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ProteinSurface4.ts
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ProteinSurface4.ts
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/* ProteinSurface.js by biochem_fan
Ported and modified for Javascript based on EDTSurf,
whose license is as follows.
Permission to use, copy, modify, and distribute this program for any
purpose, with or without fee, is hereby granted, provided that this
copyright notice and the reference information appear in all copies or
substantial portions of the Software. It is provided "as is" without
express or implied warranty.
Reference:
http://zhanglab.ccmb.med.umich.edu/EDTSurf/
D. Xu, Y. Zhang (2009) Generating Triangulated Macromolecular Surfaces
by Euclidean Distance Transform. PLoS ONE 4(12): e8140.
=======
*/
import {Vector3} from "./WebGL/math"
/**
* Surface types
* @readonly
* @enum {number}
* @property VDW - van der Waals surface
* @property MS - Molecular surface
* @property SAS - Solvent accessible surface
* @property SES - Solvent exposed surface
*/
export enum SurfaceType {
VDW = 1,
MS = 2,
SAS = 3,
SES = 4
};
/**
* Render surface synchronously if true
* @param {boolean} [$3Dmol.syncSurface=false]
* @type {boolean} */
export var syncSurface = false;
/**
*
* @param {boolean} val - Whether surfaces should be rendered synchronously or in parallel.
*/
export function setSyncSurface(val:boolean) {
syncSurface = val;
}
// Internet Explorer refuses to allow webworkers in data blobs. I can find
// no way of checking for this feature directly, so must do a browser check
if (window.navigator.userAgent.indexOf('MSIE ') >= 0 ||
window.navigator.userAgent.indexOf('Trident/') >= 0) {
syncSurface = true; // can't use webworkers
}
//Encapsulate marching cube algorithm for isosurface generation
// (currently used by protein surface rendering and generic volumetric data reading)
export class MarchingCubeInitializer {
//Marching cube algorithm - assume data has been pre-treated so isovalue is 0
// (i.e. select points greater than 0)
//origin - vector of origin of volumetric data (default is (0,0,0))
// nX, nY, nZ - specifies number of voxels in each dimension
// scale - cube diagonal unit vector scale (3Dmol vector) (specifying distance between data points); diagonal of cube
// - default is 1 - assumes unit cube (1,1,1) diag)
// fulltable - if true, use full marching cubes and tritables - else use trimmed table (e.g. surf render)
// voxel - if true, draws with a blocky voxel style (default false)
// verts, faces - vertex and face arrays to fill up
//to match with protein surface...
ISDONE: number = 2;
constructor() {
}
march(data, verts, faces, spec) {
let fulltable = !!(spec.fulltable);
let origin = (spec.hasOwnProperty('origin') && spec.origin.hasOwnProperty('x')) ? spec.origin : {x:0, y:0, z:0};
let voxel = !!(spec.voxel);
let transform = spec.matrix; //if this is set, it overrides origin and unitCube
let nX = spec.nX || 0;
let nY = spec.nY || 0;
let nZ = spec.nZ || 0;
let scale = spec.scale || 1.0;
let unitCube = null;
if(spec.unitCube) {
unitCube = spec.unitCube;
} else {
unitCube = {x:scale,y:scale,z:scale};
}
//keep track of calculated vertices to avoid repeats
let vertnums = new Int32Array(nX*nY*nZ);
let i, il;
for (i = 0, il = vertnums.length; i < il; ++i)
vertnums[i] = -1;
