molstar
Version:
A comprehensive macromolecular library.
111 lines (110 loc) • 5.06 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019-2020 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.GroFormat = void 0;
exports.trajectoryFromGRO = trajectoryFromGRO;
const mol_task_1 = require("../../mol-task");
const db_1 = require("../../mol-data/db");
const util_1 = require("./util");
const types_1 = require("../../mol-model/structure/model/types");
const component_1 = require("./common/component");
const util_2 = require("./common/util");
const entity_1 = require("./common/entity");
const schema_1 = require("./basic/schema");
const parser_1 = require("./basic/parser");
const trajectory_1 = require("../../mol-model/structure/trajectory");
function getBasic(atoms, modelNum) {
const auth_atom_id = atoms.atomName;
const auth_comp_id = atoms.residueName;
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 entity_1.EntityBuilder();
const componentBuilder = new component_1.ComponentBuilder(atoms.residueNumber, atoms.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 = atoms.count; i < il; ++i) {
const residueNumber = atoms.residueNumber.value(i);
if (residueNumber !== prevResidueNumber) {
const compId = atoms.residueName.value(i);
const moleculeType = (0, types_1.getMoleculeType)(componentBuilder.add(compId, i).type, compId);
if (moleculeType !== prevMoleculeType || (residueNumber !== prevResidueNumber + 1 && !(
// gro format allows only for 5 character residueNumbers, handle overflow here
prevResidueNumber === 99999 && residueNumber === 0))) {
currentAsymId = (0, util_2.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] = (0, util_1.guessElementSymbolString)(atoms.atomName.value(i), atoms.residueName.value(i));
}
const auth_asym_id = db_1.Column.ofStringArray(asymIds);
const atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
auth_asym_id,
auth_atom_id,
auth_comp_id,
auth_seq_id: atoms.residueNumber,
Cartn_x: db_1.Column.ofFloatArray(db_1.Column.mapToArray(atoms.x, x => x * 10, Float32Array)),
Cartn_y: db_1.Column.ofFloatArray(db_1.Column.mapToArray(atoms.y, y => y * 10, Float32Array)),
Cartn_z: db_1.Column.ofFloatArray(db_1.Column.mapToArray(atoms.z, z => z * 10, Float32Array)),
id: db_1.Column.ofIntArray(ids),
label_asym_id: auth_asym_id,
label_atom_id: auth_atom_id,
label_comp_id: auth_comp_id,
label_seq_id: db_1.Column.ofIntArray(seqIds),
label_entity_id: db_1.Column.ofStringArray(entityIds),
occupancy: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.float),
type_symbol: db_1.Column.ofStringArray(typeSymbol),
pdbx_PDB_model_num: db_1.Column.ofConst(modelNum, atoms.count, db_1.Column.Schema.int),
}, atoms.count);
return (0, schema_1.createBasic)({
entity: entityBuilder.getEntityTable(),
chem_comp: componentBuilder.getChemCompTable(),
atom_site
});
}
var GroFormat;
(function (GroFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'gro';
}
GroFormat.is = is;
function fromGro(gro) {
return { kind: 'gro', name: gro.structures[0].header.title, data: gro };
}
GroFormat.fromGro = fromGro;
})(GroFormat || (exports.GroFormat = GroFormat = {}));
// TODO reuse static model parts when hierarchy is identical
// need to pass all gro.structures as one table into createModels
function trajectoryFromGRO(gro) {
return mol_task_1.Task.create('Parse GRO', async (ctx) => {
const format = GroFormat.fromGro(gro);
const models = [];
for (let i = 0, il = gro.structures.length; i < il; ++i) {
const basic = getBasic(gro.structures[i].atoms, i + 1);
const m = await (0, parser_1.createModels)(basic, format, ctx);
if (m.frameCount === 1) {
models.push(m.representative);
}
}
return new trajectory_1.ArrayTrajectory(models);
});
}