pdbe-molstar
Version:
Molstar implementation for PDBe
128 lines (127 loc) • 5.84 kB
JavaScript
;
Object.defineProperty(exports, "__esModule", { value: true });
exports.lociDetails = lociDetails;
exports.bondLabel = bondLabel;
exports._bundleLabel = _bundleLabel;
const int_1 = require("molstar/lib/mol-data/int");
const sifts_mapping_1 = require("molstar/lib/mol-model-props/sequence/sifts-mapping");
const structure_1 = require("molstar/lib/mol-model/structure");
function lociDetails(loci) {
switch (loci.kind) {
case 'structure-loci':
return { models: loci.structure.models.map(m => m.entry).filter(l => !!l) };
case 'element-loci':
return structureElementStatsDetail(structure_1.StructureElement.Stats.ofLoci(loci));
case 'bond-loci': {
const bond = loci.bonds[0];
return bond ? bondLabel(bond, 'element') : {};
}
default:
return undefined;
}
}
function structureElementStatsDetail(stats) {
const { chainCount, residueCount, elementCount } = stats;
if (elementCount === 1 && residueCount === 0 && chainCount === 0) {
return getElementDetails(stats.firstElementLoc, 'element');
}
else if (elementCount === 0 && residueCount === 1 && chainCount === 0) {
return getElementDetails(stats.firstResidueLoc, 'residue');
}
else {
return undefined;
}
}
function getElementDetails(location, granularity = 'element') {
const basicDetails = {};
let entry = location.unit.model.entry;
if (entry.length > 30)
entry = entry.substr(0, 27) + '\u2026'; // ellipsis
basicDetails['entry_id'] = entry; // entry
if (granularity !== 'structure') {
basicDetails['model'] = location.unit.model.modelNum; // model
basicDetails['instance'] = location.unit.conformation.operator.name; // instance
}
let elementDetails;
if (structure_1.Unit.isAtomic(location.unit)) {
elementDetails = atomicElementDetails(location, granularity);
}
else if (structure_1.Unit.isCoarse(location.unit)) {
elementDetails = coarseElementDetails(location, granularity);
}
return Object.assign(Object.assign({}, basicDetails), elementDetails);
}
function atomicElementDetails(location, granularity) {
const elementDetails = {
entity_id: structure_1.StructureProperties.chain.label_entity_id(location),
label_asym_id: structure_1.StructureProperties.chain.label_asym_id(location),
auth_asym_id: structure_1.StructureProperties.chain.auth_asym_id(location),
unp_accession: undefined,
unp_seq_id: undefined,
seq_id: structure_1.StructureProperties.residue.label_seq_id(location),
auth_seq_id: structure_1.StructureProperties.residue.auth_seq_id(location),
ins_code: structure_1.StructureProperties.residue.pdbx_PDB_ins_code(location),
comp_id: structure_1.StructureProperties.atom.label_comp_id(location),
atom_id: [structure_1.StructureProperties.atom.label_atom_id(location)],
alt_id: structure_1.StructureProperties.atom.label_alt_id(location),
};
const unpLabel = sifts_mapping_1.SIFTSMapping.getLabel(location);
if (unpLabel) {
const unpLabelDetails = unpLabel.split(' ');
if (unpLabelDetails[0] === 'UNP') {
elementDetails.unp_accession = unpLabelDetails[1];
elementDetails.unp_seq_id = +unpLabelDetails[2];
}
}
const microHetCompIds = structure_1.StructureProperties.residue.microheterogeneityCompIds(location);
elementDetails['micro_het_comp_ids'] = granularity === 'residue' && microHetCompIds.length > 1 ?
microHetCompIds : [elementDetails['comp_id']];
return elementDetails;
}
function coarseElementDetails(location, granularity) {
const elementDetails = {
asym_id: structure_1.StructureProperties.coarse.asym_id(location),
seq_id_begin: structure_1.StructureProperties.coarse.seq_id_begin(location),
seq_id_end: structure_1.StructureProperties.coarse.seq_id_end(location),
};
if (granularity === 'residue') {
if (elementDetails.seq_id_begin === elementDetails.seq_id_end) {
const entityIndex = structure_1.StructureProperties.coarse.entityKey(location);
const seq = location.unit.model.sequence.byEntityKey[entityIndex];
elementDetails['comp_id'] = seq.sequence.compId.value(elementDetails.seq_id_begin - 1); // 1-indexed
}
}
return elementDetails;
}
function bondLabel(bond, granularity) {
return _bundleLabel({
loci: [
structure_1.StructureElement.Loci(bond.aStructure, [{ unit: bond.aUnit, indices: int_1.OrderedSet.ofSingleton(bond.aIndex) }]),
structure_1.StructureElement.Loci(bond.bStructure, [{ unit: bond.bUnit, indices: int_1.OrderedSet.ofSingleton(bond.bIndex) }]),
],
}, granularity);
}
function _bundleLabel(bundle, granularity) {
let isSingleElements = true;
for (const l of bundle.loci) {
if (!structure_1.StructureElement.Loci.is(l) || structure_1.StructureElement.Loci.size(l) !== 1) {
isSingleElements = false;
break;
}
}
if (isSingleElements) {
const locations = bundle.loci.map(l => {
const { unit, indices } = l.elements[0];
return structure_1.StructureElement.Location.create(l.structure, unit, unit.elements[int_1.OrderedSet.start(indices)]);
});
const elementDetailsArr = locations.map(l => getElementDetails(l, granularity));
const atomIds = [elementDetailsArr[0].atom_id[0], elementDetailsArr[1].atom_id[0]];
const elementDetails = elementDetailsArr[0];
elementDetails['atom_id'] = atomIds;
return elementDetails;
}
else {
const elementDetails = bundle.loci.map(l => lociDetails(l));
return elementDetails;
}
}