// create (or retrieve) a vertex at the appropriate point for
// the edge (p1,p2)
let getVertex = function(i, j, k, code, p1, p2) {
let pt = {x:0,y:0,z:0};
let val1 = !!(code & (1 << p1));
let val2 = !!(code & (1 << p2));
// p1 if they are the same or if !val1
let p = p1;
if (!val1 && val2)
p = p2;
// adjust i,j,k by p
if (p & 1)
k++;
if (p & 2)
j++;
if (p & 4)
i++;
if(transform) {
let vpt = new Vector3(i,j,k);
vpt = vpt.applyMatrix4(transform);
pt = {x: vpt.x, y: vpt.y, z: vpt.z}; //remove vector gunk
} else {
pt.x = origin.x+unitCube.x*i;
pt.y = origin.y+unitCube.y*j;
pt.z = origin.z+unitCube.z*k;
}
let index = ((nY * i) + j) * nZ + k;
//Have to add option to do voxels
if (!voxel) {
if (vertnums[index] < 0) // not created yet
{
vertnums[index] = verts.length;
verts.push( pt );
}
return vertnums[index];
}
else {
verts.push(pt);
return verts.length - 1;
}
};
let intersects = new Int32Array(12);
let etable = (fulltable) ? this.edgeTable2 : this.edgeTable;
let tritable = (fulltable) ? this.triTable2 : this.triTable;
//Run marching cubes algorithm
for (i = 0; i < nX-1; ++i) {
for (let j = 0; j < nY-1; ++j){
for (let k = 0; k < nZ-1; ++k){
let code = 0;
for (let p = 0; p < 8; ++p) {
let index = ((nY * (i + ((p & 4) >> 2))) + j + ((p & 2) >> 1)) *
nZ + k + (p & 1);
//TODO: Need to fix vpBits in protein surface for this to work
let val:any = !!(data[index] & this.ISDONE);
//let val = !!(data[index] > 0);
code |= val << p;
}
if (code === 0 || code === 255)
continue;
let ecode = etable[code];
if (ecode === 0)
continue;
let ttable = tritable[code];
if (ecode & 1)
intersects[0] = getVertex(i, j, k, code, 0, 1);
if (ecode & 2)
intersects[1] = getVertex(i, j, k, code, 1, 3);
if (ecode & 4)
intersects[2] = getVertex(i, j, k, code, 3, 2);
if (ecode & 8)
intersects[3] = getVertex(i, j, k, code, 2, 0);
if (ecode & 16)
intersects[4] = getVertex(i, j, k, code, 4, 5);
if (ecode & 32)
intersects[5] = getVertex(i, j, k, code, 5, 7);
if (ecode & 64)
intersects[6] = getVertex(i, j, k, code, 7, 6);
if (ecode & 128)
intersects[7] = getVertex(i, j, k, code, 6, 4);
if (ecode & 256)
intersects[8] = getVertex(i, j, k, code, 0, 4);
if (ecode & 512)
intersects[9] = getVertex(i, j, k, code, 1, 5);
if (ecode & 1024)
intersects[10] = getVertex(i, j, k, code, 3, 7);
if (ecode & 2048)
intersects[11] = getVertex(i, j, k, code, 2, 6);
for (let t = 0; t < ttable.length; t += 3) {
let a = intersects[ttable[t]],
b = intersects[ttable[t+1]],
c = intersects[ttable[t+2]];
if (voxel && t >= 3) {
verts.push(verts[a]); a = verts.length - 1;
verts.push(verts[b]); b = verts.length - 1;
verts.push(verts[c]); c = verts.length - 1;
}
faces.push(a); faces.push(b); faces.push(c);
}
}
}
}
};
laplacianSmooth (numiter, verts, faces) {
let tps = new Array(verts.length);
let i, il, j, jl, k;
for (i = 0, il = verts.length; i < il; i++)
tps[i] = {
x : 0,
y : 0,
z : 0
};
let vertdeg = new Array(20);
let flagvert;
for (i = 0; i < 20; i++)
vertdeg[i] = new Array(verts.length);
for (i = 0, il = verts.length; i < il; i++)
vertdeg[0][i] = 0;
for (i = 0, il = faces.length / 3; i < il; i++) {
let aoffset = i*3, boffset = i*3 + 1, coffset = i*3 + 2;
flagvert = true;
for (j = 0, jl = vertdeg[0][faces[aoffset]]; j < jl; j++) {
if (faces[boffset] == vertdeg[j + 1][faces[aoffset]]) {
flagvert = false;
break;
}
}
if (flagvert) {
