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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
*/
/**
* Parser options specification. Used to specify the options of a GLModel. Depending on the input file format, not all fields may be defined.
* @typedef ParserOptionsSpec
* @prop {boolean} frames - true if you want to add to a new frame and false otherwise ; supported by all
* @prop {object} vibrate - object specifying the vibration behavior ; supported by all
* @prop {number} vibrate.frames - number of frames to be created, default to 10 ; supported by all
* @prop {number} vibrate.amplitude -amplitude of distortion, default to 1 (full) ; supported by all
* @prop {boolean} multimodel - specifies weather or not multiple models are being defined ; supported by xyz,sdf, or mol2
* @prop {boolean} onemol -specifies weather or not the model is of one molecule ; Supported by xyz , sdf , mol2
* @prop {boolean} keepH - do not strip hydrogens ; supported by sdf,mol2
* @prop {object} parseStyle - used to define ChemDoodle styles ; supported by cdjson
* @prop {boolean} doAssembly - boolean dictating weather or not to do assembly ; supported by mcif
* @prop {boolean} duplicateAssemblyAtoms- Set to true if you wish to duplicate assembly atoms otherwise false ; supported by all formats with symmetries. Not duplicating will result in faster rendering but it will not be possible to individually style symmetries.
* @prop {boolean} normalizeAssembly - shift symmetry mates so their centroid is in the unit cell
* @prop {boolean} dontConnectDuplicatedAtoms - do not detect bonds between symmetries generated with duplicateAssemblyAtoms (cif only - other formats never make bonds between symmetries)
* @prop {boolean} noSecondaryStructure - boolean dictating the presence of a secondary structure ; supported by pdb
* @prop {boolean} noComputeSecondaryStructure - do not compute ss ; supported by pdb
* @prop {string} altLoc -which alternate location to select, if present; '*' to load all ; supported by pdb
* @prop {number} assemblyIndex - index of the assembly in symmetry ; supported by mmtf
* @prop {boolean} assignBonds - for formats without explicit bonds (e.g. PDB, xyz) infer bonding (default true).
*/
$3Dmol.Parsers = (function() {
var parsers = {};
//Covalent radii
var bondTable = {
H :0.37, He:0.32,
Li:1.34,Be:0.90, B :0.82,C :0.77,N :0.75,O :0.73,F :0.71,Ne:0.69,
Na:1.54,Mg:1.30, Al:1.18,Si:1.11,P :1.06,S :1.02,Cl:0.99,Ar:0.97,
K :1.96,Ca:1.74,Sc:1.44,Ti:1.56,V :1.25,/* Cr */Mn:1.39,Fe:1.25,Co:1.26,Ni:1.21,Cu:1.38,Zn:1.31,Ga:1.26,Ge:1.22,/* As */Se:1.16,Br:1.14,Kr:1.10,
Rb:2.11,Sr:1.92,Y :1.62,Zr:1.48,Nb:1.37,Mo:1.45,Tc:1.56,Ru:1.26,Rh:1.35,Pd:1.31,Ag:1.53,Cd:1.48,In:1.44,Sn:1.41,Sb:1.38,Te:1.35,I :1.33,Xe:1.30,
Cs:2.25,Ba:1.98,Lu:1.60,Hf:1.50,Ta:1.38,W :1.46,Re:1.59,Os:1.44,Ir:1.37,Pt:1.28,Au:1.44,Hg:1.49,Tl:1.48,Pb:1.47,Bi:1.46,/* Po *//* At */Rn:1.45,
// None of the bottom row or any of the Lanthanides have bond lengths
};
var anumToSymbol = {
1: 'H', 2: 'He',
3:'Li',4:'Be', 5: 'B', 6: 'C', 7:'N', 8:'O', 9:'F', 10: 'Ne',
11: 'Na',12:'Mg', 13: 'Al',14:'Si',15:'P',16:'S',17:'Cl',18:'Ar',
19: 'K',20:'Ca',21:'Sc',22:'Ti',23:'V',24:'Cr',25:'Mn',26:'Fe',27:'Co',28:'Ni',29:'Cu',30:'Zn',31:'Ga',32:'Ge',33:'As',34:'Se',35:'Br',36:'Kr',
