor=!0,t.setOptionCls.setStyle("proteins","ribbon")):"off"==e&&(t.bDoublecolor=!1)}else if(0==n.indexOf("adjust dialog")){let e=n.substr(n.lastIndexOf(" ")+1);t.scapCls.adjust2DWidth(e)}else if(0==n.indexOf("glycans cartoon")){let e=n.substr(n.lastIndexOf(" ")+1);t.bGlycansCartoon="yes"==e}else if(0==n.indexOf("save html")){let e=n.substr(n.lastIndexOf(" ")+1);s.htmlCls.eventsCls.saveHtml(e)}else if(0==n.indexOf("resdef"))s.cfg.resdef=n.substr(n.indexOf(" ")+1);else if(0==n.indexOf("vast_search_chainid")){t.chainidArray=i.substr(i.indexOf(" ")+1).split(",");let e=!0,s=!0;await t.realignParserCls.realignChainOnSeqAlign(void 0,t.chainidArray,e,s)}else if(0==n.indexOf("ig refnum off"))await t.refnumCls.hideIgRefNum();else if(0==n.indexOf("custom refnum")){let e=i.split(" | ")[1].replace(/\\n/g,"\n");await t.refnumCls.parseCustomRefFile(e)}else if(0==n.indexOf("show ref number"))t.bShownRefnum=!0;else if(0==n.indexOf("hide ref number"))t.bShownRefnum=!1;else if(0==n.indexOf("translate pdb")){let e=n.substr(14).split(" ");t.transformCls.translateCoord(t.hAtoms,parseFloat(e[0]),parseFloat(e[1]),parseFloat(e[2])),t.drawCls.draw()}else if(0==n.indexOf("rotate pdb")){let e=n.substr(11).split(","),s=[];for(let t=0,i=e.length;t1&&(n=e[1].substr(e[1].indexOf(" ")+1)),e.length>2&&(l=e[2].substr(e[2].indexOf(" ")+1)),-1!==s.indexOf(" or ")?await t.selByCommCls.selectByCommand(s,n,l):await t.selByCommCls.selectBySpec(s,n,l)}s.htmlCls.clickMenuCls.setLogCmd(i,!1),t.bAddCommands=!0}setStrengthPara(e){let t=this.icn3d;if(t.icn3dui,e.length>=5){let s=e[4].split(" ");s.length>=4&&($("#"+t.pre+"hbondthreshold").val(s[1]),$("#"+t.pre+"saltbridgethreshold").val(s[2]),$("#"+t.pre+"contactthreshold").val(s[3]),s.length>=7&&($("#"+t.pre+"halogenthreshold").val(s[4]),$("#"+t.pre+"picationthreshold").val(s[5]),$("#"+t.pre+"pistackingthreshold").val(s[6])))}if(6==e.length){let s=e[5].split(" ");s.length>=6&&($("#"+t.pre+"dist_ss").val(s[0]),$("#"+t.pre+"dist_coil").val(s[1]),$("#"+t.pre+"dist_hbond").val(s[2]),$("#"+t.pre+"dist_inter").val(s[3]),$("#"+t.pre+"dist_ssbond").val(s[4]),$("#"+t.pre+"dist_ionic").val(s[5]),9==s.length&&($("#"+t.pre+"dist_halogen").val(s[6]),$("#"+t.pre+"dist_pication").val(s[7]),$("#"+t.pre+"dist_pistacking").val(s[8])))}}getThresholdNameArrays(e){this.icn3d.icn3dui.htmlCls.clickMenuCls.SetChainsAdvancedMenu();let t,s=e.split(" | "),i=parseFloat(s[0].substr(s[0].lastIndexOf(" ")+1)),n=[],l=[];if(s.length>=2&&s[1].length>4){let e=s[1].split(" ");e.length>1&&(l=e[1].split(",")),e.length>2&&(n=e[2].split(","))}else l=["selected"],n=["non-selected"];return 3==s.length&&(t="true"==s[2]),{threshold:i,nameArray2:l,nameArray:n,bHbondCalc:t}}setQueryresi2score(e){let t=this.icn3d,s=t.icn3dui,i=e[1],n=e[2].split(" ")[1].split("_"),l=e[3];void 0===t.queryresi2score&&(t.queryresi2score={}),t.queryresi2score[i]={};for(let e=parseInt(n[0]),s=0;e<=parseInt(n[1]);++e,++s)"_"!=l[s]&&(t.queryresi2score[i][e]=11.11111111111111*parseInt(l[s]));if(e.length>4){let i=e[4].split(" ");t.startColor=i[1],t.midColor=i[2],t.endColor=i[3];let n=s.htmlCls.clickMenuCls.setLegendHtml();$("#"+s.pre+"dl_legend_html").html(n),s.htmlCls.dialogCls.openDlg("dl_legend","Color Range")}}addShape(e,t){let s=this.icn3d,i=s.icn3dui,n=e.split(" | "),l=n[1].split(" "),r=n[2].substr(n[2].lastIndexOf(" ")+1),o=n[3].substr(n[3].lastIndexOf(" ")+1),a=n[4].substr(n[4].lastIndexOf(" ")+1);r="#"+r.replace(/\#/g,"");let d,c=i.parasCls.thr(r);if("x1"==l[0])d=new THREE.Vector3(parseFloat(l[1]),parseFloat(l[3]),parseFloat(l[5]));else{let e=n[1].split(","),t=s.definedSetsCls.getAtomsFromNameArray(e),i=s.contactCls.getExtent(t);d=new THREE.Vector3(i[2][0],i[2][1],i[2][2])}"sphere"==t?s.sphereCls.createSphereBase(d,c,parseFloat(a),void 0,void 0,void 0,parseFloat(o)):s.boxCls.createBox_base(d,parseFloat(a),c,void 0,void 0,void 0,parseFloat(o))}getMenuFromCmd(e){this.icn3d.icn3dui;let t="Windows > View Sequences & Annotations",s="Analysis > Interactions",i=s+" > 2D Graph(Force-Directed)",n="View > Rotate > Auto Rotation > Rotate ",l="View > Rotate > Rotate 90 deg > ",r="Select > Select on 3D > ",o="Analysis > Label > ",a="File > 3D Printing > ";return 0==(e=e.trim()).indexOf("load")?"File > Retrieve by ID, Align":0==e.indexOf("set map")&&-1==e.indexOf("set map wireframe")?"Style > Electron Density":0==e.indexOf("set emmap")&&-1==e.indexOf("set emmap wireframe")?"Style > EM Density Map":0==e.indexOf("set phi")?"Analysis > Load Potential > URL(CORS) Phi/Cube":0==e.indexOf("set delphi")?"Analysis > DelPhi Potential":0==e.indexOf("setoption map")?"Style > Remove Map":0==e.indexOf("setoption emmap")?"Style > Remove EM Map":0==e.indexOf("view annotations")?t:0==e.indexOf("set annotation all")?t+': "All" checkbox':0==e.indexOf("set annotation clinvar")?t+': "ClinVar" checkbox':0==e.indexOf("set annotation snp")?t+': "SNP" checkbox':0==e.indexOf("set annotation 3ddomain")?t+': "3D Domains" checkbox':0==e.indexOf("view interactions")?"Windows > View 2D Diagram":0==e.indexOf("symmetry")?"Analysis > Symmetry":0==e.indexOf("realign on seq align")?"File > Realign Selection > on Sequence Alignment":0==e.indexOf("realign")?"File > Realign Selection > Residue by Residue":0==e.indexOf("graph interaction pairs")?s+" > 2D Graph(Force-Directed)":0==e.indexOf("export canvas")?"File > Save File > iCn3D PNG Image":"export stl file"==e?a+"STL":"export vrml file"==e?a+"VRML(Color)":"export stl stabilizer file"==e?a+"STL W/ Stabilizers":"export vrml stabilizer file"==e?a+"VRML(Color, W/ Stabilizers)":"select all"==e?'Select > All; or Toggle to "All"(next to "Help")':"show all"==e?"View > View Full Structure":"select complement"==e?"Select > Inverse":"set pk atom"==e?r+"Atom":"set pk residue"==e?r+"Residue":"set pk strand"==e?r+"Strand/Helix":"set pk domain"==e?r+"3D Domain":"set pk chain"==e?r+"Chain":"set surface wireframe on"==e?"Style > Surface Wireframe > Yes":"set surface wireframe off"==e?"Style > Surface Wireframe > No":"set map wireframe on"==e?"Style > Map Wireframe > Yes":"set map wireframe off"==e?"Style > Map Wireframe > No":"set emmap wireframe on"==e?"Style > EM Map Wireframe > Yes":"set emmap wireframe off"==e?"Style > EM Map Wireframe > No":"set surface neighbors on"==e?"Style > Surface Type > ... with Context":"set axis on"==e?"View > XYZ-axes > Show":"set axis off"==e?"View > XYZ-axes > Hide":"set fog on"==e?"View > Fog for Selection > On":"set fog off"==e?"View > Fog for Selection > Off":"set slab on"==e?"View > Slab for Selection > On":"set slab off"==e?"View > Slab for Selection > Off":"set assembly on"==e?"Analysis > Assembly > Biological Assembly":"set assembly off"==e?"Analysis > Assembly > Asymmetric Unit":"set chemicalbinding show"==e?"Analysis > Chem. Binding > Show":"set chemicalbinding hide"==e?"Analysis > Chem. Binding > Hide":"set hbonds off"==e||"set salt bridge off"==e||"set contact off"==e||"set halogen pi off"==e?s+" > Reset":"hydrogens"==e?"Style > Hydrogens > Show":"set hydrogens off"==e?"Style > Hydrogens > Hide":"set stabilizer off"==e?"File > 3D Printing > Remove All Stabilizers":"set disulfide bonds off"==e?"Analysis > Disulfide Bonds > Hide":"set cross linkage off"==e?"Analysis > Cross-Linkages > Hide":"set lines off"==e?"Analysis > Distance > Hide":"set labels off"==e?"Analysis > Label > Remove":"set mode all"==e?'Toggle to "All"(next to "Help")':"set mode selection"==e?'Toggle to "Selection"(next to "Help")':"set view detailed view"==e?t+': "Details" tab':"set view overview"==e?t+': "Summary" tab':"set annotation custom"==e?t+': "Custom" checkbox':"set annotation interaction"==e?t+': "Interactions" checkbox':"set annotation ptm"==e?t+': "PTM" checkbox':"set annotation cdd"==e?t+': "Conserved Domains" checkbox':"set annotation site"==e?t+': "Functional Sites" checkbox':"set annotation ssbond"==e?t+': "Disulfide Bonds" checkbox':"set annotation crosslink"==e?t+': "Cross-Linkages" checkbox':"set annotation transmembrane"==e?t+': "Transmembrane" checkbox':"set annotation ig"==e?t+': "Ig Domains" checkbox':"highlight level up"==e?"Keyboard Arrow Up":"highlight level down"==e?"Keyboard Arrow Down":0==e.indexOf("hide annotation")?t+": checkboxes off":"add residue labels"==e?o+"per Residue":"add residue number labels"==e?o+"per Residue & Number":"add Ig domain labels"==e?o+"per Ig Domain":"add atom labels"==e?o+"per Atom":"add chain labels"==e?o+"per Chain":"add terminal labels"==e?o+"N- & C- Termini":"rotate left"==e?n+"Left; or Key l":"rotate right"==e?n+"Right; or Key j":"rotate up"==e?n+"Up; or Key i":"rotate down"==e?n+"Down; or Key m":"rotate x"==e?l+"X-axis":"rotate y"==e?l+"Y-axis":"rotate z"==e?l+"Z-axis":"reset"==e?"View > Reset > All":"reset orientation"==e?"View > Reset > Orientation":"clear selection"==e?"Select > Clear Selection":"zoom selection"==e?"Select > Zoom in Selection":"center selection"==e?"Select > Center Selection":"show selection"==e?"Select > View Only Selection":"hide selection"==e?"Select > Hide Selection":"output selection"==e?"Select > Clear Selection":"toggle highlight"==e?"Select > Toggle Highlight":"stabilizer"==e?"File > 3D Printing > Add all Stabilizers":"disulfide bonds"==e?"Analysis > Disulfide Bonds > Show":"cross linkage"==e?"Analysis > Cross-Linkages > Show":"back"==e?"View > Undo":"forward"==e?"View > Redo":"clear all"==e?"Select > Clear Selection":"defined sets"==e?"Windows > Defined Sets":"delete selected sets"==e?'Windows > Defined Sets: "Delete Selected Sets" button':"view interactions"==e?"Windows > View Interactions":"show annotations all chains"==e?t+': "Show All Chains" button':"save color"==e?"Color > Save Color":"apply saved color"==e?"Color > Apply Saved Color":"save style"==e?"Style > Save Style":"apply saved style"==e?"Style > Apply Saved Style":"select main chains"==e?"Select > Main Chains":"select side chains"==e?"Select > Side Chains":"select main side chains"==e?"Select > Main & Side Chains":"area"==e?"View > Surface Area":"table inter count only"==e?s+': "Set 1" button: "Show Count Only" button':"table inter details"==e?s+': "Set 1" button: "Show Details" button':0==e.indexOf("define helix sets")?t+': "Helix Sets" button':0==e.indexOf("define sheet sets")?t+': "Sheet Sets" button':0==e.indexOf("define coil sets")?t+': "Coil Sets" button':0==e.indexOf("select interaction")?"Windows > View 2D Diagram: click on edges":0==e.indexOf("select saved atoms")||0==e.indexOf("select sets")?"Windows > Defined Sets: select in menu":-1!==e.indexOf("select chain")?t+": click on chain names":-1!==e.indexOf("select alignChain")?"Windows > View Aligned Sequences: click on chain names":0==e.indexOf("select zone cutoff")?"Select > by Distance":0==e.indexOf("set surface opacity")?"Style > Surface Opacity":0==e.indexOf("set label scale")?"View > Label Scale":0==e.indexOf("set surface")?"Style > Surface Type":0==e.indexOf("set camera")?"View > Camera":0==e.indexOf("set background")?"Style > Background":0==e.indexOf("set thickness")?"File > 3D Printing > Set Thickness":0==e.indexOf("set highlight color")?"Select > Highlight Color":0==e.indexOf("set highlight style")?"Select > Highlight Style":0==e.indexOf("add line")||0==e.indexOf("add label")?"Analysis > Distance > between Two Atoms":0==e.indexOf("dist")?"Analysis > Distance > between Two Sets":0==e.indexOf("msa")?t+': "Add Track" button: "FASTA Alignment" button':0==e.indexOf("add track")?t+': "Add Track" button':0==e.indexOf("remove one stabilizer")?"File > 3D Printing > Remove One Stablizer":0==e.indexOf("add one stabilizer")?"File > 3D Printing > Add One Stablizer":0==e.indexOf("select planes z-axis")?"View > Select between Two X-Y Planes":0==e.indexOf("adjust membrane z-axis")?"View > Adjust Membrane":0==e.indexOf("toggle membrane")?"View > Toggle Membrane":0==e.indexOf("calc buried surface")?s+': "Buried Surface Area" button':0==e.indexOf("display interaction 3d")?s+': "3D Display Interactions" button':0==e.indexOf("view interaction pairs")?s+': "Highlight Interactions in Table" button':0==e.indexOf("save1 interaction pairs")?s+': "Set 1" button':0==e.indexOf("save2 interaction pairs")?s+': "Set 2" button':0==e.indexOf("line graph interaction pairs")?s+': "2D Interaction Network" button':0==e.indexOf("scatterplot interaction pairs")?s+': "2D Interaction Map" button':0==e.indexOf("graph label")?i+': "Label Size" menu':0==e.indexOf("graph force")?i+': "Force on Nodes" menu':0==e.indexOf("hide edges")?i+': "Internal Edges" menu':0==e.indexOf("reset interaction pairs")?s+" > Reset":0==e.indexOf("side by side")?"View > Side by Side":0==e.indexOf("your note")?"Windows > Your Notes / Window Title":0==e.indexOf("pickatom")?"Hold Alt key and click on 3D structure":0==e.indexOf("color")?"Color menu":0==e.indexOf("custom tube")?t+': "Custom Color/Tube" button: "Custom Tube" button':0==e.indexOf("style")?"Style menu":-1!==e.indexOf("select displayed set")?"Select > Displayed Set":-1!==e.indexOf("select prop")?"Select > by Property":0==e.indexOf("select")&&-1!==e.indexOf("name")?t+": drag on residues to select":-1!==e.indexOf("select $")||-1!==e.indexOf("select .")||-1!==e.indexOf("select :")||-1!==e.indexOf("select @")?"Select > Advanced; or other selection":-1!==e.indexOf("replay on")?"File > Replay Each Step > On":-1!==e.indexOf("replay off")?"File > Replay Each Step > Off":-1!==e.indexOf("set theme")?"Style > Theme Color":-1!==e.indexOf("set double color")?"Style > Two-color Helix":""}}class ms{constructor(e){this.icn3d=e}setProtNuclLigInMenu(){let e=this.icn3d;if(e.icn3dui,Object.keys(e.proteins).length>0&&(e.defNames2Residues.proteins=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.proteins)),e.defNames2Descr.proteins="proteins",e.defNames2Command.proteins="select :proteins"),Object.keys(e.nucleotides).length>0&&(e.defNames2Residues.nucleotides=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.nucleotides)),e.defNames2Descr.nucleotides="nucleotides",e.defNames2Command.nucleotides="select :nucleotides"),Object.keys(e.chemicals).length>0)if(e.bOpm){let t={},s={};for(let i in e.chemicals){let n=e.atoms[i],l=n.structure+"_"+n.chain+"_"+n.resi;"DUM"===n.resn?s[l]=1:t[l]=1}Object.keys(t).length>0&&(e.defNames2Residues.chemicals=Object.keys(t),e.defNames2Descr.chemicals="chemicals",e.defNames2Command.chemicals="select :chemicals"),Object.keys(s).length>0&&(e.defNames2Residues.membrane=Object.keys(s),e.defNames2Descr.membrane="membrane",e.defNames2Command.membrane="select :membrane")}else e.defNames2Residues.chemicals=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.chemicals)),e.defNames2Descr.chemicals="chemicals",e.defNames2Command.chemicals="select :chemicals";Object.keys(e.ions).length>0&&(e.defNames2Residues.ions=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.ions)),e.defNames2Descr.ions="ions",e.defNames2Command.ions="select :ions"),Object.keys(e.water).length>0&&(e.defNames2Residues.water=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.water)),e.defNames2Descr.water="water",e.defNames2Command.water="select :water"),this.setTransmemInMenu(e.halfBilayerSize,-e.halfBilayerSize)}setPredefinedInMenu(){let e=this.icn3d,t=e.icn3dui;if(this.setChainsInMenu(),this.setProtNuclLigInMenu(),void 0!==t.cfg.mmdbid||void 0!==t.cfg.gi||void 0!==t.cfg.chainalign||void 0!==t.cfg.mmdbafid)for(let t in e.tddomains)e.selectionCls.selectResidueList(e.tddomains[t],t,t,!1,!1);if((void 0!==t.cfg.align||void 0!==t.cfg.chainalign&&2==e.chainidArray.length)&&e.bFullUi){e.selectionCls.selectResidueList(e.consHash1,e.conservedName1,e.conservedName1,!1,!1),e.selectionCls.selectResidueList(e.consHash2,e.conservedName2,e.conservedName2,!1,!1),e.selectionCls.selectResidueList(e.nconsHash1,e.nonConservedName1,e.nonConservedName1,!1,!1),e.selectionCls.selectResidueList(e.nconsHash2,e.nonConservedName2,e.nonConservedName2,!1,!1),e.selectionCls.selectResidueList(e.nalignHash1,e.notAlignedName1,e.notAlignedName1,!1,!1),e.selectionCls.selectResidueList(e.nalignHash2,e.notAlignedName2,e.notAlignedName2,!1,!1);let s={};for(let i in e.alnChains)s=t.hashUtilsCls.unionHash(s,e.alnChains[i]);let i=e.firstAtomObjCls.getResiduesFromAtoms(s),n="protein_aligned",l="aligned protein and nucleotides",r="select "+e.resid2specCls.residueids2spec(Object.keys(i));e.selectionCls.addCustomSelection(Object.keys(i),n,l,r,!0)}}setAtomMenu(e){let t=this.icn3d;t.icn3dui;let s="",i=void 0!==t.defNames2Residues?Object.keys(t.defNames2Residues):[],n=void 0!==t.defNames2Atoms?Object.keys(t.defNames2Atoms):[],l=i.concat(n).sort(),r=[];l.forEach((e=>{-1===$.inArray(e,r)&&r.push(e)}));for(let i=0,n=r.length;i0&&(n=t.atoms[e[0]])}else if(void 0!==t.defNames2Residues&&t.defNames2Residues.hasOwnProperty(o)){let e=t.defNames2Residues[o];e.length>0&&(l=t.residues[e[0]],l&&(n=t.atoms[Object.keys(l)[0]]))}let a=void 0===n||void 0===n.color||"FFFFFF"===n.color.getHexString().toUpperCase()?"DDDDDD":n.color.getHexString(),d=void 0!==n&&void 0!==n.color?a:"000000";-1!=e.indexOf(o)?s+="":s+=""}return s}setChainsInMenu(){let e=this.icn3d;e.icn3dui;for(let t in e.chains)if(e.chainsSeq[t]&&e.chainsSeq[t].length>1){e.defNames2Residues[t]=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.chains[t])),e.defNames2Descr[t]=t;let s=t.indexOf("_"),i=t.substr(0,s),n=t.substr(s+1);e.defNames2Command[t]="select $"+i+"."+n}if(1==Object.keys(e.structures)){let t=Object.keys(e.structures)[0];e.defNames2Residues[t]=Object.keys(e.residues),e.defNames2Descr[t]=t,e.defNames2Command[t]="select $"+t}else{let t=Object.keys(e.residues),s={};for(let e=0,i=t.length;ee?l[a]=1:o.coord.z0&&(i.defNames2Residues["transmembrane"+o]=Object.keys(n),i.defNames2Descr["transmembrane"+o]="transmembrane"+o,i.defNames2Command["transmembrane"+o]="select :transmembrane"+o),Object.keys(l).length>0&&(i.defNames2Residues["extracellular"+o]=Object.keys(l),i.defNames2Descr["extracellular"+o]="extracellular"+o,i.defNames2Command["extracellular"+o]="select :extracellular"+o),Object.keys(r).length>0&&(i.defNames2Residues["intracellular"+o]=Object.keys(r),i.defNames2Descr["intracellular"+o]="intracellular"+o,i.defNames2Command["intracellular"+o]="select :intracellular"+o)}}showSets(){let e=this.icn3d,t=e.icn3dui;t.bNode||(t.htmlCls.dialogCls.openDlg("dl_definedsets","Select sets"),$("#"+e.pre+"dl_setsmenu").show(),$("#"+e.pre+"dl_setoperations").show(),$("#"+e.pre+"dl_command").hide(),$("#"+e.pre+"atomsCustom").resizable());let s=t.hashUtilsCls.cloneHash(e.hAtoms),i=t.hashUtilsCls.cloneHash(e.dAtoms);void 0!==e.bSetChainsAdvancedMenu&&e.bSetChainsAdvancedMenu&&!e.bResetSets||(this.setPredefinedInMenu(),e.bSetChainsAdvancedMenu=!0),e.hAtoms=t.hashUtilsCls.cloneHash(s),e.dAtoms=t.hashUtilsCls.cloneHash(i),e.hlUpdateCls.updateHlMenus()}clickCustomAtoms(){let e=this.icn3d,t=e.icn3dui,s=this;$("#"+e.pre+"atomsCustom").change((function(e){let i=s.icn3d,n=$(this).val();if(i.nameArray=n,null!==n){let e=!1;s.changeCustomAtoms(n,e),t.htmlCls.clickMenuCls.setLogCmd("select sets "+n.join(" "+i.setOperation+" "),!0),i.bSelectResidue=!1}})),t.myEventCls.onIds("#"+e.pre+"atomsCustom","focus",(function(e){let i=s.icn3d;t.utilsCls.isMobile()&&$("#"+i.pre+"atomsCustom").val("")}))}deleteSelectedSets(){let e=this.icn3d;e.icn3dui;let t=$("#"+e.pre+"atomsCustom").val();for(let s=0;s0)for(let n=0,l=t.defNames2Residues[e].length;n0)for(let s=0,n=t.defNames2Atoms[e].length;s0&&s.atoms[e[0]]}else if(void 0!==s.defNames2Residues&&s.defNames2Residues.hasOwnProperty(o)){let e=s.defNames2Residues[o];e.length>0&&(r=s.residues[e[0]],r&&s.atoms[Object.keys(r)[0]])}-1!