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parsers.js
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parsers.js
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/**
* $3Dmol.Parsers stores functions for parsing molecular data. They all take a string of molecular data
* and options. The default behavior is to only read the first model in the case of multimodel files, and
* all parsers return a list of atom list(s)
*
* $3Dmol.Parsers.<ext> corresponds to the parsers for files with extension ext
*/
$3Dmol.Parsers = (function() {
var parsers = {};
/**
* @param {AtomSpec[]}
* atomsarray
*/
var assignBonds = function(atoms) {
// assign bonds - yuck, can't count on connect records
for (var i = 0, n = atoms.length; i < n; i++) {
// Don't reindex if atoms are already indexed
if (!atoms[i].index)
atoms[i].index = i;
}
var grid = {};
var MAX_BOND_LENGTH = 4.95; // (largest bond length, Cs) 2.25 * 2 * 1.1 (fudge factor)
for (var index = 0; index < atoms.length; index++) {
var atom = atoms[index];
var x = Math.floor(atom.x / MAX_BOND_LENGTH);
var y = Math.floor(atom.y / MAX_BOND_LENGTH);
var z = Math.floor(atom.z / MAX_BOND_LENGTH);
if (!grid[x]) {
grid[x] = {};
}
if (!grid[x][y]) {
grid[x][y] = {};
}
if (!grid[x][y][z]) {
grid[x][y][z] = [];
}
grid[x][y][z].push(atom);
}
var findConnections = function(points, otherPoints) {
for (var i = 0; i < points.length; i++) {
var atom1 = points[i];
for (var j = 0; j < otherPoints.length; j++) {
var atom2 = otherPoints[j];
if (areConnected(atom1, atom2)) {
//gracefully handle one-sided bonds
var a2i = atom1.bonds.indexOf(atom2.index);
var a1i = atom2.bonds.indexOf(atom1.index);
if (a2i == -1 && a1i == -1) {
atom1.bonds.push(atom2.index);
atom1.bondOrder.push(1);
atom2.bonds.push(atom1.index);
atom2.bondOrder.push(1);
} else if (a2i == -1) {
atom1.bonds.push(atom2.index);
atom1.bondOrder.push(atom2.bondOrder[a1i])
} else if (a1i == -1) {
atom2.bonds.push(atom1.index);
atom2.bondOrder.push(atom1.bondOrder[a2i])
}
}
}
}
}
/*const*/ var OFFSETS = [
{x: 0, y: 0, z: 1},
{x: 0, y: 1, z:-1},
{x: 0, y: 1, z: 0},
{x: 0, y: 1, z: 1},
{x: 1, y:-1, z:-1},
{x: 1, y:-1, z: 0},
{x: 1, y:-1, z: 1},
{x: 1, y: 0, z:-1},
{x: 1, y: 0, z: 0},
{x: 1, y: 0, z: 1},
{x: 1, y: 1, z:-1},
{x: 1, y: 1, z: 0},
{x: 1, y: 1, z: 1}
];
for (var x in grid) {
x = parseInt(x);
for (var y in grid[x]) {
y = parseInt(y);
for (var z in grid[x][y]) {
z = parseInt(z);
var points = grid[x][y][z];
for (var i = 0; i < points.length; i++) {
var atom1 = points[i];
for (var j = i + 1; j < points.length; j++) {
var atom2 = points[j];
if (areConnected(atom1, atom2)) {
if (atom1.bonds.indexOf(atom2.index) == -1) {
atom1.bonds.push(atom2.index);
atom1.bondOrder.push(1);
atom2.bonds.push(atom1.index);
atom2.bondOrder.push(1);
}
}
}
}
for (var o = 0; o < OFFSETS.length; o++) {
var offset = OFFSETS[o];
if (!grid[x+offset.x]
|| !grid[x+offset.x][y+offset.y]
|| !grid[x+offset.x][y+offset.y][z+offset.z]) continue;
var otherPoints = grid[x + offset.x][y + offset.y][z + offset.z];