37:'Rb',38:'Sr',39:'Y',40:'Zr',41:'Nb',42:'Mo',43:'Tc',44:'Ru',45:'Rh',46:'Pd',47:'Ag',48:'Cd',49:'In',50:'Sn',51:'Sb',52:'Te',53:'I', 54:'Xe',
55:'Cs',56:'Ba',71:'Lu',72:'Hf',73:'Ta',74:'W',75:'Re',76:'Os',77:'Ir',78:'Pt',79:'Au',80:'Hg',81:'Tl',82:'Pb',83:'Bi',84:'Po',85:'At',86:'Rn',
87:'Fr',88:'Ra',104:'Rf',105:'Db',106:'Sg',107:'Bh',108:'Hs',109:'Mt',110:'Ds',111:'Rg',112:'Cn',113:'Nh',114:'Fl',115:'Mc',116:'Lv',117:'Ts',118:'Og',
57:'La',58:'Ce',59:'Pr',60:'Nd',61:'Pm',62:'Sm',63:'Eu',64:'Gd',65:'Tb',66:'Dy',67:'Ho',68:'Er',69:'Tm',70:'Yb',
89:'Ac',90:'Th',91:'Pa',92:'U',93:'Np',94:'Pu',95:'Am',96:'Cm',97:'Bk',98:'Cf',99:'Es',100:'Fm',101:'Md',102:'No',
};
var bondLength = function(elem) {
return bondTable[elem] || 1.6;
};
// return true if atom1 and atom2 are probably bonded to each other
// based on distance alone
var areConnected = function(atom1, atom2) {
var maxsq = bondLength(atom1.elem) + bondLength(atom2.elem);
maxsq += 0.25;// fudge factor, especially important for md frames, also see 1i3d
maxsq *= maxsq;
var xdiff = atom1.x - atom2.x;
xdiff *= xdiff;
if (xdiff > maxsq)
return false;
var ydiff = atom1.y - atom2.y;
ydiff *= ydiff;
if (ydiff > maxsq)
return false;
var zdiff = atom1.z - atom2.z;
zdiff *= zdiff;
if (zdiff > maxsq)
return false;
var distSquared = xdiff + ydiff + zdiff;
if (isNaN(distSquared))
return false;
else if (distSquared < 0.5)
return false; // maybe duplicate position.
else if (distSquared > maxsq)
return false;
else if(atom1.altLoc != atom2.altLoc && atom1.altLoc != ' ' && atom2.altLoc != ' ')
return false; // don't connect across alternate locations
else
return true;
};
/**
* @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 (let x in grid) {
x = parseInt(x);
for (let y in grid[x]) {
y = parseInt(y);
for (let z in grid[x][y]) {
z = parseInt(z);
let points = grid[x][y][z];
for (let i = 0; i < points.length; i++) {
let atom1 = points[i];
for (let j = i + 1; j < points.length; j++) {
let 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 (let o = 0; o < OFFSETS.length; o++) {
let 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;
let otherPoints = grid[x + offset.x][y + offset.y][z + offset.z];
findConnections(points, otherPoints);
}
}
}
}
};
var standardResidues = new Set(['ABU','ACD','ALA','ALB','ALI','ARG','AR0','ASN',
'ASP','ASX','BAS','CYS','CYH','CYX','CSS','CSH',
'GLN','GLU','GLX','GLY','HIS','HIE','HID','HIP','HYP',
'ILE','ILU','LEU','LYS','MET','PCA','PGA','PHE',
'PR0','PRO','PRZ','SER','THR','TYR','VAL',
'A','1MA','C','5MC','OMC','G','1MG','2MG','M2G',
'7MG','OMG','YG','I','T','U','+U','H2U','5MU',
'PSU','ACE','F0R','H2O','HOH','WAT']);
// 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 || !standardResidues.has(atom.resn))
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 (let i = 0, il = atomsarray.length; i < il; i++) {
atom = atomsarray[i];
if (isFinite(atom.hbondDistanceSq) && chres[atom.chain][atom.resi] == 'maybesheet') {
let other = atom.hbondOther;
let 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 (let c in chres) {
for (let r = 1; r < chres[c].length - 1; r++) {
let valbefore = chres[c][r - 1];
let valafter = chres[c][r + 1];
val = chres[c][r];
if (valbefore == 's' && valbefore == valafter && val != valbefore) {
chres[c][r] = valbefore;