=n.indexOf(o)?i+="":i+=""}return i}reset(){let e=this.icn3d;e.atoms={},e.proteins={},e.nucleotides={},e.chemicals={},e.ions={},e.water={},e.structures={},e.chains={},e.chainsSeq={},e.residues={},e.defNames2Atoms={},e.defNames2Residues={},e.ssbondpnts={},e.bShowHighlight=void 0,e.bResetSets=!0}dictionaryDifference(e,t){const s={};for(let i in t)i in e||(s[i]=t[i]);return s}clickStructure(){let e=this.icn3d,t=e.icn3dui,s=this;null==e.allData&&(e.allData={},e.allData.all={atoms:{},proteins:{},nucleotides:{},chemicals:{},ions:{},water:{},structures:{},ssbondpnts:{},residues:{},chains:{},chainsSeq:{},defNames2Atoms:{},defNames2Residues:{}},e.allData.prev={}),$("#"+e.pre+"collections_menu").change((async function(e){let i=s.icn3d,n=$(this).val(),l=$(this).find("option:selected").text();if(i.nameArray=n,null!==n){let e=!0;s.reset();for(const t of n)t in i.allData||(i.allData.prev=JSON.parse(JSON.stringify(i.allData.all)),i.atoms=i.allData.all.atoms,i.proteins=i.allData.all.proteins,i.nucleotides=i.allData.all.nucleotides,i.chemicals=i.allData.all.chemicals,i.ions=i.allData.all.ions,i.water=i.allData.all.water,i.structures=i.allData.all.structures,i.ssbondpnts=i.allData.all.ssbondpnts,i.residues=i.allData.all.residues,i.chains=i.allData.all.chains,i.chainsSeq=i.allData.all.chainsSeq,i.defalls2Atoms=i.allData.all.defalls2Atoms,i.defalls2Residues=i.allData.all.defalls2Residues,await i.chainalignParserCls.downloadMmdbAf(t,void 0,void 0,e).then((()=>{i.allData.all={atoms:i.atoms,proteins:i.proteins,nucleotides:i.nucleotides,chemicals:i.chemicals,ions:i.ions,water:i.water,structures:i.structures,ssbondpnts:i.ssbondpnts,residues:i.residues,chains:i.chains,chainsSeq:i.chainsSeq,defNames2Atoms:i.defNames2Atoms,defNames2Residues:i.defNames2Residues},i.allData[t]={atoms:s.dictionaryDifference(i.allData.prev.atoms,i.atoms),proteins:s.dictionaryDifference(i.allData.prev.proteins,i.proteins),nucleotides:s.dictionaryDifference(i.allData.prev.nucleotides,i.nucleotides),chemicals:s.dictionaryDifference(i.allData.prev.chemicals,i.chemicals),ions:s.dictionaryDifference(i.allData.prev.ions,i.ions),water:s.dictionaryDifference(i.allData.prev.water,i.water),structures:s.dictionaryDifference(i.allData.prev.structures,i.structures),ssbondpnts:s.dictionaryDifference(i.allData.prev.ssbondpnts,i.ssbondpnts),residues:s.dictionaryDifference(i.allData.prev.residues,i.residues),chains:s.dictionaryDifference(i.allData.prev.chains,i.chains),chainsSeq:s.dictionaryDifference(i.allData.prev.chainsSeq,i.chainsSeq),defNames2Atoms:s.dictionaryDifference(i.allData.prev.defNames2Atoms,i.defNames2Atoms),defNames2Residues:s.dictionaryDifference(i.allData.prev.defNames2Residues,i.defNames2Residues)},s.reset()})));for(const e of n)i.atoms=Object.assign(i.atoms,i.allData[e].atoms),i.proteins=Object.assign(i.proteins,i.allData[e].proteins),i.nucleotides=Object.assign(i.nucleotides,i.allData[e].nucleotides),i.chemicals=Object.assign(i.chemicals,i.allData[e].chemicals),i.ions=Object.assign(i.ions,i.allData[e].ions),i.water=Object.assign(i.water,i.allData[e].water),i.structures=Object.assign(i.structures,i.allData[e].structures),i.ssbondpnts=Object.assign(i.ssbondpnts,i.allData[e].ssbondpnts),i.residues=Object.assign(i.residues,i.allData[e].residues),i.chains=Object.assign(i.chains,i.allData[e].chains),i.chainsSeq=Object.assign(i.chainsSeq,i.allData[e].chainsSeq),i.defNames2Atoms=Object.assign(i.defNames2Atoms,i.allData[e].defNames2Atoms),i.defNames2Residues=Object.assign(i.defNames2Residues,i.allData[e].defNames2Residues),i.dAtoms=t.hashUtilsCls.cloneHash(i.atoms),i.hAtoms=t.hashUtilsCls.cloneHash(i.atoms);i.opts.color=1==Object.keys(i.structures).length?"chain":"structure",i.setColorCls.setColorByOptions(i.opts,i.atoms),i.transformCls.zoominSelection(),i.definedSetsCls.showSets(),i.bResetAnno=!0,i.bAnnoShown&&(await i.showAnnoCls.showAnnotations(),i.hlUpdateCls.updateHlAll(n),i.annotationCls.showAnnoSelectedChains()),await i.drawCls.draw(),i.saveFileCls.showTitle(),t.htmlCls.clickMenuCls.setLogCmd("select structure ["+l+"]",!0)}})),t.myEventCls.onIds("#"+e.pre+"collections_menu","focus",(function(e){let i=s.icn3d;t.utilsCls.isMobile()&&$("#"+i.pre+"collections_menu").val("")}))}}class gs{constructor(e){this.icn3d=e}async loadScript(e,t,s){let i=this.icn3d;if(i.icn3dui,!e)return;i.bCommandLoad=!0,i.bRender=!1,i.bStopRotate=!0,e=t?e.replace(/\+/g," "):e.replace(/\+/g," ").replace(/;/g,"\n");let n=[];!s&&i.commands.length>0&&(n[0]=i.commands[0]);let l=e.trim().split("\n");i.commands=l;let r=l[0].indexOf("command=");if(t&&-1!=r){let e=l[0].substr(0,r-1);i.commands.splice(0,1,e)}i.STATENUMBER=i.commands.length,i.commands=n.concat(i.commands),i.STATENUMBER=i.commands.length,i.CURRENTNUMBER=0,i.bReplay?await this.replayFirstStep(i.CURRENTNUMBER):await this.execCommands(i.CURRENTNUMBER,i.STATENUMBER-1,i.STATENUMBER,s)}async execCommands(e,t,s,i){let n=this.icn3d;n.icn3dui,n.bRender=!1,i||n.reinitAfterLoad(),await this.execCommandsBase(e,t,s)}getNameArray(e){let t=this.icn3d;t.icn3dui;let s=e.split(" | "),i=[];return 2==s.length&&(i=s[1].split(","),t.hAtoms=t.definedSetsCls.getAtomsFromNameArray(i)),i}updateTransformation(e){let t=this.icn3d;t.icn3dui;let s=t.commands[e-1]?t.commands[e-1].split("|||"):[];if(2==s.length){let e=JSON.parse(s[1]);t._zoomFactor=e.factor,t.mouseChange.x=e.mouseChange.x,t.mouseChange.y=e.mouseChange.y,t.quaternion._x=e.quaternion._x,t.quaternion._y=e.quaternion._y,t.quaternion._z=e.quaternion._z,t.quaternion._w=e.quaternion._w}t.drawCls.draw()}async execCommandsBase(e,t,s,i){let n,l=this.icn3d,r=l.icn3dui,o=this;for(n=e;n<=t;++n){let i=n===s-1;if(!l.commands[n].trim())continue;if(0==(l.atoms?Object.keys(l.atoms).length:0)&&-1==l.commands[n].indexOf("load"))continue;let a=l.commands[n].split("|||"),d=a[0].trim();if(-1!==d.indexOf("load")){if(0===t&&e===t)return void(l.bNotLoadStructure?(l.hAtoms=r.hashUtilsCls.cloneHash(l.atoms),1===l.commands.length&&(l.bAddCommands=!0),i&&this.renderFinalStep(s)):(await o.applyCommandLoad(l.commands[n]),1===l.commands.length&&(l.bAddCommands=!0),i&&o.renderFinalStep(s)));l.bNotLoadStructure?(l.hAtoms=r.hashUtilsCls.cloneHash(l.atoms),l.backForward&&this.renderFinalStep(1)):(await o.applyCommandLoad(l.commands[n]),l.backForward&&o.renderFinalStep(1))}else if(0==d.indexOf("set map")&&-1==d.indexOf("set map wireframe"))await o.applyCommandMap(a[0].trim());else if(0==d.indexOf("set emmap")&&-1==d.indexOf("set emmap wireframe")){let e=a[0].trim().substr(10).split(" ");2==e.length&&"percentage"==e[0]&&(e[1],await o.applyCommandEmmap(a[0].trim()))}else if(0==d.indexOf("set phi"))await l.delphiCls.applyCommandPhi(a[0].trim());else if(0==d.indexOf("set delphi"))await l.delphiCls.applyCommandDelphi(a[0].trim());else if(0==d.indexOf("view annotations"))Object.keys(l.proteins).length>0&&await o.applyCommandAnnotationsAndCddSite(a[0].trim());else if(0==d.indexOf("set annotation clinvar"))Object.keys(l.proteins).length>0&&await o.applyCommandClinvar(a[0].trim());else if(0==d.indexOf("set annotation snp"))Object.keys(l.proteins).length>0&&await o.applyCommandSnp(a[0].trim());else if(0==d.indexOf("set annotation ptm"))Object.keys(l.proteins).length>0&&await o.applyCommandPTM(a[0].trim());else if(0==d.indexOf("ig template")){let e=d.substr(d.lastIndexOf(" ")+1);await r.htmlCls.clickMenuCls.setIgTemplate(e)}else if(0==d.indexOf("set annotation 3ddomain"))Object.keys(l.proteins).length>0&&o.applyCommand3ddomain(a[0].trim());else if(0==d.indexOf("set annotation all"))Object.keys(l.proteins).length>0&&(await o.applyCommandClinvar(a[0].trim()),await o.applyCommandSnp(a[0].trim()),o.applyCommand3ddomain(a[0].trim())),await l.annotationCls.setAnnoTabAll();else if(0==d.indexOf("view interactions")&&void 0!==r.cfg.align)await o.applyCommandViewinteraction(a[0].trim());else if(0==d.indexOf("symmetry")){l.bAxisOnly=!1;let e=d.substr(d.indexOf(" ")+1);l.symmetrytitle="none"===e?void 0:e,"none"!==e&&await l.symdCls.retrieveSymmetry(Object.keys(l.structures)[0]),l.drawCls.draw()}else if(0==d.indexOf("symd symmetry"))l.bAxisOnly=!1,await l.symdCls.applyCommandSymd(d),l.drawCls.draw();else if(0==d.indexOf("scap"))await l.scapCls.applyCommandScap(d);else if(0==d.indexOf("realign on seq align"))this.getNameArray(d),await o.applyCommandRealign(d);else if(0==d.indexOf("realign on structure align msa")){let e=this.getNameArray(d);r.cfg.aligntool="vast",await l.realignParserCls.realignOnStructAlignMsa(e)}else if(0==d.indexOf("realign on structure align"))this.getNameArray(d),r.cfg.aligntool="vast",await l.realignParserCls.realignOnStructAlign();else if(0==d.indexOf("realign on tmalign msa")){let e=this.getNameArray(d);r.cfg.aligntool="tmalign",await l.realignParserCls.realignOnStructAlignMsa(e)}else if(0==d.indexOf("realign on tmalign"))this.getNameArray(d),r.cfg.aligntool="tmalign",await l.realignParserCls.realignOnStructAlign();else if(0==d.indexOf("realign on vastplus"))o.getHAtoms(l.commands[n]),await l.vastplusCls.realignOnVastplus();else if(0==d.indexOf("graph interaction pairs"))await o.applyCommandGraphinteraction(d);else if(0==d.indexOf("cartoon 2d domain"))l.bRender=!0,o.updateTransformation(s),await o.applyCommandCartoon2d(d),l.bRender=!1;else if(0==d.indexOf("set half pae map"))await o.applyCommandAfmap(d);else if(0==d.indexOf("set full pae map"))await o.applyCommandAfmap(d,!0);else if(0==d.indexOf("export pqr"))await r.htmlCls.setHtmlCls.exportPqr();else if(0==d.indexOf("cartoon 2d chain")||0==d.indexOf("cartoon 2d secondary")){let e=d.lastIndexOf(" "),t=d.substr(e+1);l.bRender=!0,o.updateTransformation(s),await l.cartoon2dCls.draw2Dcartoon(t),l.bRender=!1}else if(0==d.indexOf("add msa track")){let e=d.split(" | "),t=e[1].substr(8),s=e[2].substr(9),i=e[3].substr(5),n=e[4].substr(10);$("#"+l.pre+"anno_custom")[0]&&($("#"+l.pre+"anno_custom")[0].checked=!0),$("[id^="+l.pre+"custom]").show(),await l.addTrackCls.addMsaTracks(t,s,i,n)}else if(0==d.indexOf("add exon track")){let e=d.split(" | "),t=e[1].substr(8),s=e[2].substr(7),i=e[3].substr(9),n=e[4].substr(5);$("#"+l.pre+"anno_custom")[0]&&($("#"+l.pre+"anno_custom")[0].checked=!0),$("[id^="+l.pre+"custom]").show(),await l.addTrackCls.addExonTracks(t,s,i,n)}else await l.applyCommandCls.applyCommand(l.commands[n])}(n===s||i)&&this.renderFinalStep(n)}pressCommandtext(){let e=this.icn3d,t=e.icn3dui,s=this;$("#"+e.pre+"logtext").keypress((async function(e){let i=s.icn3d;if(i.bAddLogs=!1,13==(e.keyCode?e.keyCode:e.which)){e.preventDefault();let n=$(this).val();i.bRender=!0;let l=n.split("\n"),r=i.logs.length;for(let e=r,n=l.length;e "+i.logs.join("\n> ")+"\n> ").scrollTop($("#"+i.pre+"logtext")[0].scrollHeight)}i.bAddLogs=!0}))}async applyCommandLoad(e){let t=this.icn3d,s=t.icn3dui;t.bAddCommands=!1;let i=e.split("|||")[0].replace(/\s\s/g," ").trim();if(-1!==i.indexOf("load")){let e=i.split(" | "),n=e[0];if(e.length>1){let t=e[e.length-1].indexOf(" ");s.cfg.inpara=e[e.length-1].substr(t+1),"undefined"===s.cfg.inpara&&(s.cfg.inpara="")}let l=n.substr(n.lastIndexOf(" ")+1);4==l.length&&(l=l.toUpperCase());let r=l.split(","),o="";for(let e=0,s=r.length;e1&&-1!=e[1].indexOf("resnum")&&(s.cfg.resnum=e[1].substr(e[1].indexOf("resnum")+7)),e.length>2&&-1!=e[2].indexOf("resdef")&&(s.cfg.resdef=e[2].substr(e[1].indexOf("resdef")+7)),e.length>3&&-1!=e[3].indexOf("aligntool")&&(s.cfg.aligntool=e[3].substr(e[1].indexOf("aligntool")+10)),s.cfg.chainalign=l,await t.chainalignParserCls.downloadChainalignment(l,s.cfg.resnum,s.cfg.resdef)}else if(-1!==i.indexOf("load url")){let i=e[1],n=void 0!==i?i.indexOf("type "):-1,r="pdb";-1!==n&&(r=i.substr(n+5)),s.cfg.url=l,await t.pdbParserCls.downloadUrl(l,r)}}t.bAddCommands=!0}async applyCommandMap(e){let t=this.icn3d;t.icn3dui;let s=e.split(" | "),i=s[0].substr(8).split(" ");if("sigma"==i[1]){let e=i[2],n=i[0],l="dsn6";if(5==i.length&&(l=i[4]),2==s.length){let i=!0;"dsn6"==l?await t.dsn6ParserCls.dsn6ParserBase(s[1],n,e,"url",i):"ccp4"==l?await t.ccp4ParserCls.ccp4ParserBase(s[1],n,e,"url",i):"mtz"==l?await t.mtzParserCls.mtzParserBase(s[1],n,e,"url",i):"rcsbmtz"==l&&await t.mtzParserCls.mtzParserBase(s[1],n,e,"url",i,!0)}else await t.dsn6ParserCls.dsn6Parser(t.inputid,n,e)}}async applyCommandEmmap(e){let t=this.icn3d;t.icn3dui;let s=e.substr(10).split(" ");if(2==s.length&&"percentage"==s[0]){let e=s[1],i="em";await t.densityCifParserCls.densityCifParser(t.inputid,i,e,t.emd)}}async applyCommandRealign(e){let t=this.icn3d;t.icn3dui,await t.realignParserCls.realignOnSeqAlign()}async applyCommandRealignByStruct(e){let t=this.icn3d;t.icn3dui,t.drawCls.draw(),await t.realignParserCls.realignOnStructAlign()}async applyCommandAfmap(e,t){let s=this.icn3d;s.icn3dui;let i=e.substr(e.lastIndexOf(" ")+1);await s.contactMapCls.afErrorMap(i,t)}async applyCommandGraphinteraction(e){let t=this.icn3d;t.icn3dui;let s=e.split(" | ");if(s.length>=3){let e,i=s[1].split(" "),n=i[0].split(","),l=i[1].split(","),r=-1!==s[2].indexOf("hbonds"),o=-1!==s[2].indexOf("salt bridge"),a=-1!==s[2].indexOf("interactions"),d=-1!==s[2].indexOf("halogen"),c=-1!==s[2].indexOf("pi-cation"),h=-1!==s[2].indexOf("pi-stacking");s.length>=4&&(e="true"==s[3]),t.applyCommandCls.setStrengthPara(s),await t.viewInterPairsCls.viewInteractionPairs(n,l,e,"graph",r,o,a,d,c,h)}}async applyCommandCartoon2d(e){let t=this.icn3d;t.icn3dui;let s=e.substr(e.lastIndexOf(" ")+1);await t.cartoon2dCls.draw2Dcartoon(s)}async applyCommandAnnotationsAndCddSite(e){let t=this.icn3d;t.icn3dui,"view annotations"==e&&await t.showAnnoCls.showAnnotations()}async applyCommandClinvar(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" ");e.substr(s+1),await t.annotationCls.setAnnoTabClinvar()}async applyCommandSnp(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" ");e.substr(s+1),await t.annotationCls.setAnnoTabSnp()}async applyCommandPTM(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" ");e.substr(s+1),await t.annotationCls.setAnnoTabPTM()}applyCommand3ddomain(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" "),i=e.substr(s+1);"3ddomain"!=i&&"all"!=i||t.annotationCls.setAnnoTab3ddomain()}async applyCommandViewinteraction(e){let t=this.icn3d,s=t.icn3dui;if(void 0!==s.cfg.align||void 0!==s.cfg.chainalign){let e=Object.keys(t.structures);await t.ParserUtilsCls.set2DDiagramsForAlign(e[0].toUpperCase(),e[1].toUpperCase())}}async renderFinalStep(e){let t=this.icn3d,s=t.icn3dui;t.bCommandLoad=!1,t.ParserUtilsCls.hideLoading(),e+1===t.commands.length&&(t.bAddCommands=!0),t.bRender=!0;let i=t.commands[e-1]?t.commands[e-1].split("|||"):[];if(2==i.length){let e=JSON.parse(i[1]);t._zoomFactor=e.factor,t.mouseChange.x=e.mouseChange.x,t.mouseChange.y=e.mouseChange.y,t.quaternion._x=e.quaternion._x,t.quaternion._y=e.quaternion._y,t.quaternion._z=e.quaternion._z,t.quaternion._w=e.quaternion._w}if(t.selectionCls.oneStructurePerWindow(),1===e||t.hAtoms&&t.atoms&&Object.keys(t.hAtoms).length===Object.keys(t.atoms).length||void 0!==t.optsHistory[e-1]&&t.optsHistory[e-1].hasOwnProperty("hlatomcount")&&t.optsHistory[e-1].hlatomcount===Object.keys(t.atoms).length)if(t.optsHistory.length>=e){let s=t.optsHistory[e-1].pk;"no"===s?t.pk=0:"atom"===s?t.pk=1:"residue"===s?t.pk=2:"strand"===s&&(t.pk=3),t.hlUpdateCls.updateHlAll(),t.drawCls.draw()}else t.hlUpdateCls.updateHlAll(),t.drawCls.draw();else t.hlUpdateCls.updateHlAll(),t.drawCls.draw();(s.cfg.closepopup||s.cfg.imageonly)&&(setTimeout((function(){t.resizeCanvasCls.closeDialogs()}),100),t.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH,s.htmlCls.HEIGHT,!0)),t.bTransparentSurface&&t.bRender&&t.drawCls.render(),s.cfg.imageonly&&t.saveFileCls.saveFile(void 0,"png",void 0,!0)}async replayFirstStep(e){let t=this.icn3d,s=t.icn3dui;t.reinitAfterLoad(),await this.execCommandsBase(e,e,t.STATENUMBER);let i=t.commands[e],n=t.commands[e].indexOf("|");-1!=n&&(i=t.commands[e].substr(0,n));let l=i.length>20?i.substr(0,20)+"...":i,r=t.applyCommandCls.getMenuFromCmd(i);$("#"+t.pre+"replay_cmd").html("Cmd: "+l),$("#"+t.pre+"replay_menu").html("Menu: "+r),s.htmlCls.clickMenuCls.setLogCmd(i,!0),t.bCommandLoad=!1,t.ParserUtilsCls.hideLoading(),t.bRender=!0,t.drawCls.draw()}getHAtoms(e){let t=this.icn3d;t.icn3dui;let s=e.split("|||")[0].trim().split(" | ");if(2==s.length){let e=s[1].split(",");t.hAtoms=t.definedSetsCls.getAtomsFromNameArray(e)}}}class fs{constructor(e){this.icn3d=e}async selectByCommand(e,t,s){let i=this.icn3d,n=i.icn3dui;if(0===e.indexOf("saved atoms")){let s=12,n=e.substr(s);i.definedSetsCls.selectCombinedSets(n,t)}else{let l=e.replace(/ AND /g," and ").replace(/ OR /g," or ").replace(/ or and /g," and ").replace(/ and /g," or and ").replace(/ or not /g," not ").replace(/ not /g," or not "),r=("select"===l.trim().substr(0,6)?l.trim().substr(7):l.trim()).split(" or "),o={};for(let e=0,t=r.length;e1||1==o.length&&"*"!==o[0])&&(h=!1);let b,y,v,_,w=[],S=[];if(w="*"===t?Object.keys(l.structures):t.split(","),"*"===s){let e=Object.keys(l.chains);for(let t=0,s=e.length;t1&&"3"===x[t][0]&&isNaN(x[t][1])&&"-"!==x[t][0]){i=x[t].toUpperCase().substr(1),m=!0}else if(""===x[t]||isNaN(parseInt(x[t]))){if("*"===x[t])h=!0;else if("proteins"!==x[t]&&"nucleotides"!==x[t]&&"chemicals"!==x[t]&&"ions"!==x[t]&&"water"!==x[t]&&"anchors"!==x[t]&&"strands"!==x[t]&&"loops"!==x[t]){s=x[t].toUpperCase(),p=!0}}else v=x[t],_=v,n=!0;for(let a=0,u=S.length;a1?e.substr(0,l-1)===n.atoms[i].name.substr(0,l-1)&&(0===s?t[i]=1:t.hasOwnProperty(i)||delete t[i]):"*"!==e&&e!==n.atoms[i].name||(0===s?t[i]=1:t.hasOwnProperty(i)||delete t[i]),t}}class Cs{constructor(e){this.icn3d=e}selectAll(){let e=this.icn3d;e.icn3dui,this.selectAll_base(),e.hlObjectsCls.removeHlObjects(),e.hlUpdateCls.removeHl2D(),e.hlUpdateCls.removeHlMenus(),e.bSelectResidue=!1,e.bSelectAlignResidue=!1,e.hlUpdateCls.removeSeqResidueBkgd(),e.hlUpdateCls.update2DdgmContent(),$("#"+e.pre+"dl_annotations > .icn3d-annotation").show(),e.definedSetsCls.setMode("all"),e.saveFileCls.showTitle()}selectAll_base(){let e=this.icn3d,t=e.icn3dui;e.hAtoms={},e.dAtoms={};for(let s in e.chains)e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.chains[s]);e.dAtoms=t.hashUtilsCls.cloneHash(e.hAtoms),e.viewSelectionAtoms=t.hashUtilsCls.cloneHash(e.hAtoms),e.ALTERNATE_STRUCTURE=-1}selectAChain(e,t,s,i){let n=this.icn3d,l=n.icn3dui;t=t.replace(/\s/g,"");let r=void 0!==s||s?"select alignChain "+e:"select chain "+e;void 0!==i&&i?(n.hAtoms=l.hashUtilsCls.unionHash(n.hAtoms,n.chains[e]),void 0===n.nameArray&&(n.nameArray=[])):(n.hAtoms={},n.nameArray=[]),n.nameArray.push(e);let o,a=s?n.alnChainsSeq[e]:n.chainsSeq[e];o=void 0===a?0:a.length;let d={};for(let t=0,s=o;t0){if(void 0!==i&&i?void 0===r.nameArray&&(r.nameArray=[]):(r.hAtoms={},r.nameArray=[]),l)for(let t in e)r.hAtoms[t]=1;else for(let t in e)for(let e in r.residues[t])r.hAtoms[e]=1;let o,a;t=t.replace(/\s/g,""),r.nameArray.push(t),l?(o="select "+r.resid2specCls.atoms2spec(r.hAtoms),a=!1):(o="select "+r.resid2specCls.residueids2spec(Object.keys(e)),a=!0);let d=Object.keys(e);this.addCustomSelection(d,t,s,o,a),(void 0===n||n)&&r.hlUpdateCls.updateHlAll(r.nameArray,void 0,i)}}selectMainChains(){let e=this.icn3d,t=e.icn3dui.hashUtilsCls.cloneHash(e.hAtoms);e.hAtoms=e.applyDisplayCls.selectMainChainSubset(t),e.hlUpdateCls.showHighlight()}selectSideChains(){let e=this.icn3d,t=e.icn3dui,s=t.hashUtilsCls.cloneHash(e.hAtoms);e.hAtoms={};for(let i in s)(e.proteins.hasOwnProperty(i)&&"N"!==e.atoms[i].name&&"H"!==e.atoms[i].name&&"C"!==e.atoms[i].name&&"O"!==e.atoms[i].name&&("CA"!==e.atoms[i].name||"C"!==e.atoms[i].elem)&&"HA"!