molstar
Version:
A comprehensive macromolecular library.
131 lines (130 loc) • 5.8 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.PolymerIdColorThemeParams = void 0;
exports.getPolymerIdColorThemeParams = getPolymerIdColorThemeParams;
exports.PolymerIdColorTheme = PolymerIdColorTheme;
const structure_1 = require("../../mol-model/structure");
const color_1 = require("../../mol-util/color");
const param_definition_1 = require("../../mol-util/param-definition");
const palette_1 = require("../../mol-util/color/palette");
const int_1 = require("../../mol-data/int");
const lists_1 = require("../../mol-util/color/lists");
const categories_1 = require("./categories");
const DefaultList = 'dark-2';
const DefaultColor = (0, color_1.Color)(0xFAFAFA);
const Description = 'Gives every polymer chain a color based on its `asym_id` value.';
exports.PolymerIdColorThemeParams = {
...(0, palette_1.getPaletteParams)({ type: 'colors', colorList: DefaultList }),
};
function getPolymerIdColorThemeParams(ctx) {
const 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 = {
...params.palette.defaultValue.params,
list: { kind: 'interpolate', colors: (0, lists_1.getColorListFromName)(DefaultList).list }
};
}
}
return params;
}
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 getPolymerAsymIdSerialMap(structure) {
const map = new Map();
for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
const unit = structure.unitSymmetryGroups[i].units[0];
const { model } = unit;
if (structure_1.Unit.isAtomic(unit)) {
const { chainAtomSegments, chains } = model.atomicHierarchy;
const chainIt = int_1.Segmentation.transientSegments(chainAtomSegments, unit.elements);
while (chainIt.hasNext) {
const { index: chainIndex } = chainIt.move();
const entityId = chains.label_entity_id.value(chainIndex);
const eI = model.entities.getEntityIndex(entityId);
if (model.entities.data.type.value(eI) === 'polymer') {
const asymId = chains.label_asym_id.value(chainIndex);
if (!map.has(asymId))
map.set(asymId, map.size);
}
}
}
else if (structure_1.Unit.isCoarse(unit)) {
const { chainElementSegments, asym_id, entity_id } = structure_1.Unit.isSpheres(unit)
? model.coarseHierarchy.spheres
: model.coarseHierarchy.gaussians;
const chainIt = int_1.Segmentation.transientSegments(chainElementSegments, unit.elements);
while (chainIt.hasNext) {
const { index: chainIndex } = chainIt.move();
const elementIndex = chainElementSegments.offsets[chainIndex];
const entityId = entity_id.value(elementIndex);
const eI = model.entities.getEntityIndex(entityId);
if (model.entities.data.type.value(eI) === 'polymer') {
const asymId = asym_id.value(elementIndex);
if (!map.has(asymId))
map.set(asymId, map.size);
}
}
}
}
return map;
}
function PolymerIdColorTheme(ctx, props) {
let color;
let legend;
if (ctx.structure) {
const l = structure_1.StructureElement.Location.create(ctx.structure);
const polymerAsymIdSerialMap = getPolymerAsymIdSerialMap(ctx.structure.root);
const labelTable = Array.from(polymerAsymIdSerialMap.keys());
const valueLabel = (i) => labelTable[i];
const palette = (0, palette_1.getPalette)(polymerAsymIdSerialMap.size, props, { valueLabel });
legend = palette.legend;
color = (location) => {
let serial = undefined;
if (structure_1.StructureElement.Location.is(location)) {
const asym_id = getAsymId(location.unit);
serial = polymerAsymIdSerialMap.get(asym_id(location));
}
else if (structure_1.Bond.isLocation(location)) {
const asym_id = getAsymId(location.aUnit);
l.unit = location.aUnit;
l.element = location.aUnit.elements[location.aIndex];
serial = polymerAsymIdSerialMap.get(asym_id(l));
}
return serial === undefined ? DefaultColor : palette.color(serial);
};
}
else {
color = () => DefaultColor;
}
return {
factory: PolymerIdColorTheme,
granularity: 'group',
color,
props,
description: Description,
legend
};
}
exports.PolymerIdColorThemeProvider = {
name: 'polymer-id',
label: 'Polymer Chain Id',
category: categories_1.ColorThemeCategory.Chain,
factory: PolymerIdColorTheme,
getParams: getPolymerIdColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerIdColorThemeParams),
isApplicable: (ctx) => !!ctx.structure
};