vertdeg[0][faces[aoffset]]++;
vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]] = faces[boffset];
}
flagvert = true;
for (j = 0, jl = vertdeg[0][faces[aoffset]]; j < jl; j++) {
if (faces[coffset] == vertdeg[j + 1][faces[aoffset]]) {
flagvert = false;
break;
}
}
if (flagvert) {
vertdeg[0][faces[aoffset]]++;
vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]] = faces[coffset];
}
// b
flagvert = true;
for (j = 0, jl = vertdeg[0][faces[boffset]]; j < jl; j++) {
if (faces[aoffset] == vertdeg[j + 1][faces[boffset]]) {
flagvert = false;
break;
}
}
if (flagvert) {
vertdeg[0][faces[boffset]]++;
vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]] = faces[aoffset];
}
flagvert = true;
for (j = 0, jl = vertdeg[0][faces[boffset]]; j < jl; j++) {
if (faces[coffset] == vertdeg[j + 1][faces[boffset]]) {
flagvert = false;
break;
}
}
if (flagvert) {
vertdeg[0][faces[boffset]]++;
vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]] = faces[coffset];
}
// c
flagvert = true;
for (j = 0; j < vertdeg[0][faces[coffset]]; j++) {
if (faces[aoffset] == vertdeg[j + 1][faces[coffset]]) {
flagvert = false;
break;
}
}
if (flagvert) {
vertdeg[0][faces[coffset]]++;
vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]] = faces[aoffset];
}
flagvert = true;
for (j = 0, jl = vertdeg[0][faces[coffset]]; j < jl; j++) {
if (faces[boffset] == vertdeg[j + 1][faces[coffset]]) {
flagvert = false;
break;
}
}
if (flagvert) {
vertdeg[0][faces[coffset]]++;
vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]] = faces[boffset];
}
}
let wt = 1.00;
let wt2 = 0.50;
for (k = 0; k < numiter; k++) {
for (i = 0, il = verts.length; i < il; i++) {
if (vertdeg[0][i] < 3) {
tps[i].x = verts[i].x;
tps[i].y = verts[i].y;
tps[i].z = verts[i].z;
} else if (vertdeg[0][i] == 3 || vertdeg[0][i] == 4) {
tps[i].x = 0;
tps[i].y = 0;
tps[i].z = 0;
for (j = 0, jl = vertdeg[0][i]; j < jl; j++) {
tps[i].x += verts[vertdeg[j + 1][i]].x;
tps[i].y += verts[vertdeg[j + 1][i]].y;
tps[i].z += verts[vertdeg[j + 1][i]].z;
}
tps[i].x += wt2 * verts[i].x;
tps[i].y += wt2 * verts[i].y;
tps[i].z += wt2 * verts[i].z;
tps[i].x /= wt2 + vertdeg[0][i];
tps[i].y /= wt2 + vertdeg[0][i];
tps[i].z /= wt2 + vertdeg[0][i];
} else {
tps[i].x = 0;
tps[i].y = 0;
tps[i].z = 0;
for (j = 0, jl = vertdeg[0][i]; j < jl; j++) {
tps[i].x += verts[vertdeg[j + 1][i]].x;
tps[i].y += verts[vertdeg[j + 1][i]].y;
tps[i].z += verts[vertdeg[j + 1][i]].z;
}
tps[i].x += wt * verts[i].x;
tps[i].y += wt * verts[i].y;
tps[i].z += wt * verts[i].z;
tps[i].x /= wt + vertdeg[0][i];
tps[i].y /= wt + vertdeg[0][i];
tps[i].z /= wt + vertdeg[0][i];
}
}
for (i = 0, il = verts.length; i < il; i++) {
verts[i].x = tps[i].x;
verts[i].y = tps[i].y;
verts[i].z = tps[i].z;
}
/*
* computenorm(); for (let i = 0; i < vertnumber; i++) { if
* (verts[i].inout) ssign = 1; else ssign = -1; verts[i].x += ssign *
* outwt * verts[i].pn.x; verts[i].y += ssign * outwt *
* verts[i].pn.y; verts[i].z += ssign * outwt * verts[i].pn.z; }
*/
}
};
/*
* These tables are based off those by Paul Bourke and Geoffrey Heller:
* http://paulbourke.net/geometry/polygonise/
* http://paulbourke.net/geometry/polygonise/table2.txt
*
* However, they have been substantially modified to reflect a more
* sensible corner numbering scheme and the discrete nature of our voxel data
* (resulting in fewer faces).
