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colors.js
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colors.js
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(function() {
/**
* Color representation.
* @typedef ColorSpec
* @prop {string} 0xAF10AB - any hex number
* @prop {string} <html color name>
*/
/**
* @typedef ColorschemeSpec
* Built in colorschemes
*
* @example //Using a function in order to define the colors.
$3Dmol.download("pdb:4UAA",viewer,{},function(){
viewer.setBackgroundColor(0xffffffff);
var colorAsSnake = function(atom) {
return atom.resi % 2 ? 'white': 'green'
};
viewer.setStyle( {chain:'A'}, { cartoon: {colorfunc: colorAsSnake }});
viewer.setStyle( {chain:'B'}, { stick: {colorscheme: 'yellowCarbon'}});
viewer.render();
});
* @prop {string} <html color>Carbon - use default element colors but with carbon set to specify html color string
* @prop {string} ssPyMOL - PyMol secondary colorscheme
* @prop {string} ssJmol - Jmol secondary colorscheme
* @prop {string} Jmol - Jmol primary colorscheme
* @prop {string} default - default colorscheme
* @prop {string} amino - amino acid colorscheme
* @prop {string} shapely - shapely protien colorscheme
* @prop {string} nucleic - nucleic acid colorscheme
* @prop {string} chain - standard chain colorscheme
* @prop {string} chainHetatm - chain Hetatm colorscheme
* @prop {string} prop - atomSpec property. Example 'b'. See AtomSpec.
* @prop {Gradient} gradient - Allows the user to provide a gradient to the colorscheme.
* @prop {object} map - map of a certain AtomSpec property to a color.: {}} elementMap - Allows the user to provide a mapping of elements to colors to the colorscheme. This can be done with any properties, and not just 'elem'.
* @prop {function} colorfunc - Allows the user to provide a function for setting the colorschemes.
*/
})();
var htmlColors = $3Dmol.htmlColors = {
"aliceblue" : 0xF0F8FF,
"antiquewhite" : 0xFAEBD7,
"aqua" : 0x00FFFF,
"aquamarine" : 0x7FFFD4,
"azure" : 0xF0FFFF,
"beige" : 0xF5F5DC,
"bisque" : 0xFFE4C4,
"black" : 0x000000,
"blanchedalmond" : 0xFFEBCD,
"blue" : 0x0000FF,
"blueviolet" : 0x8A2BE2,
"brown" : 0xA52A2A,
"burlywood" : 0xDEB887,
"cadetblue" : 0x5F9EA0,
"chartreuse" : 0x7FFF00,
"chocolate" : 0xD2691E,
"coral" : 0xFF7F50,
"cornflowerblue" : 0x6495ED,
"cornsilk" : 0xFFF8DC,
"crimson" : 0xDC143C,
"cyan" : 0x00FFFF,
"darkblue" : 0x00008B,
"darkcyan" : 0x008B8B,
"darkgoldenrod" : 0xB8860B,
"darkgray" : 0xA9A9A9,
"darkgrey" : 0xA9A9A9,
"darkgreen" : 0x006400,