==e.atoms[i].name||e.nucleotides.hasOwnProperty(i)&&-1===t.parasCls.nuclMainArray.indexOf(e.atoms[i].name))&&(e.hAtoms[i]=1);e.hlUpdateCls.showHighlight()}selectMainSideChains(){let e=this.icn3d,t=e.icn3dui,s=e.firstAtomObjCls.getResiduesFromAtoms(e.hAtoms);e.hAtoms={};for(let i in s)e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.residues[i]),e.dAtoms=t.hashUtilsCls.unionHash(e.dAtoms,e.residues[i]);e.drawCls.draw(),e.hlUpdateCls.showHighlight()}clickShow_selected(){let e=this.icn3d,t=e.icn3dui,s=this;t.myEventCls.onIds(["#"+e.pre+"show_selected","#"+e.pre+"mn2_show_selected"],"click",(function(e){s.icn3d,s.showSelection(),t.htmlCls.clickMenuCls.setLogCmd("show selection",!0)}))}clickHide_selected(){let e=this.icn3d,t=e.icn3dui,s=this;t.myEventCls.onIds("#"+e.pre+"mn2_hide_selected","click",(function(e){s.icn3d,s.hideSelection(),t.htmlCls.clickMenuCls.setLogCmd("hide selection",!0)}))}getGraphDataForDisplayed(){let e=this.icn3d;e.icn3dui;let t=JSON.parse(e.graphStr),s=e.firstAtomObjCls.getResiduesFromAtoms(e.dAtoms),i=[],n=[],l={};for(let e=0,n=t.nodes.length;e0)if(1==i.pk){let l=!0;this.selectResidueList(i.hAtoms,e,t,void 0,void 0,l),this.updateSelectionNameDesc(),s?n.htmlCls.clickMenuCls.setLogCmd("select "+i.resid2specCls.atoms2spec(i.hAtoms),!0):n.htmlCls.clickMenuCls.setLogCmd("select "+i.resid2specCls.atoms2spec(i.hAtoms)+" | name "+e,!0)}else this.selectResidueList(i.selectedResidues,e,t,void 0,void 0,void 0),this.updateSelectionNameDesc(),s?n.htmlCls.clickMenuCls.setLogCmd("select "+i.resid2specCls.residueids2spec(Object.keys(i.selectedResidues)),!0):n.htmlCls.clickMenuCls.setLogCmd("select "+i.resid2specCls.residueids2spec(Object.keys(i.selectedResidues))+" | name "+e,!0)}saveSelInCommand(){let e=this.icn3d,t=e.icn3dui;e.selectedResidues=e.firstAtomObjCls.getResiduesFromCalphaAtoms(e.hAtoms),t.htmlCls.clickMenuCls.setLogCmd("select "+e.resid2specCls.residueids2spec(Object.keys(e.selectedResidues)),!0)}saveEachResiInSel(){let e=this.icn3d;e.icn3dui,e.selectionCls.saveSelectionPrep(),e.selectedResidues={},e.selectedResidues=e.firstAtomObjCls.getResiduesFromCalphaAtoms(e.hAtoms);for(let t in e.selectedResidues){let s={};s[t]=1;let i=t+"_"+e.selectedResidues[t];this.selectResidueList(s,i,i)}}removeSelection(){let e=this.icn3d;e.icn3dui,e.bAnnotations||e.hlUpdateCls.removeSeqChainBkgd(),e.bCtrl||e.bShift||(e.hlUpdateCls.removeSeqResidueBkgd(),e.hlUpdateCls.removeSeqChainBkgd()),e.selectedResidues={},e.bSelectResidue=!1,e.hAtoms={},e.hlObjectsCls.removeHlObjects(),e.hlUpdateCls.removeHl2D()}resetAll(){let e=this.icn3d,t=e.icn3dui;e.maxD=e.oriMaxD,e.center=e.oriCenter.clone(),e.opts=t.hashUtilsCls.cloneHash(e.optsOri),e.setOptionCls.setStyle("sidec","nothing"),e.reinitAfterLoad(),e.definedSetsCls.setMode("all"),e.selectionCls.selectAll(),t.htmlCls.clickMenuCls.setLogCmd("reset",!0),e.hlUpdateCls.removeSeqChainBkgd(),e.hlUpdateCls.removeSeqResidueBkgd(),e.hlUpdateCls.removeHl2D(),e.hlUpdateCls.removeHlMenus(),e.loadScriptCls.renderFinalStep(1)}async loadSelection(e){let t=this.icn3d,s=t.icn3dui,i=e.trim().split("\n");for(let e=0,n=i.length;e=t&&l.coord.z<=e)){i[l.structure+"_"+l.chain+"_"+l.resi]=1}}let n="z_planes_"+e+"_"+t,l=n;this.selectResidueList(i,n,l,!1)}}class bs{constructor(e){this.icn3d=e}residueids2spec(e){var t=this.icn3d;t.icn3dui;let s="";if(void 0!==e){let i,n,l,r,o,a,d,c=e.sort((function(e,t){if(""!==e&&!isNaN(e))return parseInt(e)-parseInt(t);{let s=e.lastIndexOf("_"),i=t.lastIndexOf("_");if(e.substr(0,s)t.substr(0,i))return 1;if(e.substr(0,s)==t.substr(0,i)){if(parseInt(e.substr(s+1))parseInt(t.substr(i+1)))return 1;if(parseInt(e.substr(s+1))==parseInt(t.substr(i+1)))return 0}}})),h="",p=0,m=1!=Object.keys(t.structures).length;for(let e=0,u=c.length;e0&&(s+=p===d?m?"$"+o+"."+a+":"+d+" or ":"."+a+":"+d+" or ":m?"$"+o+"."+a+":"+d+"-"+p+" or ":"."+a+":"+d+"-"+p+" or "),d=n;else if(h===i){let e=t.ParserUtilsCls.getResiNCBI(h,p);t.ParserUtilsCls.getResiNCBI(i,n)!=e+1&&(s+=p===d?m?"$"+o+"."+a+":"+d+" or ":"."+a+":"+d+" or ":m?"$"+o+"."+a+":"+d+"-"+p+" or ":"."+a+":"+d+"-"+p+" or ",d=n)}h=i,p=n}}r=h.indexOf("_"),o=h.substr(0,r),a=h.substr(r+1),s+=p===d?m?"$"+o+"."+a+":"+d:"."+a+":"+d:m?"$"+o+"."+a+":"+d+"-"+p:"."+a+":"+d+"-"+p}return s}resi2range(e){this.icn3d.icn3dui;let t,s,i=[],n=e.sort((function(e,t){return parseInt(e)-parseInt(t)})),l=n[0];for(let e=0,r=n.length;e0&&(i+=" or "),i+="$"+s.structure+"."+s.chain+":"+s.resi+"@"+s.name,l[s.structure]=1,r[s.structure+"_"+s.chain]=1,o[s.structure+"_"+s.chain+"_"+s.resi]=1,++n;if(1==Object.keys(o).length){let e="\\$"+s.structure+"\\."+s.chain+":"+s.resi;i=i.replace(new RegExp(e,"g"),"")}else if(1==Object.keys(r).length){let e="\\$"+s.structure+"\\."+s.chain;i=i.replace(new RegExp(e,"g"),"")}else if(1==Object.keys(l).length){let e="\\$"+s.structure;i=i.replace(new RegExp(e,"g"),"")}return i}atoms2residues(e){var t=this.icn3d;t.icn3dui;let s={};for(let t=0,i=e.length;t=parseInt(t)&&e.b<=parseInt(s)&&(i.hAtoms=n.hashUtilsCls.unionHash(i.hAtoms,i.residues[e.structure+"_"+e.chain+"_"+e.resi]))}}else if("percent out"==e){i.bCalcArea=!0,i.opts.surface="solvent accessible surface",i.applyMapCls.applySurfaceOptions(),i.bCalcArea=!1,i.hAtoms={};for(let e in i.resid2area){let l=e.lastIndexOf("_"),r=e.substr(l+1);if(n.parasCls.residueArea.hasOwnProperty(r)){let o=parseInt(i.resid2area[e]/n.parasCls.residueArea[r]*100);if(o>=t&&o<=s){let t=e.substr(0,l);i.hAtoms=n.hashUtilsCls.unionHash(i.hAtoms,i.residues[t])}}}}i.hAtoms=n.hashUtilsCls.intHash(i.hAtoms,l),i.drawCls.draw(),i.hlUpdateCls.updateHlAll()}selectComplement(){let e=this.icn3d,t=e.icn3dui,s={};for(let t in e.atoms)e.hAtoms.hasOwnProperty(t)||(s[t]=1);e.hAtoms=t.hashUtilsCls.cloneHash(s),e.hlUpdateCls.updateHlAll()}switchHighlightLevel(){var e=this.icn3d.icn3dui;if(e.bNode)return;let t=this;document.addEventListener("keydown",(function(s){let i=t.icn3d;38===s.keyCode?(s.preventDefault(),0!=Object.keys(i.pickedAtomList).length&&i.hAtoms.hasOwnProperty(i.firstAtomObjCls.getFirstAtomObj(i.pickedAtomList).serial)||(i.pickedAtomList=e.hashUtilsCls.cloneHash(i.hAtoms)),t.switchHighlightLevelUp(),e.htmlCls.clickMenuCls.setLogCmd("highlight level up",!0)):40===s.keyCode&&(s.preventDefault(),0!=Object.keys(i.pickedAtomList).length&&i.hAtoms.hasOwnProperty(i.firstAtomObjCls.getFirstAtomObj(i.pickedAtomList).serial)||(i.pickedAtomList=e.hashUtilsCls.cloneHash(i.hAtoms)),t.switchHighlightLevelDown(),e.htmlCls.clickMenuCls.setLogCmd("highlight level down",!0))}))}switchHighlightLevelUp(){var e=this.icn3d,t=e.icn3dui;if(!t.bNode){if(e.bShift||e.bCtrl||e.hlObjectsCls.removeHlObjects(),void 0!==e.pickedAtomList&&0!==Object.keys(e.pickedAtomList).length||(e.pickedAtomList=t.hashUtilsCls.cloneHash(e.hAtoms)),0===Object.keys(e.pickedAtomList).length&&(e.pickedAtomList=e.dAtoms),1===e.highlightlevel){e.highlightlevel=2;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.residues[s.structure+"_"+s.chain+"_"+s.resi]):e.hAtoms=t.hashUtilsCls.cloneHash(e.residues[s.structure+"_"+s.chain+"_"+s.resi])}else if(2===e.highlightlevel){e.highlightlevel=3;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.pickingCls.selectStrandHelixFromAtom(s)):e.hAtoms=t.hashUtilsCls.cloneHash(e.pickingCls.selectStrandHelixFromAtom(s))}else if(3===e.highlightlevel){let s;if(void 0!==t.cfg.mmdbid||void 0!==t.cfg.gi){e.highlightlevel=4;let i=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);s=e.pickingCls.select3ddomainFromAtom(i),e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,s):e.hAtoms=t.hashUtilsCls.cloneHash(s)}if(void 0===t.cfg.mmdbid&&void 0===t.cfg.gi||0==Object.keys(s).length){e.highlightlevel=5;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.chains[s.structure+"_"+s.chain]):e.hAtoms=t.hashUtilsCls.cloneHash(e.chains[s.structure+"_"+s.chain])}}else if(4===e.highlightlevel){e.highlightlevel=5;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.chains[s.structure+"_"+s.chain]):e.hAtoms=t.hashUtilsCls.cloneHash(e.chains[s.structure+"_"+s.chain])}else if(5===e.highlightlevel||6===e.highlightlevel){e.highlightlevel=6;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl||(e.hAtoms={});let i=e.structures[s.structure];for(let s=0,n=i.length;s3e4)return void(e?console.log("The maximum number of allowed atoms is 30,000. Please try it again with selected chains..."):alert("The maximum number of allowed atoms is 30,000. Please try it again with selected chains..."));let o="";return o+=s.cfg.cid?t.saveFileCls.getAtomPDB(n,!0,void 0,void 0,void 0,void 0,true):t.saveFileCls.getAtomPDB(n,void 0,void 0,void 0,void 0,void 0,true),o+=t.saveFileCls.getAtomPDB(i,!0,void 0,!0),o}async CalcPhi(e,t,s,i,n){let l=this.icn3d;l.icn3dui;let r=await this.CalcPhiPrms(e,t,s,i,n);this.loadPhiData(r,s,i),l.bAjaxPhi=!0,i?l.setOptionCls.setOption("phisurface","phi"):l.setOptionCls.setOption("phimap","phi")}CalcPhiPrms(e,t,s,i,n){let l=this.icn3d,r=l.icn3dui;l.loadPhiFrom="delphi";let o=r.htmlCls.baseUrl+"delphi/delphi.cgi",a=r.cfg.cid?r.cfg.cid:Object.keys(l.structures).toString(),d={};if(n)d={pqr2phi:n,gsize:e,salt:t,pdbid:a};else{let s=this.getPdbStr();d={pdb2phi:s,gsize:e,salt:t,pdbid:a}}return new Promise((function(e,t){$.ajax({url:o,type:"POST",data:d,dataType:"binary",responseType:"arraybuffer",cache:!0,beforeSend:function(){l.ParserUtilsCls.showLoading()},complete:function(){l.ParserUtilsCls.hideLoading()},success:function(t){e(t)},error:function(e,t,s){}})}))}async PhiParser(e,t,s,i){let n,l=this.icn3d,r=l.icn3dui,o=this;n="phiurl"==t||"phiurl2"==t?"arraybuffer":"text";let a=await r.getXMLHttpRqstPromise(e,"GET",n,"potential");"phiurl"==t||"phiurl2"==t?o.loadPhiData(a,s,i):o.loadCubeData(a,s,i),l.bAjaxPhi=!0,i?l.setOptionCls.setOption("phisurface","phi"):l.setOptionCls.setOption("phimap","phi")}loadPhiData(e,t,s){let i=this.icn3d;i.icn3dui;let n={filetype:"phi"},l=e.buffer&&e.buffer instanceof ArrayBuffer?e.buffer:e,r=new Float32Array(l.slice(l.byteLength-24,l.byteLength-8));n.scale=r[0];let o=r[1],a=r[2],d=r[3];n.n=new Int32Array(l.slice(l.byteLength-8,l.byteLength-4)),n.xExtent=n.yExtent=n.zExtent=n.n;let c=1/n.scale*((n.n-1)/2);n.ori=new THREE.Vector3(o-c,a-c,d-c);let h=new Float32Array(l.slice(110,l.byteLength-56));n.bSurface=s,i.mapData.headerPhi=n,i.mapData.dataPhi=h,i.mapData.contourPhi=t;let p=new THREE.Matrix4;p.identity(),p.multiply((new THREE.Matrix4).makeTranslation(n.ori.x,n.ori.y,n.ori.z)),i.mapData.matrixPhi=p}loadCubeData(e,t,s){let i=this.icn3d;i.icn3dui;let n={filetype:"cube"},l=e.split("\n"),r=[];r.push(parseFloat(l[0].substr(0,10))),r.push(parseFloat(l[0].substr(10,6))),r.push(parseFloat(l[0].substr(16,10))),r.push(parseFloat(l[0].substr(26,10))),r.push(parseFloat(l[0].substr(36,10))),n.scale=r[0];let o=r[2],a=r[3],d=r[4];n.n=r[1],n.xExtent=n.yExtent=n.zExtent=n.n;let c=1/n.scale*((n.n-1)/2);n.ori=new THREE.Vector3(o-c,a-c,d-c);let h=[];for(let e=7,t=l.length;e=1)for(let t=0,l=r.length;t2540&&u<2560?e=!0:u>3540&&u<3560?t=!0:u>7540&&u<7560?s=!0:u>8540&&u<8560&&(l=!0),2550==u){"helix"==i.firstAtomObjCls.getFirstAtomObj(i.residues[h]).ss&&(r=!1)}else if(3550==u){"helix"==i.firstAtomObjCls.getFirstAtomObj(i.residues[h]).ss&&(o=!1)}else if(7550==u){"helix"==i.firstAtomObjCls.getFirstAtomObj(i.residues[h]).ss&&(d=!1)}else if(8550==u){"helix"==i.firstAtomObjCls.getFirstAtomObj(i.residues[h]).ss&&(p=!1)}if(e&&t&&s&&l)break}if(!(e&&t&&s&&l&&r&&o&&d&&p)){n.bNode||e&&t&&s&&l||console.log("Some of the Ig strands B, C, E, F are missing in the domain "+c+"..."),n.bNode||r&&o&&d&&p||console.log("Some of the Ig strands B, C, E, F are not beta sheets..."),i.domainid2refpdbname[c][0]==h&&(delete i.domainid2refpdbname[c],delete i.domainid2score[c]);continue}}s||n.bNode||console.log("domainid: "+c),(!l.hasOwnProperty(c)||d>=parseFloat(i.domainid2score[c].split("_")[0]))&&(i.domainid2score[c]=a[0].score+"_"+a[0].frac_identical+"_"+a[0].num_res,i.domainid2refpdbname[c]=s?d>=this.TMThresholdIgType?[h]:["all_templates"]:[h],l[c]=a[0].segs,i.domainid2ig2kabat[c]=a[0].ig2kabat,i.domainid2ig2imgt[c]=a[0].ig2imgt)}if(s)for(let e in r)if(!n.bNode&&"all_templates"==i.domainid2refpdbname[e][0]){let t=r[e],s=Object.keys(t);s.sort((function(e,s){return t[s]-t[e]})),i.domainid2refpdbname[e]=s.slice(0,this.topClusters)}return l}async parseAlignData(e,t,s){let i=this.icn3d,n=i.icn3dui,l=!1,r=this.parseAlignData_part1(e,t,s);if(0==Object.keys(r).length)return l=!0,l;if(s){n.bNode||console.log("Start round 2 alignment with the reference culsters "+JSON.stringify(i.domainid2refpdbname));let e=[],t=[],s=n.htmlCls.tmalignUrl;for(let l in i.domainid2refpdbname){let r=[],o=i.domainid2refpdbname[l],a=l.substr(0,l.indexOf(","));i.refpdbHash.hasOwnProperty(a)&&(o=[a],n.bNode||console.log("Adjusted refpdbname for domainid "+l+": "+a));let d=[];for(let e=0,t=o.length;e=3545&&i.q_start<=3555){let e=t.firstAtomObjCls.getFirstCalphaAtomObj(t.residues[r]);e&&w.push(e)}else if(i.q_start>=7545&&i.q_start<=7555){let e=t.firstAtomObjCls.getFirstCalphaAtomObj(t.residues[r]);e&&S.push(e)}if(-1!=i.q_start.indexOf("8550")&&1==g&&h&&u&&(p||m)){let e=999,t=999;for(let t=0,s=w.length;tt+l||e==t+l&&i>n+l)&&(A.push(p.resi),s.bNode||console.log("Rename strand C' to D: distToC "+e+" distToE "+t+" resiDistToC "+i+" resiDistToE "+n)):v&&(e+l0){for(let e=0,t=A.length;eparseInt(A[e])-10){h="D";break}}else if("D"==f&&x.length>0)for(let e=0,t=x.length;eparseInt(x[e])-10){h="C'";break}f!=h&&(c=this.getLabelFromRefnum(d,o,h)),"helix"!=t.firstAtomObjCls.getFirstAtomObj(t.residues[a]).ss&&(t.resid2refnum[a]=c,t.resid2domainid[a]=i)}}Object.keys(t.resid2refnum).length>0?t.bShowRefnum=!0:s.bNode||t.bNoIg||(console.log("No Ig reference numbers are assigned based on the reference structures in iCn3D..."),t.bNoIg=!0),t.chainid2igtrack||(t.chainid2igtrack={});for(let e in t.chains){let s=t.firstAtomObjCls.getFirstAtomObj(t.chains[e]);if(t.proteins.hasOwnProperty(s.serial)){let s=t.showSeqCls.getSeq(e);t.chainid2igtrack[e]=this.ajdustRefnum(s,e)}}}getStrandFromRefnum(e,t){this.icn3d.icn3dui;let s,i=parseInt(e);return s=i<1e3?void 0:i>=1200&&i<1320?"A---":i>=1320&&i<1420?"A--":i>=1420&&i<1520?"A-":i>=1520&&i<1620?"A":i>=1620&&i<1720?"A+":i>=1720&&i<1820?"A++":i>=1820&&i<2e3?"A'":i>=2e3&&i<3e3?"B":i>=3e3&&i<3420?"C--":i>=3420&&i<3520?"C-":i>=3520&&i<4e3?"C":i>=4e3&&i<5e3?"C'":i>=5e3&&i<6e3?"C''":i>=6e3&&i<7e3?"D":i>=7e3&&i<7620?"E":i>=7620&&i<8e3?"E+":i>=8e3&&i<9e3?"F":i>=9e3&&i<9620?"G":i>=9620&&i<9720?"G+":i>=9720&&i<9820?"G++":i>=9820&&i<9900?"G+++":i>9900?void 0:" ",t&&(s=t),s}getLabelFromRefnum(e,t,s){this.icn3d.icn3dui;let i=this.getStrandFromRefnum(e,s),n=e.toString();return"C'"==s&&"6"==n.substr(0,1)?n="4"+n.substr(1):"D"==s&&"4"==n.substr(0,1)&&(n="6"+n.substr(1)),i?i+n+t:void 0}async parseCustomRefFile(e){let t=this.icn3d;t.icn3dui,t.bShowCustomRefnum=!0;let s=e.split("\n");t.resid2refnum||(t.resid2refnum={}),t.refnum2residArray||(t.refnum2residArray={}),t.chainsMapping||(t.chainsMapping={});let i=[];for(let e=0,t=s.length;e0){l+='{"'+r+'": {\n';for(let t=0,n=o.length;t=46&&t<=54){let e=t-50;y[_].anchorRefnum=d-e,y[_].resCntBfAnchor=S-e,A=e,x=!0}g&&(y[_].anchorRefnum=0),y[_].strandPostfix=a,y[_].strand=p,y[_].postfix=o,y[_].loopResCnt=w-1,++_,w=0}else if(v[p+o]){if(50==t&&(y[_-1].anchorRefnum=d,y[_-1].resCntBfAnchor=S,y[_-1].startRefnum=y[_-1].anchorRefnum-y[_-1].resCntBfAnchor,A=0,x=!0),!x&&(51==t||52==t||53==t||54==t)){let e=t-50;y[_-1].anchorRefnum=d-e,y[_-1].resCntBfAnchor=S-e,y[_-1].startRefnum=y[_-1].anchorRefnum-y[_-1].resCntBfAnchor,A=e,x=!0}g&&(y[_-1].anchorRefnum=0),y[_-1].domainid=e,y[_-1].endResi=k,y[_-1].endRefnum=d,y[_-1].resCntAtAnchor=A,y[_-1].anchorRefnum&&(y[_-1].endRefnum=y[_-1].anchorRefnum+y[_-1].resCntAtAnchor),w=0}}u=p}}m=p}for(let e=0,i=y.length;e0&&parseInt(l)<=parseInt(y[e-1].endResi))break;let o=t+"_"+l,a=s.firstAtomObjCls.getFirstAtomObj(s.residues[o]),d=s.resid2domainid[o];if(a.ssbegin){let o=y[e].startRefnum;y[e].startResi=l,y[e].startRefnum-=i,y[e].loopResCnt-=i,y[e].loopResCnt<0&&(y[e].loopResCnt=0),y[e].resCntBfAnchor+=i;for(let a=1;a<=i;++a){n=r-a,l=s.ParserUtilsCls.getResi(t,n);let i=t+"_"+l;delete s.residIgLoop[i],s.resid2refnum[i]=y[e].strand+(o-a).toString(),s.resid2domainid[i]=d}break}}if("sheet"==l.ss&&!l.ssend)for(let n=1;n<=8;++n){let l=o+n,r=s.ParserUtilsCls.getResi(t,l);if(e=parseInt(y[e+1].startResi))break;let a=t+"_"+r,d=s.firstAtomObjCls.getFirstAtomObj(s.residues[a]),c=s.resid2domainid[a];if(d.ssend){let a=y[e].endRefnum;y[e].endResi=r,y[e].endRefnum+=n,e=0;--e){"G"!=y[e].strand&&y[e].endRefnum-y[e].startRefnum+1<3&&(y[e+1]&&(y[e+1].loopResCnt+=y[e].loopResCnt+parseInt(y[e].endResi)-parseInt(y[e].startResi)+1),y[e].startResi,y.splice(e,1))}_=0;let O,R,I=0,E=!0,T=!0,D=0;b=!1;let P=0;if(y.length>0)for(let i=0,l=e.length;iy[_].endResi:parseInt(l)>parseInt(y[_].endResi),i=!t&&!r,t)if(s.residIgLoop[o]=1,E)b?(R=y[_].startRefnum-y[_].loopResCnt+I,O=y[_].strand+R,n=O+y[_].strandPostfix,e=y[_].domainid):(O=void 0,n=void 0);else if(D>=0&&("G"==y[D].strand.substr(0,1)||"F"==y[D].strand.substr(0,1)&&"G"!=y[_].strand.substr(0,1)))T?b&&s.resid2refnum[o]?(T=!0,R=y[D].endRefnum+I,O=y[D].strand+R,n=O+y[D].strandPostfix,e=y[D].domainid):(b=!1,E=!0,T=!1,O=void 0,n=void 0):(O=void 0,n=void 0);else{T=!0;let t=y[_].loopResCnt;I<=parseInt(t/2+.5)?y[D]&&(R=y[D].endRefnum+I,O=y[D].strand+R,n=O+y[D].strandPostfix,e=y[D].domainid):(R=y[_].startRefnum-t+I-1,O=y[_].strand+R,n=O+y[_].strandPostfix,e=y[_].domainid)}else i?(E=!1,y[_].anchorRefnum&&(l==y[_].startResi?(P=y[_].anchorRefnum-y[_].resCntBfAnchor,y[_].startRefnum=P):l==y[_].endResi&&(y[_].endRefnum=P),O=y[_].strand+P,n=O+y[_].strandPostfix,e=y[_].domainid),l==y[_].endResi&&(++_,I=0,y[_]||--_)):r&&(s.residIgLoop[o]=1,T?s.resid2refnum[o]?(T=!0,R=y[_].endRefnum+I,O=y[_].strand+R,n=O+y[_].strandPostfix,e=y[_].domainid):(T=!1,O=void 0,n=void 0):(O=void 0,n=void 0))}else n=void 0;m=p,D=_-1,k.hasOwnProperty(e)?(delete s.resid2refnum[o],delete s.residIgLoop[o],delete s.resid2domainid[o]):(s.resid2refnum[o]=n,s.resid2domainid[o]=e,r=s.refnumCls.rmStrandFromRefnumlabel(n),s.refnum2residArray.hasOwnProperty(r)?s.refnum2residArray[r].push(o):s.refnum2residArray[r]=[o],s.chainsMapping.hasOwnProperty(t)||(s.chainsMapping[t]={}),s.chainsMapping[t][o]=O||l)}return!0}}class Ss{constructor(e){this.icn3d=e}async applyCommandScap(e){this.icn3d.icn3dui;let t=e.substr(e.lastIndexOf(" ")+1);0==e.indexOf("scap 3d")?await this.retrieveScap(t):0==e.indexOf("scap interaction")?await this.retrieveScap(t,!0):0==e.indexOf("scap pdb")&&await this.retrieveScap(t,void 0,!0)}adjust2DWidth(e){let t,s,i,n=this.icn3d;if(n.icn3dui,e=n.pre+e,$("#"+n.pre+"dl_selectannotations").hasClass("ui-dialog-content")){t=$("#"+n.pre+"dl_selectannotations").dialog("option","width"),s=.5*$("#"+n.pre+"dl_selectannotations").dialog("option","height"),i=s,$("#"+n.pre+"dl_selectannotations").dialog("option","height",s),$("#"+e).dialog("option","width",t),$("#"+e).dialog("option","height",s);let l={my:"left top",at:"right top+"+i,of:"#"+n.pre+"viewer",collision:"none"};$("#"+e).dialog("option","position",l)}}async retrieveScap(e,t,s){let i=this.icn3d,n=i.icn3dui,l=this;i.bScap=!0;let r="",o=e.split(","),a={},d=[],c={};for(let e=0,t=o.length;e1e4)return void alert("The maximum number of allowed atoms is 10,000. Please try it again with smaller sets...");let o="";o+=e.saveFileCls.getAtomPDB(n);let a,d={pdb:o,pdbid:Object.keys(e.structures).toString()};try{a=await t.getAjaxPostPromise(i,d,!0);let n,l,o,c=a.rcsb_struct_symmetry,h="none";if(void 0!==c){let i;void 0!==e.rmsd_supr&&void 0!==e.rmsd_supr.rot&&(n=e.rmsd_supr.rot,l=e.rmsd_supr.trans1,o=e.rmsd_supr.trans2),void 0===e.symdArray&&(e.symdArray=[]);for(let t=0,n=c.length;tThe selected residues have no detected symmetry with a Z score of "+a.zscore+" from the program SymD."),t.htmlCls.dialogCls.openDlg("dl_symd","Dynamically Calculated Symmetry Using SymD");else{let n=a.seqalign.replace(/ /g,"").split(","),l=a.nres,o=a.shift,d=a.rmsd,h=Object.keys(r),p={},m={},u=[],g=[],f=0,C=0,b={};for(let e=0,s=n[0].length;et&&(t=b[s].length,e=s);let s=Object.keys(p),i=Object.keys(m);for(let t=0,n=b[e].length;tSymD. The Z score "+a.zscore+" is greater than the threshold Z score 8. The RMSD is "+d+' angstrom.

