Skip to content

Dynamic coloring #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
JieqiongZhao wants to merge 5 commits into
base: master
Choose a base branch
from
Open

Dynamic coloring #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
968cc7f
implemented VTF
Apr 30, 2012
8864325
implemented sequence view (proof of concept; click residue to make it…
Apr 30, 2012
a0891e2
VTF for line shader. Three.js had to be patched.
Apr 30, 2012
ab6a035
enlarged sequence view
May 2, 2012
470c496
now VTF should work on Win & Mac
May 2, 2012
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
100 changes: 77 additions & 23 deletions src/js/GLmol.js
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
GLmol - Molecular Viewer on WebGL/Javascript (0.40)
GLmol - Molecular Viewer on WebGL/Javascript (0.40 + VTF)
(C) Copyright 2011-2012, biochem_fan

License: dual license of MIT or LGPL3
Expand Down Expand Up @@ -31,6 +31,38 @@ THREE.Matrix4.prototype.isIdentity = function() {
return true;
};

function hookShader() { // Lambert Shader and Line Shader ONLY
// For texture-coordinates, see
// http://stackoverflow.com/questions/5879403/opengl-texture-coordinates-in-pixel-space/5879551#5879551
// This is the heart of this trick.
// FaceColors, VertexColors: USE_COLOR is defined, color is passed as "color" attribute
// Other cases: color is passed as "diffuse" uniform

// USE_MAP has to be disabled; otherwise, mesh without uv will not be displayed.
// Inject Color picker into vertex shader
THREE.ShaderLib.lambert.vertexShader = THREE.ShaderLib.lambert.vertexShader.replace("void main", "#undef USE_MAP\n uniform sampler2D map; \n \n\nvec3 pickColor(vec3 color){\n int serial = int(color.b * 255.0 + color.g * 65280.0 + color.r * 16711680.0 + 0.01); float x = ((mod(float(serial), 512.0))* 2.0 + 1.0) / 1024.0, y = (float(serial / 512) * 2.0 + 1.0) / 1024.0;\n \n return texture2D(map, vec2(x, y)).rgb;\n} \n\n\nvoid main");
// Hook Material color ("diffuse" uniform)
THREE.ShaderLib.lambert.vertexShader = THREE.ShaderLib.lambert.vertexShader.replace(/\* diffuse/g, "* diffuse2");
THREE.ShaderLib.lambert.vertexShader = THREE.ShaderLib.lambert.vertexShader.replace("vLightFront = vLightFront *", "///////////////////////////////////////\n\n#ifndef USE_COLOR\nvec3 diffuse2 = pickColor(diffuse).rgb;\n#else\nvec3 diffuse2 = diffuse;\n#endif\nvLightFront = vLightFront *");
// Hook vertex color & face color ("color" attribute)
THREE.ShaderLib.lambert.vertexShader = THREE.ShaderLib.lambert.vertexShader.replace("vColor = color;", "vColor = pickColor(color);");
THREE.ShaderLib.lambert.vertexShader = THREE.ShaderLib.lambert.vertexShader.replace("vColor = color * color;", "vColor = pickColor(color) * pickColor(color);");
// Disable normal texture mapping
THREE.ShaderLib.lambert.fragmentShader = THREE.ShaderLib.lambert.fragmentShader.replace("void main", "#undef USE_MAP\n void main");
THREE.ShaderLib.lambert.fragmentShader = THREE.ShaderLib.lambert.fragmentShader.replace("gl_FragColor = gl_FragColor * texture2D( map, vUv );", "");
THREE.ShaderLib.lambert.fragmentShader = THREE.ShaderLib.lambert.fragmentShader.replace("gl_FragColor = gl_FragColor * texelColor;", "a1");

