molstar
Version:
A comprehensive macromolecular library.
103 lines (102 loc) • 5.15 kB
JavaScript
;
/**
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.AssemblySymmetryClusterColorThemeProvider = exports.AssemblySymmetryClusterColorThemeParams = void 0;
exports.getAssemblySymmetryClusterColorThemeParams = getAssemblySymmetryClusterColorThemeParams;
exports.AssemblySymmetryClusterColorTheme = AssemblySymmetryClusterColorTheme;
const param_definition_1 = require("../../mol-util/param-definition");
const prop_1 = require("./prop");
const color_1 = require("../../mol-util/color");
const structure_1 = require("../../mol-model/structure");
const palette_1 = require("../../mol-util/color/palette");
const categories_1 = require("../../mol-theme/color/categories");
const DefaultColor = (0, color_1.Color)(0xCCCCCC);
function getAsymId(unit) {
switch (unit.kind) {
case 0 /* Unit.Kind.Atomic */:
return structure_1.StructureProperties.chain.label_asym_id;
case 1 /* Unit.Kind.Spheres */:
case 2 /* Unit.Kind.Gaussians */:
return structure_1.StructureProperties.coarse.asym_id;
}
}
function clusterMemberKey(asymId, operList) {
return `${asymId}-${operList.join('|')}`;
}
exports.AssemblySymmetryClusterColorThemeParams = {
...(0, palette_1.getPaletteParams)({ colorList: 'red-yellow-blue' }),
};
function getAssemblySymmetryClusterColorThemeParams(ctx) {
const params = param_definition_1.ParamDefinition.clone(exports.AssemblySymmetryClusterColorThemeParams);
return params;
}
function AssemblySymmetryClusterColorTheme(ctx, props) {
var _a;
let color = () => DefaultColor;
let legend;
const assemblySymmetry = ctx.structure && prop_1.AssemblySymmetryProvider.get(ctx.structure);
const contextHash = assemblySymmetry === null || assemblySymmetry === void 0 ? void 0 : assemblySymmetry.version;
const clusters = (_a = assemblySymmetry === null || assemblySymmetry === void 0 ? void 0 : assemblySymmetry.value) === null || _a === void 0 ? void 0 : _a.clusters;
if ((clusters === null || clusters === void 0 ? void 0 : clusters.length) && ctx.structure) {
const l = structure_1.StructureElement.Location.create(ctx.structure);
const clusterByMember = new Map();
for (let i = 0, il = clusters.length; i < il; ++i) {
const { members } = clusters[i];
for (let j = 0, jl = members.length; j < jl; ++j) {
const asymId = members[j].asym_id;
const operList = [...members[j].pdbx_struct_oper_list_ids || []];
clusterByMember.set(clusterMemberKey(asymId, operList), i);
if (operList.length === 0) {
operList.push('1'); // TODO hack assuming '1' is the id of the identity operator
clusterByMember.set(clusterMemberKey(asymId, operList), i);
}
}
}
const palette = (0, palette_1.getPalette)(clusters.length, props);
legend = palette.legend;
const _emptyList = [];
const getColor = (location) => {
const { assembly } = location.unit.conformation.operator;
const asymId = getAsymId(location.unit)(location);
const cluster = clusterByMember.get(clusterMemberKey(asymId, (assembly === null || assembly === void 0 ? void 0 : assembly.operList) || _emptyList));
return cluster !== undefined ? palette.color(cluster) : DefaultColor;
};
color = (location) => {
if (structure_1.StructureElement.Location.is(location)) {
return getColor(location);
}
else if (structure_1.Bond.isLocation(location)) {
l.unit = location.aUnit;
l.element = location.aUnit.elements[location.aIndex];
return getColor(l);
}
return DefaultColor;
};
}
return {
factory: AssemblySymmetryClusterColorTheme,
granularity: 'instance',
color,
props,
contextHash,
description: 'Assigns chain colors according to assembly symmetry cluster membership data provided by RCSB PDB (calculated with BioJava) or by PDBe.',
legend
};
}
exports.AssemblySymmetryClusterColorThemeProvider = {
name: prop_1.AssemblySymmetryData.Tag.Cluster,
label: 'Assembly Symmetry Cluster',
category: categories_1.ColorThemeCategory.Symmetry,
factory: AssemblySymmetryClusterColorTheme,
getParams: getAssemblySymmetryClusterColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.AssemblySymmetryClusterColorThemeParams),
isApplicable: (ctx) => prop_1.AssemblySymmetryData.isApplicable(ctx.structure),
ensureCustomProperties: {
attach: (ctx, data) => data.structure ? prop_1.AssemblySymmetryProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
detach: (data) => data.structure && prop_1.AssemblySymmetryProvider.ref(data.structure, false)
}
};