    The following sequence alignment shows the residue mapping of the best aligned sets: "symOri" and "symPerm", which are also available in the menu "Analysis > Defined Sets".
    ',$("#"+e.pre+"symd_info").html(A),s.setSeqAlignForSymmetry(_,w,S);let x=!1,k=t.htmlCls.alignSeqCls.getAlignSequencesAnnotations(Object.keys(e.alnChains),void 0,void 0,x,S);A=$("#"+e.pre+"dl_sequence2").html()+k.sequencesHtml,$("#"+e.pre+"dl_sequence2").html(A),$("#"+e.pre+"dl_sequence2").width(t.htmlCls.RESIDUE_WIDTH*k.maxSeqCnt+200),t.htmlCls.dialogCls.openDlg("dl_alignment","Select residues in aligned sequences from SymD");let O=Object.keys(e.defNames2Residues).length+Object.keys(e.defNames2Atoms).length,R="symOri"+O;e.selectionCls.selectResidueList(y,R,R),e.selectionCls.updateSelectionNameDesc(),t.htmlCls.clickMenuCls.setLogCmd("select "+e.resid2specCls.residueids2spec(Object.keys(y))+" | name "+R,!1),R="symPerm"+O,e.selectionCls.selectResidueList(v,R,R),e.selectionCls.updateSelectionNameDesc(),t.htmlCls.clickMenuCls.setLogCmd("select "+e.resid2specCls.residueids2spec(Object.keys(v))+" | name "+R,!1),R="symBoth"+O,y=t.hashUtilsCls.unionHash(y,v),e.selectionCls.selectResidueList(y,R,R),e.selectionCls.updateSelectionNameDesc(),t.htmlCls.clickMenuCls.setLogCmd("select "+e.resid2specCls.residueids2spec(Object.keys(y))+" | name "+R,!1)}}else $("#"+e.pre+"dl_symd").html("
    The selected residues have no detected symmetry with a Z score of "+a.zscore+" from the program SymD."),t.htmlCls.dialogCls.openDlg("dl_symd","Dynamically Calculated Symmetry Using SymD");e.symdtitle="none"===h?void 0:h,e.drawCls.draw()}catch(s){return $("#"+e.pre+"dl_symd").html("
    The web service can not determine the symmetry of the input set."),t.htmlCls.dialogCls.openDlg("dl_symd","Dynamically Calculated Symmetry Using SymD"),void e.ParserUtilsCls.hideLoading()}}getResObj(e){this.icn3d.icn3dui;let t=e.substr(0,e.indexOf(" ")),s=e.indexOf("$"),i=e.indexOf("."),n=e.indexOf(":"),l=e.substr(s+1,i-s-1),r=e.substr(i+1,n-i-1),o=e.substr(n+1);return{resn:t,resid:l+"_"+r+"_"+o,resi:o,aligned:!0}}setSeqAlignForSymmetry(e,t,s){let i=this.icn3d,n=i.icn3dui;i.conservedName1="symOri_cons",i.conservedName2="symPerm_cons",i.consHash1={},i.consHash2={},i.alnChainsAnTtl={},i.alnChainsAnno={},i.alnChainsSeq={},i.alnChains={},i.alnChainsSeq={};let l={};for(let r=0,o=e.length;rThis structure has no symmetry."),void i.htmlCls.dialogCls.openDlg("dl_symmetry","Symmetry")}let r,o,a,d=t.rcsb_struct_symmetry;if(void 0!==d){void 0!==s.rmsd_supr&&void 0!==s.rmsd_supr.rot&&(r=s.rmsd_supr.rot,o=s.rmsd_supr.trans1,a=s.rmsd_supr.trans2),s.symmetryHash={};for(let e=0,t=d.length;eThis structure has no symmetry.");else{let e="",t=0;for(let i in s.symmetryHash){e+="",++t}$("#"+s.pre+"selectSymmetry").html(e)}}else $("#"+s.pre+"dl_symmetry").html("
    This structure has no symmetry.");i.htmlCls.dialogCls.openDlg("dl_symmetry","Symmetry")}getPolygonColor(e){let t=this.icn3d.icn3dui,s=e.substr(0,1);return"C"==s?t.parasCls.thr(16747520):"D"==s?t.parasCls.thr(65535):"T"==s?t.parasCls.thr(15631086):"O"==s?t.parasCls.thr(16753920):"I"==s?t.parasCls.thr(65280):t.parasCls.thr(11119017)}getAxisColor(e,t){let s=this.icn3d.icn3dui,i=e.substr(0,1);return"C"==i?s.parasCls.thr(16711680):"D"==i?2==t?s.parasCls.thr(65535):s.parasCls.thr(16711680):"T"==i?2==t?s.parasCls.thr(65535):s.parasCls.thr(65280):"O"==i||"I"==i?2==t?s.parasCls.thr(65535):3==t?s.parasCls.thr(65280):s.parasCls.thr(16711680):s.parasCls.thr(16711680)}}class xs{constructor(e){this.icn3d=e}alignSW(e,t,s,i,n,l,r){this.icn3d.icn3dui;let o=this.bsa_align(r,e,t,[s,i],[n,l]),a="score: "+o[0]+"\n";a+="start: "+o[1]+"\n",a+="cigar: "+this.bsa_cigar2str(o[2])+"\n\n",a+="alignment:\n\n";let d=this.bsa_cigar2gaps(e,t,o[1],o[2]),c={};return c.score=o[0],c.start=o[1],c.cigar=this.bsa_cigar2str(o[2]),c.target=d[0],c.query=d[1],c}bsg_enc_seq(e,t){if(this.icn3d.icn3dui,null==t)return null;let s=[];s.length=e.length;for(let i=0;i0&&(s=-s),i=0;i=2&&"number"==typeof t[0]&&"number"==typeof t[1]){if(null==s)return null;let e="number"==typeof s?s:s[s.length-1]+1;i=this.bsa_gen_score_matrix(e,t[0],t[1])}else i=t;for(let e=0;eo.length?d:o.length;l=null==l||l<0?c:l;let h,p,m=o.target>d?o.target-d:d-o.target;l=l>m?l:m,"number"==typeof n?(h=0,p=n>0?n:-n):(h=n[0]>0?n[0]:-n[0],p=n[1]>0?n[1]:-n[1]);let u,g=h+p,f=-1073741824,C=[],b=[],y=[],v=0,_=-1,w=-1;if(e)for(let e=0;e<=d;++e)C[e]=b[e]=0;else{C[0]=0,b[0]=-g-g;for(let e=1;e<=d;++e)e>=l?C[e]=b[e]=f:(C[e]=-(g+p*(e-1)),b[e]=-(g+g+p*e))}for(let t=0;tl?t-l:0,u=t+l+10?f:-(g+p*t),n=m>0?f:-(g+g+p*t));for(let t=m;t=o?0:1,a=a>=o?a:o,l=a>=n?l:2,a=a>=n?a:n,l=!e||a>0?l:64,i=a,c=r>a?c:t,r=r>a?r:a,a-=g,a=!e||a>0?a:0,o-=p,l|=o>a?4:0,o=o>a?o:a,b[t]=o,n-=p,l|=n>a?32:0,n=n>a?n:a,s[t]=l}C[u]=i,b[u]=e?0:f,r>v&&(v=r,_=t,w=c)}if(e&&0==v)return null;u=e?v:C[d];let S,A,x,k=[],O=0,R=0;for(e?(A=_,x=w,w!=d-1&&this.push_cigar(k,4,d-1-w)):(A=o.length-1,x=(A+l+1=0&&x>=0&&(S=y[A][x-(A>l?A-l:0)],O=S>>(O<<1)&3,!(0==O&&S>>6));)0==O&&(O=3&S),0==O?(this.push_cigar(k,0,1),--A,--x):1==O?(this.push_cigar(k,2,1),--A):(this.push_cigar(k,1,1),--x);e?(x>=0&&this.push_cigar(k,4,x+1),R=A+1):(A>=0&&this.push_cigar(k,2,A+1),x>=0&&this.push_cigar(k,1,x+1));for(let e=0;e>1;++e)S=k[e],k[e]=k[k.length-1-e],k[k.length-1-e]=S;return[u,R,k]}push_cigar(e,t,s){this.icn3d.icn3dui,0==e.length||t!=(15&e[e.length-1])?e.push(s<<4|t):e[e.length-1]+=s<<4}bsa_cigar2gaps(e,t,s,i){this.icn3d.icn3dui;let n="",l="",r="",o=0,a=s;for(let s=0;s>4;0==r?(n+=t.substr(o,d),l+=e.substr(a,d),o+=d,a+=d):1==r?(n+=t.substr(o,d),l+=Array(d+1).join("-"),o+=d):2==r?(n+=Array(d+1).join("-"),l+=e.substr(a,d),a+=d):4==r&&(o+=d)}let d=l.toUpperCase(),c=n.toUpperCase();for(let e=0;e>4).toString()+"MIDNSHP=XB".charAt(15&e[s]));return t.join("")}}class ks{constructor(e){this.icn3d=e}calculateArea(){var e=this.icn3d,t=e.icn3dui;e.bCalcArea=!0,e.opts.surface="solvent accessible surface",e.applyMapCls.applySurfaceOptions(),$("#"+e.pre+"areavalue").val(e.areavalue),$("#"+e.pre+"areatable").html(e.areahtml),t.htmlCls.dialogCls.openDlg("dl_area","Surface area calculation"),e.bCalcArea=!1}calcBuriedSurface(e,t){var s=this.icn3d,i=s.icn3dui;if(0==e.length)alert("Please select the first set");else{let n=i.hashUtilsCls.cloneHash(s.hAtoms),l=s.definedSetsCls.getAtomsFromNameArray(e),r=s.definedSetsCls.getAtomsFromNameArray(t);s.bCalcArea=!0,s.opts.surface="solvent accessible surface",s.hAtoms=i.hashUtilsCls.cloneHash(l),s.applyMapCls.applySurfaceOptions();let o=s.areavalue,a=i.hashUtilsCls.cloneHash(s.resid2area);s.hAtoms=i.hashUtilsCls.cloneHash(r),s.applyMapCls.applySurfaceOptions();let d=s.areavalue,c=i.hashUtilsCls.cloneHash(s.resid2area);s.hAtoms=i.hashUtilsCls.unionHash(s.hAtoms,l),s.applyMapCls.applySurfaceOptions();let h=s.areavalue,p=i.hashUtilsCls.cloneHash(s.resid2area),m=0,u=0,g=0,f=0;for(let e in a)p.hasOwnProperty(e)&&(f+=parseFloat(p[e]));u=(o-f).toFixed(2);for(let e in c)p.hasOwnProperty(e)&&(g+=parseFloat(p[e]));m=(d-g).toFixed(2),s.bCalcArea=!1,s.hAtoms=i.hashUtilsCls.cloneHash(n);let C=(parseFloat(d)+parseFloat(o)-parseFloat(h)).toFixed(2),b="
    Calculate solvent accessible surface area in the interface:

    ";b+="Set 1: "+e+", Surface: "+o+" Å2
    ",b+="Set 2: "+t+", Surface: "+d+" Å2
    ",b+="Total Surface: "+h+" Å2
    ",b+="Buried Surface for Set 1: "+u+" Å2
    ",b+="Buried Surface for Set 2: "+m+" Å2

    ",$("#"+s.pre+"dl_buriedarea_html").html(b),i.htmlCls.dialogCls.openDlg("dl_buriedarea","Buried solvent accessible surface area in the interface"),i.htmlCls.clickMenuCls.setLogCmd("buried surface "+C,!1)}}measureDistTwoSets(e,t){var s=this.icn3d,i=s.icn3dui;if(0==e.length||0==t.length)alert("Please select two sets");else{let n=i.hashUtilsCls.cloneHash(s.hAtoms),l=s.definedSetsCls.getAtomsFromNameArray(e),r=s.definedSetsCls.getAtomsFromNameArray(t),o=s.contactCls.getExtent(l),a=s.contactCls.getExtent(r),d=new THREE.Vector3(o[2][0],o[2][1],o[2][2]),c=new THREE.Vector3(a[2][0],a[2][1],a[2][2]);s.hAtoms=i.hashUtilsCls.cloneHash(n),void 0===s.distPnts&&(s.distPnts=[]),s.distPnts.push(d),s.distPnts.push(c);let h=$("#"+s.pre+"distancecolor2").val();this.addLine(d.x,d.y,d.z,c.x,c.y,c.z,h,!0,"distance");let p=0,m=0,u=d.clone().add(c).multiplyScalar(.5),g=(parseInt(10*d.distanceTo(c))/10).toString()+" A";this.addLabel(g,u.x,u.y,u.z,p,h,m,"distance"),s.drawCls.draw()}}measureDistManySets(e,t){var s=this.icn3d,i=s.icn3dui;if(0==e.length||0==t.length)alert("Please select sets for distance calculation...");else{let n=i.hashUtilsCls.cloneHash(s.hAtoms),l={};for(let i=0,n=e.length;i"+t[e]+" (Å)"}r+="";for(let s=0,i=e.length;s"+i+" (Å)";for(let e=0,s=t.length;e'+l[i][s]+"":r+="0"}r+=""}r+="

    ",$("#"+i.pre+"dl_disttable_html").html(r)}}addLine(e,t,s,i,n,l,r,o,a,d,c){var h=this.icn3d;h.icn3dui;let p={};p.position1=new THREE.Vector3(e,t,s),p.position2=new THREE.Vector3(i,n,l),p.color=r,p.dashed=o,p.radius=d,p.opacity=c,void 0===h.lines[a]&&(h.lines[a]=[]),void 0!==a?h.lines[a].push(p):(void 0===h.lines.custom&&(h.lines.custom=[]),h.lines.custom.push(p)),h.hlObjectsCls.removeHlObjects()}addLineFromPicking(e){var t=this.icn3d,s=t.icn3dui;let i=$("#"+t.pre+e+"color").val();t.pAtom.coord.x,t.pAtom2.coord.x,t.pAtom.coord.y,t.pAtom2.coord.y,t.pAtom.coord.z,t.pAtom2.coord.z;let n="stabilizer"!=e;s.htmlCls.clickMenuCls.setLogCmd("add line | x1 "+t.pAtom.coord.x.toPrecision(4)+" y1 "+t.pAtom.coord.y.toPrecision(4)+" z1 "+t.pAtom.coord.z.toPrecision(4)+" | x2 "+t.pAtom2.coord.x.toPrecision(4)+" y2 "+t.pAtom2.coord.y.toPrecision(4)+" z2 "+t.pAtom2.coord.z.toPrecision(4)+" | color "+i+" | dashed "+n+" | type "+e,!0),this.addLine(t.pAtom.coord.x,t.pAtom.coord.y,t.pAtom.coord.z,t.pAtom2.coord.x,t.pAtom2.coord.y,t.pAtom2.coord.z,i,n,e),t.pickpair=!1}addLabel(e,t,s,i,n,l,r,o){var a=this.icn3d;a.icn3dui;let d={};"0"!==n&&""!==n&&"undefined"!==n||(n=void 0),"0"!==l&&""!==l&&"undefined"!==l||(l=void 0),"0"!==r&&""!==r&&"undefined"!==r||(r=void 0);let c=new THREE.Vector3;c.x=t,c.y=s,c.z=i,d.position=c,d.text=e,d.size=n,d.color=l,d.background=r,void 0===a.labels[o]&&(a.labels[o]=[]),void 0!==o?a.labels[o].push(d):(void 0===a.labels.custom&&(a.labels.custom=[]),a.labels.custom.push(d)),a.hlObjectsCls.removeHlObjects()}addChainLabels(e){var t=this.icn3d;let s=t.icn3dui.hashUtilsCls.intHash(t.hAtoms,e);void 0===t.labels.chain&&(t.labels.chain=[]);let i=t.firstAtomObjCls.getChainsFromAtoms(s);for(let e in i){let s={};s.position=t.applyCenterCls.centerAtoms(t.chains[e]).center;let i=e.indexOf("_"),n=e.substr(i+1),l=t.showSeqCls.getProteinName(e);l.length>20&&(l=l.substr(0,20)+"..."),s.text="Chain "+n+": "+l,s.size=18,t.firstAtomObjCls.getFirstCalphaAtomObj(t.chains[e]).color.getHexString().toUpperCase(),s.color="black"!=t.opts.background?t.colorWhitebkgd:t.colorBlackbkgd,s.background="#FFFFFF",t.labels.chain.push(s)}t.hlObjectsCls.removeHlObjects()}addTerminiLabels(e){var t=this.icn3d,s=t.icn3dui;let i,n="#FFFFFF";i=s.hashUtilsCls.unionHash(i,t.proteins),i=s.hashUtilsCls.unionHash(i,t.nucleotides);let l=s.hashUtilsCls.intHash(t.dAtoms,i),r=s.hashUtilsCls.intHash(l,e);void 0===t.labels.chain&&(t.labels.chain=[]);let o=t.firstAtomObjCls.getChainsFromAtoms(r);for(let e in o){let i=s.hashUtilsCls.intHash(l,t.chains[e]),r=Object.keys(i),o=t.atoms[r[0]],a=t.atoms[r[r.length-1]],d={},c={};d.position=o.coord,c.position=a.coord,d.text="N-",c.text="C-",t.nucleotides.hasOwnProperty(o.serial)&&(d.text="5'",c.text="3'"),d.size=18,c.size=18,o.color.getHexString().toUpperCase(),a.color.getHexString().toUpperCase(),d.color="black"!=t.opts.background?t.colorWhitebkgd:t.colorBlackbkgd,c.color="black"!=t.opts.background?t.colorWhitebkgd:t.colorBlackbkgd,d.background=n,c.background=n,t.labels.chain.push(d),t.labels.chain.push(c)}t.hlObjectsCls.removeHlObjects()}}class Os{constructor(e){this.icn3d=e}draw2Ddgm(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=.667,o={},a={},d={},c={},h={};if(void 0===e)return"";for(let s in e.moleculeInfor){let i="#"+("000000"+e.moleculeInfor[s].color.toString(16)).slice(-6),l=e.moleculeInfor[s].chain.trim();void 0===h[l]?h[l]=1:++h[l];let r=t+"_"+(1===h[l]?l:l+h[l].toString());void 0!==n.mmdbid_q&&(n.mmdbid_q,n.mmdbid_t),o[s]=r,a[s]=i,d[s]=e.moleculeInfor[s].name,c[r]=s}if(void 0===i||!i)for(let s=0,i=e.intracResidues.length;s";p+=""+t.toUpperCase()+"
    ",p+="";let m={},u=[],g="",f="",C={};if(i)for(let e in n.dAtoms){let t=n.atoms[e];C[c[t.structure+"_"+t.chain]]=1}let b=Object.keys(e.moleculeInfor),y=Object.keys(e.intrac),v=[];for(let e=0,t=b.length;e0)for(let t in e.intrac){let s=e.intrac[t];for(let e=0,i=s.intrac.length;e0&&(y="#"+n.atoms[e[0]].color.getHexString().toUpperCase())}let S="";n.bInitial&&void 0!==s&&(void 0!==n.alignmolid2color&&n.alignmolid2color[s].hasOwnProperty(l)?(S=n.alignmolid2color[s][l],y="#FF0000"):y="#FFFFFF");let A=d[l],x=" ",k=" ";if(void 0!==c){let e=c.indexOf("_");k=c.substr(e+1),x=k.length>1?k.substr(0,1)+"..":k}else c="Misc";void 0===y&&(y="#FFFFFF");let O=1;if(n.bInitial&&void 0!==n.alnChains[c]){let e=0;for(let t in n.alnChains[c]){let s=n.atoms[t].color.getHexString().toUpperCase();"FF0000"!==s&&"00FF00"!==s||++e}O=1*e/Object.keys(n.chains[c]).length}if(O<.2&&(O=.2),-1===v.indexOf(l)){for(let e=0,t=h.intrac.length;e1){let s=0,i=0;for(let e=0,t=_[l].length;e",p+="Interaction of chain "+c+" with chain "+h+"",p+="",p+="",p+="Interaction of chain "+h+" with chain "+c+"",p+=""}return p+=f+g,p+="",p+="",n.html2ddgm+=p,$("#"+n.pre+"dl_2ddgm_html").html(n.html2ddgm),p}set2DdgmNote(e){let t="
    Nodes:
    ";return this.icn3d.icn3dui.utilsCls.isMac()?(t+="◯Protein
    ",t+="▢Nucleotide
    ",t+="♢Chemical
    ",t+="▢Biopolymer
    "):(t+="OProtein
    ",t+="▢Nucleotide
    ",t+="◇Chemical
    ",t+="▢Biopolymer
    "),t+="
    Lines:
    Interactions at 4 Å
    ",e&&(t+="Numbers in red:
    Aligned chains"),t+="

    ",t}highlightNode(e,t,s,i){let n=this.icn3d.icn3dui;i<.2&&(i=.2);if("rect"===e){$(t).attr("stroke",n.htmlCls.ORANGE),$(t).attr("stroke-width",3);let e=Number($(s).attr("x")),l=Number($(s).attr("y")),r=Number($(s).attr("width")),o=Number($(s).attr("height"));$(t).attr("x",e+r/2*(1-i)),$(t).attr("y",l+o/2*(1-i)),$(t).attr("width",r*i),$(t).attr("height",o*i)}else if("circle"===e)$(t).attr("stroke",n.htmlCls.ORANGE),$(t).attr("stroke-width",3),$(t).attr("r",Number($(s).attr("r"))*i);else if("polygon"===e){$(t).attr("stroke",n.htmlCls.ORANGE),$(t).attr("stroke-width",3);let e=Number($(s).attr("x")),l=Number($(s).attr("y")),r=Number($(s).attr("x0d")),o=Number($(s).attr("y0d")),a=Number($(s).attr("x1d")),d=Number($(s).attr("y1d")),c=Number($(s).attr("x2d")),h=Number($(s).attr("y2d")),p=Number($(s).attr("x3d")),m=Number($(s).attr("y3d"));$(t).attr("points",(e+r*i).toString()+", "+(l+o*i).toString()+", "+(e+a*i).toString()+", "+(l+d*i).toString()+", "+(e+c*i).toString()+", "+(l+h*i).toString()+", "+(e+p*i).toString()+", "+(l+m*i).toString())}}removeLineGraphSelection(){let e=this.icn3d;e.icn3dui,$("#"+e.pre+"dl_linegraph circle").attr("stroke","#000000"),$("#"+e.pre+"dl_linegraph circle").attr("stroke-width",1),$("#"+e.pre+"dl_linegraph svg line.icn3d-hlline").attr("stroke","#FFF")}removeScatterplotSelection(){let e=this.icn3d;e.icn3dui,$("#"+e.pre+"dl_scatterplot circle").attr("stroke","#000000"),$("#"+e.pre+"dl_scatterplot circle").attr("stroke-width",1),$("#"+e.pre+"dl_scatterplot rect").attr("stroke","#000000"),$("#"+e.pre+"dl_scatterplot rect").attr("stroke-width",1)}click2Ddgm(){let e=this.icn3d,t=e.icn3dui,s=this;$(document).on("click","#"+e.pre+"dl_2ddgm .icn3d-node",(function(e){let i=s.icn3d;e.stopImmediatePropagation(),Object.keys(i.hAtoms).length1)s="inter_"+e+"_"+t;else{let i=e.indexOf("_"),n=t.indexOf("_");s="inter_"+e.substr(i+1)+"_"+t.substr(n+1)}i="select the atoms in chain "+e+" interacting with chain "+t+" in a distance of 4 angstrom";let o="select interaction "+e+","+t;n.selectionCls.addCustomSelection(r,s,i,o,!0)}draw2DProtein(e,t,s,i,n,l,r,o,a,d,c){this.icn3d.icn3dui;let h=20*d,p="";return p+="Chain "+i+": "+l+"",p+="",p+="",p+=""+n+"",""!==r&&(p+=""+r+""),p+="",p}draw2DNucleotide(e,t,s,i,n,l,r,o,a,d,c){this.icn3d.icn3dui;let h=30*d,p=30*d,m="";return m+="Chain "+i+": "+l+"",m+="",m+="",m+=""+n+"",""!==r&&(m+=""+r+""),m+="",m}draw2DChemical(e,t,s,i,n,l,r,o,a,d,c,h){this.icn3d.icn3dui;let p,m,u,g,f,C,b,y,v=30*d;if(h){let s=.5*v/Math.sqrt(3),i=.5*v;p=e-s,m=t-i,u=e+3*s,g=t-i,f=e+s,C=t+i,b=e-3*s,y=t+i}else{let s=.5*v,i=.5*v;p=e-s,m=t,u=e,g=t+i,f=e+s,C=t,b=e,y=t-i}let _=p-e,w=m-t,S=u-e,A=g-t,x=f-e,k=C-t,O=b-e,R=y-t,I="";return I+="Chain "+i+": "+l+"",I+="",I+="",I+=""+n+"",""!