molstar
Version:
A comprehensive macromolecular library.
140 lines (139 loc) • 5.72 kB
JavaScript
/**
* Copyright (c) 2022 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(prmtop) {
const { pointers, residuePointer, residueLabel, atomName } = prmtop;
const atomCount = pointers.NATOM;
const residueCount = pointers.NRES;
//
const residueIds = new Uint32Array(atomCount);
const residueNames = [];
const addResidue = (i, from, to) => {
const rn = residueLabel.value(i);
for (let j = from, jl = to; j < jl; ++j) {
residueIds[j] = i + 1;
residueNames[j] = rn;
}
};
for (let i = 0, il = residueCount - 1; i < il; ++i) {
addResidue(i, residuePointer.value(i) - 1, residuePointer.value(i + 1) - 1);
}
addResidue(residueCount - 1, residuePointer.value(residueCount - 1) - 1, atomCount);
const residueId = Column.ofIntArray(residueIds);
const residueName = Column.ofStringArray(residueNames);
//
const entityIds = new Array(atomCount);
const asymIds = new Array(atomCount);
const seqIds = new Uint32Array(atomCount);
const ids = new Uint32Array(atomCount);
const entityBuilder = new EntityBuilder();
const componentBuilder = new ComponentBuilder(residueId, atomName);
let currentEntityId = '';
let currentAsymIndex = 0;
let currentAsymId = '';
let currentSeqId = 0;
let prevMoleculeType = 0 /* MoleculeType.Unknown */;
let prevResidueNumber = -1;
for (let i = 0, il = atomCount; i < il; ++i) {
const residueNumber = residueId.value(i);
if (residueNumber !== prevResidueNumber) {
const compId = residueName.value(i);
const moleculeType = getMoleculeType(componentBuilder.add(compId, i).type, compId);
if (moleculeType !== prevMoleculeType) {
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;
}
const id = Column.ofIntArray(ids);
const asym_id = Column.ofStringArray(asymIds);
//
const type_symbol = new Array(atomCount);
for (let i = 0; i < atomCount; ++i) {
type_symbol[i] = guessElementSymbolString(atomName.value(i), residueName.value(i));
}
const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
auth_asym_id: asym_id,
auth_atom_id: Column.asArrayColumn(atomName),
auth_comp_id: residueName,
auth_seq_id: residueId,
id: Column.asArrayColumn(id),
label_asym_id: asym_id,
label_atom_id: Column.asArrayColumn(atomName),
label_comp_id: residueName,
label_seq_id: Column.ofIntArray(seqIds),
label_entity_id: Column.ofStringArray(entityIds),
occupancy: Column.ofConst(1, atomCount, Column.Schema.float),
type_symbol: Column.ofStringArray(type_symbol),
pdbx_PDB_model_num: Column.ofConst(1, atomCount, Column.Schema.int),
}, atomCount);
const basic = createBasic({
entity: entityBuilder.getEntityTable(),
chem_comp: componentBuilder.getChemCompTable(),
atom_site
});
return basic;
}
//
export { PrmtopFormat };
var PrmtopFormat;
(function (PrmtopFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'prmtop';
}
PrmtopFormat.is = is;
function fromPrmtop(prmtop) {
return { kind: 'prmtop', name: prmtop.title.join(' ') || 'PRMTOP', data: prmtop };
}
PrmtopFormat.fromPrmtop = fromPrmtop;
})(PrmtopFormat || (PrmtopFormat = {}));
export function topologyFromPrmtop(prmtop) {
return Task.create('Parse PRMTOP', async (ctx) => {
const format = PrmtopFormat.fromPrmtop(prmtop);
const basic = getBasic(prmtop);
const { pointers: { NBONH, NBONA }, bondsIncHydrogen, bondsWithoutHydrogen } = prmtop;
const bondCount = NBONH + NBONA;
const bonds = {
indexA: Column.ofLambda({
value: (row) => {
return row < NBONH
? bondsIncHydrogen.value(row * 3) / 3
: bondsWithoutHydrogen.value((row - NBONH) * 3) / 3;
},
rowCount: bondCount,
schema: Column.Schema.int,
}),
indexB: Column.ofLambda({
value: (row) => {
return row < NBONH
? bondsIncHydrogen.value(row * 3 + 1) / 3
: bondsWithoutHydrogen.value((row - NBONH) * 3 + 1) / 3;
},
rowCount: bondCount,
schema: Column.Schema.int,
}),
order: Column.ofConst(1, bondCount, Column.Schema.int)
};
return Topology.create(prmtop.title.join(' ') || 'PRMTOP', basic, bonds, format);
});
}