findConnections(points, otherPoints);
}
}
}
}
};
// this is optimized for proteins where it is assumed connected
// atoms are on the same or next residue
/**
* @param {AtomSpec[]}
* atomsarray
*/
var assignPDBBonds = function(atomsarray) {
// assign bonds - yuck, can't count on connect records
var protatoms = [];
var hetatoms = [];
var i, n;
for (i = 0, n = atomsarray.length; i < n; i++) {
var atom = atomsarray[i];
atom.index = i;
if (atom.hetflag)
hetatoms.push(atom);
else
protatoms.push(atom);
}
assignBonds(hetatoms);
// sort by resid
protatoms.sort(function(a, b) {
if (a.chain != b.chain)
return a.chain < b.chain ? -1 : 1;
return a.resi - b.resi;
});
// for identifying connected residues
var currentResi = -1;
var reschain = -1;
var lastResConnected;
for (i = 0, n = protatoms.length; i < n; i++) {
var ai = protatoms[i];
if (ai.resi !== currentResi) {
currentResi = ai.resi;
if (!lastResConnected)
reschain++;
lastResConnected = false;
}
ai.reschain = reschain;
for (var j = i + 1; j < protatoms.length; j++) {
var aj = protatoms[j];
if (aj.chain != ai.chain)
break;
if (aj.resi - ai.resi > 1) // can't be connected
break;
if (areConnected(ai, aj)) {
if (ai.bonds.indexOf(aj.index) === -1) {
// only add if not already there
ai.bonds.push(aj.index);
ai.bondOrder.push(1);
aj.bonds.push(ai.index);
aj.bondOrder.push(1);
}
if (ai.resi !== aj.resi)
lastResConnected = true;
}
}
}
};
// this will identify all hydrogen bonds between backbone
// atoms; assume atom names are correct, only identifies
// single closest hbond
var assignBackboneHBonds = function(atomsarray) {
var maxlength = 3.2;
var maxlengthSq = 10.24;
var atoms = [];
var i, j, n;
for (i = 0, n = atomsarray.length; i < n; i++) {
atomsarray[i].index = i;
// only consider 'N' and 'O'
var atom = atomsarray[i];
if (!atom.hetflag && (atom.atom === "N" || atom.atom === "O")) {
atoms.push(atom);
atom.hbondOther = null;
atom.hbondDistanceSq = Number.POSITIVE_INFINITY;
}
}
atoms.sort(function(a, b) {
return a.z - b.z;
});
for (i = 0, n = atoms.length; i < n; i++) {
var ai = atoms[i];
for (j = i + 1; j < n; j++) {
var aj = atoms[j];
var zdiff = aj.z - ai.z;
if (zdiff > maxlength) // can't be connected
break;
if (aj.atom == ai.atom)
continue; // can't be connected, but later might be
var ydiff = Math.abs(aj.y - ai.y);
if (ydiff > maxlength)
continue;
var xdiff = Math.abs(aj.x - ai.x);
if (xdiff > maxlength)
continue;
var dist = xdiff * xdiff + ydiff * ydiff + zdiff * zdiff;
if (dist > maxlengthSq)
continue;
if (aj.chain == ai.chain && Math.abs(aj.resi - ai.resi) < 4)
continue; // ignore bonds between too close residues
// select closest hbond
if (dist < ai.hbondDistanceSq) {
ai.hbondOther = aj;
ai.hbondDistanceSq = dist;
}
if (dist < aj.hbondDistanceSq) {
aj.hbondOther = ai;
aj.hbondDistanceSq = dist;
}
}
}
};
var computeSecondaryStructure = function(atomsarray) {
assignBackboneHBonds(atomsarray);
// compute, per residue, what the secondary structure is
var chres = {}; // lookup by chain and resid