==r&&(I+=""+r+""),I+="",I}}class Rs{constructor(e){this.icn3d=e}async draw2Dcartoon(e,t){let s=this.icn3d,i=s.icn3dui,n=this;if(i.htmlCls.clickMenuCls.setLogCmd("cartoon 2d "+e,!0),s.cartoon2dType=e,t){let t=n.getCartoonSvg(e,s.graphStr);$("#"+i.svgid_ct).html(t)}else{await this.getNodesLinksForSetCartoon(e),s.graphStr=n.getCartoonData(e,s.node_link);let t=n.getCartoonSvg(e,s.graphStr);$("#"+i.svgid_ct).html(t),n.setEventsForCartoon2d(),i.htmlCls.dialogCls.openDlg("dl_2dctn","2D Cartoon")}}getCartoonSvg(e,t){let s=this.icn3d,i=s.icn3dui,n="",l="",r=JSON.parse(t);s.ctnNodeHash={};for(let t=0,i=r.nodes.length;t":"domain"==e?n+="":"secondary"==e&&(a=s.ctnNodeHash[l].x2,d=i.htmlCls.width2d-s.ctnNodeHash[l].y2,c=s.ctnNodeHash[o].x1,h=i.htmlCls.width2d-s.ctnNodeHash[o].y1,n+="");let p=l+"--"+o;n+="Interaction of "+e+" "+this.getLabelFromId(l,e)+" with "+e+" "+this.getLabelFromId(o,e)+"",n+="",s.nodeid2lineid.hasOwnProperty(l)||(s.nodeid2lineid[l]=[]),s.nodeid2lineid.hasOwnProperty(o)||(s.nodeid2lineid[o]=[]),s.nodeid2lineid[l].push(p),s.nodeid2lineid[o].push(p)}return n+=l,n}setEventsForCartoon2d(){let e=this.icn3d,t=e.icn3dui;$("#"+t.svgid_ct+" .icn3d-ctnode").draggable({start:function(e,t){let s=parseFloat(e.target.getAttribute("cx")),i=parseFloat(e.target.getAttribute("cy"));e.target.setAttribute("cx",s),e.target.setAttribute("cy",i);let n=e.target.getAttribute("ang");if(n)e.target.setAttribute("transform","rotate("+n+","+s+","+i+")");else{let t=parseFloat(e.target.getAttribute("x1")),s=parseFloat(e.target.getAttribute("y1")),i=parseFloat(e.target.getAttribute("x2")),n=parseFloat(e.target.getAttribute("y2"));e.target.setAttribute("x1",t),e.target.setAttribute("y1",s),e.target.setAttribute("x2",i),e.target.setAttribute("y2",n)}},drag:function(s,i){let n=$("#"+t.svgid_ct).offset().left,l=$("#"+t.svgid_ct).offset().top,r=s.target.getAttribute("id"),o=s.target.getAttribute("ang"),a=s.clientX-n,d=s.clientY-l,c=parseFloat(s.target.getAttribute("cx")),h=parseFloat(s.target.getAttribute("cy")),p=(a-c)/e.resizeRatioX,m=(d-h)/e.resizeRatioY,u=parseFloat($("#"+r+"_text").attr("x")),g=parseFloat($("#"+r+"_text").attr("y"));if($("#"+r+"_text").attr("x",u+p),$("#"+r+"_text").attr("y",g+m),s.target.setAttribute("cx",a),s.target.setAttribute("cy",d),o)s.target.setAttribute("transform","rotate("+o+","+a+","+d+")");else{let e=parseFloat(s.target.getAttribute("x1")),t=parseFloat(s.target.getAttribute("y1")),i=parseFloat(s.target.getAttribute("x2")),n=parseFloat(s.target.getAttribute("y2"));if(s.target.setAttribute("x1",e+p),s.target.setAttribute("y1",t+m),s.target.setAttribute("x2",i+p),s.target.setAttribute("y2",n+m),"S"==r.substr(0,1)){let e=parseFloat($("#"+r+"_box").attr("x1")),t=parseFloat($("#"+r+"_box").attr("y1")),s=parseFloat($("#"+r+"_box").attr("x2")),i=parseFloat($("#"+r+"_box").attr("y2"));$("#"+r+"_box").attr("x1",e+p),$("#"+r+"_box").attr("y1",t+m),$("#"+r+"_box").attr("x2",s+p),$("#"+r+"_box").attr("y2",i+m)}}if(e.nodeid2lineid[r])for(let t=0,s=e.nodeid2lineid[r].length;t";return u+=""+e+" "+m+"","H"==t.substr(0,1)?u+="":(u+="",u+=""),u+=""+m+"",u+="",u}drawOval(e,t,s,i,n,l,r,o,a,d){let c=this.icn3d.icn3dui,h=this.getLabelFromId(t,e);i=c.htmlCls.width2d-i,r=180-r;let p="chain"==e?"":"";return p+=""+e+" "+h+"",p+="",p+="",p+=" ",p+=" ",p+="",p+="",p+="":" from='"+a+"' to='"+d+"' />",p+=""+h+"",p+="",p}getCartoonData(e,t){let s=this.icn3d;s.icn3dui;let i,n,l=[],r=[];l=t.node;let o=[],a={},d=0;for(let e=0,t=l.length;e0?n.y=s.htmlCls.width2d-n.y:n.y=-n.y,n}async getNodesLinksForSetCartoon(e){let t,s,i,n,l,r=this.icn3d,o=r.icn3dui,a=this,d=[],c=[],h=0,p=o.htmlCls.defaultValue,m="",u="",g="",f=!1,C=!0;if("chain"==e){let e={};for(let t in r.hAtoms){let s=r.atoms[t];if("DUM"==s.chain)continue;let i=s.structure+"_"+s.chain;(r.proteins.hasOwnProperty(t)||r.nucleotides.hasOwnProperty(t))&&(e.hasOwnProperty(i)||(e[i]={}),e[i][s.serial]=s)}let t=r.contactCls.getExtent(r.atoms),s=9999,i=9999,n=-9999,a=-9999,h=-9999,p=[];for(let d in e){r.hAtom={},r.hAtoms=o.hashUtilsCls.cloneHash(r.chains[d]);let e=r.axesCls.setPc1Axes(),c=e[0],m=e[1].distanceTo(e[0]),u=e[2].distanceTo(e[0]),g=180*new THREE.Vector2(e[1].x-e[0].x,e[1].y-e[0].y).angle()/Math.PI;g>180&&(g-=180);let f=Object.keys(r.hAtoms)[0],C=r.atoms[f];l=d,c=this.projectTo2d(c);let b=c.x,y=c.y;bn&&(n=b),ya&&(a=y);let v=.5;m=v*o.htmlCls.width2d*m/(t[1][0]-t[0][0]),u=v*o.htmlCls.width2d*u/(t[1][1]-t[0][1]),m>h&&(h=m),u>h&&(h=u),p.push({id:d,r:l,x:b,y:y,rx:m,ry:u,ang:g,c:C.color.getHexString()})}let m=h+2,u=n-s,g=a-i;for(let e=0,t=p.length;e1&&(e+="__"+S.structure),a.push(e)),g==S.chain&&f&&S.ssend){let o=this.projectTo2d(t.coord.clone()),d=o.x,g=o.y,x=this.projectTo2d(S.coord.clone()),k=x.x,O=x.y;s=.5*(d+k),i=.5*(g+O),d=.5*(s+d),g=.5*(i+g),k=.5*(s+k),O=.5*(i+O),d_&&(_=d),gw&&(w=g),k_&&(_=k),Ow&&(w=O),f=!1,C=!0,n+="-"+S.resi,l+="-"+S.resi,n+="__"+S.chain,Object.keys(r.structures).length>1&&(n+="__"+S.structure);for(let t=0,s=a.length;t0&&m==S.chain&&c.push('{"source": "'+u+'", "target": "'+n+'", "v": '+p+', "c": "'+t.color.getHexString().toUpperCase()+'"}'),A.push({id:n,r:l,ss:b,x:s,y:i,x1:d,y1:g,x2:k,y2:O,c:S.color.getHexString()}),m=S.chain,u=n,++h}}}let x=S+2,k=_-y,O=w-v;for(let e=0,t=A.length;e1&&(v+="__"+i.substr(0,i.indexOf("_")));let _=g[C],w=f[C];t.hAtoms={};for(let e=0,n=_.length;e180&&(O-=180);let R=Object.keys(t.hAtoms)[0],I=t.atoms[R];A=this.projectTo2d(A);let E=A.x,T=A.y;Ec&&(c=E),Th&&(h=T);let D=.5;x=D*s.htmlCls.width2d*x/(o[1][0]-o[0][0]),k=D*s.htmlCls.width2d*k/(o[1][1]-o[0][1]),x>p&&(p=x),k>p&&(p=k),void 0!==b&&n.push('{"source": "'+b+'", "target": "'+v+'", "v": '+l+', "c": "'+y.color.getHexString().toUpperCase()+'"}'),m.push({id:v,from:_+"",to:w+"",x:E,y:T,rx:x,ry:k,ang:O,c:I.color.getHexString()}),b=v,y=I}}let g=p+2,f=c-a,C=h-d;for(let e=0,t=m.length;e=2?d+"_"+e[1]:Object.keys(i.chains)[0];for(let e=0,t=o.length;e0&&(void 0===i||i)&&n.drawCls.draw()}}windowResize(){let e=this.icn3d.icn3dui,t=this;e.cfg.resize&&!e.utilsCls.isMobile()&&$(window).resize((function(){let s=t.icn3d;e.utilsCls.setViewerWidthHeight(s.icn3dui);let i=e.htmlCls.WIDTH,n=e.htmlCls.HEIGHT;void 0===s||s.bFullscreen||t.resizeCanvas(i,n)}))}openFullscreen(e){this.icn3d.icn3dui.bNode||document.fullscreenElement||document.mozFullScreenElement||document.webkitFullscreenElement||document.msFullscreenElement||(e.requestFullscreen?e.requestFullscreen():e.mozRequestFullScreen?e.mozRequestFullScreen():e.webkitRequestFullscreen?e.webkitRequestFullscreen():e.msRequestFullscreen&&e.msRequestFullscreen())}rotStruc(e,t){var s=this.icn3d;s.icn3dui;let i=this;if(s.bStopRotate)return!1;if(s.transformCls.rotateCount>s.transformCls.rotateCountMax)return s.transformCls.resetOrientation(),!1;if(++s.transformCls.rotateCount,t)if("left"===e)s.ROT_DIR="left";else if("right"===e)s.ROT_DIR="right";else if("up"===e)s.ROT_DIR="up";else{if("down"!==e)return!1;s.ROT_DIR="down"}if("left"===e&&"left"===s.ROT_DIR)s.transformCls.rotateLeft(1);else if("right"===e&&"right"===s.ROT_DIR)s.transformCls.rotateRight(1);else if("up"===e&&"up"===s.ROT_DIR)s.transformCls.rotateUp(1);else{if("down"!==e||"down"!==s.ROT_DIR)return!1;s.transformCls.rotateDown(1)}setTimeout((function(){i.rotStruc(e)}),100)}async back(){var e=this.icn3d;e.icn3dui,e.backForward=!0,e.STATENUMBER--,e.bAddCommands=!1,e.bAddLogs=!1,e.bNotLoadStructure=!0,e.STATENUMBER<1?e.STATENUMBER=1:await e.loadScriptCls.execCommands(0,e.STATENUMBER-1,e.STATENUMBER,!0),e.setStyleCls.adjustIcon(),e.bAddCommands=!0,e.bAddLogs=!0}async forward(){var e=this.icn3d;e.icn3dui,e.backForward=!0,e.STATENUMBER++,e.bAddCommands=!1,e.bAddLogs=!1,e.bNotLoadStructure=!0,e.STATENUMBER>e.commands.length?e.STATENUMBER=e.commands.length:await e.loadScriptCls.execCommands(0,e.STATENUMBER-1,e.STATENUMBER,!0),e.setStyleCls.adjustIcon(),e.bAddCommands=!0,e.bAddLogs=!0}async replayon(){var e=this.icn3d;e.icn3dui,e.CURRENTNUMBER=0,e.bReplay=1,$("#"+e.pre+"replay").show(),e.commands.length>0&&await e.loadScriptCls.replayFirstStep(e.CURRENTNUMBER)}async replayoff(){var e=this.icn3d;e.icn3dui,e.bReplay=0,$("#"+e.pre+"replay").hide(),++e.CURRENTNUMBER,await e.loadScriptCls.execCommands(e.CURRENTNUMBER,e.STATENUMBER-1,e.STATENUMBER)}closeDialogs(){var e=this.icn3d,t=e.icn3dui;let s=["dl_2ddgm","dl_2dctn","dl_alignment","dl_sequence2","dl_definedsets","dl_setsmenu","dl_command","dl_setoperations","dl_vast","dl_foldseek","dl_mmtfid","dl_pdbid","dl_afid","dl_opmid","dl_pdbfile","dl_pdbfile_app","dl_rescolorfile","dl_customcolor","dl_align","dl_alignaf","dl_chainalign","dl_chainalign2","dl_chainalign3","dl_mutation","dl_mol2file","dl_sdffile","dl_xyzfile","dl_afmapfile","dl_urlfile","dl_mmciffile","dl_mmcifid","dl_mmdbid","dl_mmdbafid","dl_blast_rep_id","dl_yournote","dl_proteinname","dl_refseqid","dl_cid","dl_pngimage","dl_state","dl_fixedversion","dl_selection","dl_dsn6","dl_dsn6url","dl_clr","dl_symmetry","dl_symd","dl_contact","dl_hbonds","dl_realign","dl_realignbystruct","dl_allinteracton","dl_interactionsorted","dl_linegraph","dl_linegraphcolor","dl_scatterplot","dl_scatterploitcolor","dl_contactmap","dl_alignerrormap","dl_elecmap2fofc","dl_elecmapfofc","dl_emmap","dl_aroundsphere","dl_adjustmem","dl_selectplane","dl_addlabel","dl_addlabelselection","dl_labelColor","dl_distance","dl_stabilizer","dl_disttwosets","dl_distmanysets","dl_stabilizer_rm","dl_thickness","dl_thickness2","dl_addtrack","dl_addtrack_tabs","dl_saveselection","dl_copyurl","dl_selectannotations","dl_annotations_tabs","dl_anno_view_tabs","dl_annotations","dl_graph","dl_svgcolor","dl_area","dl_colorbyarea","dl_rmsd","dl_buriedarea","dl_propbypercentout","dl_propbybfactor","dl_legend","dl_disttable","dl_translate"];for(let i in s){let n=s[i];t.cfg.notebook?$("#"+e.pre+n).hide():$("#"+e.pre+n).hasClass("ui-dialog-content")&&$("#"+e.pre+n).dialog("isOpen")&&$("#"+e.pre+n).dialog("close").remove()}t.cfg.notebook||this.resizeCanvas(t.htmlCls.WIDTH,t.htmlCls.HEIGHT,!0)}}class Es{constructor(e){this.icn3d=e}resetOrientation(){let e=this.icn3d;e.icn3dui;let t=!1;if(e.commands.length>0){let s=e.commands[0].split("|||");if(2==s.length){let i=JSON.parse(s[1]);e._zoomFactor=i.factor,e.mouseChange.x=i.mouseChange.x,e.mouseChange.y=i.mouseChange.y,e.quaternion._x=i.quaternion._x,e.quaternion._y=i.quaternion._y,e.quaternion._z=i.quaternion._z,e.quaternion._w=i.quaternion._w,t=!0}}t||(e._zoomFactor=1,e.mouseChange=new THREE.Vector2(0,0),e.quaternion=new THREE.Quaternion(0,0,0,1)),e.maxD=e.oriMaxD,e.center=e.oriCenter.clone(),"show"==e.ori_chemicalbinding?e.bSkipChemicalbinding=!1:"hide"==e.ori_chemicalbinding&&(e.bSkipChemicalbinding=!0)}rotateLeft(e){let t=this.icn3d,s=t.icn3dui,i=new THREE.Vector3(0,1,0),n=-e/180*Math.PI;t.bControlGl&&!s.bNode?i.applyQuaternion(window.cam.quaternion).normalize():i.applyQuaternion(t.cam.quaternion).normalize();let l=new THREE.Quaternion;l.setFromAxisAngle(i,-n);let r={};r.quaternion=l,r.update=!0,t.bControlGl&&!s.bNode?window.controls.update(r):t.controls.update(r),t.bRender&&t.drawCls.render()}rotateRight(e){let t=this.icn3d,s=t.icn3dui,i=new THREE.Vector3(0,1,0),n=e/180*Math.PI;t.bControlGl&&!s.bNode?i.applyQuaternion(window.cam.quaternion).normalize():i.applyQuaternion(t.cam.quaternion).normalize();let l=new THREE.Quaternion;l.setFromAxisAngle(i,-n);let r={};r.quaternion=l,r.update=!0,t.bControlGl&&!s.bNode?window.controls.update(r):t.controls.update(r),t.bRender&&t.drawCls.render()}rotateUp(e){this.icn3d.icn3dui,this.rotate_base(-e)}rotateDown(e){this.icn3d.icn3dui,this.rotate_base(e)}rotate_base(e){let t=this.icn3d,s=t.icn3dui,i=new THREE.Vector3(1,0,0),n=e/180*Math.PI;t.bControlGl&&!s.bNode?i.applyQuaternion(window.cam.quaternion).normalize():i.applyQuaternion(t.cam.quaternion).normalize();let l=new THREE.Quaternion;l.setFromAxisAngle(i,-n);let r={};r.quaternion=l,r.update=!0,t.bControlGl&&!s.bNode?window.controls.update(r):t.controls.update(r),t.bRender&&t.drawCls.render()}setRotation(e,t){let s=this.icn3d,i=s.icn3dui;if(!e)return;s.bControlGl&&!i.bNode&&window.cam?e.applyQuaternion(window.cam.quaternion).normalize():s.cam&&e.applyQuaternion(s.cam.quaternion).normalize();let n=new THREE.Quaternion;n.setFromAxisAngle(e,-t);let l={};l.quaternion=n,l.update=!0,s.bControlGl&&!i.bNode&&window.controls?window.controls.update(l):s.controls&&s.controls.update(l),s.bRender&&s.drawCls.render()}translateLeft(e){this.icn3d.icn3dui,this.translate_base(-e,0)}translateRight(e){this.icn3d.icn3dui,this.translate_base(e,0)}translateUp(e){this.icn3d.icn3dui,this.translate_base(0,-e)}translateDown(e){this.icn3d.icn3dui,this.translate_base(0,e)}translate_base(e,t){let s=this.icn3d,i=s.icn3dui,n=new THREE.Vector2(0,0);n.x+=e/100,n.y+=t/100;let l={};l.mouseChange=n,l.update=!0,s.bControlGl&&!i.bNode?window.controls.update(l):s.controls.update(l),s.bRender&&s.drawCls.render()}translateCoord(e,t,s,i){let n=this.icn3d;n.icn3dui;for(let l in e){let e=n.atoms[l];e.coord.x+=t,e.coord.y+=s,e.coord.z+=i}}rotateCoord(e,t){let s=this.icn3d;s.icn3dui;const i=new THREE.Matrix4;i.elements=t;for(let t in e){let e=s.atoms[t];e.coord=e.coord.applyMatrix4(i)}}zoominSelection(e){let t=this.icn3d,s=t.icn3dui,i={};if(i._zoomFactor=1/t._zoomFactor,i.update=!0,t.bControlGl&&!s.bNode?window.controls&&window.controls.update(i):t.controls&&t.controls.update(i),void 0===e&&(e=s.hashUtilsCls.hash2Atoms(t.hAtoms,t.atoms)),Object.keys(e).length>1){let s=t.applyCenterCls.centerAtoms(e);t.maxD=s.maxD,t.maxD<5&&(t.maxD=5),t.center=s.center,t.applyCenterCls.setCenter(t.center),t.cameraCls.setCamera()}}getTransformationStr(e){this.icn3d.icn3dui;let t={factor:1,mouseChange:{x:0,y:0},quaternion:{_x:0,_y:0,_z:0,_w:1}};return t.factor=parseFloat(e.factor).toPrecision(4),t.mouseChange.x=parseFloat(e.mouseChange.x).toPrecision(4),t.mouseChange.y=parseFloat(e.mouseChange.y).toPrecision(4),t.quaternion._x=parseFloat(e.quaternion._x).toPrecision(4),t.quaternion._y=parseFloat(e.quaternion._y).toPrecision(4),t.quaternion._z=parseFloat(e.quaternion._z).toPrecision(4),t.quaternion._w=parseFloat(e.quaternion._w).toPrecision(4),"1.0000"==t.factor&&(t.factor=1),"0.0000"==t.mouseChange.x&&(t.mouseChange.x=0),"0.0000"==t.mouseChange.y&&(t.mouseChange.y=0),"0.0000"==t.quaternion._x&&(t.quaternion._x=0),"0.0000"==t.quaternion._y&&(t.quaternion._y=0),"0.0000"==t.quaternion._z&&(t.quaternion._z=0),"1.0000"==t.quaternion._w&&(t.quaternion._w=1),JSON.stringify(t)}}class Ts{constructor(e){this.icn3d=e}saveFile(e,t,s,i){let n,l=this.icn3d,r=l.icn3dui,o=this;if("command"===t){let e=l.loadCmd?l.loadCmd+"\n":"";for(let t=0,s=l.commands.length;t4e3||0!==s.indexOf("http")||l.bInputfile&&!l.bInputUrlfile?$("#"+l.pre+"viewer").html(""):$("#"+l.pre+"viewer").html(""),$("#"+l.pre+"viewer").width(i),$("#"+l.pre+"viewer").height(n),$("#"+l.pre+"cmdlog").hide(),$("#"+l.pre+"title").hide(),$("#"+l.pre+"mnlist").hide(),$("#"+l.pre+"fullscreen").length>0&&$("#"+l.pre+"fullscreen").hide(),l={}}else saveAs(e,t)}saveSvg(e,t,s){if(this.icn3d.icn3dui.bNode)return"";let i=$("#"+e).width(),n=$("#"+e).height();s&&(n=i);let l=this.getSvgXml(e,i,n,s),r=new Blob([l],{type:"image/svg+xml"});saveAs(r,t)}getSvgXml(e,t,s,i){if(this.icn3d.icn3dui.bNode)return"";return(t&&s?''+""+document.getElementById(e).innerHTML+""}savePng(e,t,s){let i=this.icn3d,n=i.icn3dui;if(n.bNode)return"";let l=$("#"+e).width(),r=$("#"+e).height();s&&(r=l);let o=document.getElementById(e),a=o.getBBox(),d=o.cloneNode(!0);i.lineGraphCls.copyStylesInline(d,o);let c=document.createElement("CANVAS");c.width=l,c.height=r;let h=c.getContext("2d");h.clearRect(0,0,a.width,a.height);let p=this.getSvgXml(e,l,r,s),m=window.URL||window.webkitURL||window,u=new Blob([p],{type:"image/svg+xml;charset=utf-8"}),g=new Image;g.src=m.createObjectURL(u),g.onload=function(){if(h.drawImage(g,0,0),m.revokeObjectURL(this.src),n.utilsCls.isIE()){let e=c.msToBlob();e&&(saveAs(e,t),c.remove())}else c.toBlob((function(e){e&&(saveAs(e,t),c.remove())}))}}exportCustomAtoms(e){var t=this.icn3d;t.icn3dui;let s="",i=void 0!==t.defNames2Residues?Object.keys(t.defNames2Residues).sort():[];for(let n=0,l=i.length;n0)if(s){let s={};for(let e=0,l=t.length;eparseInt(p)+1&&(s.ss=" ",f.push(s)),"helix"==t.ss?(s.ss="H",f.push(s)):"sheet"==t.ss&&(s.ss="S",f.push(s)),t.ssend){let e=a.hashUtilsCls.cloneHash(s);e.ss=" ",f.push(e)}p=t.resi}let C,b,y=0,v=!1,_=!1;for(let e=0,t=f.length;e1,A=1,x="",k="",O=0,R="",I={};for(let l in e){let e=o.atoms[l];if(s&&e.het)continue;if(e.structure!=x){r&&S||(d+=w,w="",A>1&&(d+="\nENDMDL\n"),S&&(d+="MODEL "+A+"\n"));let t=n?"Mutated chain_residue "+Object.keys(n)+"; ":"";i||r&&S||(d+=this.getPDBHeader(A-1,g,t,e.structure)),++A}e.chain!=k&&e.structure==x&&k&&(d+="TER\n");let p=e.chain+"_"+e.resi;if(n&&n.hasOwnProperty(p)){I.hasOwnProperty(p)||(d+=n[p],I[p]=1);continue}let m="";m+=e.het?"HETATM":"ATOM ",m+=l.toString().padStart(5," "),m+=" ";let u=e.name.trim();isNaN(u.substr(0,1))||(u=u.substr(1)+u.substr(0,1)),4==u.length?m+=u:(m+=" ",u=u.replace(/\*/g,"'"),"O1P"==u?u="OP1":"O2P"==u?u="OP2":"C5M"==u&&(u="C7 "),m+=u.padEnd(3," ")),m+=" ";let f=e.resn;if(m+=f.length<=3?f.padStart(3," "):f.substr(0,3),r&&A>2&&(o.proteins.hasOwnProperty(e.serial)||o.nucleotides.hasOwnProperty(e.serial)))e.structure==x&&e.chain==k||(R=O<36?"abcdefghijklmnopqrstuvwxyz0123456789"[O]:"?",++O),m+=" "+R;else if(e.chain.length>=2){m+=e.chain.replace(/_/gi,"").substr(0,2)}else 1==e.chain.length?m+=" "+e.chain.substr(0,1):0==e.chain.length&&(m+=" A");let C=e.resi;!isNaN(C)&&e.chain.length>3&&!isNaN(e.chain.substr(3))&&(C=C-1+parseInt(e.chain.substr(3)));let b=parseInt(C);m+=b.toString().length<=4?b.toString().padStart(4," "):b.toString().substr(0,4);let y=e.resi.toString().substr(e.resi.toString().length-1,1);if(isNaN(y)?m+=y:m+=" ",m+=" ".padStart(3," "),m+=e.coord.x.toFixed(3).toString().padStart(8," "),m+=e.coord.y.toFixed(3).toString().padStart(8," "),m+=e.coord.z.toFixed(3).toString().padStart(8," "),t&&e.het){let t=1.5,s=0;"C"==e.elem?t=1.908:"N"==e.elem?t=1.824:"O"==e.elem?t=1.6612:"H"==e.elem?t=1.25:"S"==e.elem?t=2:"P"==e.elem?t=2.1:a.parasCls.vdwRadii.hasOwnProperty(e.elem)&&(t=a.parasCls.vdwRadii[e.elem]),void 0!