molstar
Version:
A comprehensive macromolecular library.
249 lines (248 loc) • 11.3 kB
JavaScript
"use strict";
/**
* Copyright (c) 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.CifCoreFormat = void 0;
exports.trajectoryFromCifCore = trajectoryFromCifCore;
const db_1 = require("../../mol-data/db");
const types_1 = require("../../mol-model/structure/model/types");
const mol_task_1 = require("../../mol-task");
const parser_1 = require("./basic/parser");
const schema_1 = require("./basic/schema");
const component_1 = require("./common/component");
const entity_1 = require("./common/entity");
const cif_1 = require("../../mol-io/reader/cif");
const geometry_1 = require("../../mol-math/geometry");
const linear_algebra_1 = require("../../mol-math/linear-algebra");
const symmetry_1 = require("./property/symmetry");
const index_pair_1 = require("./property/bonds/index-pair");
const anisotropic_1 = require("./property/anisotropic");
const util_1 = require("./util");
const util_2 = require("../../mol-data/util");
function getSpacegroupNameOrNumber(space_group) {
const groupNumber = space_group.it_number.value(0);
const groupName = space_group['name_h-m_full'].value(0).replace('-', ' ');
if (!space_group.it_number.isDefined)
return groupName;
if (!space_group['name_h-m_full'].isDefined)
return groupNumber;
return groupNumber;
}
function getSymmetry(db) {
const { cell, space_group } = db;
const nameOrNumber = getSpacegroupNameOrNumber(space_group);
const spaceCell = geometry_1.SpacegroupCell.create(nameOrNumber, linear_algebra_1.Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)), linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
return {
spacegroup: geometry_1.Spacegroup.create(spaceCell),
assemblies: [],
isNonStandardCrystalFrame: false,
ncsOperators: []
};
}
async function getModels(db, format, ctx) {
var _a;
const atomCount = db.atom_site._rowCount;
const MOL = db_1.Column.ofConst('MOL', atomCount, db_1.Column.Schema.str);
const A = db_1.Column.ofConst('A', atomCount, db_1.Column.Schema.str);
const seq_id = db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.int);
const symmetry = getSymmetry(db);
const m = symmetry.spacegroup.cell.fromFractional;
const { fract_x, fract_y, fract_z } = db.atom_site;
const x = new Float32Array(atomCount);
const y = new Float32Array(atomCount);
const z = new Float32Array(atomCount);
const v = (0, linear_algebra_1.Vec3)();
for (let i = 0; i < atomCount; ++i) {
linear_algebra_1.Vec3.set(v, fract_x.value(i), fract_y.value(i), fract_z.value(i));
linear_algebra_1.Vec3.transformMat4(v, v, m);
x[i] = v[0], y[i] = v[1], z[i] = v[2];
}
const { type_symbol, label } = db.atom_site;
let typeSymbol;
let formalCharge;
if (type_symbol.isDefined) {
const element_symbol = new Array(atomCount);
const formal_charge = new Int8Array(atomCount);
for (let i = 0; i < atomCount; ++i) {
const ts = type_symbol.value(i);
const n = ts.length;
if (ts[n - 1] === '+') {
element_symbol[i] = ts.substring(0, n - 2);
formal_charge[i] = parseInt(ts[n - 2]);
}
else if (ts[n - 2] === '+') {
element_symbol[i] = ts.substring(0, n - 2);
formal_charge[i] = parseInt(ts[n - 1]);
}
else if (ts[n - 1] === '-') {
element_symbol[i] = ts.substring(0, n - 2);
formal_charge[i] = -parseInt(ts[n - 2]);
}
else if (ts[n - 2] === '-') {
element_symbol[i] = ts.substring(0, n - 2);
formal_charge[i] = -parseInt(ts[n - 1]);
}
else {
element_symbol[i] = ts;
formal_charge[i] = 0;
}
}
typeSymbol = db_1.Column.ofStringArray(element_symbol);
formalCharge = db_1.Column.ofIntArray(formal_charge);
}
else {
const element_symbol = new Array(atomCount);
for (let i = 0; i < atomCount; ++i) {
// TODO can take as is if type_symbol not given?