var i, il, c, r; // i: used in for loop, il: length of atomsarray
var atom, val;
//identify helices first
for (i = 0, il = atomsarray.length; i < il; i++) {
atom = atomsarray[i];
if (typeof (chres[atom.chain]) === "undefined")
chres[atom.chain] = [];
if (isFinite(atom.hbondDistanceSq)) {
var other = atom.hbondOther;
if (typeof (chres[other.chain]) === "undefined")
chres[other.chain] = [];
if (Math.abs(other.resi - atom.resi) === 4) {
// helix
chres[atom.chain][atom.resi] = 'h';
}
}
}
// plug gaps in helices
for (c in chres) {
for (r = 1; r < chres[c].length - 1; r++) {
var valbefore = chres[c][r - 1];
var valafter = chres[c][r + 1];
val = chres[c][r];
if (valbefore == 'h' && valbefore == valafter && val != valbefore) {
chres[c][r] = valbefore;
}
}
}
//now potential sheets - but only if mate not part of helix
for (i = 0, il = atomsarray.length; i < il; i++) {
atom = atomsarray[i];
if (isFinite(atom.hbondDistanceSq) && chres[atom.chain][atom.resi] != 'h' && atom.ss != 'h') {
chres[atom.chain][atom.resi] = 'maybesheet';
}
}
//sheets must bond to other sheets
for (i = 0, il = atomsarray.length; i < il; i++) {
atom = atomsarray[i];
if (isFinite(atom.hbondDistanceSq) && chres[atom.chain][atom.resi] == 'maybesheet') {
var other = atom.hbondOther;
var otherval = chres[other.chain][other.resi];
if (otherval == 'maybesheet' || otherval == 's') {
// true sheet
chres[atom.chain][atom.resi] = 's';
chres[other.chain][other.resi] = 's';
}
}
}
// plug gaps in sheets and remove singletons
for (c in chres) {
for (r = 1; r < chres[c].length - 1; r++) {
var valbefore = chres[c][r - 1];
var valafter = chres[c][r + 1];
val = chres[c][r];
if (valbefore == 's' && valbefore == valafter && val != valbefore) {
chres[c][r] = valbefore;
}
}
for (r = 0; r < chres[c].length; r++) {
val = chres[c][r];
if (val == 'h' || val == 's') {
if (chres[c][r - 1] != val && chres[c][r + 1] != val)
delete chres[c][r];
}
}
}
// assign to all atoms in residue, keep track of start
var curres = null;
for (i = 0, il = atomsarray.length; i < il; i++) {
atom = atomsarray[i];
val = chres[atom.chain][atom.resi];
if (typeof (val) == "undefined" || val == 'maybesheet')
continue;
atom.ss = val;
if (chres[atom.chain][atom.resi - 1] != val)
atom.ssbegin = true;
if (chres[atom.chain][atom.resi + 1] != val)
atom.ssend = true;
}
};
//make sure bonds are actually two way
var validateBonds = function(atomsarray, serialToIndex) {
for (var i = 0, n = atomsarray.length; i < n; i++) {
var atom = atomsarray[i];
for(var b = 0; b < atom.bonds.length; b++) {
var a2i = atom.bonds[b];
var atom2 = atomsarray[a2i];
var atomi = serialToIndex[atom.serial];
if(atom2 && atomi) {
var a1i = atom2.bonds.indexOf(atomi);
if(a1i < 0) {
atom2.bonds.push(atomi);
atom2.bondOrder.push(atom.bondOrder[b]);
}
}
}
}
};
/**
* @param {string}
* str
* @param {ParserOptionsSpec}
* options
*/
parsers.vasp = parsers.VASP = function (str, options) {
var atoms = [[]];
var lattice = {};
var lines = str.replace(/^\s+/, "").split(/[\n\r]/);