==a.cfg.cid&&void 0!==e.crg?s=e.crg:c.hasOwnProperty(l)?s=1.38:h.hasOwnProperty(l)?s=-.595:a.parasCls.ionCharges.hasOwnProperty(e.elem)&&(s=a.parasCls.ionCharges[e.elem]),m+=s.toFixed(4).toString().padStart(8," "),m+=t.toFixed(4).toString().padStart(7," ")}else m+="1.00".padStart(6," "),m+=e.b?parseFloat(e.b).toFixed(2).toString().padStart(6," "):" ".padStart(6," "),m+=" ".padStart(10," "),m+=e.elem.padStart(2," "),m+=" ".padStart(2," ");if(e.het&&e.bonds.length>0){w+="CONECT"+l.toString().padStart(5," ");let t={};for(let s=0,i=e.bonds.length;s50?n.molTitle.substr(0,47)+"...":n.molTitle;-1!=e.indexOf('"')&&(e=""),s&&(e=s+e),l+="TITLE "+e+"\n"}return t&&t[r]&&(l+=t[r]),l}showTitle(){var e=this.icn3d,t=e.icn3dui;let s=e.molTitle?e.molTitle:"",i="black"==e.opts.background?t.htmlCls.GREYD:"black";if(void 0===e.inputid)s.length>40&&(s=s.substr(0,40)+"..."),$("#"+e.pre+"title").html(s);else if(void 0!==t.cfg.cid){let t=this.getLinkToStructureSummary();$("#"+e.pre+"title").html("PubChem CID "+e.inputid.toUpperCase()+": "+s)}else if(void 0!==t.cfg.align)s="VAST+ alignment of "+Object.keys(e.structures),$("#"+e.pre+"title").html(s);else if(void 0!==t.cfg.chainalign){s="Dynamic Structure Alignment of Chains: "+t.cfg.chainalign.split(","),$("#"+e.pre+"title").html(s)}else{let n=Object.keys(t.utilsCls.getStructures(e.dAtoms));if(n.length>1){s="Multiple structures: ";for(let e=0,t=n.length;e'+n[e]+"",e5?"https://alphafold.ebi.ac.uk/entry/"+n[0]:"https://www.ncbi.nlm.nih.gov/structure/?term="+n[0];this.setStructureTitle(e,s,i)}}}setStructureTitle(e,t,s){var i=this.icn3d,n=i.icn3dui;t.length>40&&(t=t.substr(0,40)+"...");let l,r,o=i.inputid;if(-1!=o.indexOf("http"))r="Data from",e=o,l=o;else{let e=n.utilsCls.getHlStructures(),s=!1,a=!1;for(let t in e)t.length>5?a=!0:s=!0;let d=Object.keys(e);if(o=d.join(","),l=n.cfg.refseqid||n.cfg.protein?i.inputid:o.toUpperCase(),s&&a?r="AlphaFold/PDB ID":s?r="PDB ID":a&&(r="AlphaFold ID"),d.length>1&&(r+="s"),i.molTitleHash){t="";for(let e=0,s=d.length;e20&&(e=e.substr(0,17)+"..."),l="Query: "+e+"; target: "+s,$("#"+i.pre+"title").html(l+", "+t)}else $("#"+i.pre+"title").html(r+" "+l+": "+t);else $("#"+i.pre+"title").html(t)}getLinkToStructureSummary(e){var t=this.icn3d,s=t.icn3dui;let i="https://www.ncbi.nlm.nih.gov/structure/?term=";if(i=void 0!==s.cfg.cid?"https://www.ncbi.nlm.nih.gov/pccompound/?term=":void 0!==s.cfg.refseqid?"https://www.ncbi.nlm.nih.gov/protein/":void 0!==s.cfg.afid?"https://alphafold.ebi.ac.uk/search/text/":Object.keys(t.structures).length>1?"https://www.ncbi.nlm.nih.gov/structure/?term=":s.htmlCls.baseUrl+"pdb/",void 0===t.inputid)i="https://www.ncbi.nlm.nih.gov/pccompound/?term="+t.molTitle;else{let n=t.inputid.split("_");1===n.length?(i+=t.inputid,e&&s.htmlCls.clickMenuCls.setLogCmd("link to "+t.inputid+": "+i,!1)):2===n.length&&(s.cfg.afid?i+=n[0]+" "+n[1]:i+=n[0]+" OR "+n[1],e&&s.htmlCls.clickMenuCls.setLogCmd("link to structures "+n[0]+" and "+n[1]+": "+i,!1))}return i}setEntrezLinks(e){var t=this.icn3d,s=t.icn3dui;let i,n=Object.keys(t.structures);if(1===n.length){i="https://www.ncbi.nlm.nih.gov/"+e+"/?term="+n[0],s.htmlCls.clickMenuCls.setLogCmd("Entrez "+e+" about PDB "+n[0]+": "+i,!1);let l=t.structures&&Object.keys(t.structures).length>0?"_blank":"_self";window.open(i,l)}else if(2===n.length){i="https://www.ncbi.nlm.nih.gov/"+e+"/?term="+n[0]+" OR "+n[1],s.htmlCls.clickMenuCls.setLogCmd("Entrez "+e+" about PDB "+n[0]+" OR "+n[1]+": "+i,!1);let l=t.structures&&Object.keys(t.structures).length>0?"_blank":"_self";window.open(i,l)}}}class Ds{constructor(e){this.icn3d=e}async shareLink(e,t){let s=this.icn3d,i=s.icn3dui,n=this.shareLinkUrl(),l=n.length>4e3||0!==n.indexOf("http"),r=Object.keys(s.structures).join("_");if(r==s.defaultPdbId&&(s.filename?r=s.filename:s.inputid&&(r=s.inputid)),e){if(t||s.bInputfile||l)return void s.saveFileCls.saveFile(r+"_icn3d_loadable.png","png")}else{if(s.bInputfile&&!s.bInputUrlfile)return void alert("Share Link does NOT work when the data are from custom files. Please save 'iCn3D PNG Image' in the File menu and open it in iCn3D.");if(l)return void alert("The url is more than 4000 characters and may not work. Please save 'iCn3D PNG Image' or 'State File' and open them in iCn3D.");i.htmlCls.clickMenuCls.setLogCmd("share link: "+n,!1)}let o="Problem in getting shortened URL";if(!i.cfg.notebook){let t=await this.getShareLinkPrms(n,e);if(void 0!==t.shortLink&&(o=t.shortLink,e)){let e=o.split("/"),t=e[e.length-1];s.saveFileCls.saveFile(r+"-"+t+".png","png");let i='\n\n",s.saveFileCls.saveFile(r+"-"+t+".html","html",i)}e&&void 0===t.shortLink&&s.saveFileCls.saveFile(r+"_icn3d_loadable.png","png");let i=o.split("page.link/");2==i.length&&(o="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?"+i[1]),$("#"+s.pre+"short_url").val(o),$("#"+s.pre+"short_url_title").val(o+"&t="+s.yournote)}let a=this.shareLinkUrl(void 0,!0),d="view = icn3dpy.view(q='"+(i.cfg.url?"url="+i.cfg.url:i.cfg.idname+"="+i.cfg.idvalue)+"',command='"+a+"')\nview";(i.cfg.url||i.cfg.idname)&&$("#"+s.pre+"jn_commands").val(d),$("#"+s.pre+"ori_url").val(n),e||i.htmlCls.dialogCls.openDlg("dl_copyurl","Copy a Share Link URL or Jupyter Notebook Commands")}getShareLinkPrms(e,t){let s=this.icn3d,i=s.icn3dui;return new Promise((function(n,l){$.ajax({url:"https://firebasedynamiclinks.googleapis.com/v1/shortLinks?key=AIzaSyBxl9CgM0dY5lagHL4UOhEpLWE1fuwdnvc",type:"POST",data:{longDynamicLink:"https://icn3d.page.link/?link="+encodeURIComponent(e)},dataType:"json",success:function(e){n(e)},error:function(n,l,r){let o="Problem in getting shortened URL";$("#"+s.pre+"ori_url").val(e),$("#"+s.pre+"short_url").val(o),$("#"+s.pre+"short_url_title").val(o+"&t="+s.yournote),t||i.htmlCls.dialogCls.openDlg("dl_copyurl","Copy a Share Link URL")}})}))}shareLinkUrl(e,t){let s=this.icn3d,i=s.icn3dui,n=i.htmlCls.baseUrl+"icn3d/?",l="";if(i.cfg.bSidebyside&&(n=i.htmlCls.baseUrl+"icn3d/full2.html?"),s.bInputUrlfile){n=window.location.href.split("?")[0]+"?"+s.inputurl+"&"}let r,o={};for(let e in s.cfg){let t=s.cfg[e];"inpara"!==e&&"command"!==e&&"usepdbnum"!==e&&"date"!==e&&"v"!==e&&void 0!==t&&("width"===e&&"100%"===t||"height"===e&&"100%"===t||"resize"===e&&!0===t||"showmenu"===e&&!0===t||"showtitle"===e&&!0===t||"showcommand"===e&&!0===t||"mobilemenu"===e&&!1===t||"showanno"===e&&!1===t||"showseq"===e&&!1===t||"showalignseq"===e&&!1===t||"show2d"===e&&!1===t||"showsets"===e&&!1===t||"rotate"===e&&"right"===t||"command"!==e&&("options"===e?Object.keys(t).length>0&&(o[e]=JSON.stringify(t)):!0===t?o[e]=1:!1===t?o[e]=0:""!==t&&(o[e]=t)))}s.bAfMem?o.afmem="on":(i.cfg.afid||1==Object.keys(s.structures).length&&Object.keys(s.structures)[0].length>5)&&(o.afmem="off");let a=-1;void 0!==i.cfg.inpara&&(a=i.cfg.inpara.indexOf("&command=")),r=-1!==a?i.cfg.inpara.substr(0,a):i.cfg.inpara;let d=!1;if(!s.bInputUrlfile){let e=r&&r.substr(1)?r.substr(1).split("&"):[];for(let t=0,s=e.length;tc){u=s.commands[c].split("|||")[0].split("&command=")[0].trim(),-1!==u.indexOf(g)&&++f}let C,b=c+1,y="";for(let e=s.commands.length;b0&&f%2==0&&u!==g&&(y+=g+"; "),y+=u+"|||"+s.transformCls.getTransformationStr(p),m+=u+"|||"+s.transformCls.getTransformationStr(p)+"\n"),n+=y,l=y,m=m.replace(/!/g,Object.keys(s.structures)[0]+"_"),(s.bEsmfold||s.bInputfile&&!s.bInputUrlfile||s.bInputUrlfile&&s.bAppend||n.length>4e3)&&(n=m),void 0!==s.structures&&1==Object.keys(s.structures).length&&void 0!==s.inputid&&(C=Object.keys(s.structures)[0],n=n.replace(new RegExp(C+"_","g"),"!"),l=l.replace(new RegExp(C+"_","g"),"!")),void 0!==i.cfg.blast_rep_id&&(n=n.replace(new RegExp("blast_rep_id=!","g"),"blast_rep_id="+C+"_")),t?l:n}getPngText(){let e,t=this.icn3d;t.icn3dui;let s="";if(t.bInputfile)e=this.shareLinkUrl(true),"http"==e.substr(0,4)?s+="\nShare Link: "+e:(s+="\nStart of type file======\n",s+=t.InputfileType+"\n",s+="End of type file======\n",s+="Start of data file======\n",s+=t.saveFileCls.getAtomPDB(t.atoms),s+="End of data file======\n",s+="Start of state file======\n",s+=e+"\n",s+="End of state file======\n");else{e=this.shareLinkUrl(),e.length>4e3||0!==e.indexOf("http")?(e=this.shareLinkUrl(true),s+="\nStart of state file======\n",s+=e+"\n",s+="End of state file======\n"):s+="\nShare Link: "+e}return s=s.replace(/!/g,Object.keys(t.structures)[0]+"_"),s}}class Ps{constructor(e){this.icn3d=e}setThichknessFor3Dprint(){let e=this.icn3d,t=e.icn3dui;e.lineRadius=1,e.coilWidth=1.2,e.cylinderRadius=.8,e.crosslinkRadius=.8,e.traceRadius=1,e.dotSphereScale=.6,e.sphereRadius=1.5,e.ribbonthickness=1,e.helixSheetWidth=2,e.nucleicAcidWidth=1.4,t.htmlCls.setHtmlCls.setCookieForThickness()}prepareFor3Dprint(){let e=this.icn3d,t=e.icn3dui;if(e.bShowHighlight=!1,e.hlObjectsCls.removeHlObjects(),e.bDashedLines=!1,e.bSetThickness||void 0!==t.cfg.cid||this.setThichknessFor3Dprint(),void 0!==e.lines.hbond)for(let t=0,s=e.lines.hbond.length;tt.substr(0,s))return 1;if(e.substr(0,s)==t.substr(0,s)){if(parseInt(e.substr(s+1))parseInt(t.substr(i+1)))return 1;if(parseInt(e.substr(s+1))==parseInt(t.substr(i+1)))return 0}}})),n="";for(let e=0,t=i.length;e"}let l=Object.keys(t.utilsCls.getHlStructures()).join(",");e.saveFileCls.saveFile(l+"_residues.txt","html",n)}addStabilizer(){let e=this.icn3d,t=e.icn3dui,s=3.5;if(Object.keys(e.dAtoms).length>0){let i,n={},l=12.25,r=3.2*3.2;for(let t in e.dAtoms){let s=e.atoms[t];!e.nucleotides.hasOwnProperty(s.serial)||"N1"!==s.name&&"N2"!==s.name&&"N3"!==s.name&&"N4"!==s.name&&"N6"!==s.name&&"O2"!==s.name&&"O6"!==s.name||(i=s.structure+"_"+s.chain+"_"+s.resi+"_"+s.name,n[i]=s)}let o=Object.keys(n),a=o.length;void 0===e.pairArray&&(e.pairArray=[]);for(let t=0;ts)continue;let h=Math.abs(n[a].coord.y-n[d].coord.y);if(h>s)continue;let p=Math.abs(n[a].coord.z-n[d].coord.z);if(p>s)continue;let m=c*c+h*h+p*p;m>l||ms+1||rs+2||rs+4||r0&&o.length>0)if(a){let t=parseInt((r.length+.5)/2);e.pairArray.push(o[0]),e.pairArray.push(r[t])}else{let t=10,s=parseInt(r.length/(t+1));for(let i=0,n=o.length;i1&&t.bAssembly&&(t.threshbox=180/Math.pow(t.biomtMatrices.length,.33),t.applyMapCls.removeSurfaces(),t.applyMapCls.applySurfaceOptions(),t.applyMapCls.removeMaps(),t.applyMapCls.applyMapOptions(),t.applyMapCls.removeEmmaps(),t.applyMapCls.applyEmmapOptions());let i=this.saveStlFile(),n=Object.keys(s.utilsCls.getHlStructures()).join(",");if(t.saveFileCls.saveFile(n+e+".stl","binary",i),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length>t.maxAtoms3DMultiFile){alert(t.biomtMatrices.length+" files will be generated for this assembly. Please merge these files using some software and 3D print the merged file.");let s=new THREE.Matrix4;s.identity();let l=1;for(let r=0;r1&&t.bAssembly&&(t.threshbox=180/Math.pow(t.biomtMatrices.length,.33),t.applyMapCls.removeSurfaces(),t.applyMapCls.applySurfaceOptions(),t.applyMapCls.removeMaps(),t.applyMapCls.applyMapOptions(),t.applyMapCls.removeEmmaps(),t.applyMapCls.applyEmmapOptions());let i=this.saveVrmlFile(),n=Object.keys(s.utilsCls.getHlStructures()).join(",");if(t.saveFileCls.saveFile(n+e+".wrl","text",i),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length>t.maxAtoms3DMultiFile){alert(t.biomtMatrices.length+" files will be generated for this assembly. Please merge these files using some software and 3D print the merged file.");let s=new THREE.Matrix4;s.identity();let n=1;for(let l=0;l7e4)return alert("Please display a subset of the structure to export 3D files. Then merge the files for 3D printing..."),[""];t.threeDPrintCls.prepareFor3Dprint();let i=0;i+=this.getFaceCnt(t.mdl),i+=this.getFaceCnt(t.mdl_ghost);let n=[],l=new Uint8Array(84),r="STL file for the structure(s) ",o=Object.keys(t.structures);for(let e=0,t=o.length;e80&&(r=r.substr(0,80));for(let e=0;e<80;++e)e1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length<=t.maxAtoms3DMultiFile?this.updateArray(l,s.convertTypeCls.passInt32([i*t.biomtMatrices.length]),80):this.updateArray(l,s.convertTypeCls.passInt32([i]),80),n.push(new Blob([l],{type:"application/octet-stream"})),n=this.processStlMeshGroup(t.mdl,n,e),n=this.processStlMeshGroup(t.mdl_ghost,n,e),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length<=t.maxAtoms3DMultiFile){let e=new THREE.Matrix4;e.identity();for(let s=0;s5e4)return alert("Please display a subset of the structure to export 3D files. Then merge the files for 3D printing..."),[""];t.threeDPrintCls.prepareFor3Dprint();let s=[];s.push("#VRML V2.0 utf8\n");let i=0,n=this.processVrmlMeshGroup(t.mdl,s,i,e);if(s=n.vrmlStrArray,i=n.vertexCnt,n=this.processVrmlMeshGroup(t.mdl_ghost,s,i,e),s=n.vrmlStrArray,i=n.vertexCnt,void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length<=t.maxAtoms3DMultiFile){let e=new THREE.Matrix4;e.identity();for(let l=0;l0?h.z=-1:h.z=1,s.cam===s.perspectiveCamera?(s.cam_z>0?h.z=-1:h.z=1,h.unproject(s.cam),s.raycaster.set(s.cam.position,h.sub(s.cam.position).normalize())):s.cam===s.orthographicCamera&&(s.cam_z>0?h.z=1:h.z=-1,h.unproject(s.cam),s.raycaster.set(h,new THREE.Vector3(0,0,-1).transformDirection(s.cam.matrixWorld)));let p=this.isIntersect(s.objects,s.mdl,t,d,c);p||(p=this.isIntersect(s.objects_ghost,s.mdl_ghost,t,d,c))}isIntersect(e,t,s,i,n){let l=this.icn3d;l.icn3dui;let r=l.raycaster.intersectObjects(e),o=!1,a=t.position;if(r.length>0){r[0].point.sub(a);let e=l.rayThreshold,t=this.getAtomsFromPosition(r[0].point,e);for(;!t&&e<10;)e+=.5,t=this.getAtomsFromPosition(r[0].point,e);t?(o=!0,l.pickpair?s&&(l.pAtomNum%2==0?l.pAtom=t:l.pAtom2=t,++l.pAtomNum):l.pAtom=t,s?l.pickingCls.showPicking(t):l.pickingCls.showPicking(t,i,n)):console.log("No atoms were found in 10 andstrom range")}return o}getAtomsFromPosition(e,t,s){let i,n=this.icn3d,l=n.icn3dui;null==t&&(t=1);let r=s||n.dAtoms;for(i in r){let s=n.atoms[i];if(n.ions.hasOwnProperty(i)&&"sphere"===n.opts.ions){let i=l.parasCls.vdwRadii[s.elem.toUpperCase()];if(Math.abs(s.coord.x-e.x)-i>t)continue;if(Math.abs(s.coord.y-e.y)-i>t)continue;if(Math.abs(s.coord.z-e.z)-i>t)continue}else{if(s.coord.xe.x+t)continue;if(s.coord.ye.y+t)continue;if(s.coord.ze.z+t)continue}return s}return null}}class Hs{constructor(e){this.icn3d=e}setControl(){let e=this.icn3d,t=e.icn3dui;if(t.bNode)return;let s=this;e.WIDTH=e.container.width(),e.HEIGHT=e.container.height(),e.applyCenterCls.setWidthHeight(e.WIDTH,e.HEIGHT),e._zoomFactor=1,e.mouseChange=new THREE.Vector2(0,0),e.quaternion=new THREE.Quaternion(0,0,0,1),e.container.bind("contextmenu",(function(e){e.preventDefault()})),e.typetext=!1,$(document).bind("keyup",(function(t){16===t.keyCode&&(e.bShift=!1),17!==t.keyCode&&224!==t.keyCode&&91!==t.keyCode||(e.bCtrl=!1)})),$("input[type=text], textarea").focus((function(){e.typetext=!0})),$("input[type=text], textarea").blur((function(){e.typetext=!1})),$(document).bind("keydown",(async function(s){if((s.shiftKey||16===s.keyCode)&&(e.bShift=!0),(s.ctrlKey||17===s.keyCode||224===s.keyCode||91===s.keyCode)&&(e.bCtrl=!0),!e.bControlGl&&!e.controls||e.bControlGl&&!window.controls)return;e.bStopRotate=!0;let i=e.bShift?90:5;if(!e.typetext)if(90===s.keyCode){let s={};e.bControlGl&&!t.bNode?window.cam===e.perspectiveCamera?s._zoomFactor=.9:window.cam===e.orthographicCamera&&(e._zoomFactor<.1?e._zoomFactor=.1:e._zoomFactor>1&&(e._zoomFactor=1),s._zoomFactor=.8*e._zoomFactor,s._zoomFactor<.1&&(s._zoomFactor=.1)):e.cam===e.perspectiveCamera?s._zoomFactor=.9:e.cam===e.orthographicCamera&&(e._zoomFactor<.1?e._zoomFactor=.1:e._zoomFactor>1&&(e._zoomFactor=1),s._zoomFactor=.8*e._zoomFactor,s._zoomFactor<.1&&(s._zoomFactor=.1)),s.update=!0,e.bControlGl&&!t.bNode?window.controls.update(s):e.controls.update(s),e.bRender&&e.drawCls.render()}else if(88===s.keyCode){let s={};e.bControlGl&&!t.bNode?window.cam===e.perspectiveCamera?s._zoomFactor=1.03:window.cam===e.orthographicCamera&&(e._zoomFactor>10?e._zoomFactor=10:e._zoomFactor<1&&(e._zoomFactor=1),s._zoomFactor=1.01*e._zoomFactor,s._zoomFactor>10&&(s._zoomFactor=10)):e.cam===e.perspectiveCamera?s._zoomFactor=1.03:e.cam===e.orthographicCamera&&(e._zoomFactor>10?e._zoomFactor=10:e._zoomFactor<1&&(e._zoomFactor=1),s._zoomFactor=1.01*e._zoomFactor,s._zoomFactor>10&&(s._zoomFactor=10)),s.update=!0,e.bControlGl&&!t.bNode?window.controls.update(s):e.controls.update(s),e.bRender&&e.drawCls.render()}else if(76===s.keyCode){let t=new THREE.Vector3(0,1,0),s=-i/180*Math.PI;e.transformCls.setRotation(t,s)}else if(74===s.keyCode){let t=new THREE.Vector3(0,1,0),s=i/180*Math.PI;e.transformCls.setRotation(t,s)}else if(73===s.keyCode){let t=new THREE.Vector3(1,0,0),s=-i/180*Math.PI;e.transformCls.setRotation(t,s)}else if(77===s.keyCode){let t=new THREE.Vector3(1,0,0),s=i/180*Math.PI;e.transformCls.setRotation(t,s)}else 65===s.keyCode&&Object.keys(e.structures).length>1&&await e.alternateCls.alternateWrapper()})),e.container.bind("mouseup",(function(t){e.isDragging=!1})),e.container.bind("touchend",(function(t){e.isDragging=!1})),e.container.bind("mousedown",(function(s){if(e.isDragging=!0,e.scene){if(e.bStopRotate=!0,e.pk&&(s.altKey||s.ctrlKey||s.shiftKey||18===s.keyCode||16===s.keyCode||17===s.keyCode||224===s.keyCode||91===s.keyCode)){e.highlightlevel=e.pk;let t=!0;e.rayCls.rayCaster(s,t)}e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render()}})),e.container.bind("touchstart",(function(s){if(s.preventDefault(),e.isDragging=!0,!e.scene)return;e.bStopRotate=!0,$("#"+e.pre+"popup").hide();e.rayCls.rayCaster(s,!0),e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render()})),e.container.bind("mousemove touchmove",(function(e){s.mouseMove(e)})),e.container.bind("mousewheel",(function(s){s.preventDefault(),e.scene&&(e.bStopRotate=!0,e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render())})),e.container.bind("DOMMouseScroll",(function(s){s.preventDefault(),e.scene&&(e.bStopRotate=!0,e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render())}))}mouseMove(e){let t=this.icn3d,s=t.icn3dui;if(s.bNode)return;if(e.preventDefault(),!t.scene)return;$("#"+t.pre+"popup").hide();if(t.rayCls.rayCaster(e,!1),t.bControlGl&&!s.bNode){window.controls.handleResize(),window.controls.update();for(let e in window.icn3duiHash){let t=window.icn3duiHash[e].icn3d;t.bRender&&t.drawCls.render()}}else t.controls.handleResize(),t.controls.update(),t.bRender&&t.drawCls.render()}}class Ls{constructor(e){this.icn3d=e}showPicking(e,t,s){let i=this.icn3d,n=i.icn3dui;if(void 0!