molstar
Version:
A comprehensive macromolecular library.
88 lines (87 loc) • 3.75 kB
JavaScript
/**
* Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Adam Midlik <midlik@gmail.com>
*/
import { Interval, OrderedSet, Segmentation, SortedArray } from '../../mol-data/int';
import { Structure, StructureElement } from '../../mol-model/structure';
import { ColorNames } from '../../mol-util/color/names';
import { SequenceWrapper } from './wrapper';
export class HeteroSequenceWrapper extends SequenceWrapper {
residueLabel(seqIdx) {
return this.sequence[seqIdx];
}
residueColor(seqIdx) {
return ColorNames.black;
}
residueClass(seqIdx) {
return 'msp-sequence-present';
}
getSeqIndices(loci) {
const { structure } = this.data;
if (StructureElement.Loci.is(loci)) {
if (!Structure.areRootsEquivalent(loci.structure, structure))
return Interval.Empty;
loci = StructureElement.Loci.remap(loci, structure);
const out = [];
for (const e of loci.elements) {
const unit = this.unitMap.get(e.unit.id);
if (unit) {
const { index: residueIndex } = e.unit.model.atomicHierarchy.residueAtomSegments;
OrderedSet.forEach(e.indices, v => {
const seqIdx = this.sequenceIndices.get(residueIndex[unit.elements[v]]);
if (seqIdx !== undefined)
out.push(seqIdx);
});
}
}
return SortedArray.deduplicate(SortedArray.ofSortedArray(out));
}
else if (Structure.isLoci(loci)) {
if (!Structure.areRootsEquivalent(loci.structure, structure))
return Interval.Empty;
return Interval.ofBounds(0, this.length);
}
return Interval.Empty;
}
getLoci(seqIdx) {
const elements = [];
const rI = this.residueIndices.get(seqIdx);
if (rI !== undefined) {
const unit = this.seqToUnit.get(seqIdx);
const { offsets } = unit.model.atomicHierarchy.residueAtomSegments;
const start = SortedArray.findPredecessorIndex(unit.elements, offsets[rI]);
const end = SortedArray.findPredecessorIndex(unit.elements, offsets[rI + 1]);
elements.push({ unit, indices: Interval.ofBounds(start, end) });
}
return StructureElement.Loci(this.data.structure, elements);
}
constructor(data) {
const sequence = [];
const sequenceIndices = new Map();
const residueIndices = new Map();
const seqToUnit = new Map();
for (let i = 0, il = data.units.length; i < il; ++i) {
const unit = data.units[i];
const { residueAtomSegments, atoms } = unit.model.atomicHierarchy;
const residueIt = Segmentation.transientSegments(residueAtomSegments, unit.elements);
while (residueIt.hasNext) {
const { index } = residueIt.move();
sequenceIndices.set(index, sequence.length);
residueIndices.set(sequence.length, index);
seqToUnit.set(sequence.length, unit);
sequence.push(atoms.label_comp_id.value(residueAtomSegments.offsets[index]));
}
}
const length = sequence.length;
super(data, length);
this.unitMap = new Map();
for (const unit of data.units)
this.unitMap.set(unit.id, unit);
this.sequence = sequence;
this.sequenceIndices = sequenceIndices;
this.residueIndices = residueIndices;
this.seqToUnit = seqToUnit;
}
}