molstar
Version:
A comprehensive macromolecular library.
69 lines (68 loc) • 2.86 kB
JavaScript
/**
* Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { CustomElementProperty } from '../../mol-model-props/common/custom-element-property';
import { Color } from '../../mol-util/color';
import { Asset } from '../../mol-util/assets';
const EvolutionaryConservationPalette = [
[255, 255, 129], // insufficient
[160, 37, 96], // 9
[240, 125, 171],
[250, 201, 222],
[252, 237, 244],
[255, 255, 255],
[234, 255, 255],
[215, 255, 255],
[140, 255, 255],
[16, 200, 209] // 1
].reverse().map(([r, g, b]) => Color.fromRgb(r, g, b));
const EvolutionaryConservationDefaultColor = Color(0x999999);
export const EvolutionaryConservation = CustomElementProperty.create({
name: 'proteopedia-wrapper-evolutionary-conservation',
label: 'Evolutionary Conservation',
type: 'static',
async getData(model, ctx) {
var _a;
const id = model.entryId.toLowerCase();
const url = Asset.getUrlAsset(ctx.assetManager, `https://proteopedia.org/cgi-bin/cnsrf?${id}`);
const json = await ctx.assetManager.resolve(url, 'json').runInContext(ctx.runtime);
const annotations = ((_a = json.data) === null || _a === void 0 ? void 0 : _a.residueAnnotations) || [];
const conservationMap = new Map();
for (const e of annotations) {
for (const r of e.ids) {
conservationMap.set(r, e.annotation);
}
}
const map = new Map();
const { _rowCount: residueCount } = model.atomicHierarchy.residues;
const { offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
const chainIndex = model.atomicHierarchy.chainAtomSegments.index;
for (let rI = 0; rI < residueCount; rI++) {
const cI = chainIndex[residueOffsets[rI]];
const key = `${model.atomicHierarchy.chains.auth_asym_id.value(cI)} ${model.atomicHierarchy.residues.auth_seq_id.value(rI)}`;
if (!conservationMap.has(key))
continue;
const ann = conservationMap.get(key);
for (let aI = residueOffsets[rI]; aI < residueOffsets[rI + 1]; aI++) {
map.set(aI, ann);
}
}
return { value: map, assets: [json] };
},
coloring: {
getColor(e) {
if (e < 1 || e > 10)
return EvolutionaryConservationDefaultColor;
return EvolutionaryConservationPalette[e - 1];
},
defaultColor: EvolutionaryConservationDefaultColor
},
getLabel(e) {
if (e === 10)
return `Evolutionary Conservation: Insufficient Data`;
return e ? `Evolutionary Conservation: ${e}` : void 0;
}
});