*/
edgeTable: Uint32Array = new Uint32Array([ 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0,
0xb00, 0x0, 0x0, 0x0, 0x700, 0x0, 0xd00, 0xe00, 0xf00, 0x0, 0x0, 0x0,
0x8a, 0x0, 0x15, 0x0, 0x86, 0x0, 0x0, 0x0, 0x28c, 0x0, 0x813, 0xf19,
0xe10, 0x0, 0x0, 0x0, 0x2a, 0x0, 0x0, 0x0, 0x126, 0x0, 0x0, 0x15, 0x1c,
0x0, 0xf23, 0x419, 0xd20, 0x0, 0xa8, 0xa2, 0xaa, 0x0, 0x285, 0x9ab,
0x8a2, 0x0, 0x2af, 0x125, 0xac, 0xfaa, 0xea3, 0xda9, 0xca0, 0x0, 0x0,
0x0, 0x0, 0x0, 0x45, 0x0, 0x384, 0x0, 0x0, 0x0, 0x700, 0x8a, 0x83,
0x648, 0x780, 0x0, 0x51, 0x0, 0x81a, 0x54, 0x55, 0x54, 0x56, 0x0, 0x51,
0x0, 0xe5c, 0x14a, 0x451, 0x759, 0x650, 0x0, 0x0, 0x0, 0x2a, 0x0, 0x45,
0x0, 0x1f6, 0x0, 0x0, 0x15, 0xdfc, 0x8a, 0x7f3, 0x4f9, 0x5f0, 0xb00,
0x68, 0x921, 0x6a, 0x348, 0x245, 0x16f, 0x66, 0xb00, 0xe6f, 0xd65,
0xc6c, 0x76a, 0x663, 0x569, 0x460, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0,
0xf46, 0x0, 0x0, 0x45, 0x24c, 0x2a, 0x823, 0x29, 0xb40, 0x0, 0x0, 0x0,
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[ 11, 6, 7, 10, 0, 9, 10, 2, 0 ], [ 2, 1, 10, 7, 11, 6, 8, 0, 3 ],
[ 1, 10, 2, 6, 7, 11 ], [ 7, 2, 6, 7, 9, 2, 2, 9, 1, 7, 8, 9 ],
[ 1, 0, 9, 3, 6, 7, 3, 2, 6 ], [ 8, 0, 7, 7, 0, 6, 0, 2, 6 ],
[ 2, 7, 3, 2, 6, 7 ], [ 7, 11, 6, 3, 9, 1, 3, 8, 9 ],
[ 9, 1, 0, 11, 6, 7 ], [ 0, 3, 8, 11, 6, 7 ], [ 11, 6, 7 ],
[ 11, 7, 5, 11, 5, 10 ], [ 3, 0, 8, 7, 5, 10, 7, 10, 11 ],
[ 9, 0, 1, 10, 11, 7, 10, 7, 5 ],
[ 3, 1, 9, 3, 9, 8, 7, 10, 11, 7, 5, 10 ],
[ 10, 2, 5, 2, 3, 5, 5, 3, 7 ],
[ 5, 10, 2, 8, 5, 2, 8, 7, 5, 8, 2, 0 ],
[ 9, 0, 1, 10, 2, 5, 5, 2, 3, 5, 3, 7 ],
[ 1, 10, 2, 5, 8, 7, 5, 9, 8 ], [ 2, 11, 1, 11, 7, 1, 1, 7, 5 ],
[ 0, 8, 3, 2, 11, 1, 1, 11, 7, 1, 7, 5 ],
[ 9, 0, 2, 9, 2, 7, 2, 11, 7, 9, 7, 5 ],
[ 11, 3, 2, 8, 5, 9, 8, 7, 5 ], [ 1, 3, 7, 1, 7, 5 ],
[ 8, 7, 0, 0, 7, 1, 7, 5, 1 ], [ 0, 3, 9, 9, 3, 5, 3, 7, 5 ],
[ 9, 7, 5, 9, 8, 7 ], [ 4, 5, 8, 5, 10, 8, 8, 10, 11 ],
[ 3, 0, 4, 3, 4, 10, 4, 5, 10, 3, 10, 11 ],
[ 0, 1, 9, 4, 5, 8, 8, 5, 10, 8, 10, 11 ],
[ 5, 9, 4, 1, 11, 3, 1, 10, 11 ],
[ 3, 8, 4, 3, 4, 2, 2, 4, 5, 2, 5, 10 ],
[ 10, 2, 5, 5, 2, 4, 2, 0, 4 ], [ 0, 3, 8, 5, 9, 4, 10, 2, 1 ],
[ 2, 1, 10, 9, 4, 5 ], [ 8, 4, 5, 2, 8, 5, 2, 11, 8, 2, 5, 1 ],
[ 3, 2, 11, 1, 4, 5, 1, 0, 4 ], [ 9, 4, 5, 8, 2, 11, 8, 0, 2 ],
[ 11, 3, 2, 9, 4, 5 ], [ 4, 5, 8, 8, 5, 3, 5, 1, 3 ],
[ 5, 0, 4, 5, 1, 0 ], [ 3, 8, 0, 4, 5, 9 ], [ 9, 4, 5 ],
[ 7, 4, 11, 4, 9, 11, 11, 9, 10 ],
[ 3, 0, 8, 7, 4, 11, 11, 4, 9, 11, 9, 10 ],
[ 11, 7, 4, 1, 11, 4, 1, 10, 11, 1, 4, 0 ],
[ 8, 7, 4, 11, 1, 10, 11, 3, 1 ],
[ 2, 3, 7, 2, 7, 9, 7, 4, 9, 2, 9, 10 ],
[ 4, 8, 7, 0, 10, 2, 0, 9, 10 ], [ 2, 1, 10, 0, 7, 4, 0, 3, 7 ],
[ 10, 2, 1, 8, 7, 4 ], [ 2, 11, 7, 2, 7, 1, 1, 7, 4, 1, 4, 9 ],
[ 3, 2, 11, 4, 8, 7, 9, 1, 0 ], [ 7, 4, 11, 11, 4, 2, 4, 0, 2 ],
