molstar
Version:
A comprehensive macromolecular library.
88 lines (87 loc) • 4.21 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>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.EvolutionaryConservation = void 0;
var tslib_1 = require("tslib");
var custom_element_property_1 = require("../../mol-model-props/common/custom-element-property");
var color_1 = require("../../mol-util/color");
var assets_1 = require("../../mol-util/assets");
var EvolutionaryConservationPalette = [
[255, 255, 129],
[160, 37, 96],
[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(function (_a) {
var r = _a[0], g = _a[1], b = _a[2];
return color_1.Color.fromRgb(r, g, b);
});
var EvolutionaryConservationDefaultColor = (0, color_1.Color)(0x999999);
exports.EvolutionaryConservation = custom_element_property_1.CustomElementProperty.create({
name: 'proteopedia-wrapper-evolutionary-conservation',
label: 'Evolutionary Conservation',
type: 'static',
getData: function (model, ctx) {
var _a;
return tslib_1.__awaiter(this, void 0, void 0, function () {
var id, url, json, annotations, conservationMap, _i, annotations_1, e, _b, _c, r, map, residueCount, residueOffsets, chainIndex, rI, cI, key, ann, aI;
return tslib_1.__generator(this, function (_d) {
switch (_d.label) {
case 0:
id = model.entryId.toLowerCase();
url = assets_1.Asset.getUrlAsset(ctx.assetManager, "https://proteopedia.org/cgi-bin/cnsrf?".concat(id));
return [4 /*yield*/, ctx.assetManager.resolve(url, 'json').runInContext(ctx.runtime)];
case 1:
json = _d.sent();
annotations = ((_a = json.data) === null || _a === void 0 ? void 0 : _a.residueAnnotations) || [];
conservationMap = new Map();
for (_i = 0, annotations_1 = annotations; _i < annotations_1.length; _i++) {
e = annotations_1[_i];
for (_b = 0, _c = e.ids; _b < _c.length; _b++) {
r = _c[_b];
conservationMap.set(r, e.annotation);
}
}
map = new Map();
residueCount = model.atomicHierarchy.residues._rowCount;
residueOffsets = model.atomicHierarchy.residueAtomSegments.offsets;
chainIndex = model.atomicHierarchy.chainAtomSegments.index;
for (rI = 0; rI < residueCount; rI++) {
cI = chainIndex[residueOffsets[rI]];
key = "".concat(model.atomicHierarchy.chains.auth_asym_id.value(cI), " ").concat(model.atomicHierarchy.residues.auth_seq_id.value(rI));
if (!conservationMap.has(key))
continue;
ann = conservationMap.get(key);
for (aI = residueOffsets[rI]; aI < residueOffsets[rI + 1]; aI++) {
map.set(aI, ann);
}
}
return [2 /*return*/, { value: map, assets: [json] }];
}
});
});
},
coloring: {
getColor: function (e) {
if (e < 1 || e > 10)
return EvolutionaryConservationDefaultColor;
return EvolutionaryConservationPalette[e - 1];
},
defaultColor: EvolutionaryConservationDefaultColor
},
getLabel: function (e) {
if (e === 10)
return "Evolutionary Conservation: Insufficient Data";
return e ? "Evolutionary Conservation: ".concat(e) : void 0;
}
});