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to-cif.ts 10.25 KiB
/**
* Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Yana Rose <yana.v.rose@gmail.com>
*/
import { substringStartsWith } from '../../../mol-util/string';
import { CifCategory, CifField, CifFrame } from '../../../mol-io/reader/cif';
import { Tokenizer } from '../../../mol-io/reader/common/text/tokenizer';
import { PdbFile } from '../../../mol-io/reader/pdb/schema';
import { parseCryst1, parseRemark350, parseMtrix } from './assembly';
import { parseHelix, parseSheet } from './secondary-structure';
import { parseCmpnd, parseHetnam } from './entity';
import { ComponentBuilder } from '../common/component';
import { EntityBuilder } from '../common/entity';
import { Column } from '../../../mol-data/db';
import { getMoleculeType } from '../../../mol-model/structure/model/types';
import { getAtomSiteTemplate, addAtom, getAtomSite } from './atom-site';
import { addAnisotropic, getAnisotropicTemplate, getAnisotropic } from './anisotropic';
import { parseConect } from './conect';
import { isDebugMode } from '../../../mol-util/debug';
import { PdbHeaderData, addHeader } from './header';
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
const { lines } = pdb;
const { data, indices } = lines;
const tokenizer = Tokenizer(data);
const isPdbqt = !!pdb.isPdbqt;
// Count the atoms
let atomCount = 0;
let anisotropicCount = 0;
for (let i = 0, _i = lines.count; i < _i; i++) {
const s = indices[2 * i], e = indices[2 * i + 1];
switch (data[s]) {
case 'A':
if (substringStartsWith(data, s, e, 'ATOM ')) atomCount++;
else if (substringStartsWith(data, s, e, 'ANISOU')) anisotropicCount++;
break;
case 'H':
if (substringStartsWith(data, s, e, 'HETATM')) atomCount++;
break;
}
}
const header: PdbHeaderData = {};
const atomSite = getAtomSiteTemplate(data, atomCount);
const anisotropic = getAnisotropicTemplate(data, anisotropicCount);
const entityBuilder = new EntityBuilder();
const helperCategories: CifCategory[] = [];
const heteroNames: [string, string][] = [];
let modelNum = 0, modelStr = '';
let conectRange: [number, number] | undefined = undefined;
let hasAssemblies = false;
const terIndices = new Set<number>();
for (let i = 0, _i = lines.count; i < _i; i++) {
let s = indices[2 * i], e = indices[2 * i + 1];
switch (data[s]) {
case 'A':
if (substringStartsWith(data, s, e, 'ATOM ')) {
if (!modelNum) { modelNum++; modelStr = '' + modelNum; }
addAtom(atomSite, modelStr, tokenizer, s, e, isPdbqt);
} else if (substringStartsWith(data, s, e, 'ANISOU')) {
addAnisotropic(anisotropic, modelStr, tokenizer, s, e);
}
break;
case 'C':
if (substringStartsWith(data, s, e, 'CRYST1')) {
helperCategories.push(...parseCryst1(pdb.id || '?', data.substring(s, e)));
} else if (substringStartsWith(data, s, e, 'CONECT')) {
let j = i + 1;
while (true) {
s = indices[2 * j]; e = indices[2 * j + 1];
if (!substringStartsWith(data, s, e, 'CONECT')) break;
j++;
}
if (conectRange) {
if (isDebugMode) {
console.log('only single CONECT block allowed, ignoring others');
}
} else {
conectRange = [i, j];
}
i = j - 1;
} else if (substringStartsWith(data, s, e, 'COMPND')) {
let j = i + 1;
while (true) {
s = indices[2 * j]; e = indices[2 * j + 1];
if (!substringStartsWith(data, s, e, 'COMPND')) break;
j++;
}
entityBuilder.setCompounds(parseCmpnd(lines, i, j));
i = j - 1;
}
break;
case 'H':
if (substringStartsWith(data, s, e, 'HEADER')) {
addHeader(data, s, e, header);
} else if (substringStartsWith(data, s, e, 'HETATM')) {
if (!modelNum) { modelNum++; modelStr = '' + modelNum; }
addAtom(atomSite, modelStr, tokenizer, s, e, isPdbqt);
} else if (substringStartsWith(data, s, e, 'HELIX')) {
let j = i + 1;
while (true) {
s = indices[2 * j]; e = indices[2 * j + 1];
if (!substringStartsWith(data, s, e, 'HELIX')) break;
j++;