[ 2, 11, 3, 7, 4, 8 ], [ 9, 1, 4, 4, 1, 7, 1, 3, 7 ],
[ 1, 0, 9, 8, 7, 4 ], [ 3, 4, 0, 3, 7, 4 ], [ 8, 7, 4 ],
[ 8, 9, 10, 8, 10, 11 ], [ 0, 9, 3, 3, 9, 11, 9, 10, 11 ],
[ 1, 10, 0, 0, 10, 8, 10, 11, 8 ], [ 10, 3, 1, 10, 11, 3 ],
[ 3, 8, 2, 2, 8, 10, 8, 9, 10 ], [ 9, 2, 0, 9, 10, 2 ],
[ 8, 0, 3, 1, 10, 2 ], [ 10, 2, 1 ], [ 2, 11, 1, 1, 11, 9, 11, 8, 9 ],
[ 11, 3, 2, 0, 9, 1 ], [ 11, 0, 2, 11, 8, 0 ], [ 11, 3, 2 ],
[ 8, 1, 3, 8, 9, 1 ], [ 9, 1, 0 ], [ 8, 0, 3 ], [] ];
};
export let MarchingCube = new MarchingCubeInitializer();
//each webworker needs its own marching cube object
// a little class for 3d array, should really generalize this and
// use throughout...
export class PointGrid {
data: Int32Array;
width: number;
height: number;
constructor(length, width, height) {
// the standard says this is zero initialized
this.data = new Int32Array(length * width * height * 3);
this.width = width;
this.height = height;
}
// set position x,y,z to pt, which has ix,iy,and iz
set(x:number, y:number, z:number, pt) {
let index = ((((x * this.width) + y) * this.height) + z) * 3;
this.data[index] = pt.ix;
this.data[index + 1] = pt.iy;
this.data[index + 2] = pt.iz;
};
// return point at x,y,z
get(x:number, y:number, z:number) {
let index = ((((x * this.width) + y) * this.height) + z) * 3;
return {
ix : this.data[index],
iy : this.data[index + 1],
iz : this.data[index + 2]
};
};
};
/*
* @type Class
*/
export class ProteinSurface {
// constants for vpbits bitmasks
readonly INOUT = 1;
readonly ISDONE = 2;
readonly ISBOUND = 4;
ptranx:number = 0;
ptrany:number = 0;
ptranz:number = 0;
probeRadius:number = 1.4;
defaultScaleFactor:number = 2;
scaleFactor:number = this.defaultScaleFactor; // 2 is .5A grid; if this is made user configurable,
// also have to adjust offset used to find non-shown
// atoms
pHeight:number = 0;
pWidth:number = 0;
pLength:number = 0;
cutRadius:number = 0;
vpBits: any = null; // uint8 array of bitmasks
vpDistance: any = null; // floatarray of _squared_ distances
vpAtomID: any = null; // intarray
pminx:number = 0;
pminy:number = 0;
pminz:number = 0;
pmaxx:number = 0;
pmaxy:number = 0;
pmaxz:number = 0;
depty = {};
widxz = {};
faces: number[] = [];
verts = [];
static MarchingCube = new MarchingCubeInitializer();
constructor() {
if(!ProteinSurface.MarchingCube) {
//this is needed by webworkers
ProteinSurface.MarchingCube = new MarchingCubeInitializer();
}
}
readonly vdwRadii = {
"H" : 1.2,
"Li" : 1.82,
"Na" : 2.27,
"K" : 2.75,
"C" : 1.7,
"N" : 1.55,
"O" : 1.52,
"F" : 1.47,
"P" : 1.80,
"S" : 1.80,
"CL" : 1.75,
"BR" : 1.85,
"SE" : 1.90,
"ZN" : 1.39,
"CU" : 1.4,
"NI" : 1.63,
"X" : 2
};
private getVDWIndex(atom:any) {
if(!atom.elem || typeof(this.vdwRadii[atom.elem]) == "undefined") {
