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apache / airavata-php-gateway / def5373a1dc21f7429da5f5c63d818b8b1b60030 / . / public / js / datacat / GLmol.js
blob: 9af612be6b55fe6da46678c0bc3b905bb1d213e5 [file] [log] [blame]
/*
GLmol - Molecular Viewer on WebGL/Javascript (0.47)
(C) Copyright 2011-2012, biochem_fan
License: dual license of MIT or LGPL3
Contributors:
Robert Hanson for parseXYZ, deferred instantiation
This program uses
Three.js
https://github.com/mrdoob/three.js
Copyright (c) 2010-2012 three.js Authors. All rights reserved.
jQuery
http://jquery.org/
Copyright (c) 2011 John Resig
*/
// Workaround for Intel GMA series (gl_FrontFacing causes compilation error)
THREE.ShaderLib.lambert.fragmentShader = THREE.ShaderLib.lambert.fragmentShader.replace("gl_FrontFacing", "true");
THREE.ShaderLib.lambert.vertexShader = THREE.ShaderLib.lambert.vertexShader.replace(/\}$/, "#ifdef DOUBLE_SIDED\n if (transformedNormal.z < 0.0) vLightFront = vLightBack;\n #endif\n }");
var TV3 = THREE.Vector3, TF3 = THREE.Face3, TCo = THREE.Color;
THREE.Geometry.prototype.colorAll = function (color) {
for (var i = 0; i < this.faces.length; i++) {
this.faces[i].color = color;
}
};
THREE.Matrix4.prototype.isIdentity = function() {
for (var i = 0; i < 4; i++)
for (var j = 0; j < 4; j++)
if (this.elements[i * 4 + j] != (i == j) ? 1 : 0) return false;
return true;
};
var GLmol = (function() {
function GLmol(id, suppressAutoload) {
if (id) this.create(id, suppressAutoload);
return true;
}
GLmol.prototype.create = function(id, suppressAutoload) {
this.Nucleotides = [' G', ' A', ' T', ' C', ' U', ' DG', ' DA', ' DT', ' DC', ' DU'];
this.ElementColors = {"H": 0xCCCCCC, "C": 0xAAAAAA, "O": 0xCC0000, "N": 0x0000CC, "S": 0xCCCC00, "P": 0x6622CC,
"F": 0x00CC00, "CL": 0x00CC00, "BR": 0x882200, "I": 0x6600AA,
"FE": 0xCC6600, "CA": 0x8888AA};
// Reference: A. Bondi, J. Phys. Chem., 1964, 68, 441.
this.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};
this.id = id;
this.aaScale = 1; // or 2
this.container = $('#' + this.id);
this.WIDTH = this.container.width() * this.aaScale, this.HEIGHT = this.container.height() * this.aaScale;
this.ASPECT = this.WIDTH / this.HEIGHT;
this.NEAR = 1, FAR = 800;
this.CAMERA_Z = -150;
this.renderer = new THREE.WebGLRenderer({antialias: true});
this.renderer.sortObjects = false; // hopefully improve performance
// 'antialias: true' now works in Firefox too!
// setting this.aaScale = 2 will enable antialias in older Firefox but GPU load increases.
this.renderer.domElement.style.width = "100%";
this.renderer.domElement.style.height = "100%";
this.container.append(this.renderer.domElement);
this.renderer.setSize(this.WIDTH, this.HEIGHT);
this.camera = new THREE.PerspectiveCamera(20, this.ASPECT, 1, 800); // will be updated anyway
this.camera.position = new TV3(0, 0, this.CAMERA_Z);
this.camera.lookAt(new TV3(0, 0, 0));
this.perspectiveCamera = this.camera;
this.orthoscopicCamera = new THREE.OrthographicCamera();
this.orthoscopicCamera.position.z = this.CAMERA_Z;
this.orthoscopicCamera.lookAt(new TV3(0, 0, 0));
var self = this;
$(window).resize(function() { // only window can capture resize event
self.WIDTH = self.container.width() * self.aaScale;
self.HEIGHT = self.container.height() * self.aaScale;
self.ASPECT = self.WIDTH / self.HEIGHT;
self.renderer.setSize(self.WIDTH, self.HEIGHT);
self.camera.aspect = self.ASPECT;
self.camera.updateProjectionMatrix();
self.show();
});
this.scene = null;
this.rotationGroup = null; // which contains modelGroup
this.modelGroup = null;
this.bgColor = 0x000000;
this.fov = 20;
this.fogStart = 0.4;
this.slabNear = -50; // relative to the center of rotationGroup
this.slabFar = +50;
// Default values
this.sphereRadius = 1.5;
this.cylinderRadius = 0.4;
this.lineWidth = 1.5 * this.aaScale;
this.curveWidth = 3 * this.aaScale;
this.defaultColor = 0xCCCCCC;
this.sphereQuality = 16; //16;
this.cylinderQuality = 16; //8;
this.axisDIV = 5; // 3 still gives acceptable quality
this.strandDIV = 6;
this.nucleicAcidStrandDIV = 4;
this.tubeDIV = 8;
this.coilWidth = 0.3;
this.helixSheetWidth = 1.3;
this.nucleicAcidWidth = 0.8;
this.thickness = 0.4;
// UI variables
this.cq = new THREE.Quaternion(1, 0, 0, 0);
this.dq = new THREE.Quaternion(1, 0, 0, 0);
this.isDragging = false;
this.mouseStartX = 0;
this.mouseStartY = 0;
this.currentModelPos = 0;
this.cz = 0;
this.enableMouse();
if (suppressAutoload) return;
this.loadMolecule();
}
GLmol.prototype.setupLights = function(scene) {
var directionalLight = new THREE.DirectionalLight(0xFFFFFF);
directionalLight.position = new TV3(0.2, 0.2, -1).normalize();
directionalLight.intensity = 1.2;
scene.add(directionalLight);
var ambientLight = new THREE.AmbientLight(0x202020);
scene.add(ambientLight);
};
GLmol.prototype.parseSDF = function(str) {
var atoms = this.atoms;
var protein = this.protein;
var lines = str.split("\n");
if (lines.length < 4) return;
var atomCount = parseInt(lines[3].substr(0, 3));
if (isNaN(atomCount) || atomCount <= 0) return;
var bondCount = parseInt(lines[3].substr(3, 3));
var offset = 4;
if (lines.length < 4 + atomCount + bondCount) return;
for (var i = 1; i <= atomCount; i++) {
var line = lines[offset];
offset++;
var atom = {};
atom.serial = i;
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.atom = atom.elem = line.substr(31, 3).replace(/ /g, "");
atom.bonds = [];
atom.bondOrder = [];
atoms[i] = atom;
}
for (i = 1; i <= bondCount; i++) {
var line = lines[offset];
offset++;
var from = parseInt(line.substr(0, 3));
var to = parseInt(line.substr(3, 3));
var order = parseInt(line.substr(6, 3));
atoms[from].bonds.push(to);
atoms[from].bondOrder.push(order);
atoms[to].bonds.push(from);
atoms[to].bondOrder.push(order);
}
protein.smallMolecule = true;
return true;
};
GLmol.prototype.parseXYZ = function(str) {
var atoms = this.atoms;
var protein = this.protein;
var lines = str.split("\n");
if (lines.length < 3) return;
var atomCount = parseInt(lines[0].substr(0, 3));
if (isNaN(atomCount) || atomCount <= 0) return;
if (lines.length < atomCount + 2) return;
var offset = 2;
for (var i = 1; i <= atomCount; i++) {
var line = lines[offset++];
var tokens = line.replace(/^\s+/, "").replace(/\s+/g," ").split(" ");
console.log(tokens);
var atom = {};
atom.serial = i;
atom.atom = atom.elem = tokens[0];
atom.x = parseFloat(tokens[1]);
atom.y = parseFloat(tokens[2]);
atom.z = parseFloat(tokens[3]);
atom.hetflag = true;
atom.bonds = [];
atom.bondOrder = [];
atoms[i] = atom;
}
for (var i = 1; i < atomCount; i++) // hopefully XYZ is small enough
for (var j = i + 1; j <= atomCount; j++)
if (this.isConnected(atoms[i], atoms[j])) {
atoms[i].bonds.push(j);
atoms[i].bondOrder.push(1);
atoms[j].bonds.push(i);
atoms[j].bondOrder.push(1);
}
protein.smallMolecule = true;
return true;
};
GLmol.prototype.parsePDB2 = function(str) {
var atoms = this.atoms;
var protein = this.protein;
var molID;
var atoms_cnt = 0;
lines = str.split("\n");
for (var i = 0; i < lines.length; i++) {
line = lines[i].replace(/^\s*/, ''); // remove indent
var recordName = line.substr(0, 6);
if (recordName == 'ATOM ' || recordName == 'HETATM') {
var atom, resn, chain, resi, x, y, z, hetflag, elem, serial, altLoc, b;
altLoc = line.substr(16, 1);
if (altLoc != ' ' && altLoc != 'A') continue; // FIXME: ad hoc
serial = parseInt(line.substr(6, 5));
atom = line.substr(12, 4).replace(/ /g, "");
resn = line.substr(17, 3);
chain = line.substr(21, 1);
resi = parseInt(line.substr(22, 5));
x = parseFloat(line.substr(30, 8));
y = parseFloat(line.substr(38, 8));
z = parseFloat(line.substr(46, 8));
b = parseFloat(line.substr(60, 8));
elem = line.substr(76, 2).replace(/ /g, "");
if (elem == '') { // for some incorrect PDB files
elem = line.substr(12, 4).replace(/ /g,"");
}
if (line[0] == 'H') hetflag = true;
else hetflag = false;
atoms[serial] = {'resn': resn, 'x': x, 'y': y, 'z': z, 'elem': elem,
'hetflag': hetflag, 'chain': chain, 'resi': resi, 'serial': serial, 'atom': atom,
'bonds': [], 'ss': 'c', 'color': 0xFFFFFF, 'bonds': [], 'bondOrder': [], 'b': b /*', altLoc': altLoc*/};
} else if (recordName == 'SHEET ') {
var startChain = line.substr(21, 1);
var startResi = parseInt(line.substr(22, 4));
var endChain = line.substr(32, 1);
var endResi = parseInt(line.substr(33, 4));
protein.sheet.push([startChain, startResi, endChain, endResi]);
} else if (recordName == 'CONECT') {
// MEMO: We don't have to parse SSBOND, LINK because both are also
// described in CONECT. But what about 2JYT???
