molstar
Version:
A comprehensive macromolecular library.
101 lines • 5.46 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.AssemblySymmetryClusterColorTheme = exports.getAssemblySymmetryClusterColorThemeParams = exports.AssemblySymmetryClusterColorThemeParams = void 0;
var tslib_1 = require("tslib");
var param_definition_1 = require("../../../mol-util/param-definition");
var prop_1 = require("./prop");
var color_1 = require("../../../mol-util/color");
var structure_1 = require("../../../mol-model/structure");
var palette_1 = require("../../../mol-util/color/palette");
var DefaultColor = (0, color_1.Color)(0xCCCCCC);
function getAsymId(unit) {
switch (unit.kind) {
case 0 /* Atomic */:
return structure_1.StructureProperties.chain.label_asym_id;
case 1 /* Spheres */:
case 2 /* Gaussians */:
return structure_1.StructureProperties.coarse.asym_id;
}
}
function clusterMemberKey(asymId, operList) {
return asymId + "-" + operList.join('|');
}
exports.AssemblySymmetryClusterColorThemeParams = (0, tslib_1.__assign)({}, (0, palette_1.getPaletteParams)({ colorList: 'red-yellow-blue' }));
function getAssemblySymmetryClusterColorThemeParams(ctx) {
var params = param_definition_1.ParamDefinition.clone(exports.AssemblySymmetryClusterColorThemeParams);
return params;
}
exports.getAssemblySymmetryClusterColorThemeParams = getAssemblySymmetryClusterColorThemeParams;
function AssemblySymmetryClusterColorTheme(ctx, props) {
var _a;
var color = function () { return DefaultColor; };
var legend;
var assemblySymmetry = ctx.structure && prop_1.AssemblySymmetryProvider.get(ctx.structure);
var contextHash = assemblySymmetry === null || assemblySymmetry === void 0 ? void 0 : assemblySymmetry.version;
var 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) {
var l_1 = structure_1.StructureElement.Location.create(ctx.structure);
var clusterByMember_1 = new Map();
for (var i = 0, il = clusters.length; i < il; ++i) {
var members = clusters[i].members;
for (var j = 0, jl = members.length; j < jl; ++j) {
var asymId = members[j].asym_id;
var operList = (0, tslib_1.__spreadArray)([], members[j].pdbx_struct_oper_list_ids || [], true);
clusterByMember_1.set(clusterMemberKey(asymId, operList), i);
if (operList.length === 0) {
operList.push('1'); // TODO hack assuming '1' is the id of the identity operator
clusterByMember_1.set(clusterMemberKey(asymId, operList), i);
}
}
}
var palette_2 = (0, palette_1.getPalette)(clusters.length, props);
legend = palette_2.legend;
var _emptyList_1 = [];
var getColor_1 = function (location) {
var assembly = location.unit.conformation.operator.assembly;
var asymId = getAsymId(location.unit)(location);
var cluster = clusterByMember_1.get(clusterMemberKey(asymId, (assembly === null || assembly === void 0 ? void 0 : assembly.operList) || _emptyList_1));
return cluster !== undefined ? palette_2.color(cluster) : DefaultColor;
};
color = function (location) {
if (structure_1.StructureElement.Location.is(location)) {
return getColor_1(location);
}
else if (structure_1.Bond.isLocation(location)) {
l_1.unit = location.aUnit;
l_1.element = location.aUnit.elements[location.aIndex];
return getColor_1(l_1);
}
return DefaultColor;
};
}
return {
factory: AssemblySymmetryClusterColorTheme,
granularity: 'instance',
color: color,
props: props,
contextHash: contextHash,
description: 'Assigns chain colors according to assembly symmetry cluster membership calculated with BioJava and obtained via RCSB PDB.',
legend: legend
};
}
exports.AssemblySymmetryClusterColorTheme = AssemblySymmetryClusterColorTheme;
exports.AssemblySymmetryClusterColorThemeProvider = {
name: prop_1.AssemblySymmetry.Tag.Cluster,
label: 'Assembly Symmetry Cluster',
category: "Symmetry" /* Symmetry */,
factory: AssemblySymmetryClusterColorTheme,
getParams: getAssemblySymmetryClusterColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.AssemblySymmetryClusterColorThemeParams),
isApplicable: function (ctx) { return prop_1.AssemblySymmetry.isApplicable(ctx.structure); },
ensureCustomProperties: {
attach: function (ctx, data) { return data.structure ? prop_1.AssemblySymmetryProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(); },
detach: function (data) { return data.structure && prop_1.AssemblySymmetryProvider.ref(data.structure, false); }
}
};
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