molstar
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A comprehensive macromolecular library.
101 lines (100 loc) • 5.01 kB
JavaScript
/**
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Michal Malý <michal.maly@ibt.cas.cz>
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
*/
import { OrderedSet, Segmentation } from '../../mol-data/int';
import { EmptyLoci } from '../../mol-model/loci';
import { StructureElement, StructureProperties } from '../../mol-model/structure';
const EmptyStepIndices = new Array();
export var DnatcoUtil;
(function (DnatcoUtil) {
function copyResidue(r) {
return r ? { index: r.index, start: r.start, end: r.end } : void 0;
}
DnatcoUtil.copyResidue = copyResidue;
function getAtomIndex(loc, residue, names, altId, insCode) {
for (let eI = residue.start; eI < residue.end; eI++) {
loc.element = loc.unit.elements[eI];
const elName = StructureProperties.atom.label_atom_id(loc);
const elAltId = StructureProperties.atom.label_alt_id(loc);
const elInsCode = StructureProperties.residue.pdbx_PDB_ins_code(loc);
if (names.includes(elName) && (elAltId === altId || elAltId.length === 0) && (elInsCode === insCode))
return loc.element;
}
return -1;
}
DnatcoUtil.getAtomIndex = getAtomIndex;
function getStepIndices(data, loc, r) {
loc.element = loc.unit.elements[r.start];
const modelIdx = StructureProperties.unit.model_num(loc) - 1;
const chainId = StructureProperties.chain.auth_asym_id(loc);
const seqId = StructureProperties.residue.auth_seq_id(loc);
const insCode = StructureProperties.residue.pdbx_PDB_ins_code(loc);
const chains = data.mapping[modelIdx];
if (!chains)
return EmptyStepIndices;
const residues = chains.get(chainId);
if (!residues)
return EmptyStepIndices;
const indices = residues.get(seqId);
if (!indices)
return EmptyStepIndices;
return insCode !== '' ? indices.filter(idx => data.steps[idx].PDB_ins_code_1 === insCode) : indices;
}
DnatcoUtil.getStepIndices = getStepIndices;
function residueAltIds(structure, unit, residue) {
const altIds = new Array();
const loc = StructureElement.Location.create(structure, unit);
for (let eI = residue.start; eI < residue.end; eI++) {
loc.element = OrderedSet.getAt(unit.elements, eI);
const altId = StructureProperties.atom.label_alt_id(loc);
if (altId !== '' && !altIds.includes(altId))
altIds.push(altId);
}
return altIds;
}
DnatcoUtil.residueAltIds = residueAltIds;
const _loc = StructureElement.Location.create();
function residueToLoci(asymId, seqId, altId, insCode, loci, source) {
_loc.structure = loci.structure;
for (const e of loci.elements) {
_loc.unit = e.unit;
const getAsymId = source === 'label' ? StructureProperties.chain.label_asym_id : StructureProperties.chain.auth_asym_id;
const getSeqId = source === 'label' ? StructureProperties.residue.label_seq_id : StructureProperties.residue.auth_seq_id;
// Walk the entire unit and look for the requested residue
const chainIt = Segmentation.transientSegments(e.unit.model.atomicHierarchy.chainAtomSegments, e.unit.elements);
const residueIt = Segmentation.transientSegments(e.unit.model.atomicHierarchy.residueAtomSegments, e.unit.elements);
const elemIndex = (idx) => OrderedSet.getAt(e.unit.elements, idx);
while (chainIt.hasNext) {
const chain = chainIt.move();
_loc.element = elemIndex(chain.start);
const _asymId = getAsymId(_loc);
if (_asymId !== asymId)
continue; // Wrong chain, skip it
residueIt.setSegment(chain);
while (residueIt.hasNext) {
const residue = residueIt.move();
_loc.element = elemIndex(residue.start);
const _seqId = getSeqId(_loc);
if (_seqId === seqId) {
const _insCode = StructureProperties.residue.pdbx_PDB_ins_code(_loc);
if (_insCode !== insCode)
continue;
if (altId) {
const _altIds = residueAltIds(loci.structure, e.unit, residue);
if (!_altIds.includes(altId))
continue;
}
const start = residue.start;
const end = residue.end;
return StructureElement.Loci(loci.structure, [{ unit: e.unit, indices: OrderedSet.ofBounds(start, end) }]);
}
}
}
}
return EmptyLoci;
}
DnatcoUtil.residueToLoci = residueToLoci;
})(DnatcoUtil || (DnatcoUtil = {}));