var from = parseInt(line.substr(6, 5));
for (var j = 0; j < 4; j++) {
var to = parseInt(line.substr([11, 16, 21, 26][j], 5));
if (isNaN(to)) continue;
if (atoms[from] != undefined) {
atoms[from].bonds.push(to);
atoms[from].bondOrder.push(1);
}
}
} else if (recordName == 'HELIX ') {
var startChain = line.substr(19, 1);
var startResi = parseInt(line.substr(21, 4));
var endChain = line.substr(31, 1);
var endResi = parseInt(line.substr(33, 4));
protein.helix.push([startChain, startResi, endChain, endResi]);
} else if (recordName == 'CRYST1') {
protein.a = parseFloat(line.substr(6, 9));
protein.b = parseFloat(line.substr(15, 9));
protein.c = parseFloat(line.substr(24, 9));
protein.alpha = parseFloat(line.substr(33, 7));
protein.beta = parseFloat(line.substr(40, 7));
protein.gamma = parseFloat(line.substr(47, 7));
protein.spacegroup = line.substr(55, 11);
this.defineCell();
} else if (recordName == 'REMARK') {
var type = parseInt(line.substr(7, 3));
if (type == 290 && line.substr(13, 5) == 'SMTRY') {
var n = parseInt(line[18]) - 1;
var m = parseInt(line.substr(21, 2));
if (protein.symMat[m] == undefined) protein.symMat[m] = new THREE.Matrix4().identity();
protein.symMat[m].elements[n] = parseFloat(line.substr(24, 9));
protein.symMat[m].elements[n + 4] = parseFloat(line.substr(34, 9));
protein.symMat[m].elements[n + 8] = parseFloat(line.substr(44, 9));
protein.symMat[m].elements[n + 12] = parseFloat(line.substr(54, 10));
} else if (type == 350 && line.substr(13, 5) == 'BIOMT') {
var n = parseInt(line[18]) - 1;
var m = parseInt(line.substr(21, 2));
if (protein.biomtMatrices[m] == undefined) protein.biomtMatrices[m] = new THREE.Matrix4().identity();
protein.biomtMatrices[m].elements[n] = parseFloat(line.substr(24, 9));
protein.biomtMatrices[m].elements[n + 4] = parseFloat(line.substr(34, 9));
protein.biomtMatrices[m].elements[n + 8] = parseFloat(line.substr(44, 9));
protein.biomtMatrices[m].elements[n + 12] = parseFloat(line.substr(54, 10));
} else if (type == 350 && line.substr(11, 11) == 'BIOMOLECULE') {
protein.biomtMatrices = []; protein.biomtChains = '';
} else if (type == 350 && line.substr(34, 6) == 'CHAINS') {
protein.biomtChains += line.substr(41, 40);
}
} else if (recordName == 'HEADER') {
protein.pdbID = line.substr(62, 4);
} else if (recordName == 'TITLE ') {
if (protein.title == undefined) protein.title = "";
protein.title += line.substr(10, 70) + "\n"; // CHECK: why 60 is not enough???
} else if (recordName == 'COMPND') {
// TODO: Implement me!
}
}
// Assign secondary structures
for (i = 0; i < atoms.length; i++) {
atom = atoms[i]; if (atom == undefined) continue;
var found = false;
// MEMO: Can start chain and end chain differ?
for (j = 0; j < protein.sheet.length; j++) {
if (atom.chain != protein.sheet[j][0]) continue;
if (atom.resi < protein.sheet[j][1]) continue;
if (atom.resi > protein.sheet[j][3]) continue;
atom.ss = 's';
if (atom.resi == protein.sheet[j][1]) atom.ssbegin = true;
if (atom.resi == protein.sheet[j][3]) atom.ssend = true;
}
for (j = 0; j < protein.helix.length; j++) {
if (atom.chain != protein.helix[j][0]) continue;
if (atom.resi < protein.helix[j][1]) continue;
if (atom.resi > protein.helix[j][3]) continue;
atom.ss = 'h';
if (atom.resi == protein.helix[j][1]) atom.ssbegin = true;
else if (atom.resi == protein.helix[j][3]) atom.ssend = true;
}
}
protein.smallMolecule = false;
return true;
};
// Catmull-Rom subdivision
GLmol.prototype.subdivide = function(_points, DIV) { // points as Vector3
var ret = [];
var points = _points;
points = new Array(); // Smoothing test
points.push(_points[0]);
for (var i = 1, lim = _points.length - 1; i < lim; i++) {
var p1 = _points[i], p2 = _points[i + 1];
if (p1.smoothen) points.push(new TV3((p1.x + p2.x) / 2, (p1.y + p2.y) / 2, (p1.z + p2.z) / 2));
else points.push(p1);
}
points.push(_points[_points.length - 1]);
for (var i = -1, size = points.length; i <= size - 3; i++) {
var p0 = points[(i == -1) ? 0 : i];
var p1 = points[i + 1], p2 = points[i + 2];
var p3 = points[(i == size - 3) ? size - 1 : i + 3];
var v0 = new TV3().sub(p2, p0).multiplyScalar(0.5);
var v1 = new TV3().sub(p3, p1).multiplyScalar(0.5);
for (var j = 0; j < DIV; j++) {
var t = 1.0 / DIV * j;
var x = p1.x + t * v0.x
+ t * t * (-3 * p1.x + 3 * p2.x - 2 * v0.x - v1.x)
+ t * t * t * (2 * p1.x - 2 * p2.x + v0.x + v1.x);
var y = p1.y + t * v0.y
+ t * t * (-3 * p1.y + 3 * p2.y - 2 * v0.y - v1.y)
+ t * t * t * (2 * p1.y - 2 * p2.y + v0.y + v1.y);
var z = p1.z + t * v0.z
+ t * t * (-3 * p1.z + 3 * p2.z - 2 * v0.z - v1.z)
+ t * t * t * (2 * p1.z - 2 * p2.z + v0.z + v1.z);
ret.push(new TV3(x, y, z));
}
}
ret.push(points[points.length - 1]);
return ret;
};
GLmol.prototype.drawAtomsAsSphere = function(group, atomlist, defaultRadius, forceDefault, scale) {
var sphereGeometry = new THREE.SphereGeometry(1, this.sphereQuality, this.sphereQuality); // r, seg, ring
for (var i = 0; i < atomlist.length; i++) {
var atom = this.atoms[atomlist[i]];
if (atom == undefined) continue;
var sphereMaterial = new THREE.MeshLambertMaterial({color: atom.color});
var sphere = new THREE.Mesh(sphereGeometry, sphereMaterial);
group.add(sphere);
var r = (!forceDefault && this.vdwRadii[atom.elem] != undefined) ? this.vdwRadii[atom.elem] : defaultRadius;
if (!forceDefault && scale) r *= scale;
sphere.scale.x = sphere.scale.y = sphere.scale.z = r;
sphere.position.x = atom.x;
sphere.position.y = atom.y;
sphere.position.z = atom.z;
}
};
// about two times faster than sphere when div = 2
GLmol.prototype.drawAtomsAsIcosahedron = function(group, atomlist, defaultRadius, forceDefault) {
var geo = this.IcosahedronGeometry();
for (var i = 0; i < atomlist.length; i++) {
var atom = this.atoms[atomlist[i]];
if (atom == undefined) continue;
var mat = new THREE.MeshLambertMaterial({color: atom.color});
var sphere = new THREE.Mesh(geo, mat);
sphere.scale.x = sphere.scale.y = sphere.scale.z = (!forceDefault && this.vdwRadii[atom.elem] != undefined) ? this.vdwRadii[atom.elem] : defaultRadius;
group.add(sphere);
sphere.position.x = atom.x;
sphere.position.y = atom.y;
sphere.position.z = atom.z;
}
};
GLmol.prototype.isConnected = function(atom1, atom2) {
var s = atom1.bonds.indexOf(atom2.serial);
if (s != -1) return atom1.bondOrder[s];
if (this.protein.smallMolecule && (atom1.hetflag || atom2.hetflag)) return 0; // CHECK: or should I ?