element_symbol[i] = (0, util_1.guessElementSymbolString)(label.value(i), '');
}
typeSymbol = db_1.Column.ofStringArray(element_symbol);
formalCharge = db_1.Column.Undefined(atomCount, db_1.Column.Schema.int);
}
const atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
auth_asym_id: A,
auth_atom_id: label,
auth_comp_id: MOL,
auth_seq_id: seq_id,
Cartn_x: db_1.Column.ofFloatArray(x),
Cartn_y: db_1.Column.ofFloatArray(y),
Cartn_z: db_1.Column.ofFloatArray(z),
id: db_1.Column.range(0, atomCount - 1),
label_asym_id: A,
label_atom_id: label,
label_comp_id: MOL,
label_seq_id: seq_id,
label_entity_id: db_1.Column.ofConst('1', atomCount, db_1.Column.Schema.str),
occupancy: db.atom_site.occupancy.isDefined
? db.atom_site.occupancy
: db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.float),
type_symbol: typeSymbol,
pdbx_formal_charge: formalCharge,
pdbx_PDB_model_num: db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.int),
B_iso_or_equiv: db.atom_site.u_iso_or_equiv,
}, atomCount);
const name = (db.chemical.name_common.value(0) ||
db.chemical.name_systematic.value(0) ||
db.chemical_formula.sum.value(0));
const entityBuilder = new entity_1.EntityBuilder();
entityBuilder.setNames([['MOL', name || 'Unknown Entity']]);
entityBuilder.getEntityId('MOL', types_1.MoleculeType.Unknown, 'A');
const componentBuilder = new component_1.ComponentBuilder(seq_id, db.atom_site.type_symbol);
componentBuilder.setNames([['MOL', name || 'Unknown Molecule']]);
componentBuilder.add('MOL', 0);
const basic = (0, schema_1.createBasic)({
entity: entityBuilder.getEntityTable(),
chem_comp: componentBuilder.getChemCompTable(),
atom_site
});
const models = await (0, parser_1.createModels)(basic, format, ctx);
if (models.frameCount > 0) {
const first = models.representative;
symmetry_1.ModelSymmetry.Provider.set(first, symmetry);
const bondCount = db.geom_bond._rowCount;
if (bondCount > 0) {
const labelIndexMap = {};
const { label } = db.atom_site;
for (let i = 0, il = label.rowCount; i < il; ++i) {
labelIndexMap[label.value(i)] = i;
}
const bond_type = (_a = format.data.frame.categories.ccdc_geom_bond_type) === null || _a === void 0 ? void 0 : _a.getField('');
const indexA = [];
const indexB = [];
const order = [];
const dist = [];
const flag = [];
const included = new Set();
let j = 0;
const { atom_site_label_1, atom_site_label_2, valence, distance } = db.geom_bond;
for (let i = 0; i < bondCount; ++i) {
const iA = labelIndexMap[atom_site_label_1.value(i)];
const iB = labelIndexMap[atom_site_label_2.value(i)];
const id = iA < iB ? (0, util_2.cantorPairing)(iA, iB) : (0, util_2.cantorPairing)(iB, iA);
if (included.has(id))
continue;
included.add(id);
indexA[j] = iA;
indexB[j] = iB;
dist[j] = distance.value(i) || -1;
if (bond_type) {
const t = bond_type.str(i);
if (t === 'D') {
order[j] = 2;
flag[j] = types_1.BondType.Flag.Covalent;
}
else if (t === 'A') {
order[j] = 1;
flag[j] = types_1.BondType.Flag.Covalent | types_1.BondType.Flag.Aromatic;
}
else if (t === 'S') {
order[j] = 1;
flag[j] = types_1.BondType.Flag.Covalent;
}
else {
order[j] = 1;
flag[j] = types_1.BondType.Flag.Covalent;
}
}
else {
flag[j] = types_1.BondType.Flag.Covalent;
// TODO derive order from bond length if undefined
order[j] = valence.isDefined ? valence.value(i) : 1;
}
j += 1;
}
index_pair_1.IndexPairBonds.Provider.set(first, index_pair_1.IndexPairBonds.fromData({ pairs: {
indexA: db_1.Column.ofIntArray(indexA),
indexB: db_1.Column.ofIntArray(indexB),
order: db_1.Column.ofIntArray(order),
distance: db_1.Column.ofFloatArray(dist),
flag: db_1.Column.ofIntArray(flag)
}, count: atomCount }));
}
}
return models;
}
function atomSiteAnisotropFromCifCore(model) {
if (!CifCoreFormat.is(model.sourceData))
return;
const { atom_site, atom_site_aniso } = model.sourceData.data.db;
const data = db_1.Table.ofPartialColumns(anisotropic_1.AtomSiteAnisotrop.Schema, {
U: atom_site_aniso.u,
}, atom_site_aniso._rowCount);
const elementToAnsiotrop = anisotropic_1.AtomSiteAnisotrop.getElementToAnsiotropFromLabel(atom_site.label, atom_site_aniso.label);
return { data, elementToAnsiotrop };
}
function atomSiteAnisotropApplicableCifCore(model) {
if (!CifCoreFormat.is(model.sourceData))
return false;
return model.sourceData.data.db.atom_site_aniso.u.isDefined;
}
anisotropic_1.AtomSiteAnisotrop.Provider.formatRegistry.add('cifCore', atomSiteAnisotropFromCifCore, atomSiteAnisotropApplicableCifCore);
var CifCoreFormat;
(function (CifCoreFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'cifCore';
}
CifCoreFormat.is = is;
function fromFrame(frame, db) {
if (!db)
db = cif_1.CIF.schema.cifCore(frame);
const name = (db.database_code.depnum_ccdc_archive.value(0) ||
db.database_code.depnum_ccdc_fiz.value(0) ||
db.database_code.icsd.value(0) ||
db.database_code.mdf.value(0) ||
db.database_code.nbs.value(0) ||
db.database_code.csd.value(0) ||
db.database_code.cod.value(0) ||
db._name);
return { kind: 'cifCore', name, data: { db, frame } };
}
CifCoreFormat.fromFrame = fromFrame;
})(CifCoreFormat || (exports.CifCoreFormat = CifCoreFormat = {}));
function trajectoryFromCifCore(frame) {
const format = CifCoreFormat.fromFrame(frame);
return mol_task_1.Task.create('Parse CIF Core', ctx => getModels(format.data.db, format, ctx));
}