==n.cfg.cid&&0!=i.pk&&(i.pk=1),i.highlightlevel=i.pk,this.showPickingBase(e,t,s),0!=i.pk)if(void 0!==t&&void 0!==s){null!=n.cfg.showmenu&&1==n.cfg.showmenu&&(s+=n.htmlCls.MENU_HEIGHT);let l,r=1==i.pk?e.resn+e.resi+"@"+e.name:e.resn+e.resi,o=e.structure+"_"+e.chain;if(void 0!==i.structures&&Object.keys(i.structures).length>1?(r=o+" "+r,l=i.chainid2refpdbname&&i.chainid2refpdbname[o]?240:160,$("#"+i.pre+"popup").css("width",l+"px")):(l=i.chainid2refpdbname&&i.chainid2refpdbname[o]?160:80,$("#"+i.pre+"popup").css("width",l+"px")),i.chainid2refpdbname&&i.chainid2refpdbname[o]){let t=i.resid2refnum[o+"_"+e.resi];t&&(r+=", Ig: "+t)}$("#"+i.pre+"popup").html(r),$("#"+i.pre+"popup").css("top",s).css("left",t+20).show()}else{i.hlUpdateCls.updateHlAll();let t={};t.factor=i._zoomFactor,t.mouseChange=i.mouseChange,t.quaternion={},t.quaternion._x=parseFloat(i.quaternion._x).toPrecision(5),t.quaternion._y=parseFloat(i.quaternion._y).toPrecision(5),t.quaternion._z=parseFloat(i.quaternion._z).toPrecision(5),t.quaternion._w=parseFloat(i.quaternion._w).toPrecision(5),n.htmlCls.clickMenuCls.setLogCmd("pickatom "+e.serial,!0),i.selectionCls.saveSelInCommand(),i.bSphereCalc=!1,i.bHbondCalc=!1}}showPickingBase(e,t,s){this.icn3d.icn3dui,void 0===t&&void 0===s&&this.showPickingHilight(e)}getPickedAtomList(e,t){let s=this.icn3d;s.icn3dui;let i={};if(1===e)i[t.serial]=1;else if(2===e){let e=t.structure+"_"+t.chain+"_"+t.resi;i=s.residues[e]}else if(3===e)i=this.selectStrandHelixFromAtom(t);else if(4===e)i=this.select3ddomainFromAtom(t);else if(5===e){let e=t.structure+"_"+t.chain;i=s.chains[e]}return i}showPickingHilight(e){let t=this.icn3d,s=t.icn3dui;t.bShift||t.bCtrl||t.hlObjectsCls.removeHlObjects(),t.pickedAtomList=this.getPickedAtomList(t.pk,e),0===t.pk?t.bShowHighlight=!1:t.bShowHighlight=!0;let i=Object.keys(t.hAtoms).length==Object.keys(t.atoms).length?{}:s.hashUtilsCls.intHash(t.hAtoms,t.pickedAtomList),n=Object.keys(i).length;if(t.bShift||t.bCtrl)if(t.bShift){if(void 0===t.prevPickedAtomList)t.hAtoms=s.hashUtilsCls.unionHash(t.hAtoms,t.pickedAtomList);else{let e=t.firstAtomObjCls.getFirstAtomObj(t.prevPickedAtomList),i=t.firstAtomObjCls.getFirstAtomObj(t.pickedAtomList);if(e.structure+"_"+e.chain!=i.structure+"_"+i.chain)t.hAtoms=s.hashUtilsCls.unionHash(t.hAtoms,t.pickedAtomList);else{let e;e=s.hashUtilsCls.unionHash(e,t.prevPickedAtomList),e=s.hashUtilsCls.unionHash(e,t.pickedAtomList);let i=t.firstAtomObjCls.getFirstAtomObj(e),n=t.firstAtomObjCls.getLastAtomObj(e);for(let e=i.serial;e<=n.serial;++e)t.hAtoms[e]=1}}t.prevPickedAtomList=s.hashUtilsCls.cloneHash(t.pickedAtomList)}else t.bCtrl&&(t.hAtoms=n>0?s.hashUtilsCls.exclHash(t.hAtoms,t.pickedAtomList):s.hashUtilsCls.unionHash(t.hAtoms,t.pickedAtomList));else t.hAtoms=s.hashUtilsCls.cloneHash(t.pickedAtomList);t.hlObjectsCls.removeHlObjects(),t.hlObjectsCls.addHlObjects()}select3ddomainFromAtom(e){let t,s=this.icn3d,i=s.icn3dui,n=e.structure+"_"+e.chain,l=n+"_"+e.resi;for(let e in s.tddomains){let i=e.indexOf("_3d_domain");if(e.substr(0,i)==n&&-1!==Object.keys(s.tddomains[e]).indexOf(l)){t=e;break}}let r={};for(let e in s.tddomains[t])r=i.hashUtilsCls.unionHash(r,s.residues[e]);return r}selectStrandHelixFromAtom(e){let t=this.icn3d,s=t.icn3dui,i=e,n=e,l={},r=i.resi;if(!i.ssbegin&&!isNaN(i.resi)){for(let e=i.resi-1;e>0;--e){let s=i.structure+"_"+i.chain+"_"+e;if(!t.residues.hasOwnProperty(s))break;let n=t.firstAtomObjCls.getFirstCalphaAtomObj(t.residues[s]);if(r=n.resi,"coil"!==i.ss&&n.ss===i.ss&&n.ssbegin||"coil"===i.ss&&n.ss!==i.ss){"coil"===i.ss&&n.ss!==i.ss&&(r=parseInt(n.resi)+1);break}}for(let e=r;e<=i.resi;++e){let n=i.structure+"_"+i.chain+"_"+e;l=s.hashUtilsCls.unionHash(l,s.hashUtilsCls.hash2Atoms(t.residues[n],t.atoms))}}let o=n.resi,a=t.firstAtomObjCls.getLastAtomObj(t.chains[n.structure+"_"+n.chain]).resi;for(let e=parseInt(n.resi)+1;e<=parseInt(a);++e){let s=n.structure+"_"+n.chain+"_"+e;if(!t.residues.hasOwnProperty(s))break;let i=t.firstAtomObjCls.getFirstCalphaAtomObj(t.residues[s]);if(o=i.resi,"coil"!==n.ss&&i.ss===n.ss&&i.ssend||"coil"===n.ss&&i.ss!==n.ss){"coil"!==n.ss||i.ss===n.ss||isNaN(i.resi)||(o=i.resi-1);break}}for(let e=parseInt(n.resi)+1;e<=parseInt(o);++e){let i=n.structure+"_"+n.chain+"_"+e;l=s.hashUtilsCls.unionHash(l,s.hashUtilsCls.hash2Atoms(t.residues[i],t.atoms))}return l}}class Ns{constructor(e){this.icn3d=e,this.xrSessionIsGranted=!1}createButton(e,t){let s=this.icn3d,i=s.icn3dui;t&&console.error('THREE.VRButton: The "options" parameter has been removed. Please set the reference space type via renderer.xr.setReferenceSpaceType() instead.');const n=document.createElement("button");function l(){n.style.display="",n.style.cursor="auto",n.style.left="calc(33% - 75px)",n.style.width="150px",n.onmouseenter=null,n.onmouseleave=null,n.onclick=null}let r=this;if("xr"in navigator)return n.id=i.pre+"VRButton",n.style.display="none",(o=n).style.position="absolute",o.style.bottom="20px",o.style.padding="12px 6px",o.style.border="1px solid #fff",o.style.borderRadius="4px",o.style.background="#000",o.style.color="#f8b84e",o.style.font="bold 13px sans-serif",o.style.textAlign="center",o.style.opacity="0.8",o.style.outline="none",o.style.zIndex="999",navigator.xr.isSessionSupported("immersive-vr").then((function(t){t?function(){let t=null;async function i(s){s.addEventListener("end",l),await e.xr.setSession(s),n.textContent="EXIT VR",t=s}function l(){s.transformCls.resetOrientation(),s.bVr=!1,s.drawCls.draw(),t.removeEventListener("end",l),n.textContent="ENTER VR",t=null}n.style.display="",n.style.cursor="pointer",n.style.left="calc(33% - 50px)",n.style.width="100px",n.textContent="ENTER VR",n.onmouseenter=function(){n.style.opacity="1.0"},n.onmouseleave=function(){n.style.opacity="0.8"},n.onclick=function(){if(s.bImpo=!1,s.bVr=!0,s.drawCls.draw(s.bVr),null===t){const e={optionalFeatures:["local-floor","bounded-floor","hand-tracking","layers"]};navigator.xr.requestSession("immersive-vr",e).then(i)}else t.end()}}():(l(),n.style.display="none"),t&&r.xrSessionIsGranted&&n.click()})).catch((function(e){l(),console.warn("Exception when trying to call xr.isSessionSupported",e),n.style.display="none"})),n;return document.createElement("span");var o}registerSessionGrantedListener(){"xr"in navigator&&navigator.xr.addEventListener("sessiongranted",(()=>{this.xrSessionIsGranted=!0}))}}class qs{constructor(e){this.icn3d=e,this.xrSessionIsGranted=!1}createButton(e,t={}){let s=this.icn3d,i=s.icn3dui;const n=document.createElement("button");function l(){n.style.display="",n.style.cursor="auto",n.style.left="calc(66% - 50px)",n.style.width="150px",n.onmouseenter=null,n.onmouseleave=null,n.onclick=null}function r(e){e.style.position="absolute",e.style.bottom="20px",e.style.padding="12px 6px",e.style.border="1px solid #fff",e.style.borderRadius="4px",e.style.background="#000",e.style.color="#f8b84e",e.style.font="bold 13px sans-serif",e.style.textAlign="center",e.style.opacity="0.8",e.style.outline="none",e.style.zIndex="999"}if(i.utilsCls.isAndroid()&&i.utilsCls.isChrome()){if("xr"in navigator)return n.id=i.pre+"ARButton",n.style.display="none",r(n),navigator.xr.isSessionSupported("immersive-ar").then((function(i){i?function(){if(void 0===t.domOverlay){const e=document.createElement("div");e.style.display="none",document.body.appendChild(e);const s=document.createElementNS("http://www.w3.org/2000/svg","svg");s.setAttribute("width",38),s.setAttribute("height",38),s.style.position="absolute",s.style.right="20px",s.style.top="20px",s.addEventListener("click",(function(){i.end()})),e.appendChild(s);const n=document.createElementNS("http://www.w3.org/2000/svg","path");n.setAttribute("d","M 12,12 L 28,28 M 28,12 12,28"),n.setAttribute("stroke","#fff"),n.setAttribute("stroke-width",2),s.appendChild(n),void 0===t.optionalFeatures&&(t.optionalFeatures=[]),t.optionalFeatures.push("dom-overlay"),t.domOverlay={root:e}}let i=null;async function l(s){s.addEventListener("end",r),e.xr.setReferenceSpaceType("local"),await e.xr.setSession(s),n.textContent="STOP AR",t.domOverlay.root.style.display="",i=s}function r(){s.transformCls.resetOrientation(),s.bAr=!1,s.drawCls.draw(),i.removeEventListener("end",r),n.textContent="START AR",t.domOverlay.root.style.display="none",i=null}n.style.display="",n.style.cursor="pointer",n.style.left="calc(66% - 50px)",n.style.width="100px",n.textContent="START AR",n.onmouseenter=function(){n.style.opacity="1.0"},n.onmouseleave=function(){n.style.opacity="0.8"},n.onclick=function(){s.bImpo=!1,s.opts.background="transparent",s.bAr=!0,s.drawCls.draw(s.bAr),null===i?navigator.xr.requestSession("immersive-ar",t).then(l):i.end()}}():(l(),n.style.display="none")})).catch((function(e){l(),console.warn("Exception when trying to call xr.isSessionSupported",e),n.style.display="none"})),n;return document.createElement("span")}return n.id=i.pre+"ARButton",n.style.display="none",r(n),l(),n.style.display="none",n}}class Us{constructor(e){let t,s,i,n=e;if(this.icn3dui=e,this.id=this.icn3dui.pre+"canvas",this.pre=this.icn3dui.pre,this.container=$("#"+this.id),this.oriContainer=$("#"+this.id),this.bControlGl=!1,this.maxatomcnt=1e5,this.overdraw=0,this.bDrawn=!1,this.bOpm=!1,this.crossstrucinter=0,this.bSecondaryStructure=!1,this.bHighlight=1,this.renderOrderPicking=-1,this.bInitial=!0,this.bDoublecolor=!1,this.originSize=1,this.ALTERNATE_STRUCTURE=-1,this.bUsePdbNum=!0,!this.icn3dui.bNode){let e=document.createElement("canvas");t=!(!window.WebGLRenderingContext||!e.getContext("webgl")&&!e.getContext("experimental-webgl")),e.remove(),e=document.createElement("canvas"),s=!(!window.WebGLRenderingContext||!e.getContext("webgl2")),e.remove(),i="xr"in navigator,t?(s&&i?(this.renderer=new THREE.WebGLRenderer({canvas:this.oriContainer.get(0),antialias:!0,preserveDrawingBuffer:!0,sortObjects:!1,alpha:!0}),this.renderer.xr.enabled=!0):this.renderer=new THREE.WebGL1Renderer({canvas:this.oriContainer.get(0),antialias:!0,preserveDrawingBuffer:!0,sortObjects:!1,alpha:!0}),this.overdraw=0):alert("Currently your web browser has a problem on WebGL. If you are using Chrome, open a new tab for the same URL and WebGL may work again.")}this.frac=new THREE.Color(.1,.1,.1),this.shininess=40,this.emissive=1118481,this.light1=.8,this.light2=.4,this.light3=.2,this.lineRadius=.1,this.coilWidth=.3,this.cylinderRadius=.4,this.crosslinkRadius=.4,this.traceRadius=.4,this.dotSphereScale=.3,this.sphereRadius=1.5,this.cylinderHelixRadius=1.6,this.ribbonthickness=.2,this.helixSheetWidth=1.3,this.nucleicAcidWidth=.8,this.scaleFactor=1,this.labelScale=1,this.resizeRatioX=1,this.resizeRatioY=1,this.bImpo=!0,this.bInstanced=!0,this.chainMissingResidueArray={},this._zoomFactor=1,this.transparentRenderOrder=!1,this.AFUniprotVersion="v4",this.defaultPdbId="stru",this.icn3dui.bNode||(s&&i?(this.bExtFragDepth=!0,this.bImpo=!0,this.bInstanced=!0):(this.bExtFragDepth=this.renderer.extensions.get("EXT_frag_depth"),this.bExtFragDepth?console.log("EXT_frag_depth is supported. All spheres and cylinders are drawn using shaders."):(this.bImpo=!1,console.log("EXT_frag_depth is NOT supported. All spheres and cylinders are drawn using geometry.")),this.bInstanced=this.renderer.extensions.get("ANGLE_instanced_arrays"),this.bInstanced?console.log("ANGLE_instanced_arrays is supported. Assembly is drawn with one copy of the asymmetric unit using hardware instancing."):console.log("ANGLE_instanced_arrays is NOT supported. Assembly is drawn by making copies of the asymmetric unit."))),this.posArray=new Array,this.colorArray=new Array,this.pos2Array=new Array,this.color2Array=new Array,this.radiusArray=new Array,this.posArraySphere=new Array,this.colorArraySphere=new Array,this.radiusArraySphere=new Array,this.axis=!1,this.pk=1,this.highlightlevel=1,this.pickpair=!1,this.pAtomNum=0,this.pAtom=void 0,this.pAtom2=void 0,this.bCtrl=!1,this.bShift=!1,this.bStopRotate=!1,this.bCalphaOnly=!1,this.bConsiderNeighbors=!1,this.bShowCrossResidueBond=!0,this.bExtrude=!0,this.effects={none:this.renderer},this.maxD=500,this.oriMaxD=this.maxD,this.cam_z=2*this.maxD,this.commands=[],this.optsHistory=[],this.logs=[],this.bRender=!0,this.hColor=new THREE.Color(16777011),this.sphereGeometry=new THREE.SphereGeometry(1,32,32),this.boxGeometry=new THREE.BoxGeometry(1,1,1),this.cylinderGeometry=new THREE.CylinderGeometry(1,1,1,32,1),this.cylinderGeometryOutline=new THREE.CylinderGeometry(1,1,1,32,1,!0),this.axisDIV=15,this.strandDIV=6,this.tubeDIV=8,this.nucleicAcidStrandDIV=6,this.linewidth=1,this.hlLineRadius=.1,this.threshbox=180,this.maxAtoms3DMultiFile=4e4,this.tsHbond=3.8,this.tsIonic=6,this.tsContact=4,this.tsHalogen=3.8,this.tsPication=6,this.tsPistacking=5.5,this.LABELSIZE=30,this.rayThreshold=.5,this.colorBlackbkgd="#ffff00",this.colorWhitebkgd="#000000",this.optsOri={},this.optsOri.camera="perspective",this.optsOri.background="black",this.optsOri.color="chain",this.optsOri.proteins="ribbon",this.optsOri.sidec="nothing",this.optsOri.nucleotides="nucleotide cartoon",this.optsOri.ntbase="nothing",this.optsOri.surface="nothing",this.optsOri.opacity="1.0",this.optsOri.wireframe="no",this.optsOri.map="nothing",this.optsOri.mapwireframe="yes",this.optsOri.emmap="nothing",this.optsOri.emmapwireframe="yes",this.optsOri.phimap="nothing",this.optsOri.phimapwireframe="yes",this.optsOri.phisurface="nothing",this.optsOri.phisurftype="nothing",this.optsOri.phisurfop="1.0",this.optsOri.phisurfwf="yes",this.optsOri.chemicals="stick",this.optsOri.water="nothing",this.optsOri.ions="sphere",this.optsOri.hbonds="no",this.optsOri.saltbridge="no",this.optsOri.contact="no",this.optsOri.halogen="no",this.optsOri["pi-cation"]="no",this.optsOri["pi-stacking"]="no",this.optsOri.ssbonds="yes",this.optsOri.clbonds="yes",this.optsOri.rotationcenter="molecule center",this.optsOri.axis="no",this.optsOri.fog="no",this.optsOri.slab="no",this.optsOri.pk="residue",this.optsOri.chemicalbinding="hide",this.opts=n.hashUtilsCls.cloneHash(this.optsOri),this.sheetcolor="green",this.bShowHighlight=!0,this.mapData={},this.bFullUi=!0,this.divid=this.icn3dui.cfg.divid,this.inputid="",this.setOperation="or",this.ROT_DIR="right",this.currSelectedSets=[],this.selectedResidues={},this.ncbi2resid={},this.resid2ncbi={},this.shapeCmdHash={},this.bHideSelection=!0,this.bSelectResidue=!1,this.bSelectAlignResidue=!1,this.bAnnoShown=!1,this.bSetChainsAdvancedMenu=!1,this.b2DShown=!1,this.bCrashed=!1,this.bAddCommands=!0,this.bAddLogs=!0,this.bNotLoadStructure=!1,this.InputfileData="",this.bVr=!1,this.bAr=!1,this.startColor="blue",this.midColor="white",this.endColor="red",this.startValue=0,this.midValue=50,this.endValue=100,this.crosslinkRadius=.4,this.sceneCls=new Ie(this),this.cameraCls=new Ee(this),this.fogCls=new Te(this),this.boxCls=new De(this),this.brickCls=new Pe(this),this.curveStripArrowCls=new Me(this),this.curveCls=new Fe(this),this.cylinderCls=new He(this),this.lineCls=new Le(this),this.reprSubCls=new Ne(this),this.sphereCls=new qe(this),this.stickCls=new Ue(this),this.strandCls=new Be(this),this.stripCls=new $e(this),this.tubeCls=new je(this),this.cartoonNuclCls=new ze(this),this.surfaceCls=new Ze(this),this.labelCls=new Ve(this),this.axesCls=new We(this),this.glycanCls=new Ye(this),this.applyCenterCls=new Qe(this),this.applyClbondsCls=new et(this),this.applyMissingResCls=new tt(this),this.applyDisplayCls=new st(this),this.applyMapCls=new rt(this),this.applyOtherCls=new it(this),this.applySsbondsCls=new nt(this),this.applySymdCls=new lt(this),this.hlObjectsCls=new Ht(this),this.residueLabelsCls=new ot(this),this.alternateCls=new ct(this),this.drawCls=new ht(this),this.firstAtomObjCls=new ys(this),this.impostorCls=new at(this),this.instancingCls=new dt(this),this.contactCls=new pt(this),this.hBondCls=new mt(this),this.piHalogenCls=new ut(this),this.saltbridgeCls=new gt(this),this.loadPDBCls=new ds(this),this.loadCIFCls=new cs(this),this.vastplusCls=new hs(this),this.transformCls=new Es(this),this.setStyleCls=new ft(this),this.setColorCls=new Ct(this),this.threeDPrintCls=new Ps(this),this.export3DCls=new Ms(this),this.annoCddSiteCls=new vt(this),this.annoContactCls=new _t(this),this.annoPTMCls=new wt(this),this.annoIgCls=new St(this),this.annoCrossLinkCls=new At(this),this.annoDomainCls=new