var distSquared = (atom1.x - atom2.x) * (atom1.x - atom2.x) +
(atom1.y - atom2.y) * (atom1.y - atom2.y) +
(atom1.z - atom2.z) * (atom1.z - atom2.z);
// if (atom1.altLoc != atom2.altLoc) return false;
if (isNaN(distSquared)) return 0;
if (distSquared < 0.5) return 0; // maybe duplicate position.
if (distSquared > 1.3 && (atom1.elem == 'H' || atom2.elem == 'H' || atom1.elem == 'D' || atom2.elem == 'D')) return 0;
if (distSquared < 3.42 && (atom1.elem == 'S' || atom2.elem == 'S')) return 1;
if (distSquared > 2.78) return 0;
return 1;
};
GLmol.prototype.drawBondAsStickSub = function(group, atom1, atom2, bondR, order) {
var delta, tmp;
if (order > 1) delta = this.calcBondDelta(atom1, atom2, bondR * 2.3);
var p1 = new TV3(atom1.x, atom1.y, atom1.z);
var p2 = new TV3(atom2.x, atom2.y, atom2.z);
var mp = p1.clone().addSelf(p2).multiplyScalar(0.5);
var c1 = new TCo(atom1.color), c2 = new TCo(atom2.color);
if (order == 1 || order == 3) {
this.drawCylinder(group, p1, mp, bondR, atom1.color);
this.drawCylinder(group, p2, mp, bondR, atom2.color);
}
if (order > 1) {
tmp = mp.clone().addSelf(delta);
this.drawCylinder(group, p1.clone().addSelf(delta), tmp, bondR, atom1.color);
this.drawCylinder(group, p2.clone().addSelf(delta), tmp, bondR, atom2.color);
tmp = mp.clone().subSelf(delta);
this.drawCylinder(group, p1.clone().subSelf(delta), tmp, bondR, atom1.color);
this.drawCylinder(group, p2.clone().subSelf(delta), tmp, bondR, atom2.color);
}
};
GLmol.prototype.drawBondsAsStick = function(group, atomlist, bondR, atomR, ignoreNonbonded, multipleBonds, scale) {
var sphereGeometry = new THREE.SphereGeometry(1, this.sphereQuality, this.sphereQuality);
var nAtoms = atomlist.length, mp;
var forSpheres = [];
if (!!multipleBonds) bondR /= 2.5;
for (var _i = 0; _i < nAtoms; _i++) {
var i = atomlist[_i];
var atom1 = this.atoms[i];
if (atom1 == undefined) continue;
for (var _j = _i + 1; _j < _i + 30 && _j < nAtoms; _j++) {
var j = atomlist[_j];
var atom2 = this.atoms[j];
if (atom2 == undefined) continue;
var order = this.isConnected(atom1, atom2);
if (order == 0) continue;
atom1.connected = atom2.connected = true;
this.drawBondAsStickSub(group, atom1, atom2, bondR, (!!multipleBonds) ? order : 1);
}
for (var _j = 0; _j < atom1.bonds.length; _j++) {
var j = atom1.bonds[_j];
if (j < i + 30) continue; // be conservative!
if (atomlist.indexOf(j) == -1) continue;
var atom2 = this.atoms[j];
if (atom2 == undefined) continue;
atom1.connected = atom2.connected = true;
this.drawBondAsStickSub(group, atom1, atom2, bondR, (!!multipleBonds) ? atom1.bondOrder[_j] : 1);
}
if (atom1.connected) forSpheres.push(i);
}
this.drawAtomsAsSphere(group, forSpheres, atomR, !scale, scale);
};
GLmol.prototype.defineCell = function() {
var p = this.protein;
if (p.a == undefined) return;
p.ax = p.a;
p.ay = 0;
p.az = 0;
p.bx = p.b * Math.cos(Math.PI / 180.0 * p.gamma);
p.by = p.b * Math.sin(Math.PI / 180.0 * p.gamma);
p.bz = 0;
p.cx = p.c * Math.cos(Math.PI / 180.0 * p.beta);
p.cy = p.c * (Math.cos(Math.PI / 180.0 * p.alpha) -
Math.cos(Math.PI / 180.0 * p.gamma)
* Math.cos(Math.PI / 180.0 * p.beta)
/ Math.sin(Math.PI / 180.0 * p.gamma));
p.cz = Math.sqrt(p.c * p.c * Math.sin(Math.PI / 180.0 * p.beta)
* Math.sin(Math.PI / 180.0 * p.beta) - p.cy * p.cy);
};
GLmol.prototype.drawUnitcell = function(group) {
var p = this.protein;
if (p.a == undefined) return;
var vertices = [[0, 0, 0], [p.ax, p.ay, p.az], [p.bx, p.by, p.bz], [p.ax + p.bx, p.ay + p.by, p.az + p.bz],
[p.cx, p.cy, p.cz], [p.cx + p.ax, p.cy + p.ay, p.cz + p.az], [p.cx + p.bx, p.cy + p.by, p.cz + p.bz], [p.cx + p.ax + p.bx, p.cy + p.ay + p.by, p.cz + p.az + p.bz]];
var edges = [0, 1, 0, 2, 1, 3, 2, 3, 4, 5, 4, 6, 5, 7, 6, 7, 0, 4, 1, 5, 2, 6, 3, 7];
var geo = new THREE.Geometry();
for (var i = 0; i < edges.length; i++) {
geo.vertices.push(new TV3(vertices[edges[i]][0], vertices[edges[i]][1], vertices[edges[i]][2]));
}
var lineMaterial = new THREE.LineBasicMaterial({linewidth: 1, color: 0xcccccc});
var line = new THREE.Line(geo, lineMaterial);
line.type = THREE.LinePieces;
group.add(line);
};
// TODO: Find inner side of a ring
GLmol.prototype.calcBondDelta = function(atom1, atom2, sep) {
var dot;
var axis = new TV3(atom1.x - atom2.x, atom1.y - atom2.y, atom1.z - atom2.z).normalize();
var found = null;
for (var i = 0; i < atom1.bonds.length && !found; i++) {
var atom = this.atoms[atom1.bonds[i]]; if (!atom) continue;
if (atom.serial != atom2.serial && atom.elem != 'H') found = atom;
}
for (var i = 0; i < atom2.bonds.length && !found; i++) {
var atom = this.atoms[atom2.bonds[i]]; if (!atom) continue;
if (atom.serial != atom1.serial && atom.elem != 'H') found = atom;
}
if (found) {
var tmp = new TV3(atom1.x - found.x, atom1.y - found.y, atom1.z - found.z).normalize();
dot = tmp.dot(axis);
delta = new TV3(tmp.x - axis.x * dot, tmp.y - axis.y * dot, tmp.z - axis.z * dot);
}
if (!found || Math.abs(dot - 1) < 0.001 || Math.abs(dot + 1) < 0.001) {
if (axis.x < 0.01 && axis.y < 0.01) {
delta = new TV3(0, -axis.z, axis.y);
} else {
delta = new TV3(-axis.y, axis.x, 0);
}
}
delta.normalize().multiplyScalar(sep);
return delta;
};
GLmol.prototype.drawBondsAsLineSub = function(geo, atom1, atom2, order) {
var delta, tmp, vs = geo.vertices, cs = geo.colors;
if (order > 1) delta = this.calcBondDelta(atom1, atom2, 0.15);
var p1 = new TV3(atom1.x, atom1.y, atom1.z);
var p2 = new TV3(atom2.x, atom2.y, atom2.z);
var mp = p1.clone().addSelf(p2).multiplyScalar(0.5);
var c1 = new TCo(atom1.color), c2 = new TCo(atom2.color);
if (order == 1 || order == 3) {
vs.push(p1); cs.push(c1); vs.push(mp); cs.push(c1);
vs.push(p2); cs.push(c2); vs.push(mp); cs.push(c2);
}
if (order > 1) {
vs.push(p1.clone().addSelf(delta)); cs.push(c1);
vs.push(tmp = mp.clone().addSelf(delta)); cs.push(c1);
vs.push(p2.clone().addSelf(delta)); cs.push(c2);
vs.push(tmp); cs.push(c2);
vs.push(p1.clone().subSelf(delta)); cs.push(c1);
vs.push(tmp = mp.clone().subSelf(delta)); cs.push(c1);
vs.push(p2.clone().subSelf(delta)); cs.push(c2);
vs.push(tmp); cs.push(c2);
}
};
GLmol.prototype.drawBondsAsLine = function(group, atomlist, lineWidth) {
var geo = new THREE.Geometry();
var nAtoms = atomlist.length;
for (var _i = 0; _i < nAtoms; _i++) {
var i = atomlist[_i];
var atom1 = this.atoms[i];
if (atom1 == undefined) continue;
for (var _j = _i + 1; _j < _i + 30 && _j < nAtoms; _j++) {
var j = atomlist[_j];
var atom2 = this.atoms[j];
if (atom2 == undefined) continue;
var order = this.isConnected(atom1, atom2);
if (order == 0) continue;
this.drawBondsAsLineSub(geo, atom1, atom2, order);
}
for (var _j = 0; _j < atom1.bonds.length; _j++) {
var j = atom1.bonds[_j];
if (j < i + 30) continue; // be conservative!
