molstar
Version:
A comprehensive macromolecular library.
156 lines • 8.1 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019 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.EntitySourceColorThemeProvider = exports.EntitySourceColorTheme = exports.getEntitySourceColorThemeParams = exports.EntitySourceColorThemeParams = void 0;
var tslib_1 = require("tslib");
var structure_1 = require("../../mol-model/structure");
var color_1 = require("../../mol-util/color");
var param_definition_1 = require("../../mol-util/param-definition");
var palette_1 = require("../../mol-util/color/palette");
var number_1 = require("../../mol-util/number");
var lists_1 = require("../../mol-util/color/lists");
var mmcif_1 = require("../../mol-model-formats/structure/mmcif");
var DefaultList = 'dark-2';
var DefaultColor = (0, color_1.Color)(0xFAFAFA);
var Description = 'Gives ranges of a polymer chain a color based on the entity source it originates from (e.g. gene, plasmid, organism).';
exports.EntitySourceColorThemeParams = (0, tslib_1.__assign)({}, (0, palette_1.getPaletteParams)({ type: 'colors', colorList: DefaultList }));
function getEntitySourceColorThemeParams(ctx) {
var params = param_definition_1.ParamDefinition.clone(exports.EntitySourceColorThemeParams);
if (ctx.structure) {
if (getMaps(ctx.structure.root.models).srcKeySerialMap.size > lists_1.ColorLists[DefaultList].list.length) {
params.palette.defaultValue.name = 'colors';
params.palette.defaultValue.params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.palette.defaultValue.params), { list: { kind: 'interpolate', colors: (0, lists_1.getColorListFromName)(DefaultList).list } });
}
}
return params;
}
exports.getEntitySourceColorThemeParams = getEntitySourceColorThemeParams;
function modelEntityKey(modelIndex, entityId) {
return modelIndex + "|" + entityId;
}
function srcKey(modelIndex, entityId, organism, srcId, plasmid, gene) {
return modelIndex + "|" + entityId + "|" + organism + "|" + (gene ? gene : (plasmid ? plasmid : srcId));
}
function addSrc(seqToSrcByModelEntity, srcKeySerialMap, modelIndex, model, entity_src, scientific_name, plasmid_name, gene_src_gene) {
var entity_id = entity_src.entity_id, pdbx_src_id = entity_src.pdbx_src_id, pdbx_beg_seq_num = entity_src.pdbx_beg_seq_num, pdbx_end_seq_num = entity_src.pdbx_end_seq_num;
for (var j = 0, jl = entity_src._rowCount; j < jl; ++j) {
var entityId = entity_id.value(j);
var mK = modelEntityKey(modelIndex, entityId);
var seqToSrc = void 0;
if (!seqToSrcByModelEntity.has(mK)) {
var entityIndex = model.entities.getEntityIndex(entityId);
var seq = model.sequence.sequences[entityIndex].sequence;
seqToSrc = new Int16Array(seq.length);
seqToSrcByModelEntity.set(mK, seqToSrc);
}
else {
seqToSrc = seqToSrcByModelEntity.get(mK);
}
var plasmid = plasmid_name ? plasmid_name.value(j) : '';
var gene = gene_src_gene ? gene_src_gene.value(j)[0] : '';
var sK = srcKey(modelIndex, entityId, scientific_name.value(j), pdbx_src_id.value(j), plasmid, gene);
// may not be given (= 0) indicating src is for the whole seq
var beg = pdbx_beg_seq_num.valueKind(j) === 0 /* Present */ ? pdbx_beg_seq_num.value(j) : 1;
var end = pdbx_end_seq_num.valueKind(j) === 0 /* Present */ ? pdbx_end_seq_num.value(j) : seqToSrc.length;
var srcIndex = void 0; // serial no starting from 1
if (srcKeySerialMap.has(sK)) {
srcIndex = srcKeySerialMap.get(sK);
}
else {
srcIndex = srcKeySerialMap.size + 1;
