TmMolStar/src/examples/ply-wrapper/annotation.ts

/**
 * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 */

import { CustomElementProperty } from 'mol-model-props/common/custom-element-property';
import { Model, ElementIndex, ResidueIndex } from 'mol-model/structure';
import { Color } from 'mol-util/color';

const EvolutionaryConservationPalette: Color[] = [
    [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<number>({
    isStatic: true,
    name: 'proteopedia-wrapper-evolutionary-conservation',
    display: 'Evolutionary Conservation',
    async getData(model: Model) {
        const id = model.label.toLowerCase();
        const req = await fetch(`https://proteopedia.org/cgi-bin/cnsrf?${id}`);
        const json = await req.json();
        const annotations = (json && json.residueAnnotations) || [];

        const conservationMap = new Map<string, number>();

        for (const e of annotations) {
            for (const r of e.ids) {
                conservationMap.set(r, e.annotation);
            }
        }

        const map = new Map<ElementIndex, number>();

        const { _rowCount: residueCount } = model.atomicHierarchy.residues;
        const { offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
        const chainIndex = model.atomicHierarchy.chainAtomSegments.index;

        for (let rI = 0 as ResidueIndex; 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 map;
    },
    coloring: {
        getColor(e: number) {
            if (e < 1 || e > 10) return EvolutionaryConservationDefaultColor;
            return EvolutionaryConservationPalette[e - 1];
        },
        defaultColor: EvolutionaryConservationDefaultColor
    },
    format(e) {
        if (e === 10) return `Evolutionary Conservation: InsufficientData`;
        return e ? `Evolutionary Conservation: ${e}` : void 0;
    }
});