if (lines.length < 3){
return atoms;
}
if (lines[1].match(/\d+/)) {
lattice.length = parseFloat(lines[1]);
} else {
console.log("Warning: second line of the vasp structure file must be a number");
return atoms;
}
if (lattice.length<0) {
console.log("Warning: Vasp implementation for negative lattice lengths is not yet available");
return atoms;
}
lattice.xVec = new Float32Array(lines[2].replace(/^\s+/, "").split(/\s+/));
lattice.yVec = new Float32Array(lines[3].replace(/^\s+/, "").split(/\s+/));
lattice.zVec = new Float32Array(lines[4].replace(/^\s+/, "").split(/\s+/));
var matrix = new $3Dmol.Matrix4(lattice.xVec[0], lattice.xVec[1], lattice.xVec[2], 0,
lattice.yVec[0], lattice.yVec[1], lattice.yVec[2], 0,
lattice.zVec[0], lattice.zVec[1], lattice.zVec[2], 0,
0, 0, 0, 1);
matrix.multiplyScalar(lattice.length)
var modelData = atoms.modelData = [{symmetries:[], cryst:{matrix:matrix}}];
var atomSymbols=lines[5].replace(/\s+/, "").replace(/\s+$/,"").split(/\s+/);
var atomSpeciesNumber=new Int16Array(lines[6].replace(/^\s+/, "").split(/\s+/));
var vaspMode=lines[7].replace(/\s+/, "");
if (vaspMode.match(/C/)) {
vaspMode = "cartesian";
}else if (vaspMode.match(/D/)){
vaspMode="direct";
} else {
console.log("Warning: Unknown vasp mode in POSCAR file: mode must be either C(artesian) or D(irect)");
return atoms;
}
if (atomSymbols.length != atomSpeciesNumber.length) {
console.log("Warning: declaration of atomary species wrong:");
console.log(atomSymbols);
console.log(atomSpeciesNumber);
return atoms;
}
lines.splice(0,8);
var atomCounter = 0;
for (var i = 0, len = atomSymbols.length; i < len; i++) {
var atomSymbol = atomSymbols[i];
for (var j = 0, atomLen = atomSpeciesNumber[i]; j < atomLen; j++) {
var coords = new Float32Array(lines[atomCounter + j].replace(/^\s+/, "").split(/\s+/));
var atom={};
atom.elem = atomSymbol;
if (vaspMode == "cartesian") {
atom.x = lattice.length*coords[0];
atom.y = lattice.length*coords[1];
atom.z = lattice.length*coords[2];
} else {
atom.x = lattice.length*(coords[0]*lattice.xVec[0] + coords[1]*lattice.yVec[0] + coords[2]*lattice.zVec[0]);
atom.y = lattice.length*(coords[0]*lattice.xVec[1] + coords[1]*lattice.yVec[1] + coords[2]*lattice.zVec[1]);
atom.z = lattice.length*(coords[0]*lattice.xVec[2] + coords[1]*lattice.yVec[2] + coords[2]*lattice.zVec[2]);
}
atom.bonds=[];
atoms[0].push(atom);
}
atomCounter += atomSpeciesNumber[i];
}
return atoms;
}
/**
* @param {string}
* str
* @param {ParserOptionsSpec}
* options
*/
parsers.cube = parsers.CUBE = function(str, options) {
var atoms = [[]];
var lines = str.replace(/^\s+/, "").split(/\n\r|\r+/);
if (lines.length < 6)
return atoms;
var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(
" ");
var natoms = Math.abs(parseFloat(lineArr[0]));
lineArr = lines[3].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
// might have to convert from bohr units to angstroms
var convFactor = (parseFloat(lineArr[0]) > 0) ? 0.529177 : 1;
// Extract atom portion; send to new GLModel...