return "X";
}
return atom.elem;
};
readonly nb = [ new Int32Array([ 1, 0, 0 ]), new Int32Array([ -1, 0, 0 ]),
new Int32Array([ 0, 1, 0 ]), new Int32Array([ 0, -1, 0 ]),
new Int32Array([ 0, 0, 1 ]),
new Int32Array([ 0, 0, -1 ]),
new Int32Array([ 1, 1, 0 ]),
new Int32Array([ 1, -1, 0 ]),
new Int32Array([ -1, 1, 0 ]),
new Int32Array([ -1, -1, 0 ]),
new Int32Array([ 1, 0, 1 ]),
new Int32Array([ 1, 0, -1 ]),
new Int32Array([ -1, 0, 1 ]),
new Int32Array([ -1, 0, -1 ]),
new Int32Array([ 0, 1, 1 ]),
new Int32Array([ 0, 1, -1 ]),
new Int32Array([ 0, -1, 1 ]),
new Int32Array([ 0, -1, -1 ]),
new Int32Array([ 1, 1, 1 ]),
new Int32Array([ 1, 1, -1 ]),
new Int32Array([ 1, -1, 1 ]),
new Int32Array([ -1, 1, 1 ]),
new Int32Array([ 1, -1, -1 ]),
new Int32Array([ -1, -1, 1 ]),
new Int32Array([ -1, 1, -1 ]),
new Int32Array([ -1, -1, -1 ]) ];
public getFacesAndVertices(atomlist: any[]) {
let atomsToShow = {};
for (let i = 0, il = atomlist.length; i < il; i++)
atomsToShow[atomlist[i]] = true;
let vertices = this.verts;
for (let i = 0, il = vertices.length; i < il; i++) {
vertices[i].x = vertices[i].x / this.scaleFactor - this.ptranx;
vertices[i].y = vertices[i].y / this.scaleFactor - this.ptrany;
vertices[i].z = vertices[i].z / this.scaleFactor - this.ptranz;
}
let finalfaces = [];
for (let i = 0, il = this.faces.length; i < il; i += 3) {
//let f = faces[i];
let fa = this.faces[i], fb = this.faces[i+1], fc = this.faces[i+2];
let a = vertices[fa].atomid, b = vertices[fb].atomid, c = vertices[fc].atomid;
// must be a unique face for each atom
let which = a;
if (b < which)
which = b;
if (c < which)
which = c;
if (!atomsToShow[which]) {
continue;
}
if (fa !== fb && fb !== fc && fa !== fc){
finalfaces.push(fa);
finalfaces.push(fb);
finalfaces.push(fc);
}
}
//try to help the garbage collector
this.vpBits = null; // uint8 array of bitmasks
this.vpDistance = null; // floatarray
this.vpAtomID = null; // intarray
return {
'vertices' : vertices,
'faces' : finalfaces
};
};
public initparm (extent: number[][], btype, volume) {
if(volume > 1000000) //heuristical decrease resolution to avoid large memory consumption
this.scaleFactor = this.defaultScaleFactor/2;
let margin = (1 / this.scaleFactor) * 5.5; // need margin to avoid
// boundary/round off effects
this.pminx = extent[0][0]; this.pmaxx = extent[1][0];
this.pminy = extent[0][1]; this.pmaxy = extent[1][1];
this.pminz = extent[0][2]; this.pmaxz = extent[1][2];
if (!btype) {
this.pminx -= margin;
this.pminy -= margin;
this.pminz -= margin;
this.pmaxx += margin;
this.pmaxy += margin;
this.pmaxz += margin;
} else {
this.pminx -= this.probeRadius + margin;
this.pminy -= this.probeRadius + margin;
this.pminz -= this.probeRadius + margin;
this.pmaxx += this.probeRadius + margin;