}
}
for (let r = 0; r < chres[c].length; r++) {
let 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
for (i = 0, il = atomsarray.length; i < il; i++) {
atom = atomsarray[i];
val = chres[atom.chain][atom.resi];
//clear hbondOther to eliminate circular references that prohibit serialization
delete atom.hbondOther;
delete atom.hbondDistanceSq;
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]);
}
}
}
}
};
//adds symmetry info to either duplicate and rotate/translate biological unit later or add extra atoms now
//matrices may be modified if normalization is requested
var processSymmetries = function(copyMatrices, atoms, options, cryst) {
var dontDuplicate = !options.duplicateAssemblyAtoms;
var end = atoms.length;
var offset = end;
var t, l, n; // Used in for loops
let modifiedIdentity = -1;
if(options.normalizeAssembly && cryst) {
//to normalize, translate every symmetry so that the centroid is
//in the unit cell. To do this, convert back to fractional coordinates,
//compute the centroid, calculate any adjustment needed to get it in [0,1],
//convert the adjustment to a cartesian translation, and then add it to
//the symmetry matrix
let conversionMatrix = $3Dmol.conversionMatrix3(cryst.a, cryst.b, cryst.c,
cryst.alpha, cryst.beta, cryst.gamma);
let toFrac = new $3Dmol.Matrix3();
toFrac.getInverse3(conversionMatrix);
for (t = 0; t < copyMatrices.length; t++) {
//transform with the symmetry, and then back to fractional coordinates
let center = new $3Dmol.Vector3(0,0,0);
for (n = 0; n < end; n++) {
let xyz = new $3Dmol.Vector3(atoms[n].x,atoms[n].y,atoms[n].z);
xyz.applyMatrix4(copyMatrices[t]);
xyz.applyMatrix3(toFrac);
//figure out
center.add(xyz);
}
center.divideScalar(end);
center = [center.x,center.y,center.z];
let adjustment = [0.0, 0.0, 0.0];
for(let i = 0; i < 3; i++) {
while(center[i] < -0.001 ) {
center[i] += 1.0;
adjustment[i] += 1.0;
}
while(center[i] > 1.001 ) {
center[i] -= 1.0;
adjustment[i] -= 1.0;
}
}
//convert adjustment to non-fractional
adjustment = new $3Dmol.Vector3(adjustment[0],adjustment[1],adjustment[2]);
adjustment.applyMatrix3(conversionMatrix);
//modify symmetry matrix to include translation
if(copyMatrices[t].isNearlyIdentity() && adjustment.lengthSq() > 0.001) {
modifiedIdentity = t; //keep track of which matrix was identity
}
copyMatrices[t].translate(adjustment);
}
}
if (!dontDuplicate) { // do full assembly
for (n = 0; n < end; n++) {
atoms[n].sym = -1; //if identity matrix is present, original labeled -1
}
for (t = 0; t < copyMatrices.length; t++) {
if (!copyMatrices[t].isNearlyIdentity() && modifiedIdentity != t) {
let xyz = new $3Dmol.Vector3();
for (n = 0; n < end; n++) {
var bondsArr = [];
for (l = 0; l < atoms[n].bonds.length; l++) {
bondsArr.push(atoms[n].bonds[l] + offset);
}
xyz.set(atoms[n].x, atoms[n].y, atoms[n].z);
xyz.applyMatrix4(copyMatrices[t]);
var newAtom = {};
for (var i in atoms[n]) {
newAtom[i] = atoms[n][i];
}
newAtom.x = xyz.x;
newAtom.y = xyz.y;
newAtom.z = xyz.z;
newAtom.bonds = bondsArr;
newAtom.sym = t; //so symmetries can be selected
newAtom.index = atoms.length;
atoms.push(newAtom);
}
offset = atoms.length;
} else {
for (n = 0; n < end; n++) {
atoms[n].sym = t;
}
}
}
if(modifiedIdentity >= 0) {
//after applying the other transformations, apply this one in place
