molstar
Version:
A comprehensive macromolecular library.
126 lines • 6.13 kB
JavaScript
;
/**
* Copyright (c) 2018-2019 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.PolymerIdColorThemeProvider = exports.PolymerIdColorTheme = exports.getPolymerIdColorThemeParams = exports.PolymerIdColorThemeParams = 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 int_1 = require("../../mol-data/int");
var lists_1 = require("../../mol-util/color/lists");
var DefaultList = 'dark-2';
var DefaultColor = (0, color_1.Color)(0xFAFAFA);
var Description = 'Gives every polymer chain a color based on its `asym_id` value.';
exports.PolymerIdColorThemeParams = (0, tslib_1.__assign)({}, (0, palette_1.getPaletteParams)({ type: 'colors', colorList: DefaultList }));
function getPolymerIdColorThemeParams(ctx) {
var params = param_definition_1.ParamDefinition.clone(exports.PolymerIdColorThemeParams);
if (ctx.structure) {
if (getPolymerAsymIdSerialMap(ctx.structure.root).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.getPolymerIdColorThemeParams = getPolymerIdColorThemeParams;
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 getPolymerAsymIdSerialMap(structure) {
var map = new Map();
for (var i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
var unit = structure.unitSymmetryGroups[i].units[0];
var model = unit.model;
if (structure_1.Unit.isAtomic(unit)) {
var _a = model.atomicHierarchy, chainAtomSegments = _a.chainAtomSegments, chains = _a.chains;
var chainIt = int_1.Segmentation.transientSegments(chainAtomSegments, unit.elements);
while (chainIt.hasNext) {
var chainIndex = chainIt.move().index;
var entityId = chains.label_entity_id.value(chainIndex);
var eI = model.entities.getEntityIndex(entityId);
if (model.entities.data.type.value(eI) === 'polymer') {
var asymId = chains.label_asym_id.value(chainIndex);
if (!map.has(asymId))
map.set(asymId, map.size);
}
}
}
else if (structure_1.Unit.isCoarse(unit)) {
var _b = structure_1.Unit.isSpheres(unit)
? model.coarseHierarchy.spheres
: model.coarseHierarchy.gaussians, chainElementSegments = _b.chainElementSegments, asym_id = _b.asym_id, entity_id = _b.entity_id;
var chainIt = int_1.Segmentation.transientSegments(chainElementSegments, unit.elements);
while (chainIt.hasNext) {
var chainIndex = chainIt.move().index;
var elementIndex = chainElementSegments.offsets[chainIndex];
var entityId = entity_id.value(elementIndex);
var eI = model.entities.getEntityIndex(entityId);
if (model.entities.data.type.value(eI) === 'polymer') {
var asymId = asym_id.value(elementIndex);
if (!map.has(asymId))
map.set(asymId, map.size);
}
}
}
}
return map;
}
function PolymerIdColorTheme(ctx, props) {
var color;
var legend;
if (ctx.structure) {
var l_1 = structure_1.StructureElement.Location.create(ctx.structure);
var polymerAsymIdSerialMap_1 = getPolymerAsymIdSerialMap(ctx.structure.root);
var labelTable_1 = Array.from(polymerAsymIdSerialMap_1.keys());
var valueLabel = function (i) { return labelTable_1[i]; };
var palette_2 = (0, palette_1.getPalette)(polymerAsymIdSerialMap_1.size, props, { valueLabel: valueLabel });
legend = palette_2.legend;
color = function (location) {
var serial = undefined;
if (structure_1.StructureElement.Location.is(location)) {
var asym_id = getAsymId(location.unit);
serial = polymerAsymIdSerialMap_1.get(asym_id(location));
}
else if (structure_1.Bond.isLocation(location)) {
var asym_id = getAsymId(location.aUnit);
l_1.unit = location.aUnit;
l_1.element = location.aUnit.elements[location.aIndex];
serial = polymerAsymIdSerialMap_1.get(asym_id(l_1));
}
return serial === undefined ? DefaultColor : palette_2.color(serial);
};
}
else {
color = function () { return DefaultColor; };
}
return {
factory: PolymerIdColorTheme,
granularity: 'group',
color: color,
props: props,
description: Description,
legend: legend
};
}
exports.PolymerIdColorTheme = PolymerIdColorTheme;
exports.PolymerIdColorThemeProvider = {
name: 'polymer-id',
label: 'Polymer Chain Id',
category: "Chain Property" /* Chain */,
factory: PolymerIdColorTheme,
getParams: getPolymerIdColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerIdColorThemeParams),
isApplicable: function (ctx) { return !!ctx.structure; }
};
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