"darkkhaki" : 0xBDB76B,
"darkmagenta" : 0x8B008B,
"darkolivegreen" : 0x556B2F,
"darkorange" : 0xFF8C00,
"darkorchid" : 0x9932CC,
"darkred" : 0x8B0000,
"darksalmon" : 0xE9967A,
"darkseagreen" : 0x8FBC8F,
"darkslateblue" : 0x483D8B,
"darkslategray" : 0x2F4F4F,
"darkslategrey" : 0x2F4F4F,
"darkturquoise" : 0x00CED1,
"darkviolet" : 0x9400D3,
"deeppink" : 0xFF1493,
"deepskyblue" : 0x00BFFF,
"dimgray" : 0x696969,
"dimgrey" : 0x696969,
"dodgerblue" : 0x1E90FF,
"firebrick" : 0xB22222,
"floralwhite" : 0xFFFAF0,
"forestgreen" : 0x228B22,
"fuchsia" : 0xFF00FF,
"gainsboro" : 0xDCDCDC,
"ghostwhite" : 0xF8F8FF,
"gold" : 0xFFD700,
"goldenrod" : 0xDAA520,
"gray" : 0x808080,
"grey" : 0x808080,
"green" : 0x008000,
"greenyellow" : 0xADFF2F,
"honeydew" : 0xF0FFF0,
"hotpink" : 0xFF69B4,
"indianred" : 0xCD5C5C,
"indigo" : 0x4B0082,
"ivory" : 0xFFFFF0,
"khaki" : 0xF0E68C,
"lavender" : 0xE6E6FA,
"lavenderblush" : 0xFFF0F5,
"lawngreen" : 0x7CFC00,
"lemonchiffon" : 0xFFFACD,
"lightblue" : 0xADD8E6,
"lightcoral" : 0xF08080,
"lightcyan" : 0xE0FFFF,
"lightgoldenrodyellow" : 0xFAFAD2,
"lightgray" : 0xD3D3D3,
"lightgrey" : 0xD3D3D3,
"lightgreen" : 0x90EE90,
"lightpink" : 0xFFB6C1,
"lightsalmon" : 0xFFA07A,
"lightseagreen" : 0x20B2AA,
"lightskyblue" : 0x87CEFA,
"lightslategray" : 0x778899,
"lightslategrey" : 0x778899,
"lightsteelblue" : 0xB0C4DE,
"lightyellow" : 0xFFFFE0,
"lime" : 0x00FF00,
"limegreen" : 0x32CD32,
"linen" : 0xFAF0E6,
"magenta" : 0xFF00FF,
"maroon" : 0x800000,
"mediumaquamarine" : 0x66CDAA,
"mediumblue" : 0x0000CD,
"mediumorchid" : 0xBA55D3,
"mediumpurple" : 0x9370DB,
"mediumseagreen" : 0x3CB371,
"mediumslateblue" : 0x7B68EE,
"mediumspringgreen" : 0x00FA9A,
"mediumturquoise" : 0x48D1CC,
"mediumvioletred" : 0xC71585,
"midnightblue" : 0x191970,
"mintcream" : 0xF5FFFA,
"mistyrose" : 0xFFE4E1,
"moccasin" : 0xFFE4B5,
"navajowhite" : 0xFFDEAD,
"navy" : 0x000080,
"oldlace" : 0xFDF5E6,
"olive" : 0x808000,
"olivedrab" : 0x6B8E23,
"orange" : 0xFFA500,
"orangered" : 0xFF4500,
"orchid" : 0xDA70D6,
"palegoldenrod" : 0xEEE8AA,
"palegreen" : 0x98FB98,
"paleturquoise" : 0xAFEEEE,
"palevioletred" : 0xDB7093,
"papayawhip" : 0xFFEFD5,
"peachpuff" : 0xFFDAB9,
"peru" : 0xCD853F,
"pink" : 0xFFC0CB,
"plum" : 0xDDA0DD,
"powderblue" : 0xB0E0E6,
"purple" : 0x800080,
"rebeccapurple" : 0x663399,
"red" : 0xFF0000,
"rosybrown" : 0xBC8F8F,
"royalblue" : 0x4169E1,
"saddlebrown" : 0x8B4513,
"salmon" : 0xFA8072,
"sandybrown" : 0xF4A460,
"seagreen" : 0x2E8B57,
"seashell" : 0xFFF5EE,
"sienna" : 0xA0522D,
"silver" : 0xC0C0C0,