lines = lines.splice(6, natoms);
var start = atoms[atoms.length-1].length;
var end = start + lines.length;
for (var i = start; i < end; ++i) {
var atom = {};
atom.serial = i;
var line = lines[i - start];
var tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
" ");
if (tokens[0] == 6)
atom.elem = "C";
else if (tokens[0] == 1)
atom.elem = "H";
else if (tokens[0] == 8)
atom.elem = "O";
else if (tokens[0] == 17)
atom.elem = "Cl";
atom.x = parseFloat(tokens[2]) * convFactor;
atom.y = parseFloat(tokens[3]) * convFactor;
atom.z = parseFloat(tokens[4]) * convFactor;
atom.hetflag = true;
atom.bonds = [];
atom.bondOrder = [];
atom.properties = {};
atoms[atoms.length-1].push(atom);
}
for (var i = 0; i < atoms.length; i++)
assignBonds(atoms[i]);
return atoms;
};
// read an XYZ file from str and return result
/**
* @param {string}
* str
* @param {ParserOptionsSpec}
* options
*/
parsers.xyz = parsers.XYZ = function(str, options) {
var atoms = [[]];
var lines = str.split(/\r?\n|\r/);
while (lines.length > 0) {
if (lines.length < 3)
break;
var atomCount = parseInt(lines[0]);
if (isNaN(atomCount) || atomCount <= 0)
break;
if (lines.length < atomCount + 2)
break;
var offset = 2;
var start = atoms[atoms.length-1].length;
var end = start + atomCount;
for (var i = start; i < end; i++) {
var line = lines[offset++];
var tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
" ");
var atom = {};
atom.serial = i;
var elem = tokens[0];
atom.atom = atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
atom.x = parseFloat(tokens[1]);
atom.y = parseFloat(tokens[2]);
atom.z = parseFloat(tokens[3]);
atom.hetflag = true;
atom.bonds = [];
atom.bondOrder = [];
atom.properties = {};
atoms[atoms.length-1][i] = atom;
if (tokens.length >= 7) {
atom.dx = parseFloat(tokens[4]);
atom.dy = parseFloat(tokens[5]);
atom.dz = parseFloat(tokens[6]);
}
}
if (options.multimodel) {
atoms.push([]);
lines.splice(0, offset);
}
else {
break;
}
}
for (var i = 0; i < atoms.length; i++) {
assignBonds(atoms[i]);
}
if (options.onemol) {
var temp = atoms;
atoms = [];
atoms.push(temp[0]);
for (var i = 1; i < temp.length; i++) {
var offset = atoms[0].length;
for (var j = 0; j < temp[i].length; j++) {
var a = temp[i][j];
for (var k = 0; k < a.bonds.length; k++) {
a.bonds[k] = a.bonds[k] + offset;
}
a.index = atoms[0].length;
a.serial = atoms[0].length;
atoms[0].push(a);
}
}
}
return atoms;
};
// put atoms specified in sdf fromat in str into atoms
// adds to atoms, does not replace
/**
* @param {string}
* str
* @param {ParserOptionsSpec}
* options
*/
parsers.sdf = parsers.SDF = function(str, options) {
var atoms = [[]];
var noH = false;
if (typeof options.keepH !== "undefined")
noH = !options.keepH;
var lines = str.split(/\r?\n|\r/);
while(lines.length > 0) {
if (lines.length < 4)
break;
var atomCount = parseInt(lines[3].substr(0, 3));
if (isNaN(atomCount) || atomCount <= 0)
break;
var bondCount = parseInt(lines[3].substr(3, 3));
var offset = 4;
if (lines.length < 4 + atomCount + bondCount)
break;
// serial is atom's index in file; index is atoms index in 'atoms'
var serialToIndex = [];
var start = atoms[atoms.length-1].length;
var end = start + atomCount;
var i, line;
for (i = start; i < end; i++,offset++) {
line = lines[offset];
var atom = {};
var elem = line.substr(31, 3).replace(/ /g, "");
atom.atom = atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
if (atom.elem != 'H' || !noH) {
atom.serial = i;
serialToIndex[i] = atoms[atoms.length-1].length;
atom.x = parseFloat(line.substr(0, 10));
atom.y = parseFloat(line.substr(10, 10));
atom.z = parseFloat(line.substr(20, 10));
atom.hetflag = true;
atom.bonds = [];
atom.bondOrder = [];
atom.properties = {};
atom.index = atoms[atoms.length-1].length;
atoms[atoms.length-1].push(atom);
}
}
for (i = 0; i < bondCount; i++,offset++) {
line = lines[offset];
var from = serialToIndex[parseInt(line.substr(0, 3)) - 1 + start];
var to = serialToIndex[parseInt(line.substr(3, 3)) - 1 + start];
var order = parseInt(line.substr(6, 3));
if (typeof (from) != 'undefined' && typeof (to) != 'undefined') {
atoms[atoms.length-1][from].bonds.push(to);
atoms[atoms.length-1][from].bondOrder.push(order);
atoms[atoms.length-1][to].bonds.push(from);
atoms[atoms.length-1][to].bondOrder.push(order);
}
}
if (options.multimodel) {
if (!options.onemol)
atoms.push([]);
while (lines[offset] != "$$$$")
offset++
lines.splice(0, ++offset);
}
else {
break;
}
}
return atoms;
};
// This parses the ChemDoodle json file format. Although this is registered
// for the json file extension, other chemical json file formats exist that
// this can not parse. Check which one you have and do not assume that
// .json can be parsed
parsers.cdjson = parsers.json = function(str, options) {
var atoms = [[]];
if (typeof str === "string") { // Str is usually automatically parsed by JQuery
str = JSON.parse(str);
}
var molecules = str.m;
var atomsInFile = molecules[0].a; // Assumes there is at least one
var bondsInFile = molecules[0].b; // molecule and ignores any more
// Ignores any shapes
var styles = molecules[0].s;
var parseStyle = options !== undefined && options.parseStyle !== undefined ? options.parseStyle : styles !== undefined;
var offset = atoms[atoms.length-1].length; // When adding atoms their index will be
// Offset by the number of existing atoms
for (var i = 0; i < atomsInFile.length; i++) {
var currentAtom = atomsInFile[i];
var atom = {};
atom.id = currentAtom.i; // Probably won't exist. Doesn't seem to
// break anything.
