molstar
Version:
A comprehensive macromolecular library.
112 lines (111 loc) • 4.49 kB
JavaScript
;
/**
* Copyright (c) 2018 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.SequenceIdColorThemeProvider = exports.SequenceIdColorThemeParams = void 0;
exports.getSequenceIdColorThemeParams = getSequenceIdColorThemeParams;
exports.SequenceIdColorTheme = SequenceIdColorTheme;
const structure_1 = require("../../mol-model/structure");
const color_1 = require("../../mol-util/color");
const param_definition_1 = require("../../mol-util/param-definition");
const categories_1 = require("./categories");
const DefaultColor = (0, color_1.Color)(0xCCCCCC);
const Description = 'Gives every polymer residue a color based on its `seq_id` value.';
exports.SequenceIdColorThemeParams = {
list: param_definition_1.ParamDefinition.ColorList('turbo', { presetKind: 'scale' }),
};
function getSequenceIdColorThemeParams(ctx) {
return exports.SequenceIdColorThemeParams; // TODO return copy
}
function getSeqId(unit, element) {
const { model } = unit;
switch (unit.kind) {
case 0 /* Unit.Kind.Atomic */:
const residueIndex = model.atomicHierarchy.residueAtomSegments.index[element];
return model.atomicHierarchy.residues.label_seq_id.value(residueIndex);
case 1 /* Unit.Kind.Spheres */:
return Math.round((model.coarseHierarchy.spheres.seq_id_begin.value(element) +
model.coarseHierarchy.spheres.seq_id_end.value(element)) / 2);
case 2 /* Unit.Kind.Gaussians */:
return Math.round((model.coarseHierarchy.gaussians.seq_id_begin.value(element) +
model.coarseHierarchy.gaussians.seq_id_end.value(element)) / 2);
}
}
function getSequenceLength(unit, element) {
const { model } = unit;
let entityId = '';
switch (unit.kind) {
case 0 /* Unit.Kind.Atomic */:
const chainIndex = model.atomicHierarchy.chainAtomSegments.index[element];
entityId = model.atomicHierarchy.chains.label_entity_id.value(chainIndex);
break;
case 1 /* Unit.Kind.Spheres */:
entityId = model.coarseHierarchy.spheres.entity_id.value(element);
break;
case 2 /* Unit.Kind.Gaussians */:
entityId = model.coarseHierarchy.gaussians.entity_id.value(element);
break;
}
if (entityId === '')
return 0;
const entityIndex = model.entities.getEntityIndex(entityId);
if (entityIndex === -1)
return 0;
const entity = model.sequence.byEntityKey[entityIndex];
if (entity === undefined)
return 0;
return entity.sequence.length;
}
function SequenceIdColorTheme(ctx, props) {
const scale = color_1.ColorScale.create({
listOrName: props.list.colors,
minLabel: 'Start',
maxLabel: 'End',
});
const color = (location) => {
if (structure_1.StructureElement.Location.is(location)) {
const { unit, element } = location;
const seq_id = getSeqId(unit, element);
if (seq_id > 0) {
const seqLen = getSequenceLength(unit, element);
if (seqLen) {
scale.setDomain(0, seqLen - 1);
return scale.color(seq_id);
}
}
}
else if (structure_1.Bond.isLocation(location)) {
const { aUnit, aIndex } = location;
const seq_id = getSeqId(aUnit, aUnit.elements[aIndex]);
if (seq_id > 0) {
const seqLen = getSequenceLength(aUnit, aUnit.elements[aIndex]);
if (seqLen) {
scale.setDomain(0, seqLen - 1);
return scale.color(seq_id);
}
}
}
return DefaultColor;
};
return {
factory: SequenceIdColorTheme,
granularity: 'group',
preferSmoothing: true,
color,
props,
description: Description,
legend: scale ? scale.legend : undefined
};
}
exports.SequenceIdColorThemeProvider = {
name: 'sequence-id',
label: 'Sequence Id',
category: categories_1.ColorThemeCategory.Residue,
factory: SequenceIdColorTheme,
getParams: getSequenceIdColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.SequenceIdColorThemeParams),
isApplicable: (ctx) => !!ctx.structure
};