"skyblue" : 0x87CEEB,
"slateblue" : 0x6A5ACD,
"slategray" : 0x708090,
"slategrey" : 0x708090,
"snow" : 0xFFFAFA,
"springgreen" : 0x00FF7F,
"steelblue" : 0x4682B4,
"tan" : 0xD2B48C,
"teal" : 0x008080,
"thistle" : 0xD8BFD8,
"tomato" : 0xFF6347,
"turquoise" : 0x40E0D0,
"violet" : 0xEE82EE,
"wheat" : 0xF5DEB3,
"white" : 0xFFFFFF,
"whitesmoke" : 0xF5F5F5,
"yellow" : 0xFFFF00,
"yellowgreen" : 0x9ACD32
};
// in an attempt to reduce memory overhead, cache all $3Dmol.Colors
// this makes things a little faster
$3Dmol.CC = {
cache : {0:new $3Dmol.Color(0)},
color : function color_(hex) {
// Undefined values default to black
if(!hex)
return this.cache[0];
// cache hits
if(typeof(this.cache[hex]) !== "undefined") {
return this.cache[hex];
}
// arrays
else if(hex && hex.constructor === Array) {
// parse elements recursively
return hex.map(color_,this);
}
// numbers and hex strings
hex = this.getHex(hex);
if(typeof hex === 'number') {
var c = new $3Dmol.Color(hex);
this.cache[hex] = c;
return c;
} else {
// pass through $3Dmol.Color & other objects
return hex;
}
},
getHex : function(hex) {
if (!isNaN(parseInt(hex)))
return parseInt(hex);
else if (typeof(hex) === 'string') {
hex = hex.trim();
if(hex.length == 4 && hex[0] == '#') {
hex = '#' + hex[1]+hex[1]+hex[2]+hex[2]+hex[3]+hex[3]; //expand to full hex number
}
if(hex.length == 7 && hex[0] == '#') {
return parseInt(hex.substring(1),16);
}
else {
return htmlColors[hex.toLowerCase()] || 0x000000;
}
}
return hex;
}
};
$3Dmol.CC = $3Dmol.CC;
$3Dmol.CC.color = $3Dmol.CC.color;
/** Preset secondary structure color scheme
* @struct
*/
$3Dmol.ssColors = $3Dmol.ssColors || {};
//names are in helix-sheet-coil order
$3Dmol.ssColors.pyMol = {'h': 0xff0000, 's': 0xffff00, 'c': 0x00ff00};
$3Dmol.ssColors.Jmol = {'h': 0xff0080, 's': 0xffc800, 'c': 0xffffff};
/** Preset element coloring - from individual element colors to entire mappings (e.g. '$3Dmol.elementColors.Jmol' colors atoms with Jmol stylings)
* @struct
*/
$3Dmol.elementColors = $3Dmol.elementColors || {};
$3Dmol.elementColors.defaultColor = 0xff1493;
/** @property Jmol-like element colors*/
$3Dmol.elementColors.Jmol = {
'H': 0xFFFFFF,
'He': 0xD9FFFF,
'HE': 0xD9FFFF,
'Li': 0xCC80FF,
'LI': 0xCC80FF,
'Be': 0xC2FF00,
'BE': 0xC2FF00,
'B': 0xFFB5B5,
'C': 0x909090,
'N': 0x3050F8,
'O': 0xFF0D0D,
'F': 0x90E050,
'Ne': 0xB3E3F5,
'NE': 0xB3E3F5,
'Na': 0xAB5CF2,
'NA': 0xAB5CF2,
'Mg': 0x8AFF00,
'MG': 0x8AFF00,
'Al': 0xBFA6A6,
'AL': 0xBFA6A6,
'Si': 0xF0C8A0,
'SI': 0xF0C8A0,
'P': 0xFF8000,
'S': 0xFFFF30,