}
helperCategories.push(parseHelix(lines, i, j));
i = j - 1;
} else if (substringStartsWith(data, s, e, 'HETNAM')) {
let j = i + 1;
while (true) {
s = indices[2 * j]; e = indices[2 * j + 1];
if (!substringStartsWith(data, s, e, 'HETNAM')) break;
j++;
}
heteroNames.push(...Array.from(parseHetnam(lines, i, j).entries()));
i = j - 1;
}
break;
case 'M':
if (substringStartsWith(data, s, e, 'MODEL ')) {
modelNum++;
modelStr = '' + modelNum;
}
if (substringStartsWith(data, s, e, 'MTRIX')) {
let j = i + 1;
while (true) {
s = indices[2 * j]; e = indices[2 * j + 1];
if (!substringStartsWith(data, s, e, 'MTRIX')) break;
j++;
}
helperCategories.push(...parseMtrix(lines, i, j));
i = j - 1;
}
// TODO: MODRES records => pdbx_struct_mod_residue
break;
case 'O':
// TODO: ORIGX record => cif.database_PDB_matrix.origx, cif.database_PDB_matrix.origx_vector
break;
case 'R':
if (substringStartsWith(data, s, e, 'REMARK 350')) {
let j = i + 1;
while (true) {
s = indices[2 * j]; e = indices[2 * j + 1];
if (!substringStartsWith(data, s, e, 'REMARK 350')) break;
j++;
}
helperCategories.push(...parseRemark350(lines, i, j));
i = j - 1;
hasAssemblies = true;
}
break;
case 'S':
if (substringStartsWith(data, s, e, 'SHEET')) {
let j = i + 1;
while (true) {
s = indices[2 * j]; e = indices[2 * j + 1];
if (!substringStartsWith(data, s, e, 'SHEET')) break;
j++;
}
helperCategories.push(parseSheet(lines, i, j));
i = j - 1;
}
// TODO: SCALE record => cif.atom_sites.fract_transf_matrix, cif.atom_sites.fract_transf_vector
break;
case 'T':
if (substringStartsWith(data, s, e, 'TER')) {
terIndices.add(atomSite.index);
}
}
}
// build entry, struct_keywords and pdbx_database_status
if (header.id_code) {
const entry: CifCategory.SomeFields<mmCIF_Schema['entry']> = {
id: CifField.ofString(header.id_code)
};
helperCategories.push(CifCategory.ofFields('entry', entry));
}
if (header.classification) {
const struct_keywords: CifCategory.SomeFields<mmCIF_Schema['struct_keywords']> = {
pdbx_keywords: CifField.ofString(header.classification)
};
helperCategories.push(CifCategory.ofFields('struct_keywords', struct_keywords));
}
if (header.dep_date) {
const pdbx_database_status: CifCategory.SomeFields<mmCIF_Schema['pdbx_database_status']> = {
recvd_initial_deposition_date: CifField.ofString(header.dep_date)
};
helperCategories.push(CifCategory.ofFields('pdbx_database_status', pdbx_database_status));
}
// build entity and chem_comp categories
const seqIds = Column.ofIntTokens(atomSite.auth_seq_id);
const atomIds = Column.ofStringTokens(atomSite.auth_atom_id);
const compIds = Column.ofStringTokens(atomSite.auth_comp_id);
const asymIds = Column.ofStringTokens(atomSite.auth_asym_id);
const componentBuilder = new ComponentBuilder(seqIds, atomIds);
componentBuilder.setNames(heteroNames);
entityBuilder.setNames(heteroNames);
for (let i = 0, il = compIds.rowCount; i < il; ++i) {
const compId = compIds.value(i);
const moleculeType = getMoleculeType(componentBuilder.add(compId, i).type, compId);
atomSite.label_entity_id[i] = entityBuilder.getEntityId(compId, moleculeType, asymIds.value(i));
}
const atom_site = getAtomSite(atomSite, terIndices, { hasAssemblies });
if (!isPdbqt) delete atom_site.partial_charge;
if (conectRange) {
helperCategories.push(parseConect(lines, conectRange[0], conectRange[1], atom_site));
}
const categories = {
entity: CifCategory.ofTable('entity', entityBuilder.getEntityTable()),
chem_comp: CifCategory.ofTable('chem_comp', componentBuilder.getChemCompTable()),
atom_site: CifCategory.ofFields('atom_site', atom_site),
atom_site_anisotrop: CifCategory.ofFields('atom_site_anisotrop', getAnisotropic(anisotropic))
} as any;
for (const c of helperCategories) {
categories[c.name] = c;
}
return {
header: pdb.id || 'PDB',
categoryNames: Object.keys(categories),
categories
};
}