I've had to do some funny stuff trying to initialize the view the way I want it... My suggestion would be to use a configuration object in the init as well as in the defineRepresentation. If you like my proposal I could add that into the newThreeJS branch.
During init provided could be merged with the default one. It is easy to modify the config object in the instance and run rebuildScene and show to update the view. This could become a default defineRepresentation and would not need any more changes:
this.drawAtomsAsSphere(this.modelGroup, hetatm, this.sphereRadius);
this.drawMainchainCurve(this.modelGroup, all, this.curveWidth, 'P');
this.drawCartoon(this.modelGroup, all, this.curveWidth);
} else {
var c = this.config,
all = this.getAllAtoms();
if (c.biomtChains) {
all = this.getChain(all, c.biomtChains);
}
var allHet = this.getHetatms(all),
hetatm = this.removeSolvents(allHet),
asu = new THREE.Object3D();
// color by
this.colorByAtom(all, {});
if (c.colorMode === 'ss') {
this.colorByStructure(all, 0xcc00cc, 0x00cccc);
} else if (c.colorMode === 'chain') {
this.colorByChain(all);
} else if (c.colorMode === 'chainbow') {
this.colorChainbow(all);
} else if (c.colorMode === 'b') {
this.colorByBFactor(all);
} else if (c.colorMode === 'polarity') {
this.colorByPolarity(all, 0xcc0000, 0xcccccc);
}
// main chain
// Don't smooth beta-sheets in ribbons: boolean
if (c.mainchainMode) {
if (c.mainchainMode === 'ribbon') {
this.drawCartoon(asu, all, c.doNotSmoothen);
this.drawCartoonNucleicAcid(asu, all);
} else if (c.mainchainMode === 'thickRibbon') {
this.drawCartoon(asu, all, c.doNotSmoothen, this.thickness);
this.drawCartoonNucleicAcid(asu, all, null, this.thickness);
} else if (c.mainchainMode === 'strand') {
this.drawStrand(asu, all, null, null, null, null, null, c.doNotSmoothen);
this.drawStrandNucleicAcid(asu, all);
} else if (c.mainchainMode === 'chain') {
this.drawMainchainCurve(asu, all, this.curveWidth, 'CA', 1);
this.drawMainchainCurve(asu, all, this.curveWidth, 'O3\'', 1);
} else if (c.mainchainMode === 'cylinderHelix') {
this.drawHelixAsCylinder(asu, all, 1.6);
this.drawCartoonNucleicAcid(asu, all);
} else if (c.mainchainMode === 'tube') {
this.drawMainchainTube(asu, all, 'CA');
this.drawMainchainTube(asu, all, 'O3\''); // FIXME: 5' end problem!
} else if (c.mainchainMode === 'bonds') {
this.drawBondsAsLine(asu, all, this.lineWidth);
}
}
// side chains as lines: boolean
if (c.sideChainsAsLines) {
this.drawBondsAsLine(this.modelGroup, this.getSidechains(all), this.lineWidth);
}
// nucleic acid bases as: sticks, lines, polygons
if (c.baseMode) {
if (c.baseMode === 'nuclStick') {
this.drawNucleicAcidStick(this.modelGroup, all);
} else if (c.baseMode === 'nuclLine') {
this.drawNucleicAcidLine(this.modelGroup, all);
} else if (c.baseMode === 'nuclPolygon') {
this.drawNucleicAcidLadder(this.modelGroup, all);
}
}
// Show HETATMs in symmetry mates (slower)
var target = c.symopHetatms ? asu : this.modelGroup;
// Non-bonded atoms (solvent/ions) as
if (c.nbMode) {
var nonBonded = this.getNonbonded(allHet);
if (c.nbMode === 'nb_sphere') {
this.drawAtomsAsIcosahedron(target, nonBonded, 0.3, true);
} else if (c.nbMode === 'nb_cross') {
this.drawAsCross(target, nonBonded, 0.3, true);
}
}
// Small molecules(HETATMs) as: hidden, sticks, ball and stick, ball and stick (multi bond), spheres, icosahedrons, lines
if (c.hetatmMode) {
if (c.hetatmMode === 'stick') {
this.drawBondsAsStick(target, hetatm, this.cylinderRadius, this.cylinderRadius, true);
} else if (c.hetatmMode === 'sphere') {
this.drawAtomsAsSphere(target, hetatm, this.sphereRadius);
} else if (c.hetatmMode === 'line') {
this.drawBondsAsLine(target, hetatm, this.curveWidth);
} else if (c.hetatmMode === 'icosahedron') {
this.drawAtomsAsIcosahedron(target, hetatm, this.sphereRadius);
} else if (c.hetatmMode === 'ballAndStick') {
this.drawBondsAsStick(target, hetatm, this.cylinderRadius / 2.0, this.cylinderRadius, true, false, 0.3);
} else if (c.hetatmMode === 'ballAndStick2') {
this.drawBondsAsStick(target, hetatm, this.cylinderRadius / 2.0, this.cylinderRadius, true, true, 0.3);
}
}
// Projection: perspective, orthoscopic
if (c.projectionMode === 'perspective') {
this.camera = this.perspectiveCamera;
} else if (c.projectionMode === 'orthoscopic') {
this.camera = this.orthoscopicCamera;
}
// Background color
if (c.bgcolor !== null) {
this.setBackground(c.bgcolor);
}
// Unit cell
if (c.unitCell) {
this.drawUnitcell(this.modelGroup);
}
// Biological assembly (the last one defined)
if (c.biomt) {
this.drawSymmetryMates2(this.modelGroup, asu, this.protein.biomtMatrices);
}
// Crystal packing
if (c.packing) {
this.drawSymmetryMatesWithTranslation2(this.modelGroup, asu, this.protein.symMat);
}
this.modelGroup.add(asu);
}
I've had to do some funny stuff trying to initialize the view the way I want it... My suggestion would be to use a configuration object in the init as well as in the defineRepresentation. If you like my proposal I could add that into the newThreeJS branch.
How about something like this for default:
config = {
colorMode: 'chainbow', // ss chain chainbow b polarity
mainchainMode: 'ribbon', // ribbon thickRibbon strand chain cylinderHelix tube bonds
doNotSmoothen: true,
sideChainsAsLines: false,
baseMode: 'nuclLine', // na base: nuclStick nuclLine nuclPolygon
symopHetatms: false,
nbMode: null, // nb_sphere nb_cross
hetatmMode: 'sphere', // stick sphere line icosahedron ballAndStick ballAndStick2
projectionMode: 'perspective', // perspective orthoscopic
unitCell: false,
biomt: false,
packing: false,
bgcolor: 0x434343,
}
During init provided could be merged with the default one. It is easy to modify the config object in the instance and run rebuildScene and show to update the view. This could become a default defineRepresentation and would not need any more changes:
// extend glMol with additional configs
glmolDefineRepresentation = function() {
if (!this.config) {
var all = this.getAllAtoms();
var hetatm = this.removeSolvents(this.getHetatms(all));
this.colorByAtom(all, {});
this.colorByChain(all);
};