if (atomlist.indexOf(j) == -1) continue;
var atom2 = this.atoms[j];
if (atom2 == undefined) continue;
this.drawBondsAsLineSub(geo, atom1, atom2, atom1.bondOrder[_j]);
}
}
var lineMaterial = new THREE.LineBasicMaterial({linewidth: lineWidth});
lineMaterial.vertexColors = true;
var line = new THREE.Line(geo, lineMaterial);
line.type = THREE.LinePieces;
group.add(line);
};
GLmol.prototype.drawSmoothCurve = function(group, _points, width, colors, div) {
if (_points.length == 0) return;
div = (div == undefined) ? 5 : div;
var geo = new THREE.Geometry();
var points = this.subdivide(_points, div);
for (var i = 0; i < points.length; i++) {
geo.vertices.push(points[i]);
geo.colors.push(new TCo(colors[(i == 0) ? 0 : Math.round((i - 1) / div)]));
}
var lineMaterial = new THREE.LineBasicMaterial({linewidth: width});
lineMaterial.vertexColors = true;
var line = new THREE.Line(geo, lineMaterial);
line.type = THREE.LineStrip;
group.add(line);
};
GLmol.prototype.drawAsCross = function(group, atomlist, delta) {
var geo = new THREE.Geometry();
var points = [[delta, 0, 0], [-delta, 0, 0], [0, delta, 0], [0, -delta, 0], [0, 0, delta], [0, 0, -delta]];
for (var i = 0, lim = atomlist.length; i < lim; i++) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
var c = new TCo(atom.color);
for (var j = 0; j < 6; j++) {
geo.vertices.push(new TV3(atom.x + points[j][0], atom.y + points[j][1], atom.z + points[j][2]));
geo.colors.push(c);
}
}
var lineMaterial = new THREE.LineBasicMaterial({linewidth: this.lineWidth});
lineMaterial.vertexColors = true;
var line = new THREE.Line(geo, lineMaterial, THREE.LinePieces);
group.add(line);
};
// FIXME: Winkled...
GLmol.prototype.drawSmoothTube = function(group, _points, colors, radii) {
if (_points.length < 2) return;
var circleDiv = this.tubeDIV, axisDiv = this.axisDIV;
var geo = new THREE.Geometry();
var points = this.subdivide(_points, axisDiv);
var prevAxis1 = new TV3(), prevAxis2;
for (var i = 0, lim = points.length; i < lim; i++) {
var r, idx = (i - 1) / axisDiv;
if (i == 0) r = radii[0];
else {
if (idx % 1 == 0) r = radii[idx];
else {
var floored = Math.floor(idx);
var tmp = idx - floored;
r = radii[floored] * tmp + radii[floored + 1] * (1 - tmp);
}
}
var delta, axis1, axis2;
if (i < lim - 1) {
delta = new TV3().sub(points[i], points[i + 1]);
axis1 = new TV3(0, - delta.z, delta.y).normalize().multiplyScalar(r);
axis2 = new TV3().cross(delta, axis1).normalize().multiplyScalar(r);
// var dir = 1, offset = 0;
if (prevAxis1.dot(axis1) < 0) {
axis1.negate(); axis2.negate(); //dir = -1;//offset = 2 * Math.PI / axisDiv;
}
prevAxis1 = axis1; prevAxis2 = axis2;
} else {
axis1 = prevAxis1; axis2 = prevAxis2;
}
for (var j = 0; j < circleDiv; j++) {
var angle = 2 * Math.PI / circleDiv * j; //* dir + offset;
var c = Math.cos(angle), s = Math.sin(angle);
geo.vertices.push(new TV3(
points[i].x + c * axis1.x + s * axis2.x,
points[i].y + c * axis1.y + s * axis2.y,
points[i].z + c * axis1.z + s * axis2.z));
}
}
var offset = 0;
for (var i = 0, lim = points.length - 1; i < lim; i++) {
var c = new TCo(colors[Math.round((i - 1)/ axisDiv)]);
var reg = 0;
var r1 = new TV3().sub(geo.vertices[offset], geo.vertices[offset + circleDiv]).lengthSq();
var r2 = new TV3().sub(geo.vertices[offset], geo.vertices[offset + circleDiv + 1]).lengthSq();
if (r1 > r2) {r1 = r2; reg = 1;};
for (var j = 0; j < circleDiv; j++) {
geo.faces.push(new TF3(offset + j, offset + (j + reg) % circleDiv + circleDiv, offset + (j + 1) % circleDiv));
geo.faces.push(new TF3(offset + (j + 1) % circleDiv, offset + (j + reg) % circleDiv + circleDiv, offset + (j + reg + 1) % circleDiv + circleDiv));
geo.faces[geo.faces.length -2].color = c;
geo.faces[geo.faces.length -1].color = c;
}
offset += circleDiv;
}
geo.computeFaceNormals();
geo.computeVertexNormals(false);
var mat = new THREE.MeshLambertMaterial();
mat.vertexColors = THREE.FaceColors;
var mesh = new THREE.Mesh(geo, mat);
mesh.doubleSided = true;
group.add(mesh);
};
GLmol.prototype.drawMainchainCurve = function(group, atomlist, curveWidth, atomName, div) {
var points = [], colors = [];
var currentChain, currentResi;
if (div == undefined) div = 5;
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]];
if (atom == undefined) continue;
if ((atom.atom == atomName) && !atom.hetflag) {
if (currentChain != atom.chain || currentResi + 1 != atom.resi) {
this.drawSmoothCurve(group, points, curveWidth, colors, div);
points = [];
colors = [];
}
points.push(new TV3(atom.x, atom.y, atom.z));
colors.push(atom.color);
currentChain = atom.chain;
currentResi = atom.resi;
}
}
this.drawSmoothCurve(group, points, curveWidth, colors, div);
};
GLmol.prototype.drawMainchainTube = function(group, atomlist, atomName, radius) {
var points = [], colors = [], radii = [];
var currentChain, currentResi;
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]];
if (atom == undefined) continue;
if ((atom.atom == atomName) && !atom.hetflag) {
if (currentChain != atom.chain || currentResi + 1 != atom.resi) {
this.drawSmoothTube(group, points, colors, radii);
points = []; colors = []; radii = [];
}
points.push(new TV3(atom.x, atom.y, atom.z));
if (radius == undefined) {
radii.push((atom.b > 0) ? atom.b / 100 : 0.3);
} else {
radii.push(radius);
}
colors.push(atom.color);
currentChain = atom.chain;
currentResi = atom.resi;
}
}
this.drawSmoothTube(group, points, colors, radii);
};
GLmol.prototype.drawStrip = function(group, p1, p2, colors, div, thickness) {
if ((p1.length) < 2) return;
div = div || this.axisDIV;
p1 = this.subdivide(p1, div);
p2 = this.subdivide(p2, div);
if (!thickness) return this.drawThinStrip(group, p1, p2, colors, div);
var geo = new THREE.Geometry();
var vs = geo.vertices, fs = geo.faces;
var axis, p1v, p2v, a1v, a2v;
for (var i = 0, lim = p1.length; i < lim; i++) {
vs.push(p1v = p1[i]); // 0
vs.push(p1v); // 1
vs.push(p2v = p2[i]); // 2
vs.push(p2v); // 3
if (i < lim - 1) {
var toNext = p1[i + 1].clone().subSelf(p1[i]);
var toSide = p2[i].clone().subSelf(p1[i]);
axis = toSide.crossSelf(toNext).normalize().multiplyScalar(thickness);
}
vs.push(a1v = p1[i].clone().addSelf(axis)); // 4
vs.push(a1v); // 5
vs.push(a2v = p2[i].clone().addSelf(axis)); // 6
vs.push(a2v); // 7
}
var faces = [[0, 2, -6, -8], [-4, -2, 6, 4], [7, 3, -5, -1], [-3, -7, 1, 5]];
for (var i = 1, lim = p1.length; i < lim; i++) {
var offset = 8 * i, color = new TCo(colors[Math.round((i - 1)/ div)]);
for (var j = 0; j < 4; j++) {
var f = new THREE.Face4(offset + faces[j][0], offset + faces[j][1], offset + faces[j][2], offset + faces[j][3], undefined, color);
fs.push(f);
}
}
var vsize = vs.length - 8; // Cap