'Cl': 0x1FF01F,
'CL': 0x1FF01F,
'Ar': 0x80D1E3,
'AR': 0x80D1E3,
'K': 0x8F40D4,
'Ca': 0x3DFF00,
'CA': 0x3DFF00,
'Sc': 0xE6E6E6,
'SC': 0xE6E6E6,
'Ti': 0xBFC2C7,
'TI': 0xBFC2C7,
'V': 0xA6A6AB,
'Cr': 0x8A99C7,
'CR': 0x8A99C7,
'Mn': 0x9C7AC7,
'MN': 0x9C7AC7,
'Fe': 0xE06633,
'FE': 0xE06633,
'Co': 0xF090A0,
'CO': 0xF090A0,
'Ni': 0x50D050,
'NI': 0x50D050,
'Cu': 0xC88033,
'CU': 0xC88033,
'Zn': 0x7D80B0,
'ZN': 0x7D80B0,
'Ga': 0xC28F8F,
'GA': 0xC28F8F,
'Ge': 0x668F8F,
'GE': 0x668F8F,
'As': 0xBD80E3,
'AS': 0xBD80E3,
'Se': 0xFFA100,
'SE': 0xFFA100,
'Br': 0xA62929,
'BR': 0xA62929,
'Kr': 0x5CB8D1,
'KR': 0x5CB8D1,
'Rb': 0x702EB0,
'RB': 0x702EB0,
'Sr': 0x00FF00,
'SR': 0x00FF00,
'Y': 0x94FFFF,
'Zr': 0x94E0E0,
'ZR': 0x94E0E0,
'Nb': 0x73C2C9,
'NB': 0x73C2C9,
'Mo': 0x54B5B5,
'MO': 0x54B5B5,
'Tc': 0x3B9E9E,
'TC': 0x3B9E9E,
'Ru': 0x248F8F,
'RU': 0x248F8F,
'Rh': 0x0A7D8C,
'RH': 0x0A7D8C,
'Pd': 0x006985,
'PD': 0x006985,
'Ag': 0xC0C0C0,
'AG': 0xC0C0C0,
'Cd': 0xFFD98F,
'CD': 0xFFD98F,
'In': 0xA67573,
'IN': 0xA67573,
'Sn': 0x668080,
'SN': 0x668080,
'Sb': 0x9E63B5,
'SB': 0x9E63B5,
'Te': 0xD47A00,
'TE': 0xD47A00,
'I': 0x940094,
'Xe': 0x429EB0,
'XE': 0x429EB0,
'Cs': 0x57178F,
'CS': 0x57178F,
'Ba': 0x00C900,
'BA': 0x00C900,
'La': 0x70D4FF,
'LA': 0x70D4FF,
'Ce': 0xFFFFC7,
'CE': 0xFFFFC7,
'Pr': 0xD9FFC7,
'PR': 0xD9FFC7,
'Nd': 0xC7FFC7,
'ND': 0xC7FFC7,
'Pm': 0xA3FFC7,
'PM': 0xA3FFC7,
'Sm': 0x8FFFC7,
'SM': 0x8FFFC7,
'Eu': 0x61FFC7,
'EU': 0x61FFC7,
'Gd': 0x45FFC7,
'GD': 0x45FFC7,
'Tb': 0x30FFC7,
'TB': 0x30FFC7,
'Dy': 0x1FFFC7,
'DY': 0x1FFFC7,
'Ho': 0x00FF9C,
'HO': 0x00FF9C,
'Er': 0x00E675,
'ER': 0x00E675,
'Tm': 0x00D452,
'TM': 0x00D452,
'Yb': 0x00BF38,
'YB': 0x00BF38,
'Lu': 0x00AB24,
'LU': 0x00AB24,
'Hf': 0x4DC2FF,
'HF': 0x4DC2FF,
'Ta': 0x4DA6FF,
'TA': 0x4DA6FF,
'W': 0x2194D6,
'Re': 0x267DAB,
'RE': 0x267DAB,
'Os': 0x266696,
'OS': 0x266696,
'Ir': 0x175487,
'IR': 0x175487,
'Pt': 0xD0D0E0,
'PT': 0xD0D0E0,
'Au': 0xFFD123,
'AU': 0xFFD123,
'Hg': 0xB8B8D0,
'HG': 0xB8B8D0,
'Tl': 0xA6544D,
'TL': 0xA6544D,
'Pb': 0x575961,
'PB': 0x575961,
'Bi': 0x9E4FB5,
'BI': 0x9E4FB5,
'Po': 0xAB5C00,
'PO': 0xAB5C00,
'At': 0x754F45,
'AT': 0x754F45,
'Rn': 0x428296,
'RN': 0x428296,
'Fr': 0x420066,
'FR': 0x420066,
'Ra': 0x007D00,
'RA': 0x007D00,
'Ac': 0x70ABFA,
'AC': 0x70ABFA,
'Th': 0x00BAFF,
'TH': 0x00BAFF,
'Pa': 0x00A1FF,
'PA': 0x00A1FF,
'U': 0x008FFF,
'Np': 0x0080FF,
'NP': 0x0080FF,
'Pu': 0x006BFF,
'PU': 0x006BFF,
'Am': 0x545CF2,
'AM': 0x545CF2,
'Cm': 0x785CE3,
'CM': 0x785CE3,
'Bk': 0x8A4FE3,
'BK': 0x8A4FE3,
'Cf': 0xA136D4,
'CF': 0xA136D4,
