molstar
Version:
A comprehensive macromolecular library.
122 lines (121 loc) • 5.28 kB
JavaScript
/**
* Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { __awaiter, __generator } from "tslib";
import { Column, Table } from '../../mol-data/db';
import { getMoleculeType } from '../../mol-model/structure/model/types';
import { Topology } from '../../mol-model/structure/topology/topology';
import { Task } from '../../mol-task';
import { BasicSchema, createBasic } from './basic/schema';
import { ComponentBuilder } from './common/component';
import { EntityBuilder } from './common/entity';
import { getChainId } from './common/util';
import { guessElementSymbolString } from './util';
function getBasic(atoms) {
var entityIds = new Array(atoms.count);
var asymIds = new Array(atoms.count);
var seqIds = new Uint32Array(atoms.count);
var ids = new Uint32Array(atoms.count);
var typeSymbol = new Array(atoms.count);
var entityBuilder = new EntityBuilder();
var componentBuilder = new ComponentBuilder(atoms.residueId, atoms.atomName);
var currentEntityId = '';
var currentAsymIndex = 0;
var currentAsymId = '';
var currentSeqId = 0;
var currentSegmentName = atoms.segmentName.value(0), segmentChanged = false;
var prevMoleculeType = 0 /* MoleculeType.Unknown */;
var prevResidueNumber = -1;
for (var i = 0, il = atoms.count; i < il; ++i) {
var residueNumber = atoms.residueId.value(i);
var segmentName = atoms.segmentName.value(i);
if (currentSegmentName !== segmentName) {
currentAsymId = getChainId(currentAsymIndex);
currentAsymIndex += 1;
currentSeqId = 0;
segmentChanged = true;
currentSegmentName = segmentName;
}
else {
segmentChanged = false;
}
if (segmentChanged || residueNumber !== prevResidueNumber) {
var compId = atoms.residueName.value(i);
var moleculeType = getMoleculeType(componentBuilder.add(compId, i).type, compId);
if (!segmentChanged && (moleculeType !== prevMoleculeType || residueNumber !== prevResidueNumber + 1)) {
currentAsymId = getChainId(currentAsymIndex);
currentAsymIndex += 1;
currentSeqId = 0;
}
currentEntityId = entityBuilder.getEntityId(compId, moleculeType, currentAsymId);
currentSeqId += 1;
prevResidueNumber = residueNumber;
prevMoleculeType = moleculeType;
}
entityIds[i] = currentEntityId;
asymIds[i] = currentAsymId;
seqIds[i] = currentSeqId;
ids[i] = i;
typeSymbol[i] = guessElementSymbolString(atoms.atomName.value(i), atoms.residueName.value(i));
}
var atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
auth_asym_id: atoms.segmentName,
auth_atom_id: atoms.atomName,
auth_comp_id: atoms.residueName,
auth_seq_id: atoms.residueId,
id: Column.ofIntArray(ids),
label_asym_id: Column.ofStringArray(asymIds),
label_atom_id: atoms.atomName,
label_comp_id: atoms.residueName,
label_seq_id: Column.ofIntArray(seqIds),
label_entity_id: Column.ofStringArray(entityIds),
occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
type_symbol: Column.ofStringArray(typeSymbol),
pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
}, atoms.count);
return createBasic({
entity: entityBuilder.getEntityTable(),
chem_comp: componentBuilder.getChemCompTable(),
atom_site: atom_site
});
}
//
export { PsfFormat };
var PsfFormat;
(function (PsfFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'psf';
}
PsfFormat.is = is;
function fromPsf(psf) {
return { kind: 'psf', name: psf.id, data: psf };
}
PsfFormat.fromPsf = fromPsf;
})(PsfFormat || (PsfFormat = {}));
export function topologyFromPsf(psf) {
var _this = this;
return Task.create('Parse PSF', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
var format, basic, _a, atomIdA, atomIdB, bonds;
return __generator(this, function (_b) {
format = PsfFormat.fromPsf(psf);
basic = getBasic(psf.atoms);
_a = psf.bonds, atomIdA = _a.atomIdA, atomIdB = _a.atomIdB;
bonds = {
indexA: Column.ofLambda({
value: function (row) { return atomIdA.value(row) - 1; },
rowCount: atomIdA.rowCount,
schema: atomIdA.schema,
}),
indexB: Column.ofLambda({
value: function (row) { return atomIdB.value(row) - 1; },
rowCount: atomIdB.rowCount,
schema: atomIdB.schema,
}),
order: Column.ofConst(1, psf.bonds.count, Column.Schema.int)
};
return [2 /*return*/, Topology.create(psf.id, basic, bonds, format)];
});
}); });
}