this.pmaxy += this.probeRadius + margin;
this.pmaxz += this.probeRadius + margin;
}
this.pminx = Math.floor(this.pminx * this.scaleFactor) / this.scaleFactor;
this.pminy = Math.floor(this.pminy * this.scaleFactor) / this.scaleFactor;
this.pminz = Math.floor(this.pminz * this.scaleFactor) / this.scaleFactor;
this.pmaxx = Math.ceil(this.pmaxx * this.scaleFactor) / this.scaleFactor;
this.pmaxy = Math.ceil(this.pmaxy * this.scaleFactor) / this.scaleFactor;
this.pmaxz = Math.ceil(this.pmaxz * this.scaleFactor) / this.scaleFactor;
this.ptranx = -this.pminx;
this.ptrany = -this.pminy;
this.ptranz = -this.pminz;
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(btype);
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); // float 32
// doesn't
// play
// nicely
// with
// native
// floats
this.vpAtomID = new Int32Array(this.pLength * this.pWidth * this.pHeight);
};
public boundingatom(btype) {
let tradius = {};
for ( const i in this.vdwRadii) {
let r = this.vdwRadii[i];
if (!btype)
tradius[i] = r * this.scaleFactor + 0.5;
else
tradius[i] = (r + this.probeRadius) * this.scaleFactor + 0.5;
let sradius = tradius[i] * tradius[i];
this.widxz[i] = Math.floor(tradius[i]) + 1;
this.depty[i] = new Int32Array(this.widxz[i] * this.widxz[i]);
let indx = 0;
for (let j = 0; j < this.widxz[i]; j++) {
for (let k = 0; k < this.widxz[i]; k++) {
let txz = j * j + k * k;
if (txz > sradius)
this.depty[i][indx] = -1; // outside
else {
let tdept = Math.sqrt(sradius - txz);
this.depty[i][indx] = Math.floor(tdept);
}
indx++;
}
}
}
};
public fillvoxels(atoms, atomlist) { // (int seqinit,int
// seqterm,bool
// atomtype,atom*
// proseq,bool bcolor)
for (let i = 0, il = this.vpBits.length; i < il; i++) {
this.vpBits[i] = 0;
this.vpDistance[i] = -1.0;
this.vpAtomID[i] = -1;
}
for (let i in atomlist) {
let atom = atoms[atomlist[i]];
if (atom === undefined)
continue;
this.fillAtom(atom, atoms);
}
for (let i = 0, il = this.vpBits.length; i < il; i++)
if (this.vpBits[i] & this.INOUT)
this.vpBits[i] |= this.ISDONE;
};
public fillAtom(atom, atoms) {
let cx = Math.floor(0.5 + this.scaleFactor * (atom.x + this.ptranx));
let cy = Math.floor(0.5 + this.scaleFactor * (atom.y + this.ptrany));
let cz = Math.floor(0.5 + this.scaleFactor * (atom.z + this.ptranz));
let at = this.getVDWIndex(atom);
let nind = 0;
let pWH = this.pWidth*this.pHeight;
for (let i = 0, n = this.widxz[at]; i < n; i++) {
for (let j = 0; j < n; j++) {
if (this.depty[at][nind] != -1) {
for (let ii = -1; ii < 2; ii++) {
for (let jj = -1; jj < 2; jj++) {
for (let kk = -1; kk < 2; kk++) {
if (ii !== 0 && jj !== 0 && kk !== 0) {
let mi = ii * i;
let mk = kk * j;
for (let k = 0; k <= this.depty[at][nind]; k++) {
let mj = k * jj;
let si = cx + mi;