'Es': 0xB31FD4,
'ES': 0xB31FD4,
'Fm': 0xB31FBA,
'FM': 0xB31FBA,
'Md': 0xB30DA6,
'MD': 0xB30DA6,
'No': 0xBD0D87,
'NO': 0xBD0D87,
'Lr': 0xC70066,
'LR': 0xC70066,
'Rf': 0xCC0059,
'RF': 0xCC0059,
'Db': 0xD1004F,
'DB': 0xD1004F,
'Sg': 0xD90045,
'SG': 0xD90045,
'Bh': 0xE00038,
'BH': 0xE00038,
'Hs': 0xE6002E,
'HS': 0xE6002E,
'Mt': 0xEB0026,
'MT': 0xEB0026
};
/** @property rasmol-like element colors */
$3Dmol.elementColors.rasmol = {
'H': 0xFFFFFF,
'He': 0xFFC0CB,
'HE': 0xFFC0CB,
'Li': 0xB22222,
'LI': 0xB22222,
'B': 0x00FF00,
'C': 0xC8C8C8,
'N': 0x8F8FFF,
'O': 0xF00000,
'F': 0xDAA520,
'Na': 0x0000FF,
'NA': 0x0000FF,
'Mg': 0x228B22,
'MG': 0x228B22,
'Al': 0x808090,
'AL': 0x808090,
'Si': 0xDAA520,
'SI': 0xDAA520,
'P': 0xFFA500,
'S': 0xFFC832,
'Cl': 0x00FF00,
'CL': 0x00FF00,
'Ca': 0x808090,
'CA': 0x808090,
'Ti': 0x808090,
'TI': 0x808090,
'Cr': 0x808090,
'CR': 0x808090,
'Mn': 0x808090,
'MN': 0x808090,
'Fe': 0xFFA500,
'FE': 0xFFA500,
'Ni': 0xA52A2A,
'NI': 0xA52A2A,
'Cu': 0xA52A2A,
'CU': 0xA52A2A,
'Zn': 0xA52A2A,
'ZN': 0xA52A2A,
'Br': 0xA52A2A,
'BR': 0xA52A2A,
'Ag': 0x808090,
'AG': 0x808090,
'I': 0xA020F0,
'Ba': 0xFFA500,
'BA': 0xFFA500,
'Au': 0xDAA520,
'AU': 0xDAA520
};
$3Dmol.elementColors.defaultColors = $3Dmol.elementColors.rasmol;
$3Dmol.elementColors.greenCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
$3Dmol.elementColors.greenCarbon.C = 0x00ff00; //bright green
$3Dmol.elementColors.cyanCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
$3Dmol.elementColors.cyanCarbon.C = 0x00ffff;
$3Dmol.elementColors.magentaCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
$3Dmol.elementColors.magentaCarbon.C = 0xff00ff;
$3Dmol.elementColors.yellowCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
$3Dmol.elementColors.yellowCarbon.C = 0xffff00;
$3Dmol.elementColors.whiteCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
$3Dmol.elementColors.whiteCarbon.C = 0xffffff;
$3Dmol.elementColors.orangeCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
$3Dmol.elementColors.orangeCarbon.C = 0xffa500;
$3Dmol.elementColors.purpleCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
$3Dmol.elementColors.purpleCarbon.C = 0x800080;
$3Dmol.elementColors.blueCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
$3Dmol.elementColors.blueCarbon.C = 0x0000ff;
$3Dmol.residues = {};
/** @property standard amino acid color scheme*/
$3Dmol.residues.amino ={
'ALA' : 0xC8C8C8,
'ARG' : 0x145AFF,
'ASN' : 0x00DCDC,
'ASP' : 0xE60A0A,
'CYS' : 0xE6E600,
'GLN' : 0x00DCDC,
'GLU' : 0xE60A0A,
'GLY' : 0xEBEBEB,