// Same for 'basic' shader
// For this to work, WebGLRenderer.js has to be patched beforehand.
THREE.ShaderLib.basic.vertexShader = THREE.ShaderLib.basic.vertexShader.replace("void main", "uniform sampler2D map; \n \n\nvec3 pickColor(vec3 color){\n int serial = int(color.b * 255.0 + color.g * 65280.0 + color.r * 16711680.0 + 0.01); float x = ((mod(float(serial), 512.0))* 2.0 + 1.0) / 1024.0, y = (float(serial / 512) * 2.0 + 1.0) / 1024.0;\n \n return texture2D(map, vec2(x, y)).rgb;\n} \n\n\nvoid main");
THREE.ShaderLib.basic.vertexShader = THREE.ShaderLib.basic.vertexShader.replace(/\* diffuse/g, "* diffuse2");
THREE.ShaderLib.basic.vertexShader = THREE.ShaderLib.basic.vertexShader.replace("vLightFront = vLightFront *", "///////////////////////////////////////\n\n#ifndef USE_COLOR\nvec3 diffuse2 = pickColor(diffuse).rgb;\n#else\nvec3 diffuse2 = diffuse;\n#endif\nvLightFront = vLightFront *");
THREE.ShaderLib.basic.vertexShader = THREE.ShaderLib.basic.vertexShader.replace("vColor = color;", "vColor = pickColor(color);");
THREE.ShaderLib.basic.fragmentShader = THREE.ShaderLib.basic.fragmentShader.replace("gl_FragColor = gl_FragColor * texture2D( map, vUv );", "");
}

hookShader();

var GLmol = (function() {
function GLmol(id, suppressAutoload) {
this.Nucleotides = [' G', ' A', ' T', ' C', ' U', ' DG', ' DA', ' DT', ' DC', ' DU'];
Expand Down Expand Up @@ -113,11 +145,31 @@ function GLmol(id, suppressAutoload) {
this.currentModelPos = 0;
this.cz = 0;
this.enableMouse();
this.colortable = new Uint8Array(512 * 512 * 3);
this.colormap = new THREE.DataTexture(this.colortable, 512, 512, THREE.RGBFormat);
// this.colormap.generateMipmaps = false;
this.colormap.onUpdate = function() {console.log('texture updated');};
this.colormap.magFilter = this.colormap.minFilter = THREE.NearestFilter;
this.colormap.generateMipmaps = false;
for (var i = 0; i < 512 * 512; i++) {
this.setColor(i, 0x0000ff);
}

if (suppressAutoload) return;
this.loadMolecule();
}

GLmol.prototype.setColor = function(serial, color) {
var b = color % 256;
var g = Math.floor((color % 65536) / 256);
var r = Math.floor(color / 65536);
this.colortable[serial * 3] = r;
this.colortable[serial * 3 + 1] = g;
this.colortable[serial * 3 + 2] = b;
this.colormap.needsUpdate = true;
}


GLmol.prototype.setupLights = function(scene) {
var directionalLight = new THREE.DirectionalLight(0xFFFFFF);
directionalLight.position = new TV3(0.2, 0.2, -1).normalize();
Expand Down Expand Up @@ -198,7 +250,7 @@ GLmol.prototype.parsePDB2 = function(str) {
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*/};
'bonds': [], 'ss': 'c', 'color': serial, 'bonds': [], 'bondOrder': [], 'b': b /*', altLoc': altLoc*/};
} else if (recordName == 'SHEET ') {
var startChain = line.substr(21, 1);
var startResi = parseInt(line.substr(22, 4));
Expand Down Expand Up @@ -325,11 +377,12 @@ GLmol.prototype.subdivide = function(_points, DIV) { // points as Vector3

GLmol.prototype.drawAtomsAsSphere = function(group, atomlist, defaultRadius, forceDefault) {
var sphereGeometry = new THREE.SphereGeometry(1, this.sphereQuality, this.sphereQuality); // r, seg, ring
sphereGeometry.faceVertexUvs = [];
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 sphereMaterial = new THREE.MeshLambertMaterial({color: atom.color, map:this.colormap});
var sphere = new THREE.Mesh(sphereGeometry, sphereMaterial);
group.add(sphere);
var r = (!forceDefault && this.vdwRadii[atom.elem] != undefined) ? this.vdwRadii[atom.elem] : defaultRadius
Expand All @@ -347,7 +400,7 @@ GLmol.prototype.drawAtomsAsIcosahedron = function(group, atomlist, defaultRadius
var atom = this.atoms[atomlist[i]];
if (atom == undefined) continue;