atom.x = currentAtom.x;
atom.y = currentAtom.y;
atom.z = currentAtom.z || 0; // Default value if file is 2D
atom.bonds = [];
atom.bondOrder = [];
var elem = currentAtom.l || 'C';
atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
atom.serial = atoms[atoms.length-1].length;
if (parseStyle) {
atom.style = styles[currentAtom.s || 0];
}
atoms[atoms.length-1].push(atom);
}
for (var i = 0; i < bondsInFile.length; i++) {
var currentBond = bondsInFile[i];
var beginIndex = currentBond.b + offset;
var endIndex = currentBond.e + offset;
var bondOrder = currentBond.o || 1;
var firstAtom = atoms[atoms.length-1][beginIndex];
var secondAtom = atoms[atoms.length-1][endIndex];
firstAtom.bonds.push(endIndex);
firstAtom.bondOrder.push(bondOrder);
secondAtom.bonds.push(beginIndex);
secondAtom.bondOrder.push(bondOrder);
}
return atoms;
}
// puts atoms specified in mmCIF fromat in str into atoms
/**
* @param {string}
* str
* @param {ParserOptionsSpec}
* options
*/
parsers.mcif = parsers.cif = function(str, options) {
var atoms = [];
var noAssembly = !options.doAssembly; // don't assemble by default
var copyMatrix = !options.duplicateAssemblyAtoms;
var modelData = atoms.modelData = [];
// Used to handle quotes correctly
function splitRespectingQuotes(string, separator) {
var sections = [];
var sectionStart = 0;
var sectionEnd = 0;
while (sectionEnd < string.length) {
while (string.substr(sectionEnd, separator.length) !== separator
&& sectionEnd < string.length) {
// currently does not support escaping quotes
if (string[sectionEnd] === "'") {
sectionEnd++;
while (sectionEnd < string.length
&& string[sectionEnd] !== "'") {
sectionEnd++;
}
} else if (string[sectionEnd] === '"') {
sectionEnd++;
while (sectionEnd < string.length
&& string[sectionEnd] !== '"') {
sectionEnd++;
}
}
sectionEnd++;
}
sections.push(string.substr(sectionStart, sectionEnd
- sectionStart));
sectionStart = sectionEnd = sectionEnd + separator.length;
}
return sections;
}
var lines = str.split(/\r?\n|\r/);
// Filter text to remove comments, trailing spaces, and empty lines
var linesFiltered = [];
var trimDisabled = false;
for (var lineNum = 0; lineNum < lines.length; lineNum++) {
// first remove comments
// incorrect if #'s are allowed in strings
// comments might only be allowed at beginning of line, not sure
var line = lines[lineNum].split('#')[0];
// inside data blocks, the string must be left verbatim
// datablocks are started with a ';' at the beginning of a line
// and ended with a ';' on its own line.
if (trimDisabled) {
if (line[0] === ';') {
trimDisabled = false;
}
} else {
if (line[0] === ';') {
trimDisabled = true;
}
}
if (trimDisabled || line !== "") {
if (!trimDisabled) {
line = line.trim();
if (line[0] === '_') {
// Replace dot separating category from data item with underscore. Dots aren't guarenteed, to makes
// files consistent.