xt(this),this.annoSnpClinVarCls=new kt(this),this.annoSsbondCls=new Ot(this),this.annoTransMemCls=new Rt(this),this.domain3dCls=new It(this),this.addTrackCls=new Et(this),this.annotationCls=new Tt(this),this.showAnnoCls=new Dt(this),this.showSeqCls=new Pt(this),this.hlSeqCls=new Mt(this),this.hlUpdateCls=new Ft(this),this.lineGraphCls=new Lt(this),this.getGraphCls=new Nt(this),this.showInterCls=new qt(this),this.viewInterPairsCls=new Ut(this),this.drawGraphCls=new Bt(this),this.contactMapCls=new $t(this),this.alignParserCls=new jt(this),this.chainalignParserCls=new zt(this),this.dsn6ParserCls=new Gt(this),this.ccp4ParserCls=new Vt(this),this.mtzParserCls=new Xt(this),this.mmcifParserCls=new Kt(this),this.mmdbParserCls=new Jt(this),this.bcifParserCls=new Zt(this),this.mol2ParserCls=new Qt(this),this.opmParserCls=new es(this),this.pdbParserCls=new ts(this),this.sdfParserCls=new ss(this),this.xyzParserCls=new is(this),this.realignParserCls=new ns(this),this.densityCifParserCls=new ls(this),this.ParserUtilsCls=new rs(this),this.loadAtomDataCls=new os(this),this.setSeqAlignCls=new as(this),this.applyCommandCls=new ps(this),this.definedSetsCls=new ms(this),this.selectCollectionsCls=new us(this),this.legendTableCls=new yt(this),this.loadScriptCls=new gs(this),this.selByCommCls=new fs(this),this.selectionCls=new Cs(this),this.resid2specCls=new bs(this),this.delphiCls=new vs(this),this.dsspCls=new _s(this),this.refnumCls=new ws(this),this.scapCls=new Ss(this),this.symdCls=new As(this),this.alignSWCls=new xs(this),this.analysisCls=new ks(this),this.resizeCanvasCls=new Is(this),this.saveFileCls=new Ts(this),this.setOptionCls=new bt(this),this.shareLinkCls=new Ds(this),this.diagram2dCls=new Os(this),this.cartoon2dCls=new Rs(this),this.rayCls=new Fs(this),this.controlCls=new Hs(this),this.pickingCls=new Ls(this),this.VRButtonCls=new Ns(this),this.ARButtonCls=new qs(this),this.matShader=this.setColorCls.setOutlineColor("yellow")}}Us.prototype.init=function(e){this.init_base(),this.molTitle="",this.ssbondpnts={},this.clbondpnts={},this.biomtMatrices=[],this.bAssembly=!0,this.bDrawn=!1,this.bSecondaryStructure=!1,this.bHighlight=1,this.axes=[]},Us.prototype.init_base=function(e){this.resetConfig(),this.structures={},this.chains={},this.tddomains={},this.residues={},this.secondaries={},this.alnChains={},this.chainsSeq={},this.chainsColor={},this.chainsGene={},this.chainsAn={},this.chainsAnTitle={},this.chainsMapping={},this.resid2refnum={},this.residIgLoop={},this.refnum2residArray={},this.bShowRefnum=!1,this.alnChainsSeq={},this.alnChainsAnno={},this.alnChainsAnTtl={},this.pickedAtomList={},this.prevHighlightObjects=[],this.prevHighlightObjects_ghost=[],this.prevSurfaces=[],this.prevMaps=[],this.prevEmmaps=[],this.prevPhimaps=[],this.prevOtherMesh=[],this.defNames2Residues={},this.defNames2Atoms={},this.defNames2Descr={},this.defNames2Command={},this.residueId2Name={},this.atoms={},this.dAtoms={},this.hAtoms={},this.proteins={},this.sidec={},this.ntbase={},this.nucleotides={},this.nucleotidesO3={},this.chemicals={},this.ions={},this.water={},this.calphas={},this.hbondpnts=[],this.saltbridgepnts=[],this.contactpnts=[],this.stabilizerpnts=[],this.halogenpnts=[],this.picationpnts=[],this.pistackingpnts=[],this.distPnts=[],this.doublebonds={},this.triplebonds={},this.aromaticbonds={},this.atomPrevColors={},this.style2atoms={},this.labels={},this.lines={},this.resids2inter={},this.resids2interAll={},this.transformCls.rotateCount=0,this.transformCls.rotateCountMax=20,e&&(this.commands=[]),this.axes=[],this.bGlycansCartoon=0,this.bMembrane=1,this.bCmdWindow=0,this.chainMissingResidueArray={},this.nTotalGap=0},Us.prototype.reinitAfterLoad=function(){let e=this,t=e.icn3dui;e.resetConfig(),e.setStyleCls.setAtomStyleByOptions(),e.setColorCls.setColorByOptions(e.opts,e.atoms),e.dAtoms=t.hashUtilsCls.cloneHash(e.atoms),e.hAtoms=t.hashUtilsCls.cloneHash(e.atoms),e.prevHighlightObjects=[],e.prevHighlightObjects_ghost=[],e.prevSurfaces=[],e.prevMaps=[],e.prevEmmaps=[],e.prevPhimaps=[],e.prevOtherMesh=[],e.labels={},e.lines={},e.shapeCmdHash={},e.bAssembly=!0},Us.prototype.resetConfig=function(){let e=this,t=e.icn3dui;if(this.opts=t.hashUtilsCls.cloneHash(this.optsOri),void 0===t.cfg.align&&void 0===t.cfg.chainalign||(this.opts.color="identity",this.opts.proteins="c alpha trace",this.opts.nucleotides="o3 trace"),void 0!==t.cfg.cid&&(this.opts.color="atom",this.opts.pk="atom",this.opts.chemicals="ball and stick"),(void 0!==t.cfg.afid||e.bEsmfold)&&(this.opts.color="confidence"),void 0!==t.cfg.blast_rep_id&&(this.opts.color="conservation"),void 0!==t.cfg.mmdbafid){let s=t.cfg.mmdbafid.split(",");if(s.length>1)e.opts.color="structure";else if(1==s.length){let t=s[0];isNaN(t)&&t.length>5?this.opts.color="confidence":e.opts.color="chain"}}void 0!==t.cfg.options&&$.extend(this.opts,t.cfg.options)};class Bs{constructor(e){this.cfg=e,this.pre=this.cfg.divid+"_",this.REVISION="3.33.1",this.bNode=Object.keys(window).length<2,void 0===this.cfg.command&&(this.cfg.command=""),void 0===this.cfg.width&&(this.cfg.width="100%"),void 0===this.cfg.height&&(this.cfg.height="100%"),void 0===this.cfg.resize&&(this.cfg.resize=!0),void 0===this.cfg.showmenu&&(this.cfg.showmenu=!0),void 0===this.cfg.showtitle&&(this.cfg.showtitle=!0),void 0===this.cfg.showcommand&&(this.cfg.showcommand=!0),void 0===this.cfg.mobilemenu&&(this.cfg.mobilemenu=!1),void 0===this.cfg.imageonly&&(this.cfg.imageonly=!1),void 0===this.cfg.closepopup&&(this.cfg.closepopup=!1),void 0===this.cfg.showanno&&(this.cfg.showanno=!1),void 0===this.cfg.showseq&&(this.cfg.showseq=!1),void 0===this.cfg.showalignseq&&(this.cfg.showalignseq=!1),void 0===this.cfg.show2d&&(this.cfg.show2d=!1),void 0===this.cfg.showsets&&(this.cfg.showsets=!1),void 0===this.cfg.rotate&&(this.cfg.rotate="right"),void 0===this.cfg.hidelicense&&(this.cfg.hidelicense=!1),this.hashUtilsCls=new t(this),this.utilsCls=new s(this),this.parasCls=new i(this),this.myEventCls=new n(this),this.rmsdSuprCls=new l(this),this.subdivideCls=new r(this),this.convertTypeCls=new o(this),this.htmlCls=new g(this)}allCustomEvents(){}}Bs.prototype.show3DStructure=async function(e){let t=this;t.cfg.menuicon?(t.htmlCls.wifiStr=' ',t.htmlCls.licenseStr=' '):(t.htmlCls.wifiStr="",t.htmlCls.licenseStr=""),t.setIcn3d();let s=t.icn3d;t.utilsCls.isSessionStorageSupported()&&s.setStyleCls.getCommandsBeforeCrash();let i=t.htmlCls.WIDTH,n=t.htmlCls.HEIGHT;t.oriWidth=i,t.oriHeight=n,t.htmlCls.eventsCls.allEventFunctions(),this.allCustomEvents();let l=0;if((null==t.cfg.showmenu||t.cfg.showmenu)&&(l+=t.htmlCls.MENU_HEIGHT),(null==t.cfg.showcommand||t.cfg.showcommand)&&(l+=t.htmlCls.CMD_HEIGHT),null!=t.cfg.showmenu&&0==t.cfg.showmenu?t.htmlCls.setMenuCls.hideMenu():t.htmlCls.setMenuCls.showMenu(),null!=t.cfg.showtitle&&0==t.cfg.showtitle?$("#"+s.pre+"title").hide():$("#"+s.pre+"title").show(),$("#"+s.pre+"viewer").width(i).height(parseInt(n)+l),$("#"+s.pre+"canvas").width(i).height(parseInt(n)),$("#"+s.pre+"canvas").resizable({resize:function(e,i){t.htmlCls.WIDTH=i.size.width,t.htmlCls.HEIGHT=i.size.height,void 0===s||t.icn3d.bFullscreen||s.resizeCanvasCls.resizeCanvas(t.htmlCls.WIDTH,t.htmlCls.HEIGHT,!0)}}),void 0!==t.cfg.usepdbnum?t.icn3d.bUsePdbNum=t.cfg.usepdbnum:void 0!==t.cfg.date?t.icn3d.bUsePdbNum=parseInt(t.cfg.date)>=20201222:"1tup"==t.cfg.mmdbid&&1==t.cfg.showanno&&1==t.cfg.show2d&&1==t.cfg.showsets||"118496"==t.cfg.mmdbid&&0==t.cfg.showanno&&-1!=t.cfg.inpara.indexOf("bu=1")||"163605,1,91105,1,1,1"==t.cfg.align&&-1!=t.cfg.inpara.indexOf("atype=1")?t.icn3d.bUsePdbNum=!1:t.icn3d.bUsePdbNum=!0,t.cfg.replay?(s.bReplay=1,$("#"+s.pre+"replay").show()):(s.bReplay=0,$("#"+s.pre+"replay").hide()),t.utilsCls.isMobile()&&(s.threshbox=60),t.cfg.controlGl&&(s.bControlGl=!0,s.container=s.bControlGl&&!t.bNode?$(document):$("#"+s.id)),s.setStyleCls.handleContextLost(),s.applyCenterCls.setWidthHeight(i,n),s.ori_chemicalbinding=s.opts.chemicalbinding,void 0!==t.cfg.bCalphaOnly&&(s.bCalphaOnly=t.cfg.bCalphaOnly),s.opts=t.hashUtilsCls.cloneHash(s.opts),s.STATENUMBER=s.commands.length,t.utilsCls.isSessionStorageSupported()&&s.bCrashed){s.bCrashed=!1;let e=s.commandsBeforeCrash.split("|||")[0],i=e.substr(e.lastIndexOf(" ")+1);if(i===t.cfg.bcifid||i===t.cfg.mmtfid||i===t.cfg.pdbid||i===t.cfg.opmid||i===t.cfg.mmdbid||i===t.cfg.gi||i===t.cfg.blast_rep_id||i===t.cfg.cid||i===t.cfg.mmcifid||i===t.cfg.align||i===t.cfg.chainalign||i===t.cfg.mmdbafid)return void await s.loadScriptCls.loadScript(s.commandsBeforeCrash,!0)}if(s.molTitle="",s.loadCmd,t.htmlCls.clickMenuCls.getHiddenMenusFromCache(),t.htmlCls.clickMenuCls.applyShownMenus(),e){if(s.init(),s.bInputfile=!0,s.InputfileType="pdb",s.InputfileData=s.InputfileData?s.InputfileData+"\nENDMDL\n"+e:e,await s.pdbParserCls.loadPdbData(e),void 0!==t.cfg.resdef&&void 0!==t.cfg.chains){let e=Object.keys(s.structures),i=t.cfg.chains.split(" | "),n=[];if(e.length==i.length){for(let t=0,s=e.length;t0&&(l+=","),l+=n[e].substr(0,n[e].indexOf("_"));s.chainidArray=[e].concat(n),s.chainidArray=s.chainalignParserCls.addPostfixForChainids(s.chainidArray),t.htmlCls.clickMenuCls.setLogCmd("resdef "+t.cfg.resdef,!0),s.loadCmd="vast_search_chainid "+s.chainidArray,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),s.bMmdbafid=!0;let r=!0;await s.chainalignParserCls.downloadMmdbAf(l,r)}}else if(void 0!==t.cfg.url){s.bInputUrlfile=!0;let e=t.cfg.url.split("|"),i=e[0],n=e[1];s.molTitle="",s.inputid=n,s.inputurl="type="+i+"&url="+encodeURIComponent(n),s.loadCmd="load url "+n+" | type "+i,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.pdbParserCls.downloadUrl(n,i,t.cfg.command)}else if(void 0!==t.cfg.mmtfid)s.inputid=t.cfg.mmtfid,s.loadCmd="load mmtf "+t.cfg.mmtfid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.bcifParserCls.downloadBcif(t.cfg.mmtfid);else if(void 0!==t.cfg.bcifid)s.inputid=t.cfg.bcifid,s.loadCmd="load bcif "+t.cfg.bcifid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.bcifParserCls.downloadBcif(t.cfg.bcifid);else if(void 0!==t.cfg.pdbid)s.inputid=t.cfg.pdbid,s.loadCmd="load pdb "+t.cfg.pdbid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.pdbParserCls.downloadPdb(t.cfg.pdbid);else if(void 0!==t.cfg.afid){s.inputid=t.cfg.afid,s.loadCmd="load af "+t.cfg.afid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0);let e=!0;await s.pdbParserCls.downloadPdb(t.cfg.afid,e)}else if(void 0!==t.cfg.opmid)s.inputid=t.cfg.opmid,s.loadCmd="load opm "+t.cfg.opmid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.opmParserCls.downloadOpm(t.cfg.opmid);else if(void 0!==t.cfg.mmdbid)s.inputid=t.cfg.mmdbid,s.loadCmd="load mmdb "+t.cfg.mmdbid+" | parameters "+t.cfg.inpara,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadMmdb(t.cfg.mmdbid);else if(void 0!==t.cfg.gi)s.loadCmd="load gi "+t.cfg.gi,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadGi(t.cfg.gi);else if(void 0!==t.cfg.refseqid)s.inputid=t.cfg.refseqid,s.loadCmd="load refseq "+t.cfg.refseqid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadRefseq(t.cfg.refseqid);else if(void 0!==t.cfg.protein)s.inputid=t.cfg.protein,s.loadCmd="load protein "+t.cfg.protein,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadProteinname(t.cfg.protein);else if(void 0!==t.cfg.blast_rep_id)if(s.inputid=t.cfg.query_id+","+t.cfg.blast_rep_id,t.cfg.oriQuery_id=t.cfg.query_id,t.cfg.oriBlast_rep_id=t.cfg.blast_rep_id,"Query"!==t.cfg.query_id.substr(0,5)&&void 0===t.cfg.rid)"icn3d"==t.cfg.from&&"1TSR_A"==t.cfg.blast_rep_id&&"NP_001108451.1"==t.cfg.query_id&&(t.cfg.command="view annotations; set annotation cdd; set annotation site; set view detailed view; select chain 1TSR_A; show selection"),"smithwm"==t.cfg.alg?(s.loadCmd="load seq_struct_ids_smithwm "+t.cfg.query_id+","+t.cfg.blast_rep_id,s.bSmithwm=!0):"local_smithwm"==t.cfg.alg?(s.loadCmd="load seq_struct_ids_local_smithwm "+t.cfg.query_id+","+t.cfg.blast_rep_id,s.bLocalSmithwm=!0):(s.loadCmd="load seq_struct_ids "+t.cfg.query_id+","+t.cfg.blast_rep_id,s.bSmithwm=!1,s.bLocalSmithwm=!1),t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadBlast_rep_id(t.cfg.query_id+","+t.cfg.blast_rep_id);else if(void 0!==t.cfg.rid){let e="https://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment&CMD=Get&RID="+t.cfg.rid,i=await t.getAjaxPromise(e,"json",!1,"The RID "+t.cfg.rid+" may have expired...");for(let e=0,n=i.BlastOutput2.length;e
    ",s="All atoms  ";e.utilsCls.setViewerWidthHeight(e),e.utilsCls.isMobile()||e.cfg.mobilemenu?e.htmlCls.setMenuCls.setTopMenusHtmlMobile(e.cfg.divid,t,s):e.htmlCls.setMenuCls.setTopMenusHtml(e.cfg.divid,t,s),e.icn3d=new Us(e),e.icn3d.controlCls.setControl(),e.setDialogAjax()},Bs.prototype.getMmtfPromise=function(e){return new Promise((function(t,s){MMTF.fetch(e,(async function(e){t(e)}),(function(e){s("error")}))}))},Bs.prototype.getMmtfReducedPromise=function(e){return new Promise((function(t,s){MMTF.fetchReduced(e,(async function(e){t(e)}),(function(e){s("error")}))}))},Bs.prototype.getXMLHttpRqstPromise=function(e,t,s,i){let n=this;return new Promise((function(l,r){let o=new XMLHttpRequest;o.open(t,e,!0),o.responseType=s,o.onreadystatechange=function(){if(4==this.readyState)if(200==this.status){let e=o.response;l(e)}else"2fofc"==i||"fofc"==i?alert("Density server at EBI has no corresponding electron density map for this structure."):"em"==i?alert("Density server at EBI has no corresponding EM density map for this structure."):"rcsbEdmaps"==i?alert("RCSB server has no corresponding electron density map for this structure."):alert("The "+i+" file is unavailable..."),r("error");else n.icn3d.ParserUtilsCls.showLoading()},o.send()}))},Bs.prototype.getAjaxPromise=function(e,t,s,i,n,l,r){let o=this;return new Promise((function(r,a){$.ajax({url:e,dataType:t,cache:!0,beforeSend:function(){s&&o.icn3d.ParserUtilsCls.showLoading()},complete:function(){l&&o.icn3d.ParserUtilsCls.hideLoading()},success:function(e){r(e)},error:function(){i&&alert(i),n&&console.log(n),a("error")}})}))},Bs.prototype.getAjaxPostPromise=async function(e,t,s,i,n,l,r,o){let a=this;return r=r||"json",new Promise((function(o,d){$.ajax({url:e,type:"POST",data:t,dataType:r,cache:!0,beforeSend:function(){s&&a.icn3d.ParserUtilsCls.showLoading()},complete:function(){l&&a.icn3d.ParserUtilsCls.hideLoading()},success:function(e){o(e)},error:function(){!a.bNode&&i&&console.log(i),!a.bNode&&n&&console.log(n),o("error")}})}))},Bs.prototype.setDialogAjax=function(){this.bNode||$.ui.dialog.prototype._makeDraggableBase||($.ui.dialog.prototype._makeDraggableBase=$.ui.dialog.prototype._makeDraggable,$.ui.dialog.prototype._makeDraggable=function(){this._makeDraggableBase(),this.uiDialog.draggable("option","containment",!1)}),$.ajaxTransport("+binary",(function(e,t,s){if(window.FormData&&(e.dataType&&"binary"==e.dataType||e.data&&(window.ArrayBuffer&&e.data instanceof ArrayBuffer||window.Blob&&e.data instanceof Blob)))return{send:function(t,s){let i=new XMLHttpRequest,n=e.url,l=e.type,r=e.async||!0,o=e.responseType||"blob",a=e.data||null;i.addEventListener("load",(function(){let t={};t[e.dataType]=i.response,s(i.status,i.statusText,t,i.getAllResponseHeaders())})),i.open(l,n,r);for(let e in t)i.setRequestHeader(e,t[e]);i.responseType=o,i.send(a)},abort:function(){s.abort()}}}))};return e.ARButton=qs,e.AddTrack=Et,e.AlignParser=jt,e.AlignSW=xs,e.AlignSeq=m,e.Alternate=ct,e.Analysis=ks,e.AnnoCddSite=vt,e.AnnoContact=_t,e.AnnoCrossLink=At,e.AnnoDomain=xt,e.AnnoSnpClinVar=kt,e.AnnoSsbond=Ot,e.AnnoTransMem=Rt,e.Annotation=Tt,e.ApplyCenter=Qe,e.ApplyClbonds=et,e.ApplyCommand=ps,e.ApplyDisplay=st,e.ApplyMap=rt,e.ApplyOther=it,e.ApplySsbonds=nt,e.ApplySymd=lt,e.Axes=We,e.Box=De,e.Brick=Pe,e.Camera=Ee,e.CartoonNucl=ze,e.ChainalignParser=zt,e.ClickMenu=a,e.Contact=pt,e.Control=Hs,e.ConvertTypeCls=o,e.Curve=Fe,e.CurveStripArrow=Me,e.Cylinder=He,e.DefinedSets=ms,e.Delphi=vs,e.DensityCifParser=ls,e.Diagram2d=Os,e.Dialog=c,e.Domain3d=It,e.Draw=ht,e.DrawGraph=Bt,e.Dsn6Parser=Gt,e.Dssp=_s,e.ElectronMap=Je,e.Events=p,e.Export3D=Ms,e.FirstAtomObj=ys,e.Fog=Te,e.GetGraph=Nt,e.Glycan=Ye,e.HBond=mt,e.HashUtilsCls=t,e.HlObjects=Ht,e.HlSeq=Mt,e.HlUpdate=Ft,e.Html=g,e.Impostor=at,e.Instancing=dt,e.Label=Ve,e.Line=Le,e.LineGraph=Lt,e.LoadAtomData=os,e.LoadCIF=cs,e.LoadPDB=ds,e.LoadScript=gs,e.MarchingCube=Xe,e.MmcifParser=Kt,e.MmdbParser=Jt,e.Mol2Parser=Qt,e.MyEventCls=n,e.OpmParser=es,e.ParasCls=i,e.ParserUtils=rs,e.PdbParser=ts,e.PiHalogen=ut,e.Picking=Ls,e.ProteinSurface=Ke,e.Ray=Fs,e.RealignParser=ns,e.Refnum=ws,e.ReprSub=Ne,e.Resid2spec=bs,e.ResidueLabels=ot,e.ResizeCanvas=Is,e.RmsdSuprCls=l,e.Saltbridge=gt,e.SaveFile=Ts,e.Scap=Ss,e.Scene=Ie,e.SdfParser=ss,e.SelectByCommand=fs,e.Selection=Cs,e.SetColor=Ct,e.SetDialog=h,e.SetHtml=u,e.SetMenu=d,e.SetOption=bt,e.SetSeqAlign=as,e.SetStyle=ft,e.ShareLink=Ds,e.ShowAnno=Dt,e.ShowInter=qt,e.ShowSeq=Pt,e.Sphere=qe,e.Stick=Ue,e.Strand=Be,e.Strip=$e,e.SubdivideCls=r,e.Surface=Ze,e.Symd=As,e.ThreeDPrint=Ps,e.Transform=Es,e.Tube=je,e.UtilsCls=s,e.VRButton=Ns,e.Vastplus=hs,e.ViewInterPairs=Ut,e.XyzParser=is,e.iCn3D=Us,e.iCn3DUI=Bs,e.printMsg=class{constructor(){console.log("This is a message from the icn3d package")}},Object.defineProperty(e,"__esModule",{value:!0}),e}({});
    StructureChainResidue Number
    "+i[e].substr(0,t)+""+i[e].substr(t+1,s-t-1)+""+i[e].substr(s+1)+"