let xyz = new $3Dmol.Vector3();
for (n = 0; n < end; n++) {
xyz.set(atoms[n].x, atoms[n].y, atoms[n].z);
xyz.applyMatrix4(copyMatrices[modifiedIdentity]);
atoms[n].x = xyz.x;
atoms[n].y = xyz.y;
atoms[n].z = xyz.z;
}
}
//we have explicitly duplicated the atoms, remove model symmetry information
copyMatrices.length = 0;
}
else if(copyMatrices.length > 1) {
for (t = 0; t < atoms.length; t++) {
var symmetries = [];
for (l = 0; l < copyMatrices.length; l++) {
if (!copyMatrices[l].isNearlyIdentity()) {
var newXYZ = new $3Dmol.Vector3();
newXYZ.set(atoms[t].x, atoms[t].y, atoms[t].z);
newXYZ.applyMatrix4(copyMatrices[l]);
symmetries.push(newXYZ);
}
}
atoms[t].symmetries = symmetries;
}
}
};
/**
* @param {string}
* str
* @param {ParserOptionsSpec}
* options
*/
parsers.vasp = parsers.VASP = function (str /*,options*/) {
var atoms = [[]];
var lattice = {};
var lines = str.replace(/^\s+/, "").split(/\r?\n/);
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 $3Dmol.Matrix3(
lattice.xVec[0], lattice.xVec[1], lattice.xVec[2],
lattice.yVec[0], lattice.yVec[1], lattice.yVec[2],
lattice.zVec[0], lattice.zVec[1], lattice.zVec[2]
);
matrix.multiplyScalar(lattice.length);
atoms.modelData = [{symmetries:[], cryst:{matrix:matrix}}];
var atomSymbols=lines[5].replace(/\s+/, "").replace(/\s+$/,"").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) {
options = options || {};
var atoms = [[]];
var lines = str.split(/\r?\n/);
var assignbonds = options.assignBonds === undefined ? true : options.assignBonds;
if (lines.length < 6)
return atoms;
var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
var natoms = Math.abs(parseFloat(lineArr[0]));
let cryst = {};
var origin = cryst.origin = new $3Dmol.Vector3(parseFloat(lineArr[1]),
parseFloat(lineArr[2]), parseFloat(lineArr[3]));
lineArr = lines[3].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
lineArr = lines[3].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
// might have to convert from bohr units to angstroms
// there is a great deal of confusion here:
// n>0 means angstroms: http://www.gaussian.com/g_tech/g_ur/u_cubegen.htm
// n<0 means angstroms: http://paulbourke.net/dataformats/cube/
// always assume bohr: openbabel source code
// always assume angstrom: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html
// we are going to go with n<0 means angstrom - note this is just the first n
var convFactor = (lineArr[0] > 0) ? 0.529177 : 1;
origin.multiplyScalar(convFactor);
var nX = Math.abs(lineArr[0]);
var xVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
parseFloat(lineArr[2]), parseFloat(lineArr[3]))
.multiplyScalar(convFactor);
lineArr = lines[4].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
var nY = Math.abs(lineArr[0]);
var yVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
parseFloat(lineArr[2]), parseFloat(lineArr[3]))
.multiplyScalar(convFactor);
lineArr = lines[5].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
var nZ = Math.abs(lineArr[0]);
var zVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
parseFloat(lineArr[2]), parseFloat(lineArr[3]))
.multiplyScalar(convFactor);
cryst.size = {x:nX, y:nY, z:nZ};
cryst.unit = new $3Dmol.Vector3(xVec.x, yVec.y, zVec.z);
if (xVec.y != 0 || xVec.z != 0 || yVec.x != 0 || yVec.z != 0 || zVec.x != 0