var dot = line.split(/\s/)[0].indexOf('.');
if (dot > -1) {
line[dot] = '_';
line = line.substr(0,dot) + '_' + line.substr(dot + 1)
}
}
}
linesFiltered.push(line);
}
}
var lineNum = 0;
while (lineNum < linesFiltered.length) {
while (! linesFiltered[lineNum].startsWith("data_") ||
linesFiltered[lineNum] === "data_global") {
lineNum++;
}
lineNum++;
// Process the lines and puts all of the data into an object.
var mmCIF = {};
while (lineNum < linesFiltered.length &&
! linesFiltered[lineNum].startsWith("data_")) {
if (linesFiltered[lineNum][0] === undefined) {
lineNum++;
} else if (linesFiltered[lineNum][0] === '_') {
var dataItemName = (linesFiltered[lineNum].split(/\s/)[0]).toLowerCase();
var dataItem = (mmCIF[dataItemName] = mmCIF[dataItemName] || []);
// if nothing left on the line go to the next one
var restOfLine = linesFiltered[lineNum]
.substr(linesFiltered[lineNum].indexOf(dataItemName)
+ dataItemName.length);
if (restOfLine === "") {
lineNum++;
if (linesFiltered[lineNum][0] === ';') {
var dataBlock = linesFiltered[lineNum].substr(1);
lineNum++;
while (linesFiltered[lineNum] !== ';') {
dataBlock = dataBlock + '\n'
+ linesFiltered[lineNum];
lineNum++;
}
dataItem.push(dataBlock);
} else {
dataItem.push(linesFiltered[lineNum]);
}
} else {
dataItem.push(restOfLine.trim());
}
lineNum++;
} else if (linesFiltered[lineNum].substr(0, 5) === "loop_") {
lineNum++;
var dataItems = [];
while (linesFiltered[lineNum] === ""
|| linesFiltered[lineNum][0] === '_') {
if (linesFiltered[lineNum] !== "") {
var dataItemName = (linesFiltered[lineNum].split(/\s/)[0]).toLowerCase();
var dataItem = (mmCIF[dataItemName] = mmCIF[dataItemName] || []);
dataItems.push(dataItem);
}
lineNum++;
}
var currentDataItem = 0;
while (lineNum < linesFiltered.length
&& linesFiltered[lineNum][0] !== '_'
&& !linesFiltered[lineNum].startsWith("loop_")
&& !linesFiltered[lineNum].startsWith("data_")) {
var line = splitRespectingQuotes(linesFiltered[lineNum], " ");
for (var field = 0; field < line.length; field++) {
if (line[field] !== "") {
dataItems[currentDataItem].push(line[field]);
currentDataItem = (currentDataItem + 1) % dataItems.length;
}
}
lineNum++;
}
} else {
lineNum++;
}
}
modelData.push({symmetries:[]});
// Pulls atom information out of the data
atoms.push([]);
var currentIndex = 0;
var atomCount = mmCIF._atom_site_id !== undefined ? mmCIF._atom_site_id.length
: mmCIF._atom_site_label.length;
function sqr(n) {
return n*n;
}
var conversionMatrix;
if (mmCIF._cell_length_a !== undefined) {
var a = parseFloat(mmCIF._cell_length_a);
var b = parseFloat(mmCIF._cell_length_b);
var c = parseFloat(mmCIF._cell_length_c);
var alpha_deg = parseFloat(mmCIF._cell_angle_alpha) || 90;
var beta_deg = parseFloat(mmCIF._cell_angle_beta) || 90;
var gamma_deg = parseFloat(mmCIF._cell_angle_gamma) || 90;
var alpha = alpha_deg * Math.PI / 180;
var beta = beta_deg * Math.PI / 180;
var gamma = gamma_deg * Math.PI / 180;
var cos_alpha = Math.cos(alpha);
var cos_beta = Math.cos(beta);
var cos_gamma = Math.cos(gamma);
var sin_gamma = Math.sin(gamma);
conversionMatrix = [
[a, b*cos_gamma, c*cos_beta],
[0, b*sin_gamma, c*(cos_alpha-cos_beta*cos_gamma)/sin_gamma],
