molstar
Version:
A comprehensive macromolecular library.
231 lines • 12.5 kB
JavaScript
;
/**
* 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>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.pdbToMmCif = void 0;
var tslib_1 = require("tslib");
var string_1 = require("../../../mol-util/string");
var cif_1 = require("../../../mol-io/reader/cif");
var tokenizer_1 = require("../../../mol-io/reader/common/text/tokenizer");
var assembly_1 = require("./assembly");
var secondary_structure_1 = require("./secondary-structure");
var entity_1 = require("./entity");
var component_1 = require("../common/component");
var entity_2 = require("../common/entity");
var db_1 = require("../../../mol-data/db");
var types_1 = require("../../../mol-model/structure/model/types");
var atom_site_1 = require("./atom-site");
var anisotropic_1 = require("./anisotropic");
var conect_1 = require("./conect");
var debug_1 = require("../../../mol-util/debug");
function pdbToMmCif(pdb) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var lines, data, indices, tokenizer, isPdbqt, atomCount, anisotropicCount, i, _i, s, e, atomSite, anisotropic, entityBuilder, helperCategories, heteroNames, modelNum, modelStr, conectRange, i, _i, s, e, j, j, j, j, j, j, j, seqIds, atomIds, compIds, asymIds, componentBuilder, i, il, compId, moleculeType, atom_site, categories, _a, helperCategories_1, c;
return (0, tslib_1.__generator)(this, function (_b) {
lines = pdb.lines;
data = lines.data, indices = lines.indices;
tokenizer = (0, tokenizer_1.Tokenizer)(data);
isPdbqt = !!pdb.isPdbqt;
atomCount = 0;
anisotropicCount = 0;
for (i = 0, _i = lines.count; i < _i; i++) {
s = indices[2 * i], e = indices[2 * i + 1];
switch (data[s]) {
case 'A':
if ((0, string_1.substringStartsWith)(data, s, e, 'ATOM '))
atomCount++;
else if ((0, string_1.substringStartsWith)(data, s, e, 'ANISOU'))
anisotropicCount++;
break;
case 'H':
if ((0, string_1.substringStartsWith)(data, s, e, 'HETATM'))
atomCount++;
break;
}
}
atomSite = (0, atom_site_1.getAtomSiteTemplate)(data, atomCount);
anisotropic = (0, anisotropic_1.getAnisotropicTemplate)(data, anisotropicCount);
entityBuilder = new entity_2.EntityBuilder();
helperCategories = [];
heteroNames = [];
modelNum = 0, modelStr = '';
conectRange = undefined;
for (i = 0, _i = lines.count; i < _i; i++) {
s = indices[2 * i], e = indices[2 * i + 1];
switch (data[s]) {
case 'A':
if ((0, string_1.substringStartsWith)(data, s, e, 'ATOM ')) {
if (!modelNum) {
modelNum++;
modelStr = '' + modelNum;
}
(0, atom_site_1.addAtom)(atomSite, modelStr, tokenizer, s, e, isPdbqt);
}
else if ((0, string_1.substringStartsWith)(data, s, e, 'ANISOU')) {
(0, anisotropic_1.addAnisotropic)(anisotropic, modelStr, tokenizer, s, e);
}
break;
case 'C':
if ((0, string_1.substringStartsWith)(data, s, e, 'CRYST1')) {
helperCategories.push.apply(helperCategories, (0, assembly_1.parseCryst1)(pdb.id || '?', data.substring(s, e)));
}
else if ((0, string_1.substringStartsWith)(data, s, e, 'CONECT')) {
j = i + 1;
while (true) {
s = indices[2 * j];
e = indices[2 * j + 1];
if (!(0, string_1.substringStartsWith)(data, s, e, 'CONECT'))