srcKeySerialMap.set(sK, srcIndex);
}
// set src index
for (var i = beg, il = end; i <= il; ++i) {
seqToSrc[i - 1] = srcIndex;
}
}
}
function getMaps(models) {
var seqToSrcByModelEntity = new Map();
var srcKeySerialMap = new Map(); // serial no starting from 1
for (var i = 0, il = models.length; i < il; ++i) {
var m = models[i];
if (!mmcif_1.MmcifFormat.is(m.sourceData))
continue;
var _a = m.sourceData.data.db, entity_src_gen = _a.entity_src_gen, entity_src_nat = _a.entity_src_nat, pdbx_entity_src_syn = _a.pdbx_entity_src_syn;
addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_gen, entity_src_gen.pdbx_gene_src_scientific_name, entity_src_gen.plasmid_name, entity_src_gen.pdbx_gene_src_gene);
addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_nat, entity_src_nat.pdbx_organism_scientific, entity_src_nat.pdbx_plasmid_name);
addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, pdbx_entity_src_syn, pdbx_entity_src_syn.organism_scientific);
}
return { seqToSrcByModelEntity: seqToSrcByModelEntity, srcKeySerialMap: srcKeySerialMap };
}
function getLabelTable(srcKeySerialMap) {
var unnamedCount = 0;
return Array.from(srcKeySerialMap.keys()).map(function (v) {
var vs = v.split('|');
var organism = vs[2];
var name = (0, number_1.isInteger)(vs[3]) ? "Unnamed " + ++unnamedCount : vs[3];
return "" + name + (organism ? " (" + organism + ")" : '');
});
}
function EntitySourceColorTheme(ctx, props) {
var color;
var legend;
if (ctx.structure) {
var l_1 = structure_1.StructureElement.Location.create(ctx.structure);
var models_1 = ctx.structure.root.models;
var _a = getMaps(models_1), seqToSrcByModelEntity_1 = _a.seqToSrcByModelEntity, srcKeySerialMap = _a.srcKeySerialMap;
var labelTable_1 = getLabelTable(srcKeySerialMap);
var valueLabel = function (i) { return labelTable_1[i]; };
var palette_2 = (0, palette_1.getPalette)(srcKeySerialMap.size, props, { valueLabel: valueLabel });
legend = palette_2.legend;
var getSrcColor_1 = function (location) {
var modelIndex = models_1.indexOf(location.unit.model);
var entityId = structure_1.StructureProperties.entity.id(location);
var mK = modelEntityKey(modelIndex, entityId);
var seqToSrc = seqToSrcByModelEntity_1.get(mK);
if (seqToSrc) {
// minus 1 to convert seqId to array index
var src = seqToSrc[structure_1.StructureProperties.residue.label_seq_id(location) - 1] - 1;
// check for -1 as not all sequence ids have a src given
return src === -1 ? DefaultColor : palette_2.color(src);
}
else {
return DefaultColor;
}
};
color = function (location) {
if (structure_1.StructureElement.Location.is(location)) {
return getSrcColor_1(location);
}
else if (structure_1.Bond.isLocation(location)) {
l_1.unit = location.aUnit;
l_1.element = location.aUnit.elements[location.aIndex];
return getSrcColor_1(l_1);
}
return DefaultColor;
};
}
else {
color = function () { return DefaultColor; };
}
return {
factory: EntitySourceColorTheme,
granularity: 'group',
color: color,
props: props,
description: Description,
legend: legend
};
}
exports.EntitySourceColorTheme = EntitySourceColorTheme;
exports.EntitySourceColorThemeProvider = {
name: 'entity-source',
label: 'Entity Source',
category: "Chain Property" /* Chain */,
factory: EntitySourceColorTheme,
getParams: getEntitySourceColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.EntitySourceColorThemeParams),
isApplicable: function (ctx) { return !!ctx.structure; }
};
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