[0, 0, c*Math.sqrt(1-sqr(cos_alpha)-sqr(cos_beta)-sqr(cos_gamma)+2*cos_alpha*cos_beta*cos_gamma)/sin_gamma]
];
modelData[modelData.length-1].cryst = {'a' : a, 'b' : b, 'c' : c, 'alpha' : alpha_deg, 'beta' : beta_deg, 'gamma' : gamma_deg};
}
function fractionalToCartesian(a, b, c) {
var x = conversionMatrix[0][0]*a + conversionMatrix[0][1]*b + conversionMatrix[0][2]*c;
var y = conversionMatrix[1][0]*a + conversionMatrix[1][1]*b + conversionMatrix[1][2]*c;
var z = conversionMatrix[2][0]*a + conversionMatrix[2][1]*b + conversionMatrix[2][2]*c;
return {x:x, y:y, z:z};
}
for (var i = 0; i < atomCount; i++) {
if (mmCIF._atom_site_group_pdb !== undefined && mmCIF._atom_site_group_pdb[i] === "TER")
continue;
var atom = {};
if (mmCIF._atom_site_cartn_x !== undefined) {
atom.x = parseFloat(mmCIF._atom_site_cartn_x[i]);
atom.y = parseFloat(mmCIF._atom_site_cartn_y[i]);
atom.z = parseFloat(mmCIF._atom_site_cartn_z[i]);
}
else {
var coords = fractionalToCartesian(
parseFloat(mmCIF._atom_site_fract_x[i]),
parseFloat(mmCIF._atom_site_fract_y[i]),
parseFloat(mmCIF._atom_site_fract_z[i]));
atom.x = coords.x;
atom.y = coords.y;
atom.z = coords.z;
}
atom.chain = mmCIF._atom_site_auth_asym_id ? mmCIF._atom_site_auth_asym_id[i] : undefined;
atom.resi = mmCIF._atom_site_auth_seq_id ? parseInt(mmCIF._atom_site_auth_seq_id[i]) : undefined;
atom.resn = mmCIF._atom_site_auth_comp_id ? mmCIF._atom_site_auth_comp_id[i].trim() : undefined;
atom.atom = mmCIF._atom_site_auth_atom_id ? mmCIF._atom_site_auth_atom_id[i].replace(/"/gm,'') : undefined; //"primed" names are in quotes
atom.hetflag = !mmCIF._atom_site_group_pdb || mmCIF._atom_site_group_pdb[i] === "HETA" || mmCIF._atom_site_group_pdb[i] === "HETATM";
var elem = mmCIF._atom_site_type_symbol[i];
atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
atom.bonds = [];
atom.ss = 'c';
atom.serial = i;
atom.bondOrder = [];
atom.properties = {};
atoms[atoms.length-1].push(atom);
}
if (mmCIF._pdbx_struct_oper_list_id !== undefined && !noAssembly) {
for (var i = 0; i < mmCIF._pdbx_struct_oper_list_id.length; i++) {
var matrix11 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[1][1]'][i]);
var matrix12 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[1][2]'][i]);
var matrix13 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[1][3]'][i]);
var vector1 = parseFloat(mmCIF['_pdbx_struct_oper_list_vector[1]'][i]);
var matrix21 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[2][1]'][i]);
var matrix22 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[2][2]'][i]);
var matrix23 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[2][3]'][i]);
var vector2 = parseFloat(mmCIF['_pdbx_struct_oper_list_vector[2]'][i]);
var matrix31 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[3][1]'][i]);
var matrix32 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[3][2]'][i]);
var matrix33 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[3][3]'][i]);
var vector3 = parseFloat(mmCIF['_pdbx_struct_oper_list_vector[3]'][i]);
var matrix = new $3Dmol.Matrix4(matrix11, matrix12, matrix13, vector1,
matrix21, matrix22, matrix23, vector2,
matrix31, matrix32, matrix33, vector3);
modelData[modelData.length-1].symmetries.push(matrix);
}
for (var i = 0; i < atoms.length; i++) {