'HIS' : 0x8282D2,
'ILE' :0x0F820F,
'LEU':0x0F820F,
'LYS' :0x145AFF,
'MET' :0xE6E600,
'PHE':0x3232AA,
'PRO' : 0xDC9682,
'SER': 0xFA9600,
'THR': 0xFA9600,
'TRP' : 0xB45AB4,
'TYR' :0x3232AA,
'VAL' :0x0F820F,
'ASX' :0xFF69B4,
'GLX' :0xFF69B4,
};
/** @property shapely amino acid color scheme*/
$3Dmol.residues.shapely ={
'ALA' : 0x8CFF8C,
'ARG' : 0x00007C,
'ASN' : 0xFF7C70,
'ASP' : 0xA00042,
'CYS' : 0xFFFF70,
'GLN' : 0xFF4C4C,
'GLU' : 0x660000,
'GLY' : 0xFFFFFF,
'HIS' : 0x7070FF,
'ILE' :0x004C00,
'LEU':0x455E45,
'LYS' :0x4747B8,
'MET' :0xB8A042,
'PHE':0x534C52,
'PRO' : 0x525252,
'SER': 0xFF7042,
'THR': 0xB84C00,
'TRP' : 0x4F4600,
'TYR' :0x8C704C,
'VAL' :0xFF8CFF,
'ASX' :0xFF00FF,
'GLX' :0xFF00FF,
};
/** @property nucleic acid color scheme*/
$3Dmol.residues.nucleic = {
'A':0xA0A0FF,
'G': 0xFF7070,
'I': 0x80FFFF,
'C': 0xFF8C4B,
'T': 0xA0FFA0,
'U': 0xFF8080
};
$3Dmol.chains ={};
/** @property chain based standard color scheme */
$3Dmol.chains.atom = {
'A' : 0xC0D0FF,
'B' : 0xB0FFB0,
'C' : 0xFFC0C8 ,
'D' : 0xFFFF80,
'E' : 0xFFC0FF,
'F' : 0xB0F0F0,
'G' : 0xFFD070,
'H' : 0xF08080,
'I' : 0xF5DEB3,
'J' :0x00BFFF,
'K':0xCD5C5C ,
'L' :0x66CDAA,
'M' :0x9ACD32,
'N':0xEE82EE ,
'O' : 0x00CED1,
'P': 0x00FF7F,
'Q': 0x3CB371 ,
'R' : 0x00008B,
'S' :0xBDB76B,
'T' :0x006400,
'U' :0x800000,
'V' :0x808000,
'W' :0x800080,
'X' :0x008080 ,
'Y':0xB8860B,
'Z':0xB22222,
};
/** @property hetatm color scheme */
$3Dmol.chains.hetatm = {
'A' : 0x90A0CF,
'B' : 0x80CF98,
'C' : 0xCF90B0 ,
'D' : 0xCFCF70,
'E' : 0xCF90CF,
'F' : 0x80C0C0,
'G' : 0xCFA060,
'H' : 0xC05070,
'I' : 0xC5AE83,
'J' :0x00A7CF,
'K':0xB54C4C ,
'L' :0x56B592,
'M' :0x8AB52A,
'N':0xBE72BE ,
'O' : 0x00B6A1,
'P': 0x00CF6F,
'Q': 0x349B61 ,
'R' : 0x0000BB ,
'S' :0xA59F5B,
'T' :0x009400,
'U' :0xB00000,
'V' :0xB0B000,
'W' :0xB000B0,
'X' :0x00B0B0 ,
'Y':0xE8B613,
'Z':0xC23232,
};
/** @property built in color schemes
* The user can pass all of these values directly as the colorscheme and they will use the respective colorscheme */
$3Dmol.builtinColorSchemes = {
'ssPyMol' : {'prop':'ss', map:$3Dmol.ssColors.pyMol},
'ssJmol' :{'prop':'ss', map:$3Dmol.ssColors.Jmol},
'Jmol' :{'prop':'elem', map:$3Dmol.elementColors.Jmol},
'greenCarbon': {'prop': 'elem', map:$3Dmol.elementColors.greenCarbon},
'default' : {'prop': 'elem', map:$3Dmol.elementColors.defaultColors},
'amino' : {'prop':'resn', map:$3Dmol.residues.amino},
'shapely' :{'prop':'resn', map:$3Dmol.residues.shapely},
'nucleic' :{'prop':'resn', map:$3Dmol.residues.nucleic},
'chain' :{'prop':'chain', map:$3Dmol.chains.atom},