|| zVec.y != 0) {
//need a transformation matrix
cryst.matrix4 = new $3Dmol.Matrix4(xVec.x, yVec.x, zVec.x, 0, xVec.y, yVec.y, zVec.y, 0, xVec.z, yVec.z, zVec.z, 0, 0,0,0,1);
// include translation in matrix
let t = new $3Dmol.Matrix4().makeTranslation(origin.x, origin.y, origin.z);
cryst.matrix4 = cryst.matrix4.multiplyMatrices(t,cryst.matrix4);
cryst.matrix = cryst.matrix4.matrix3FromTopLeft();
// all translation and scaling done by matrix, so reset origin and unit
cryst.origin = new $3Dmol.Vector3(0,0,0);
cryst.unit = new $3Dmol.Vector3(1,1,1);
}
atoms.modelData = [{cryst:cryst}];
// 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(
" ");
atom.elem = anumToSymbol[tokens[0]];
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);
}
if(assignbonds) {
for (let 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) {
options = options || {};
var atoms = [[]];
var assignbonds = options.assignBonds === undefined ? true : options.assignBonds;
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 lattice_re = /Lattice\s*=\s*["\{\}]([^"\{\}]+)["\{\}]\s*/gi;
var lattice_match = lattice_re.exec(lines[1]);
if ((lattice_match != null) && (lattice_match.length > 1)) {
var lattice = new Float32Array(lattice_match[1].split(/\s+/));
var matrix = new $3Dmol.Matrix3(
lattice[0], lattice[3], lattice[6],
lattice[1], lattice[4], lattice[7],
lattice[2], lattice[5], lattice[8]
);
atoms.modelData = [{cryst:{matrix:matrix}}];
}
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(1,1).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;
}
}
if(assignbonds) {
for (let i = 0; i < atoms.length; i++) {
assignBonds(atoms[i]);
}
}
if (options.onemol) {
var temp = atoms;
atoms = [];
atoms.push(temp[0]);
for (let i = 1; i < temp.length; i++) {
let offset = atoms[0].length;
for (let j = 0; j < temp[i].length; j++) {
let a = temp[i][j];
for (let 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;
};
/**
* @param {!Array.<string>} lines
* @param {ParserOptionsSpec} options
* @returns {!Array.<Array<Object>>}
*/
var parseV2000 = function(lines, options) {
var atoms = [[]];
var noH = false;
if (typeof options.keepH !== "undefined")
noH = !options.keepH;
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;
};
/**
* @param {!Array.<string>} lines
* @param {ParserOptionsSpec} options
* @returns {!Array.<!Array<!Object>>}
*/
var parseV3000 = function(lines, options) {
var atoms = [[]];
var noH = false;
if (typeof options.keepH !== "undefined")
noH = !options.keepH;
while(lines.length > 0) {
if (lines.length < 8)
break;
if (!lines[4].startsWith("M V30 BEGIN CTAB"))
break;
if (!lines[5].startsWith("M V30 COUNTS") || lines[5].length < 14)
break;
var counts = lines[5].substr(13).match(/\S+/g);
if (counts.length < 2)
break;
var atomCount = parseInt(counts[0]);
if (isNaN(atomCount) || atomCount <= 0)
break;
var bondCount = parseInt(counts[1]);
var offset = 7;
if (lines.length < 8 + atomCount + bondCount) //header, bgn+end CTAB, counts, END
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 atomParts = line.substr(6).match(/\S+/g);
if (atomParts.length > 4) {
var atom = {};
var elem = atomParts[1].replace(/ /g, "");
atom.atom = atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
if (atom.elem !== 'H' || !noH) {