for (var i = 0; i < 4; i++) {vs.push(vs[i * 2]); vs.push(vs[vsize + i * 2])};
vsize += 8;
fs.push(new THREE.Face4(vsize, vsize + 2, vsize + 6, vsize + 4, undefined, fs[0].color));
fs.push(new THREE.Face4(vsize + 1, vsize + 5, vsize + 7, vsize + 3, undefined, fs[fs.length - 3].color));
geo.computeFaceNormals();
geo.computeVertexNormals(false);
var material = new THREE.MeshLambertMaterial();
material.vertexColors = THREE.FaceColors;
var mesh = new THREE.Mesh(geo, material);
mesh.doubleSided = true;
group.add(mesh);
};
GLmol.prototype.drawThinStrip = function(group, p1, p2, colors, div) {
var geo = new THREE.Geometry();
for (var i = 0, lim = p1.length; i < lim; i++) {
geo.vertices.push(p1[i]); // 2i
geo.vertices.push(p2[i]); // 2i + 1
}
for (var i = 1, lim = p1.length; i < lim; i++) {
var f = new THREE.Face4(2 * i, 2 * i + 1, 2 * i - 1, 2 * i - 2);
f.color = new TCo(colors[Math.round((i - 1)/ div)]);
geo.faces.push(f);
}
geo.computeFaceNormals();
geo.computeVertexNormals(false);
var material = new THREE.MeshLambertMaterial();
material.vertexColors = THREE.FaceColors;
var mesh = new THREE.Mesh(geo, material);
mesh.doubleSided = true;
group.add(mesh);
};
GLmol.prototype.IcosahedronGeometry = function() {
if (!this.icosahedron) this.icosahedron = new THREE.IcosahedronGeometry(1);
return this.icosahedron;
};
GLmol.prototype.drawCylinder = function(group, from, to, radius, color, cap) {
if (!from || !to) return;
var midpoint = new TV3().add(from, to).multiplyScalar(0.5);
var color = new TCo(color);
if (!this.cylinderGeometry) {
this.cylinderGeometry = new THREE.CylinderGeometry(1, 1, 1, this.cylinderQuality, 1, !cap);
this.cylinderGeometry.faceUvs = [];
this.faceVertexUvs = [];
}
var cylinderMaterial = new THREE.MeshLambertMaterial({color: color.getHex()});
var cylinder = new THREE.Mesh(this.cylinderGeometry, cylinderMaterial);
cylinder.position = midpoint;
cylinder.lookAt(from);
cylinder.updateMatrix();
cylinder.matrixAutoUpdate = false;
var m = new THREE.Matrix4().makeScale(radius, radius, from.distanceTo(to));
m.rotateX(Math.PI / 2);
cylinder.matrix.multiplySelf(m);
group.add(cylinder);
};
// FIXME: transition!
GLmol.prototype.drawHelixAsCylinder = function(group, atomlist, radius) {
var start = null;
var currentChain, currentResi;
var others = [], beta = [];
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]];
if (atom == undefined || atom.hetflag) continue;
if ((atom.ss != 'h' && atom.ss != 's') || atom.ssend || atom.ssbegin) others.push(atom.serial);
if (atom.ss == 's') beta.push(atom.serial);
if (atom.atom != 'CA') continue;
if (atom.ss == 'h' && atom.ssend) {
if (start != null) this.drawCylinder(group, new TV3(start.x, start.y, start.z), new TV3(atom.x, atom.y, atom.z), radius, atom.color, true);
start = null;
}
currentChain = atom.chain;
currentResi = atom.resi;
if (start == null && atom.ss == 'h' && atom.ssbegin) start = atom;
}
if (start != null) this.drawCylinder(group, new TV3(start.x, start.y, start.z), new TV3(atom.x, atom.y, atom.z), radius, atom.color);
this.drawMainchainTube(group, others, "CA", 0.3);
this.drawStrand(group, beta, undefined, undefined, true, 0, this.helixSheetWidth, false, this.thickness * 2);
};
GLmol.prototype.drawCartoon = function(group, atomlist, doNotSmoothen, thickness) {
this.drawStrand(group, atomlist, 2, undefined, true, undefined, undefined, doNotSmoothen, thickness);
};
GLmol.prototype.drawStrand = function(group, atomlist, num, div, fill, coilWidth, helixSheetWidth, doNotSmoothen, thickness) {
num = num || this.strandDIV;
div = div || this.axisDIV;
coilWidth = coilWidth || this.coilWidth;
doNotSmoothen == (doNotSmoothen == undefined) ? false : doNotSmoothen;
helixSheetWidth = helixSheetWidth || this.helixSheetWidth;
var points = []; for (var k = 0; k < num; k++) points[k] = [];
var colors = [];
var currentChain, currentResi, currentCA;
var prevCO = null, ss=null, ssborder = false;
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]];
if (atom == undefined) continue;
if ((atom.atom == 'O' || atom.atom == 'CA') && !atom.hetflag) {
if (atom.atom == 'CA') {
if (currentChain != atom.chain || currentResi + 1 != atom.resi) {
for (var j = 0; !thickness && j < num; j++)
this.drawSmoothCurve(group, points[j], 1 ,colors, div);
if (fill) this.drawStrip(group, points[0], points[num - 1], colors, div, thickness);
var points = []; for (var k = 0; k < num; k++) points[k] = [];
colors = [];
prevCO = null; ss = null; ssborder = false;
}
currentCA = new TV3(atom.x, atom.y, atom.z);
currentChain = atom.chain;
currentResi = atom.resi;
ss = atom.ss; ssborder = atom.ssstart || atom.ssend;
colors.push(atom.color);
} else { // O
var O = new TV3(atom.x, atom.y, atom.z);
O.subSelf(currentCA);
O.normalize(); // can be omitted for performance
O.multiplyScalar((ss == 'c') ? coilWidth : helixSheetWidth);
if (prevCO != undefined && O.dot(prevCO) < 0) O.negate();
prevCO = O;
for (var j = 0; j < num; j++) {
var delta = -1 + 2 / (num - 1) * j;
var v = new TV3(currentCA.x + prevCO.x * delta,
currentCA.y + prevCO.y * delta, currentCA.z + prevCO.z * delta);
if (!doNotSmoothen && ss == 's') v.smoothen = true;
points[j].push(v);
}
}
}
}
for (var j = 0; !thickness && j < num; j++)
this.drawSmoothCurve(group, points[j], 1 ,colors, div);
if (fill) this.drawStrip(group, points[0], points[num - 1], colors, div, thickness);
};
GLmol.prototype.drawNucleicAcidLadderSub = function(geo, lineGeo, atoms, color) {
// color.r *= 0.9; color.g *= 0.9; color.b *= 0.9;
if (atoms[0] != undefined && atoms[1] != undefined && atoms[2] != undefined &&
atoms[3] != undefined && atoms[4] != undefined && atoms[5] != undefined) {
var baseFaceId = geo.vertices.length;
for (var i = 0; i <= 5; i++) geo.vertices.push(atoms[i]);
geo.faces.push(new TF3(baseFaceId, baseFaceId + 1, baseFaceId + 2));
geo.faces.push(new TF3(baseFaceId, baseFaceId + 2, baseFaceId + 3));
geo.faces.push(new TF3(baseFaceId, baseFaceId + 3, baseFaceId + 4));
geo.faces.push(new TF3(baseFaceId, baseFaceId + 4, baseFaceId + 5));
for (var j = geo.faces.length - 4, lim = geo.faces.length; j < lim; j++) geo.faces[j].color = color;
}
if (atoms[4] != undefined && atoms[3] != undefined && atoms[6] != undefined &&
atoms[7] != undefined && atoms[8] != undefined) {
var baseFaceId = geo.vertices.length;
geo.vertices.push(atoms[4]);
geo.vertices.push(atoms[3]);
geo.vertices.push(atoms[6]);
geo.vertices.push(atoms[7]);
geo.vertices.push(atoms[8]);
for (var i = 0; i <= 4; i++) geo.colors.push(color);
geo.faces.push(new TF3(baseFaceId, baseFaceId + 1, baseFaceId + 2));
geo.faces.push(new TF3(baseFaceId, baseFaceId + 2, baseFaceId + 3));
geo.faces.push(new TF3(baseFaceId, baseFaceId + 3, baseFaceId + 4));