'chainHetatm' :{'prop':'chain', map:$3Dmol.chains.hetatm},
};
/** Return proper color for atom given style
* @param {AtomSpec} atom
* @param {AtomStyle} style
* @return {$3Dmol.Color}
*/
$3Dmol.getColorFromStyle = function(atom, style) {
var scheme = style.colorscheme;
if(typeof($3Dmol.builtinColorSchemes[scheme]) != "undefined") {
scheme = $3Dmol.builtinColorSchemes[scheme];
} else if(typeof(scheme) == 'string' && scheme.endsWith('Carbon')) {
//any color you want of carbon
var ccolor = scheme.substring(0,scheme.lastIndexOf("Carbon")).toLowerCase();
if(typeof(htmlColors[ccolor]) != "undefined") {
var newscheme = $.extend({},$3Dmol.elementColors.defaultColors);
newscheme.C = htmlColors[ccolor];
$3Dmol.builtinColorSchemes[scheme] = {'prop': 'elem', map:newscheme};
scheme = $3Dmol.builtinColorSchemes[scheme];
}
}
var color = atom.color;
if (typeof (style.color) != "undefined" && style.color != "spectrum")
color = style.color;
if(typeof(scheme) != "undefined") {
var prop, val;
if(typeof($3Dmol.elementColors[scheme]) != "undefined") {
//name of builtin colorscheme
scheme = $3Dmol.elementColors[scheme];
if(typeof(scheme[atom[scheme.prop]]) != "undefined") {
color = scheme.map[atom[scheme.prop]];
}
} else if(typeof(scheme[atom[scheme.prop]]) != 'undefined') {
//actual color scheme provided
color = scheme.map[atom[scheme.prop]];
} else if(typeof(scheme.prop) != 'undefined' &&
typeof(scheme.gradient) != 'undefined') {
//apply a property mapping
prop = scheme.prop;
var grad = scheme.gradient; //redefining scheme
if(typeof($3Dmol.Gradient.builtinGradients[grad]) != "undefined") {
grad = new $3Dmol.Gradient.builtinGradients[grad](scheme.min, scheme.max, scheme.mid);
}
var range = grad.range() || [-1,1]; //sensible default
val = $3Dmol.getAtomProperty(atom, prop);
if(val != null) {
color = grad.valueToHex(val, range);
}
} else if(typeof(scheme.prop) != 'undefined' &&
typeof(scheme.map) != 'undefined') {
//apply a discrete property mapping
prop = scheme.prop;
val = $3Dmol.getAtomProperty(atom, prop);
if( typeof scheme.map[val] != 'undefined' ) {
color = scheme.map[val];
}
} else if(typeof(style.colorscheme[atom.elem]) != 'undefined') {
//actual color scheme provided
color = style.colorscheme[atom.elem];
} else {
console.log("Could not interpret colorscheme "+scheme);
}
}
else if(typeof(style.colorfunc) != "undefined") {
//this is a user provided function for turning an atom into a color
color = style.colorfunc(atom);
}
var C = $3Dmol.CC.color(color);
return C;
};