molstar
Version:
A comprehensive macromolecular library.
117 lines (116 loc) • 4.81 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 { 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) {
const entityIds = new Array(atoms.count);
const asymIds = new Array(atoms.count);
const seqIds = new Uint32Array(atoms.count);
const ids = new Uint32Array(atoms.count);
const typeSymbol = new Array(atoms.count);
const entityBuilder = new EntityBuilder();
const componentBuilder = new ComponentBuilder(atoms.residueId, atoms.atomName);
let currentEntityId = '';
let currentAsymIndex = 0;
let currentAsymId = '';
let currentSeqId = 0;
let currentSegmentName = atoms.segmentName.value(0), segmentChanged = false;
let prevMoleculeType = 0 /* MoleculeType.Unknown */;
let prevResidueNumber = -1;
for (let i = 0, il = atoms.count; i < il; ++i) {
const residueNumber = atoms.residueId.value(i);
const 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) {
const compId = atoms.residueName.value(i);
const 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));
}
const 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
});
}
//
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) {
return Task.create('Parse PSF', async (ctx) => {
const format = PsfFormat.fromPsf(psf);
const basic = getBasic(psf.atoms);
const { atomIdA, atomIdB } = psf.bonds;
const bonds = {
indexA: Column.ofLambda({
value: (row) => atomIdA.value(row) - 1,
rowCount: atomIdA.rowCount,
schema: atomIdA.schema,
}),
indexB: Column.ofLambda({
value: (row) => atomIdB.value(row) - 1,
rowCount: atomIdB.rowCount,
schema: atomIdB.schema,
}),
order: Column.ofConst(1, psf.bonds.count, Column.Schema.int)
};
return Topology.create(psf.id, basic, bonds, format);
});
}