for (var j = geo.faces.length - 3, lim = geo.faces.length; j < lim; j++) geo.faces[j].color = color;
}
};
GLmol.prototype.drawNucleicAcidLadder = function(group, atomlist) {
var geo = new THREE.Geometry();
var lineGeo = new THREE.Geometry();
var baseAtoms = ["N1", "C2", "N3", "C4", "C5", "C6", "N9", "C8", "N7"];
var currentChain, currentResi, currentComponent = new Array(baseAtoms.length);
var color = new TCo(0xcc0000);
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]];
if (atom == undefined || atom.hetflag) continue;
if (atom.resi != currentResi || atom.chain != currentChain) {
this.drawNucleicAcidLadderSub(geo, lineGeo, currentComponent, color);
currentComponent = new Array(baseAtoms.length);
}
var pos = baseAtoms.indexOf(atom.atom);
if (pos != -1) currentComponent[pos] = new TV3(atom.x, atom.y, atom.z);
if (atom.atom == 'O3\'') color = new TCo(atom.color);
currentResi = atom.resi; currentChain = atom.chain;
}
this.drawNucleicAcidLadderSub(geo, lineGeo, currentComponent, color);
geo.computeFaceNormals();
var mat = new THREE.MeshLambertMaterial();
mat.vertexColors = THREE.VertexColors;
var mesh = new THREE.Mesh(geo, mat);
mesh.doubleSided = true;
group.add(mesh);
};
GLmol.prototype.drawNucleicAcidStick = function(group, atomlist) {
var currentChain, currentResi, start = null, end = null;
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]];
if (atom == undefined || atom.hetflag) continue;
if (atom.resi != currentResi || atom.chain != currentChain) {
if (start != null && end != null)
this.drawCylinder(group, new TV3(start.x, start.y, start.z),
new TV3(end.x, end.y, end.z), 0.3, start.color, true);
start = null; end = null;
}
if (atom.atom == 'O3\'') start = atom;
if (atom.resn == ' A' || atom.resn == ' G' || atom.resn == ' DA' || atom.resn == ' DG') {
if (atom.atom == 'N1') end = atom; // N1(AG), N3(CTU)
} else if (atom.atom == 'N3') {
end = atom;
}
currentResi = atom.resi; currentChain = atom.chain;
}
if (start != null && end != null)
this.drawCylinder(group, new TV3(start.x, start.y, start.z),
new TV3(end.x, end.y, end.z), 0.3, start.color, true);
};
GLmol.prototype.drawNucleicAcidLine = function(group, atomlist) {
var currentChain, currentResi, start = null, end = null;
var geo = new THREE.Geometry();
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]];
if (atom == undefined || atom.hetflag) continue;
if (atom.resi != currentResi || atom.chain != currentChain) {
if (start != null && end != null) {
geo.vertices.push(new TV3(start.x, start.y, start.z));
geo.colors.push(new TCo(start.color));
geo.vertices.push(new TV3(end.x, end.y, end.z));
geo.colors.push(new TCo(start.color));
}
start = null; end = null;
}
if (atom.atom == 'O3\'') start = atom;
if (atom.resn == ' A' || atom.resn == ' G' || atom.resn == ' DA' || atom.resn == ' DG') {
if (atom.atom == 'N1') end = atom; // N1(AG), N3(CTU)
} else if (atom.atom == 'N3') {
end = atom;
}
currentResi = atom.resi; currentChain = atom.chain;
}
if (start != null && end != null) {
geo.vertices.push(new TV3(start.x, start.y, start.z));
geo.colors.push(new TCo(start.color));
geo.vertices.push(new TV3(end.x, end.y, end.z));
geo.colors.push(new TCo(start.color));
}
var mat = new THREE.LineBasicMaterial({linewidth: 1, linejoin: false});
mat.linewidth = 1.5; mat.vertexColors = true;
var line = new THREE.Line(geo, mat, THREE.LinePieces);
group.add(line);
};
GLmol.prototype.drawCartoonNucleicAcid = function(group, atomlist, div, thickness) {
this.drawStrandNucleicAcid(group, atomlist, 2, div, true, undefined, thickness);
};
GLmol.prototype.drawStrandNucleicAcid = function(group, atomlist, num, div, fill, nucleicAcidWidth, thickness) {
nucleicAcidWidth = nucleicAcidWidth || this.nucleicAcidWidth;
div = div || this.axisDIV;
num = num || this.nucleicAcidStrandDIV;
var points = []; for (var k = 0; k < num; k++) points[k] = [];
var colors = [];
var currentChain, currentResi, currentO3;
var prevOO = null;
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]];
if (atom == undefined) continue;
if ((atom.atom == 'O3\'' || atom.atom == 'OP2') && !atom.hetflag) {
if (atom.atom == 'O3\'') { // to connect 3' end. FIXME: better way to do?
if (currentChain != atom.chain || currentResi + 1 != atom.resi) {
if (currentO3) {
for (var j = 0; j < num; j++) {
var delta = -1 + 2 / (num - 1) * j;
points[j].push(new TV3(currentO3.x + prevOO.x * delta,
currentO3.y + prevOO.y * delta, currentO3.z + prevOO.z * delta));
}
}
if (fill) this.drawStrip(group, points[0], points[1], colors, div, thickness);
for (var j = 0; !thickness && j < num; j++)
this.drawSmoothCurve(group, points[j], 1 ,colors, div);
var points = []; for (var k = 0; k < num; k++) points[k] = [];
colors = [];
prevOO = null;
}
currentO3 = new TV3(atom.x, atom.y, atom.z);
currentChain = atom.chain;
currentResi = atom.resi;
colors.push(atom.color);
} else { // OP2
if (!currentO3) {prevOO = null; continue;} // for 5' phosphate (e.g. 3QX3)
var O = new TV3(atom.x, atom.y, atom.z);
O.subSelf(currentO3);
O.normalize().multiplyScalar(nucleicAcidWidth); // TODO: refactor
if (prevOO != undefined && O.dot(prevOO) < 0) {
O.negate();
}
prevOO = O;
for (var j = 0; j < num; j++) {
var delta = -1 + 2 / (num - 1) * j;
points[j].push(new TV3(currentO3.x + prevOO.x * delta,
currentO3.y + prevOO.y * delta, currentO3.z + prevOO.z * delta));
}
currentO3 = null;
}
}
}
if (currentO3) {
for (var j = 0; j < num; j++) {
var delta = -1 + 2 / (num - 1) * j;
points[j].push(new TV3(currentO3.x + prevOO.x * delta,
currentO3.y + prevOO.y * delta, currentO3.z + prevOO.z * delta));
}
}
if (fill) this.drawStrip(group, points[0], points[1], colors, div, thickness);
for (var j = 0; !thickness && j < num; j++)
this.drawSmoothCurve(group, points[j], 1 ,colors, div);
};
GLmol.prototype.drawDottedLines = function(group, points, color) {
var geo = new THREE.Geometry();
var step = 0.3;
for (var i = 0, lim = Math.floor(points.length / 2); i < lim; i++) {
var p1 = points[2 * i], p2 = points[2 * i + 1];
var delta = p2.clone().subSelf(p1);
var dist = delta.length();
delta.normalize().multiplyScalar(step);
var jlim = Math.floor(dist / step);
for (var j = 0; j < jlim; j++) {
var p = new TV3(p1.x + delta.x * j, p1.y + delta.y * j, p1.z + delta.z * j);
geo.vertices.push(p);
}
if (jlim % 2 == 1) geo.vertices.push(p2);
}
var mat = new THREE.LineBasicMaterial({'color': color.getHex()});
mat.linewidth = 2;
var line = new THREE.Line(geo, mat, THREE.LinePieces);
group.add(line);
};
GLmol.prototype.getAllAtoms = function() {
var ret = [];
for (var i in this.atoms) {
ret.push(this.atoms[i].serial);
}
return ret;
};
// Probably I can refactor using higher-order functions.
