/** * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author Alexander Rose */ import { Column, Table } from '../../mol-data/db'; import { Model, Symmetry } from '../../mol-model/structure/model'; import { BondType, MoleculeType } from '../../mol-model/structure/model/types'; import { RuntimeContext, Task } from '../../mol-task'; import { createModels } from './basic/parser'; import { BasicSchema, createBasic } from './basic/schema'; import { ComponentBuilder } from './common/component'; import { EntityBuilder } from './common/entity'; import { ModelFormat } from '../format'; import { IndexPairBonds } from './property/bonds/index-pair'; import { Mol2Crysin, Mol2File } from '../../mol-io/reader/mol2/schema'; import { AtomPartialCharge } from './property/partial-charge'; import { Trajectory, ArrayTrajectory } from '../../mol-model/structure'; import { guessElementSymbolString } from './util'; import { ModelSymmetry } from './property/symmetry'; import { Spacegroup, SpacegroupCell } from '../../mol-math/geometry'; import { Vec3 } from '../../mol-math/linear-algebra'; async function getModels(mol2: Mol2File, ctx: RuntimeContext) { const models: Model[] = []; for (let i = 0, il = mol2.structures.length; i < il; ++i) { const { molecule, atoms, bonds, crysin } = mol2.structures[i]; const A = Column.ofConst('A', atoms.count, Column.Schema.str); const type_symbol = new Array(atoms.count); let hasAtomType = false; for (let i = 0; i < atoms.count; ++i) { if (atoms.atom_type.value(i).includes('.')) { hasAtomType = true; break; } } for (let i = 0; i < atoms.count; ++i) { type_symbol[i] = hasAtomType ? atoms.atom_type.value(i).split('.')[0].toUpperCase() : guessElementSymbolString(atoms.atom_name.value(i), atoms.subst_name.value(i)); } const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, { auth_asym_id: A, auth_atom_id: Column.asArrayColumn(atoms.atom_name), auth_comp_id: atoms.subst_name, auth_seq_id: atoms.subst_id, Cartn_x: Column.asArrayColumn(atoms.x, Float32Array), Cartn_y: Column.asArrayColumn(atoms.y, Float32Array), Cartn_z: Column.asArrayColumn(atoms.z, Float32Array), id: Column.asArrayColumn(atoms.atom_id), label_asym_id: A, label_atom_id: Column.asArrayColumn(atoms.atom_name), label_comp_id: atoms.subst_name, label_seq_id: atoms.subst_id, label_entity_id: Column.ofConst('1', atoms.count, Column.Schema.str), occupancy: Column.ofConst(1, atoms.count, Column.Schema.float), type_symbol: Column.ofStringArray(type_symbol), pdbx_PDB_model_num: Column.ofConst(i, atoms.count, Column.Schema.int), }, atoms.count); const entityBuilder = new EntityBuilder(); entityBuilder.setNames([['MOL', molecule.mol_name || 'Unknown Entity']]); entityBuilder.getEntityId('MOL', MoleculeType.Unknown, 'A'); const componentBuilder = new ComponentBuilder(atoms.subst_id, atoms.atom_name); for (let i = 0, il = atoms.subst_name.rowCount; i < il; ++i) { componentBuilder.add(atoms.subst_name.value(i), i); } const basic = createBasic({ entity: entityBuilder.getEntityTable(), chem_comp: componentBuilder.getChemCompTable(), atom_site }); const _models = await createModels(basic, Mol2Format.create(mol2), ctx); if (_models.frameCount > 0) { const indexA = Column.ofIntArray(Column.mapToArray(bonds.origin_atom_id, x => x - 1, Int32Array)); const indexB = Column.ofIntArray(Column.mapToArray(bonds.target_atom_id, x => x - 1, Int32Array)); const key = bonds.bond_id; const order = Column.ofIntArray(Column.mapToArray(bonds.bond_type, 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)); const flag = Column.ofIntArray(Column.mapToArray(bonds.bond_type, x => { switch (x) { case 'ar': // aromatic case 'am': // amide return BondType.Flag.Aromatic | BondType.Flag.Covalent; case 'du': // dummy case 'nc': // not connected return BondType.Flag.None; case 'un': // unknown default: return BondType.Flag.Covalent; } }, Int8Array)); const pairBonds = IndexPairBonds.fromData( { pairs: { key, indexA, indexB, order, flag }, count: atoms.count }, { maxDistance: crysin ? -1 : Infinity } ); const first = _models.representative; IndexPairBonds.Provider.set(first, pairBonds); AtomPartialCharge.Provider.set(first, { data: atoms.charge, type: molecule.charge_type }); if (crysin) { const symmetry = getSymmetry(crysin); if (symmetry) ModelSymmetry.Provider.set(first, symmetry); } models.push(first); } } return new ArrayTrajectory(models); } function getSymmetry(crysin: Mol2Crysin): Symmetry | undefined { // TODO handle `crysin.setting` if (crysin.setting !== 1) return; const spaceCell = SpacegroupCell.create( crysin.spaceGroup, Vec3.create(crysin.a, crysin.b, crysin.c), Vec3.scale(Vec3(), Vec3.create(crysin.alpha, crysin.beta, crysin.gamma), Math.PI / 180) ); return { spacegroup: Spacegroup.create(spaceCell), assemblies: [], isNonStandardCrystalFrame: false, ncsOperators: [] }; } // export { Mol2Format }; type Mol2Format = ModelFormat namespace Mol2Format { export function is(x?: ModelFormat): x is Mol2Format { return x?.kind === 'mol2'; } export function create(mol2: Mol2File): Mol2Format { return { kind: 'mol2', name: mol2.name, data: mol2 }; } } export function trajectoryFromMol2(mol2: Mol2File): Task { return Task.create('Parse MOL2', ctx => getModels(mol2, ctx)); }