var mat = new THREE.MeshLambertMaterial({color: atom.color});
var mat = new THREE.MeshLambertMaterial({color: atom.color, map:this.colormap});
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);
Expand Down Expand Up @@ -408,7 +461,7 @@ GLmol.prototype.drawBondsAsStick = function(group, atomlist, bondR, atomR, ignor
this.drawCylinder(group, new TV3(atom2.x, atom2.y, atom2.z), mp, bondR, atom2.color);
}
if (!atom1.connected) continue;
var sphereMaterial = new THREE.MeshLambertMaterial({color: atom1.color});
var sphereMaterial = new THREE.MeshLambertMaterial({color: atom1.color, map:this.colormap});
var sphere = new THREE.Mesh(sphereGeometry, sphereMaterial);
sphere.scale.x = sphere.scale.y = sphere.scale.z = atomR;
group.add(sphere);
Expand Down Expand Up @@ -449,7 +502,7 @@ GLmol.prototype.drawUnitcell = function(group) {
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 lineMaterial = new THREE.LineBasicMaterial({linewidth: 1, color: 0xcccccc}); // TODO: fix color
var line = new THREE.Line(geo, lineMaterial);
line.type = THREE.LinePieces;
group.add(line);
Expand Down Expand Up @@ -556,7 +609,8 @@ GLmol.prototype.drawBondsAsLine = function(group, atomlist, lineWidth) {
}
var lineMaterial = new THREE.LineBasicMaterial({linewidth: lineWidth});
lineMaterial.vertexColors = true;

lineMaterial.map = this.colormap;
console.log(lineMaterial);
var line = new THREE.Line(geo, lineMaterial);
line.type = THREE.LinePieces;
group.add(line);
Expand All @@ -574,7 +628,7 @@ GLmol.prototype.drawSmoothCurve = function(group, _points, width, colors, div) {
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});
var lineMaterial = new THREE.LineBasicMaterial({linewidth: width, map: this.colormap});
lineMaterial.vertexColors = true;
var line = new THREE.Line(geo, lineMaterial);
line.type = THREE.LineStrip;
Expand Down Expand Up @@ -663,7 +717,7 @@ GLmol.prototype.drawSmoothTube = function(group, _points, colors, radii) {
}
geo.computeFaceNormals();
geo.computeVertexNormals(false);
var mat = new THREE.MeshLambertMaterial();// mat.wireframe = true;
var mat = new THREE.MeshLambertMaterial({map:this.colormap});// mat.wireframe = true;
mat.vertexColors = THREE.FaceColors;
var mesh = new THREE.Mesh(geo, mat);
mesh.doubleSided = true;
Expand Down Expand Up @@ -726,7 +780,7 @@ GLmol.prototype.drawStrip = function(group, p1, p2, colors, div, thickness) {
div = div || this.axisDIV;
p1 = this.subdivide(p1, div);
p2 = this.subdivide(p2, div);
if (!thickness) this.drawThinStrip(group, p1, p2, colors, div)
if (!thickness) {this.drawThinStrip(group, p1, p2, colors, div); return;}