GLmol.prototype.getHetatms = function(atomlist) {
var ret = [];
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (atom.hetflag) ret.push(atom.serial);
}
return ret;
};
GLmol.prototype.removeSolvents = function(atomlist) {
var ret = [];
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (atom.resn != 'HOH') ret.push(atom.serial);
}
return ret;
};
GLmol.prototype.getProteins = function(atomlist) {
var ret = [];
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (!atom.hetflag) ret.push(atom.serial);
}
return ret;
};
// TODO: Test
GLmol.prototype.excludeAtoms = function(atomlist, deleteList) {
var ret = [];
var blackList = new Object();
for (var _i in deleteList) blackList[deleteList[_i]] = true;
for (var _i in atomlist) {
var i = atomlist[_i];
if (!blackList[i]) ret.push(i);
}
return ret;
};
GLmol.prototype.getSidechains = function(atomlist) {
var ret = [];
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (atom.hetflag) continue;
if (atom.atom == 'C' || atom.atom == 'O' || (atom.atom == 'N' && atom.resn != "PRO")) continue;
ret.push(atom.serial);
}
return ret;
};
GLmol.prototype.getAtomsWithin = function(atomlist, extent) {
var ret = [];
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (atom.x < extent[0][0] || atom.x > extent[1][0]) continue;
if (atom.y < extent[0][1] || atom.y > extent[1][1]) continue;
if (atom.z < extent[0][2] || atom.z > extent[1][2]) continue;
ret.push(atom.serial);
}
return ret;
};
GLmol.prototype.getExtent = function(atomlist) {
var xmin = ymin = zmin = 9999;
var xmax = ymax = zmax = -9999;
var xsum = ysum = zsum = cnt = 0;
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
cnt++;
xsum += atom.x; ysum += atom.y; zsum += atom.z;
xmin = (xmin < atom.x) ? xmin : atom.x;
ymin = (ymin < atom.y) ? ymin : atom.y;
zmin = (zmin < atom.z) ? zmin : atom.z;
xmax = (xmax > atom.x) ? xmax : atom.x;
ymax = (ymax > atom.y) ? ymax : atom.y;
zmax = (zmax > atom.z) ? zmax : atom.z;
}
return [[xmin, ymin, zmin], [xmax, ymax, zmax], [xsum / cnt, ysum / cnt, zsum / cnt]];
};
GLmol.prototype.getResiduesById = function(atomlist, resi) {
var ret = [];
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (resi.indexOf(atom.resi) != -1) ret.push(atom.serial);
}
return ret;
};
GLmol.prototype.getResidueBySS = function(atomlist, ss) {
var ret = [];
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (ss.indexOf(atom.ss) != -1) ret.push(atom.serial);
}
return ret;
};
GLmol.prototype.getChain = function(atomlist, chain) {
var ret = [], chains = {};
chain = chain.toString(); // concat if Array
for (var i = 0, lim = chain.length; i < lim; i++) chains[chain.substr(i, 1)] = true;
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (chains[atom.chain]) ret.push(atom.serial);
}
return ret;
};
// for HETATM only
GLmol.prototype.getNonbonded = function(atomlist, chain) {
var ret = [];
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (atom.hetflag && atom.bonds.length == 0) ret.push(atom.serial);
}
return ret;
};
GLmol.prototype.colorByAtom = function(atomlist, colors) {
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
var c = colors[atom.elem];
if (c == undefined) c = this.ElementColors[atom.elem];
if (c == undefined) c = this.defaultColor;
atom.color = c;
}
};
// MEMO: Color only CA. maybe I should add atom.cartoonColor.
GLmol.prototype.colorByStructure = function(atomlist, helixColor, sheetColor, colorSidechains) {
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (!colorSidechains && (atom.atom != 'CA' || atom.hetflag)) continue;
if (atom.ss[0] == 's') atom.color = sheetColor;
else if (atom.ss[0] == 'h') atom.color = helixColor;
}
};
GLmol.prototype.colorByBFactor = function(atomlist, colorSidechains) {
var minB = 1000, maxB = -1000;
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (atom.hetflag) continue;
if (colorSidechains || atom.atom == 'CA' || atom.atom == 'O3\'') {
if (minB > atom.b) minB = atom.b;
if (maxB < atom.b) maxB = atom.b;
}
}
var mid = (maxB + minB) / 2;
var range = (maxB - minB) / 2;
if (range < 0.01 && range > -0.01) return;
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (atom.hetflag) continue;
if (colorSidechains || atom.atom == 'CA' || atom.atom == 'O3\'') {
var color = new TCo(0);
if (atom.b < mid)
color.setHSV(0.667, (mid - atom.b) / range, 1);
else
color.setHSV(0, (atom.b - mid) / range, 1);
atom.color = color.getHex();
}
}
};
GLmol.prototype.colorByChain = function(atomlist, colorSidechains) {
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if (atom.hetflag) continue;
if (colorSidechains || atom.atom == 'CA' || atom.atom == 'O3\'') {
var color = new TCo(0);
color.setHSV((atom.chain.charCodeAt(0) * 5) % 17 / 17.0, 1, 0.9);
atom.color = color.getHex();
}
}
};
GLmol.prototype.colorByResidue = function(atomlist, residueColors) {
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
c = residueColors[atom.resn]
if (c != undefined) atom.color = c;
}
};
GLmol.prototype.colorAtoms = function(atomlist, c) {
for (var i in atomlist) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
atom.color = c;
}
};
GLmol.prototype.colorByPolarity = function(atomlist, polar, nonpolar) {
var polarResidues = ['ARG', 'HIS', 'LYS', 'ASP', 'GLU', 'SER', 'THR', 'ASN', 'GLN', 'CYS'];
var nonPolarResidues = ['GLY', 'PRO', 'ALA', 'VAL', 'LEU', 'ILE', 'MET', 'PHE', 'TYR', 'TRP'];
var colorMap = {};
for (var i in polarResidues) colorMap[polarResidues[i]] = polar;
for (i in nonPolarResidues) colorMap[nonPolarResidues[i]] = nonpolar;
this.colorByResidue(atomlist, colorMap);
};
// TODO: Add near(atomlist, neighbor, distanceCutoff)
// TODO: Add expandToResidue(atomlist)
GLmol.prototype.colorChainbow = function(atomlist, colorSidechains) {
var cnt = 0;
var atom, i;
for (i in atomlist) {
atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if ((colorSidechains || atom.atom != 'CA' || atom.atom != 'O3\'') && !atom.hetflag)
cnt++;
}
var total = cnt;
cnt = 0;
for (i in atomlist) {
atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;
if ((colorSidechains || atom.atom != 'CA' || atom.atom != 'O3\'') && !atom.hetflag) {
var color = new TCo(0);
color.setHSV(240.0 / 360 * (1 - cnt / total), 1, 0.9);
atom.color = color.getHex();
cnt++;
}
}
};
GLmol.prototype.drawSymmetryMates2 = function(group, asu, matrices) {
if (matrices == undefined) return;
asu.matrixAutoUpdate = false;
var cnt = 1;
this.protein.appliedMatrix = new THREE.Matrix4();
for (var i = 0; i < matrices.length; i++) {
var mat = matrices[i];
if (mat == undefined || mat.isIdentity()) continue;
console.log(mat);
var symmetryMate = THREE.SceneUtils.cloneObject(asu);
symmetryMate.matrix = mat;
group.add(symmetryMate);
for (var j = 0; j < 16; j++) this.protein.appliedMatrix.elements[j] += mat.elements[j];
cnt++;
}
this.protein.appliedMatrix.multiplyScalar(cnt);
};
GLmol.prototype.drawSymmetryMatesWithTranslation2 = function(group, asu, matrices) {
if (matrices == undefined) return;
var p = this.protein;
asu.matrixAutoUpdate = false;
for (var i = 0; i < matrices.length; i++) {
var mat = matrices[i];
if (mat == undefined) continue;
for (var a = -1; a <=0; a++) {
for (var b = -1; b <= 0; b++) {
for (var c = -1; c <= 0; c++) {
var translationMat = new THREE.Matrix4().makeTranslation(
p.ax * a + p.bx * b + p.cx * c,
p.ay * a + p.by * b + p.cy * c,
p.az * a + p.bz * b + p.cz * c);
var symop = mat.clone().multiplySelf(translationMat);
if (symop.isIdentity()) continue;
var symmetryMate = THREE.SceneUtils.cloneObject(asu);
symmetryMate.matrix = symop;
group.add(symmetryMate);
}
}
}
}
};
GLmol.prototype.defineRepresentation = function() {
var all = this.getAllAtoms();
var hetatm = this.removeSolvents(this.getHetatms(all));
this.colorByAtom(all, {});
this.colorByChain(all);
this.drawAtomsAsSphere(this.modelGroup, hetatm, this.sphereRadius);
this.drawMainchainCurve(this.modelGroup, all, this.curveWidth, 'P');
this.drawCartoon(this.modelGroup, all, this.curveWidth);
};
GLmol.prototype.getView = function() {
if (!this.modelGroup) return [0, 0, 0, 0, 0, 0, 0, 1];
var pos = this.modelGroup.position;
var q = this.rotationGroup.quaternion;
return [pos.x, pos.y, pos.z, this.rotationGroup.position.z, q.x, q.y, q.z, q.w];
};
GLmol.prototype.setView = function(arg) {
if (!this.modelGroup || !this.rotationGroup) return;
this.modelGroup.position.x = arg[0];
this.modelGroup.position.y = arg[1];
this.modelGroup.position.z = arg[2];
this.rotationGroup.position.z = arg[3];
this.rotationGroup.quaternion.x = arg[4];
this.rotationGroup.quaternion.y = arg[5];
this.rotationGroup.quaternion.z = arg[6];
this.rotationGroup.quaternion.w = arg[7];
this.show();
};
GLmol.prototype.setBackground = function(hex, a) {
a = a | 1.0;
this.bgColor = hex;
this.renderer.setClearColorHex(hex, a);
this.scene.fog.color = new TCo(hex);
};
GLmol.prototype.initializeScene = function() {
// CHECK: Should I explicitly call scene.deallocateObject?
this.scene = new THREE.Scene();
this.scene.fog = new THREE.Fog(this.bgColor, 100, 200);
this.modelGroup = new THREE.Object3D();
this.rotationGroup = new THREE.Object3D();
this.rotationGroup.useQuaternion = true;
this.rotationGroup.quaternion = new THREE.Quaternion(1, 0, 0, 0);
this.rotationGroup.add(this.modelGroup);
this.scene.add(this.rotationGroup);
this.setupLights(this.scene);
};
GLmol.prototype.zoomInto = function(atomlist, keepSlab) {
var tmp = this.getExtent(atomlist);
var center = new TV3(tmp[2][0], tmp[2][1], tmp[2][2]);//(tmp[0][0] + tmp[1][0]) / 2, (tmp[0][1] + tmp[1][1]) / 2, (tmp[0][2] + tmp[1][2]) / 2);
if (this.protein.appliedMatrix) {center = this.protein.appliedMatrix.multiplyVector3(center);}
this.modelGroup.position = center.multiplyScalar(-1);
var x = tmp[1][0] - tmp[0][0], y = tmp[1][1] - tmp[0][1], z = tmp[1][2] - tmp[0][2];
var maxD = Math.sqrt(x * x + y * y + z * z);
if (maxD < 25) maxD = 25;
if (!keepSlab) {
this.slabNear = -maxD / 1.9;
this.slabFar = maxD / 3;
}
this.rotationGroup.position.z = maxD * 0.35 / Math.tan(Math.PI / 180.0 * this.camera.fov / 2) - 150;
this.rotationGroup.quaternion = new THREE.Quaternion(1, 0, 0, 0);
};
GLmol.prototype.rebuildScene = function() {
time = new Date();
var view = this.getView();
this.initializeScene();
this.defineRepresentation();
this.setView(view);
console.log("builded scene in " + (+new Date() - time) + "ms");
};
GLmol.prototype.loadMolecule = function(repressZoom) {
this.loadMoleculeStr(repressZoom, $('#' + this.id + '_src').val());
};
GLmol.prototype.loadMoleculeStr = function(repressZoom, source) {
var time = new Date();
this.protein = {sheet: [], helix: [], biomtChains: '', biomtMatrices: [], symMat: [], pdbID: '', title: ''};
this.atoms = [];
this.parsePDB2(source);
if (!this.parseSDF(source)) this.parseXYZ(source);
console.log("parsed in " + (+new Date() - time) + "ms");
var title = $('#' + this.id + '_pdbTitle');
var titleStr = '';
if (this.protein.pdbID != '') titleStr += '<a href="http://www.rcsb.org/pdb/explore/explore.do?structureId=' + this.protein.pdbID + '">' + this.protein.pdbID + '</a>';
if (this.protein.title != '') titleStr += '<br>' + this.protein.title;
title.html(titleStr);
this.rebuildScene(true);
if (repressZoom == undefined || !repressZoom) this.zoomInto(this.getAllAtoms());
this.show();
};
GLmol.prototype.setSlabAndFog = function() {
var center = this.rotationGroup.position.z - this.camera.position.z;
if (center < 1) center = 1;
this.camera.near = center + this.slabNear;
if (this.camera.near < 1) this.camera.near = 1;
this.camera.far = center + this.slabFar;
if (this.camera.near + 1 > this.camera.far) this.camera.far = this.camera.near + 1;
if (this.camera instanceof THREE.PerspectiveCamera) {
this.camera.fov = this.fov;
} else {
this.camera.right = center * Math.tan(Math.PI / 180 * this.fov);
this.camera.left = - this.camera.right;
this.camera.top = this.camera.right / this.ASPECT;
this.camera.bottom = - this.camera.top;
}
this.camera.updateProjectionMatrix();
this.scene.fog.near = this.camera.near + this.fogStart * (this.camera.far - this.camera.near);
// if (this.scene.fog.near > center) this.scene.fog.near = center;
this.scene.fog.far = this.camera.far;
};
GLmol.prototype.enableMouse = function() {
var me = this, glDOM = $(this.renderer.domElement);
// TODO: Better touch panel support.
// Contribution is needed as I don't own any iOS or Android device with WebGL support.
glDOM.bind('mousedown touchstart', function(ev) {
ev.preventDefault();
if (!me.scene) return;
var x = ev.pageX, y = ev.pageY;
if (ev.originalEvent.targetTouches && ev.originalEvent.targetTouches[0]) {
x = ev.originalEvent.targetTouches[0].pageX;
y = ev.originalEvent.targetTouches[0].pageY;
}
if (x == undefined) return;
me.isDragging = true;
me.mouseButton = ev.which;
me.mouseStartX = x;
me.mouseStartY = y;
me.cq = me.rotationGroup.quaternion;
me.cz = me.rotationGroup.position.z;
me.currentModelPos = me.modelGroup.position.clone();
me.cslabNear = me.slabNear;
me.cslabFar = me.slabFar;
});
glDOM.bind('DOMMouseScroll mousewheel', function(ev) { // Zoom
ev.preventDefault();
if (!me.scene) return;
var scaleFactor = (me.rotationGroup.position.z - me.CAMERA_Z) * 0.85;
if (ev.originalEvent.detail) { // Webkit
me.rotationGroup.position.z += scaleFactor * ev.originalEvent.detail / 10;
} else if (ev.originalEvent.wheelDelta) { // Firefox
me.rotationGroup.position.z -= scaleFactor * ev.originalEvent.wheelDelta / 400;
}
console.log(ev.originalEvent.wheelDelta, ev.originalEvent.detail, me.rotationGroup.position.z);
me.show();
});
glDOM.bind("contextmenu", function(ev) {ev.preventDefault();});
$('body').bind('mouseup touchend', function(ev) {
me.isDragging = false;
});
glDOM.bind('mousemove touchmove', function(ev) { // touchmove
ev.preventDefault();
if (!me.scene) return;
if (!me.isDragging) return;
var mode = 0;
var modeRadio = $('input[name=' + me.id + '_mouseMode]:checked');
if (modeRadio.length > 0) mode = parseInt(modeRadio.val());
var x = ev.pageX, y = ev.pageY;
if (ev.originalEvent.targetTouches && ev.originalEvent.targetTouches[0]) {
x = ev.originalEvent.targetTouches[0].pageX;
y = ev.originalEvent.targetTouches[0].pageY;
}
if (x == undefined) return;
var dx = (x - me.mouseStartX) / me.WIDTH;
var dy = (y - me.mouseStartY) / me.HEIGHT;
var r = Math.sqrt(dx * dx + dy * dy);
if (mode == 3 || (me.mouseButton == 3 && ev.ctrlKey)) { // Slab
me.slabNear = me.cslabNear + dx * 100;
me.slabFar = me.cslabFar + dy * 100;
} else if (mode == 2 || me.mouseButton == 3 || ev.shiftKey) { // Zoom
var scaleFactor = (me.rotationGroup.position.z - me.CAMERA_Z) * 0.85;
if (scaleFactor < 80) scaleFactor = 80;
me.rotationGroup.position.z = me.cz - dy * scaleFactor;
} else if (mode == 1 || me.mouseButton == 2 || ev.ctrlKey) { // Translate
var scaleFactor = (me.rotationGroup.position.z - me.CAMERA_Z) * 0.85;
if (scaleFactor < 20) scaleFactor = 20;
var translationByScreen = new TV3(- dx * scaleFactor, - dy * scaleFactor, 0);
var q = me.rotationGroup.quaternion;
var qinv = new THREE.Quaternion(q.x, q.y, q.z, q.w).inverse().normalize();
var translation = qinv.multiplyVector3(translationByScreen);
me.modelGroup.position.x = me.currentModelPos.x + translation.x;
me.modelGroup.position.y = me.currentModelPos.y + translation.y;
me.modelGroup.position.z = me.currentModelPos.z + translation.z;
} else if ((mode == 0 || me.mouseButton == 1) && r != 0) { // Rotate
var rs = Math.sin(r * Math.PI) / r;
me.dq.x = Math.cos(r * Math.PI);
me.dq.y = 0;
me.dq.z = rs * dx;
me.dq.w = rs * dy;
me.rotationGroup.quaternion = new THREE.Quaternion(1, 0, 0, 0);
me.rotationGroup.quaternion.multiplySelf(me.dq);
me.rotationGroup.quaternion.multiplySelf(me.cq);
}
me.show();
});
};
GLmol.prototype.show = function() {
if (!this.scene) return;
var time = new Date();
this.setSlabAndFog();
this.renderer.render(this.scene, this.camera);
console.log("rendered in " + (+new Date() - time) + "ms");
};
// For scripting
GLmol.prototype.doFunc = function(func) {
func(this);
};
return GLmol;
}());