molstar
Version:
A comprehensive macromolecular library.
184 lines (183 loc) • 7.3 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.TopFormat = void 0;
exports.topologyFromTop = topologyFromTop;
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(top) {
const { molecules, compounds } = top;
const singleResidue = {};
let atomCount = 0;
for (let i = 0, il = molecules._rowCount; i < il; ++i) {
const mol = molecules.compound.value(i);
const count = molecules.molCount.value(i);
const { atoms } = compounds[mol];
db_1.Column.asArrayColumn(atoms.atom);
db_1.Column.asArrayColumn(atoms.resnr);
db_1.Column.asArrayColumn(atoms.residu);
atomCount += count * atoms._rowCount;
let prevResnr = atoms.resnr.value(0);
singleResidue[mol] = true;
for (let j = 1, jl = atoms._rowCount; j < jl; ++j) {
const resnr = atoms.resnr.value(j);
if (resnr !== prevResnr) {
singleResidue[mol] = false;
break;
}
prevResnr = resnr;
}
}
//
const atomNames = new Array(atomCount);
const residueIds = new Uint32Array(atomCount);
const residueNames = new Array(atomCount);
let k = 0;
for (let i = 0, il = molecules._rowCount; i < il; ++i) {
const mol = molecules.compound.value(i);
const count = molecules.molCount.value(i);
const { atoms } = compounds[mol];
const isSingleResidue = singleResidue[mol];
for (let j = 0; j < count; ++j) {
for (let l = 0, ll = atoms._rowCount; l < ll; ++l) {
atomNames[k] = atoms.atom.value(l);
residueIds[k] = atoms.resnr.value(l);
residueNames[k] = atoms.residu.value(l);
if (isSingleResidue)
residueIds[k] += j;
k += 1;
}
}
}
const atomName = db_1.Column.ofStringArray(atomNames);
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;
}
function getBonds(top) {
const { molecules, compounds } = top;
const indexA = [];
const indexB = [];
let atomOffset = 0;
for (let i = 0, il = molecules._rowCount; i < il; ++i) {
const mol = molecules.compound.value(i);
const count = molecules.molCount.value(i);
const { atoms, bonds } = compounds[mol];
if (bonds) {
for (let j = 0; j < count; ++j) {
for (let l = 0, ll = bonds._rowCount; l < ll; ++l) {
indexA.push(bonds.ai.value(l) - 1 + atomOffset);
indexB.push(bonds.aj.value(l) - 1 + atomOffset);
}
atomOffset += atoms._rowCount;
}
}
else if (mol === 'TIP3') {
for (let j = 0; j < count; ++j) {
indexA.push(0 + atomOffset);
indexB.push(1 + atomOffset);
indexA.push(0 + atomOffset);
indexB.push(2 + atomOffset);
atomOffset += atoms._rowCount;
}
}
else {
atomOffset += count * atoms._rowCount;
}
}
return {
indexA: db_1.Column.ofIntArray(indexA),
indexB: db_1.Column.ofIntArray(indexB),
order: db_1.Column.ofConst(1, indexA.length, db_1.Column.Schema.int)
};
}
var TopFormat;
(function (TopFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'top';
}
TopFormat.is = is;
function fromTop(top) {
return { kind: 'top', name: top.system || 'TOP', data: top };
}
TopFormat.fromTop = fromTop;
})(TopFormat || (exports.TopFormat = TopFormat = {}));
function topologyFromTop(top) {
return mol_task_1.Task.create('Parse TOP', async (ctx) => {
const format = TopFormat.fromTop(top);
const basic = getBasic(top);
const bonds = getBonds(top);
return topology_1.Topology.create(top.system || 'TOP', basic, bonds, format);
});
}