molstar
Version:
A comprehensive macromolecular library.
90 lines (89 loc) • 3.7 kB
JavaScript
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { StructureProperties, StructureElement, Bond } from '../../mol-model/structure';
import { Color } from '../../mol-util/color';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
const Description = 'Gives every chain a color from a list based on its `asym_id` value.';
export function createProteopediaCustomTheme(colors) {
const ProteopediaCustomColorThemeParams = {
colors: PD.ObjectList({ color: PD.Color(Color(0xffffff)) }, ({ color }) => Color.toHexString(color), { defaultValue: colors.map(c => ({ color: Color(c) })) })
};
function getChainIdColorThemeParams(ctx) {
return ProteopediaCustomColorThemeParams; // TODO return copy
}
function getAsymId(unit) {
switch (unit.kind) {
case 0 /* Unit.Kind.Atomic */:
return StructureProperties.chain.label_asym_id;
case 1 /* Unit.Kind.Spheres */:
case 2 /* Unit.Kind.Gaussians */:
return StructureProperties.coarse.asym_id;
}
}
function addAsymIds(map, data) {
let j = map.size;
for (let o = 0, ol = data.rowCount; o < ol; ++o) {
const k = data.value(o);
if (!map.has(k)) {
map.set(k, j);
j += 1;
}
}
}
function ProteopediaCustomColorTheme(ctx, props) {
let color;
const colors = props.colors, colorCount = colors.length, defaultColor = colors[0].color;
if (ctx.structure) {
const l = StructureElement.Location.create(ctx.structure);
const { models } = ctx.structure;
const asymIdSerialMap = new Map();
for (let i = 0, il = models.length; i < il; ++i) {
const m = models[i];
addAsymIds(asymIdSerialMap, m.atomicHierarchy.chains.label_asym_id);
if (m.coarseHierarchy.isDefined) {
addAsymIds(asymIdSerialMap, m.coarseHierarchy.spheres.asym_id);
addAsymIds(asymIdSerialMap, m.coarseHierarchy.gaussians.asym_id);
}
}
color = (location) => {
if (StructureElement.Location.is(location)) {
const asym_id = getAsymId(location.unit);
const o = asymIdSerialMap.get(asym_id(location)) || 0;
return colors[o % colorCount].color;
}
else if (Bond.isLocation(location)) {
const asym_id = getAsymId(location.aUnit);
l.unit = location.aUnit;
l.element = location.aUnit.elements[location.aIndex];
const o = asymIdSerialMap.get(asym_id(l)) || 0;
return colors[o % colorCount].color;
}
return defaultColor;
};
}
else {
color = () => defaultColor;
}
return {
factory: ProteopediaCustomColorTheme,
granularity: 'group',
color,
props,
description: Description,
legend: undefined
};
}
return {
name: 'proteopedia-custom',
label: 'Proteopedia Custom',
category: 'Custom',
factory: ProteopediaCustomColorTheme,
getParams: getChainIdColorThemeParams,
defaultValues: PD.getDefaultValues(ProteopediaCustomColorThemeParams),
isApplicable: (ctx) => !!ctx.structure
};
}