var geo = new THREE.Geometry();
var vs = geo.vertices, fs = geo.faces;
Expand Down Expand Up @@ -761,7 +815,7 @@ GLmol.prototype.drawStrip = function(group, p1, p2, colors, div, thickness) {
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();
var material = new THREE.MeshLambertMaterial({map: this.colormap});
material.vertexColors = THREE.FaceColors;
var mesh = new THREE.Mesh(geo, material);
mesh.doubleSided = true;
Expand All @@ -782,7 +836,7 @@ GLmol.prototype.drawThinStrip = function(group, p1, p2, colors, div) {
}
geo.computeFaceNormals();
geo.computeVertexNormals(false);
var material = new THREE.MeshLambertMaterial();
var material = new THREE.MeshLambertMaterial({map:this.colormap});
material.vertexColors = THREE.FaceColors;
var mesh = new THREE.Mesh(geo, material);
mesh.doubleSided = true;
Expand All @@ -806,7 +860,7 @@ GLmol.prototype.drawCylinder = function(group, from, to, radius, color, cap) {
this.cylinderGeometry.faceUvs = [];
this.faceVertexUvs = [];
}
var cylinderMaterial = new THREE.MeshLambertMaterial({color: color.getHex()});
var cylinderMaterial = new THREE.MeshLambertMaterial({color: color.getHex(), map:this.colormap});
var cylinder = new THREE.Mesh(this.cylinderGeometry, cylinderMaterial);
cylinder.position = midpoint;
cylinder.lookAt(from);
Expand Down Expand Up @@ -952,7 +1006,7 @@ GLmol.prototype.drawNucleicAcidLadder = function(group, atomlist) {
}
this.drawNucleicAcidLadderSub(geo, lineGeo, currentComponent, color);
geo.computeFaceNormals();
var mat = new THREE.MeshLambertMaterial();
var mat = new THREE.MeshLambertMaterial({map:this.colormap});
mat.vertexColors = THREE.VertexColors;
var mesh = new THREE.Mesh(geo, mat);
mesh.doubleSided = true;
Expand Down Expand Up @@ -1257,7 +1311,7 @@ GLmol.prototype.colorByAtom = function(atomlist, colors) {
var c = colors[atom.elem];
if (c == undefined) c = this.ElementColors[atom.elem];
if (c == undefined) c = this.defaultColor;
atom.color = c;
this.setColor(atom.serial, c);
}
};

Expand All @@ -1268,8 +1322,8 @@ GLmol.prototype.colorByStructure = function(atomlist, helixColor, sheetColor, co
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;
if (atom.ss[0] == 's') this.setColor(atom.serial, sheetColor);
else if (atom.ss[0] == 'h') this.setColor(atom.serial, helixColor);
}
};

Expand Down Expand Up @@ -1300,7 +1354,7 @@ GLmol.prototype.colorByBFactor = function(atomlist, colorSidechains) {
color.setHSV(0.667, (mid - atom.b) / range, 1);
else
color.setHSV(0, (atom.b - mid) / range, 1);
atom.color = color.getHex();
this.setColor(atom.serial, color.getHex());
}
}
};
Expand All @@ -1313,7 +1367,7 @@ GLmol.prototype.colorByChain = function(atomlist, colorSidechains) {
if (colorSidechains || atom.atom == 'CA' || atom.atom == 'O3\'') {
var color = new TCo(0);
color.setHSV((atom.chain.charCodeAt(0)) % 15 / 15.0, 1, 0.9);
atom.color = color.getHex();
this.setColor(atom.serial, color.getHex());
}
}
};
Expand All @@ -1323,15 +1377,15 @@ GLmol.prototype.colorByResidue = function(atomlist, residueColors) {
var atom = this.atoms[atomlist[i]]; if (atom == undefined) continue;

c = residueColors[atom.resn]
if (c != undefined) atom.color = c;
if (c != undefined) this.setColor(atom.serial, 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;
this.setColor(atom.serial, c);
}
};

Expand All @@ -1341,7 +1395,7 @@ GLmol.prototype.colorByPolarity = function(atomlist, polar, nonpolar) {
var colorMap = {};
for (var i in polarResidues) colorMap[polarResidues[i]] = polar;
for (i in nonPolarResidues) colorMap[nonPolarResidues[i]] = nonpolar;
this.colorByResidue(atomlist, colorMap);
this.colorByResidue(atomlist, colorMap);
};

// TODO: Add near(atomlist, neighbor, distanceCutoff)
Expand All @@ -1365,7 +1419,7 @@ GLmol.prototype.colorChainbow = function(atomlist, colorSidechains) {
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();
this.setColor(atom.serial, color.getHex());
cnt++;
}
}
Expand Down
2 changes: 1 addition & 1 deletion src/js/Three49custom.js
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading