Return-Path: X-Original-To: apmail-airavata-commits-archive@www.apache.org Delivered-To: apmail-airavata-commits-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 66FE318229 for ; Tue, 9 Feb 2016 15:55:31 +0000 (UTC) Received: (qmail 38598 invoked by uid 500); 9 Feb 2016 15:55:30 -0000 Delivered-To: apmail-airavata-commits-archive@airavata.apache.org Received: (qmail 38347 invoked by uid 500); 9 Feb 2016 15:55:30 -0000 Mailing-List: contact commits-help@airavata.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@airavata.apache.org Delivered-To: mailing list commits@airavata.apache.org Received: (qmail 37401 invoked by uid 99); 9 Feb 2016 15:55:30 -0000 Received: from git1-us-west.apache.org (HELO git1-us-west.apache.org) (140.211.11.23) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 09 Feb 2016 15:55:30 +0000 Received: by git1-us-west.apache.org (ASF Mail Server at git1-us-west.apache.org, from userid 33) id D7800E6994; Tue, 9 Feb 2016 15:55:29 +0000 (UTC) Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit From: scnakandala@apache.org To: commits@airavata.apache.org Date: Tue, 09 Feb 2016 15:55:42 -0000 Message-Id: <64f7a284d0ab4abb8bf2f6159a604f15@git.apache.org> In-Reply-To: References: X-Mailer: ASF-Git Admin Mailer Subject: [14/50] [abbrv] airavata-php-gateway git commit: adding datacat web browser initial files adding datacat web browser initial files Project: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/commit/bac76ae5 Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/bac76ae5 Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/bac76ae5 Branch: refs/heads/master Commit: bac76ae50087fe8c66604ee6e54628d2da9a884c Parents: e675d4d Author: scnakandala Authored: Wed Jan 27 15:08:16 2016 -0500 Committer: scnakandala Committed: Wed Jan 27 15:08:16 2016 -0500 ---------------------------------------------------------------------- app/controllers/DataCatController.php | 16 + app/routes.php | 5 + app/views/datacat/select.blade.php | 80 ++ public/js/datacat/GLmol.js | 1708 ++++++++++++++++++++++++++++ public/js/datacat/Three.js | 382 +++++++ public/js/datacat/jquery-1.7.min.js | 4 + 6 files changed, 2195 insertions(+) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/bac76ae5/app/controllers/DataCatController.php ---------------------------------------------------------------------- diff --git a/app/controllers/DataCatController.php b/app/controllers/DataCatController.php new file mode 100755 index 0000000..fb821f6 --- /dev/null +++ b/app/controllers/DataCatController.php @@ -0,0 +1,16 @@ + $results)); + } + +} http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/bac76ae5/app/routes.php ---------------------------------------------------------------------- diff --git a/app/routes.php b/app/routes.php index a180cba..e183220 100755 --- a/app/routes.php +++ b/app/routes.php @@ -204,6 +204,11 @@ Route::post("gp/remove-sr", "GatewayprofileController@delete"); Route::post("gp/credential-store-token-change", "GatewayprofileController@cstChange"); + +//DataCat +Route::get("datacat/select", "DataCatController@select"); + + //Management Dashboard Route::get("admin/dashboard", "AdminController@dashboard"); http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/bac76ae5/app/views/datacat/select.blade.php ---------------------------------------------------------------------- diff --git a/app/views/datacat/select.blade.php b/app/views/datacat/select.blade.php new file mode 100755 index 0000000..ada2902 --- /dev/null +++ b/app/views/datacat/select.blade.php @@ -0,0 +1,80 @@ +@extends('layout.basic') +{{ HTML::script('js/datacat/jquery-1.7.min.js')}} +{{ HTML::script('js/datacat/Three.js')}} +{{ HTML::script('js/datacat/GLmol.js')}} + +@section('page-header') + @parent +@stop +@section('content') +
+ @if ( isset($results)) + @if (sizeof($results) != 0) +
+ + + + + + + + + + + + + + + @foreach($results as $key=>$result) + @if(isset($result['Formula'])) + + + + + + + + + + + + + + @endif + @endforeach +
FinalGeomFormulaEnergyZPECalcTypeMethodsBasisEnthalpyGibbsNImagCodeVersion
+
+ @if(isset($result['PDB'])) + + + @endif + 		@if(isset($result['Formula'])){{$result['Formula']}}@endif@if(isset($result['Energy'])){{$result['Energy']}}@endif@if(isset($result['ZPE'])){{$result['ZPE']}}@endif@if(isset($result['CalcType'])){{$result['CalcType']}}@endif@if(isset($result['Methods'])){{$result['Methods']}}@endif@if(isset($result['Basis'])){{$result['Basis']}}@endif@if(isset($result['Enthalpy'])){{$result['Enthalpy']}}@endif@if(isset($result['Gibbs'])){{$result['Gibbs']}}@endif@if(isset($result['NImag'])){{$result['NImag']}}@endif@if(isset($result['CodeVersion'])){{$result['CodeVersion']}}@endif
+
+ @endif + @endif +
+@stop \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/bac76ae5/public/js/datacat/GLmol.js ---------------------------------------------------------------------- diff --git a/public/js/datacat/GLmol.js b/public/js/datacat/GLmol.js new file mode 100644 index 0000000..9af612b --- /dev/null +++ b/public/js/datacat/GLmol.js @@ -0,0 +1,1708 @@ +/* + 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 += '' + this.protein.pdbID + ''; + if (this.protein.title != '') titleStr += '
' + 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; +}());