molstar
Version:
A comprehensive macromolecular library.
142 lines (141 loc) • 6.03 kB
JavaScript
"use strict";
/**
* Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.PrmtopFormat = void 0;
exports.topologyFromPrmtop = topologyFromPrmtop;
const db_1 = require("../../mol-data/db");
const types_1 = require("../../mol-model/structure/model/types");
const topology_1 = require("../../mol-model/structure/topology/topology");
const mol_task_1 = require("../../mol-task");
const schema_1 = require("./basic/schema");
const component_1 = require("./common/component");
const entity_1 = require("./common/entity");
const util_1 = require("./common/util");
const util_2 = require("./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 = db_1.Column.ofIntArray(residueIds);
const residueName = db_1.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 entity_1.EntityBuilder();
const componentBuilder = new component_1.ComponentBuilder(residueId, atomName);
let currentEntityId = '';
let currentAsymIndex = 0;
let currentAsymId = '';
let currentSeqId = 0;
let prevMoleculeType = types_1.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 = (0, types_1.getMoleculeType)(componentBuilder.add(compId, i).type, compId);
if (moleculeType !== prevMoleculeType) {
currentAsymId = (0, util_1.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 = db_1.Column.ofIntArray(ids);
const asym_id = db_1.Column.ofStringArray(asymIds);
//
const type_symbol = new Array(atomCount);
for (let i = 0; i < atomCount; ++i) {
type_symbol[i] = (0, util_2.guessElementSymbolString)(atomName.value(i), residueName.value(i));
}
const atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
auth_asym_id: asym_id,
auth_atom_id: db_1.Column.asArrayColumn(atomName),
auth_comp_id: residueName,
auth_seq_id: residueId,
id: db_1.Column.asArrayColumn(id),
label_asym_id: asym_id,
label_atom_id: db_1.Column.asArrayColumn(atomName),
label_comp_id: residueName,
label_seq_id: db_1.Column.ofIntArray(seqIds),
label_entity_id: db_1.Column.ofStringArray(entityIds),
occupancy: db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.float),
type_symbol: db_1.Column.ofStringArray(type_symbol),
pdbx_PDB_model_num: db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.int),
}, atomCount);
const basic = (0, schema_1.createBasic)({
entity: entityBuilder.getEntityTable(),
chem_comp: componentBuilder.getChemCompTable(),
atom_site
});
return basic;
}
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 || (exports.PrmtopFormat = PrmtopFormat = {}));
function topologyFromPrmtop(prmtop) {
return mol_task_1.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: db_1.Column.ofLambda({
value: (row) => {
return row < NBONH
? bondsIncHydrogen.value(row * 3) / 3
: bondsWithoutHydrogen.value((row - NBONH) * 3) / 3;
},
rowCount: bondCount,
schema: db_1.Column.Schema.int,
}),
indexB: db_1.Column.ofLambda({
value: (row) => {
return row < NBONH
? bondsIncHydrogen.value(row * 3 + 1) / 3
: bondsWithoutHydrogen.value((row - NBONH) * 3 + 1) / 3;
},
rowCount: bondCount,
schema: db_1.Column.Schema.int,
}),
order: db_1.Column.ofConst(1, bondCount, db_1.Column.Schema.int)
};
return topology_1.Topology.create(prmtop.title.join(' ') || 'PRMTOP', basic, bonds, format);
});
}