molstar
Version:
A comprehensive macromolecular library.
163 lines (162 loc) • 9.11 kB
JavaScript
;
/**
* Copyright (c) 2020-2022 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.trajectoryFromMol2 = exports.Mol2Format = void 0;
var tslib_1 = require("tslib");
var db_1 = require("../../mol-data/db");
var mol_task_1 = require("../../mol-task");
var parser_1 = require("./basic/parser");
var schema_1 = require("./basic/schema");
var component_1 = require("./common/component");
var entity_1 = require("./common/entity");
var index_pair_1 = require("./property/bonds/index-pair");
var partial_charge_1 = require("./property/partial-charge");
var structure_1 = require("../../mol-model/structure");
var util_1 = require("./util");
var symmetry_1 = require("./property/symmetry");
var geometry_1 = require("../../mol-math/geometry");
var linear_algebra_1 = require("../../mol-math/linear-algebra");
function getModels(mol2, ctx) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var models, i, il, _a, molecule, atoms, bonds, crysin, A, type_symbol, hasAtomType, i_1, i_2, atom_site, entityBuilder, componentBuilder, i_3, il_1, basic, _models, indexA, indexB, key, order, flag, pairBonds, first, symmetry;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
models = [];
i = 0, il = mol2.structures.length;
_b.label = 1;
case 1:
if (!(i < il)) return [3 /*break*/, 4];
_a = mol2.structures[i], molecule = _a.molecule, atoms = _a.atoms, bonds = _a.bonds, crysin = _a.crysin;
A = db_1.Column.ofConst('A', atoms.count, db_1.Column.Schema.str);
type_symbol = new Array(atoms.count);
hasAtomType = false;
for (i_1 = 0; i_1 < atoms.count; ++i_1) {
if (atoms.atom_type.value(i_1).includes('.')) {
hasAtomType = true;
break;
}
}
for (i_2 = 0; i_2 < atoms.count; ++i_2) {
type_symbol[i_2] = hasAtomType
? atoms.atom_type.value(i_2).split('.')[0].toUpperCase()
: (0, util_1.guessElementSymbolString)(atoms.atom_name.value(i_2), atoms.subst_name.value(i_2));
}
atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
auth_asym_id: A,
auth_atom_id: db_1.Column.asArrayColumn(atoms.atom_name),
auth_comp_id: atoms.subst_name,
auth_seq_id: atoms.subst_id,
Cartn_x: db_1.Column.asArrayColumn(atoms.x, Float32Array),
Cartn_y: db_1.Column.asArrayColumn(atoms.y, Float32Array),
Cartn_z: db_1.Column.asArrayColumn(atoms.z, Float32Array),
id: db_1.Column.asArrayColumn(atoms.atom_id),
label_asym_id: A,
label_atom_id: db_1.Column.asArrayColumn(atoms.atom_name),
label_comp_id: atoms.subst_name,
label_seq_id: atoms.subst_id,
label_entity_id: db_1.Column.ofConst('1', atoms.count, db_1.Column.Schema.str),
occupancy: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.float),
type_symbol: db_1.Column.ofStringArray(type_symbol),
pdbx_PDB_model_num: db_1.Column.ofConst(i, atoms.count, db_1.Column.Schema.int),
}, atoms.count);
entityBuilder = new entity_1.EntityBuilder();
entityBuilder.setNames([['MOL', molecule.mol_name || 'Unknown Entity']]);
entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
componentBuilder = new component_1.ComponentBuilder(atoms.subst_id, atoms.atom_name);
for (i_3 = 0, il_1 = atoms.subst_name.rowCount; i_3 < il_1; ++i_3) {
componentBuilder.add(atoms.subst_name.value(i_3), i_3);
}
basic = (0, schema_1.createBasic)({
entity: entityBuilder.getEntityTable(),
chem_comp: componentBuilder.getChemCompTable(),
atom_site: atom_site
});
return [4 /*yield*/, (0, parser_1.createModels)(basic, Mol2Format.create(mol2), ctx)];
case 2:
_models = _b.sent();
if (_models.frameCount > 0) {
indexA = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.origin_atom_id, function (x) { return x - 1; }, Int32Array));
indexB = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.target_atom_id, function (x) { return x - 1; }, Int32Array));
key = bonds.bond_id;
order = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.bond_type, function (x) {
switch (x) {
case 'ar': // aromatic
case 'am': // amide
case 'un': // unknown
return 1;
case 'du': // dummy
case 'nc': // not connected
return 0;
default:
return parseInt(x);
}
}, Int8Array));
flag = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.bond_type, function (x) {
switch (x) {
case 'ar': // aromatic
case 'am': // amide
return 16 /* BondType.Flag.Aromatic */ | 1 /* BondType.Flag.Covalent */;
case 'du': // dummy
case 'nc': // not connected
return 0 /* BondType.Flag.None */;
case 'un': // unknown
default:
return 1 /* BondType.Flag.Covalent */;
}
}, Int8Array));
pairBonds = index_pair_1.IndexPairBonds.fromData({ pairs: { key: key, indexA: indexA, indexB: indexB, order: order, flag: flag }, count: atoms.count }, { maxDistance: crysin ? -1 : Infinity });
first = _models.representative;
index_pair_1.IndexPairBonds.Provider.set(first, pairBonds);
partial_charge_1.AtomPartialCharge.Provider.set(first, {
data: atoms.charge,
type: molecule.charge_type
});
if (crysin) {
symmetry = getSymmetry(crysin);
if (symmetry)
symmetry_1.ModelSymmetry.Provider.set(first, symmetry);
}
models.push(first);
}
_b.label = 3;
case 3:
++i;
return [3 /*break*/, 1];
case 4: return [2 /*return*/, new structure_1.ArrayTrajectory(models)];
}
});
});
}
function getSymmetry(crysin) {
// TODO handle `crysin.setting`
if (crysin.setting !== 1)
return;
var spaceCell = geometry_1.SpacegroupCell.create(crysin.spaceGroup, linear_algebra_1.Vec3.create(crysin.a, crysin.b, crysin.c), linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.create(crysin.alpha, crysin.beta, crysin.gamma), Math.PI / 180));
return {
spacegroup: geometry_1.Spacegroup.create(spaceCell),
assemblies: [],
isNonStandardCrystalFrame: false,
ncsOperators: []
};
}
var Mol2Format;
(function (Mol2Format) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'mol2';
}
Mol2Format.is = is;
function create(mol2) {
return { kind: 'mol2', name: mol2.name, data: mol2 };
}
Mol2Format.create = create;
})(Mol2Format || (Mol2Format = {}));
exports.Mol2Format = Mol2Format;
function trajectoryFromMol2(mol2) {
return mol_task_1.Task.create('Parse MOL2', function (ctx) { return getModels(mol2, ctx); });
}
exports.trajectoryFromMol2 = trajectoryFromMol2;