break;
j++;
}
if (conectRange) {
if (debug_1.isDebugMode) {
console.log('only single CONECT block allowed, ignoring others');
}
}
else {
conectRange = [i, j];
}
i = j - 1;
}
else if ((0, string_1.substringStartsWith)(data, s, e, 'COMPND')) {
j = i + 1;
while (true) {
s = indices[2 * j];
e = indices[2 * j + 1];
if (!(0, string_1.substringStartsWith)(data, s, e, 'COMPND'))
break;
j++;
}
entityBuilder.setCompounds((0, entity_1.parseCmpnd)(lines, i, j));
i = j - 1;
}
break;
case 'H':
if ((0, string_1.substringStartsWith)(data, s, e, 'HETATM')) {
if (!modelNum) {
modelNum++;
modelStr = '' + modelNum;
}
(0, atom_site_1.addAtom)(atomSite, modelStr, tokenizer, s, e, isPdbqt);
}
else if ((0, string_1.substringStartsWith)(data, s, e, 'HELIX')) {
j = i + 1;
while (true) {
s = indices[2 * j];
e = indices[2 * j + 1];
if (!(0, string_1.substringStartsWith)(data, s, e, 'HELIX'))
break;
j++;
}
helperCategories.push((0, secondary_structure_1.parseHelix)(lines, i, j));
i = j - 1;
}
else if ((0, string_1.substringStartsWith)(data, s, e, 'HETNAM')) {
j = i + 1;
while (true) {
s = indices[2 * j];
e = indices[2 * j + 1];
if (!(0, string_1.substringStartsWith)(data, s, e, 'HETNAM'))
break;
j++;
}
heteroNames.push.apply(heteroNames, Array.from((0, entity_1.parseHetnam)(lines, i, j).entries()));
i = j - 1;
}
break;
case 'M':
if ((0, string_1.substringStartsWith)(data, s, e, 'MODEL ')) {
modelNum++;
modelStr = '' + modelNum;
}
if ((0, string_1.substringStartsWith)(data, s, e, 'MTRIX')) {
j = i + 1;
while (true) {
s = indices[2 * j];
e = indices[2 * j + 1];
if (!(0, string_1.substringStartsWith)(data, s, e, 'MTRIX'))
break;
j++;
}
helperCategories.push.apply(helperCategories, (0, assembly_1.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 ((0, string_1.substringStartsWith)(data, s, e, 'REMARK 350')) {
j = i + 1;
while (true) {
s = indices[2 * j];
e = indices[2 * j + 1];
if (!(0, string_1.substringStartsWith)(data, s, e, 'REMARK 350'))
break;
j++;
}
helperCategories.push.apply(helperCategories, (0, assembly_1.parseRemark350)(lines, i, j));
i = j - 1;
}
break;
case 'S':
if ((0, string_1.substringStartsWith)(data, s, e, 'SHEET')) {
j = i + 1;
while (true) {
s = indices[2 * j];
e = indices[2 * j + 1];
if (!(0, string_1.substringStartsWith)(data, s, e, 'SHEET'))
break;
j++;
}
helperCategories.push((0, secondary_structure_1.parseSheet)(lines, i, j));
i = j - 1;
}
// TODO: SCALE record => cif.atom_sites.fract_transf_matrix, cif.atom_sites.fract_transf_vector
break;
}
}
seqIds = db_1.Column.ofIntTokens(atomSite.auth_seq_id);
atomIds = db_1.Column.ofStringTokens(atomSite.auth_atom_id);
compIds = db_1.Column.ofStringTokens(atomSite.auth_comp_id);
asymIds = db_1.Column.ofStringTokens(atomSite.auth_asym_id);
componentBuilder = new component_1.ComponentBuilder(seqIds, atomIds);
componentBuilder.setNames(heteroNames);
entityBuilder.setNames(heteroNames);
for (i = 0, il = compIds.rowCount; i < il; ++i) {
compId = compIds.value(i);
moleculeType = (0, types_1.getMoleculeType)(componentBuilder.add(compId, i).type, compId);
atomSite.label_entity_id[i] = entityBuilder.getEntityId(compId, moleculeType, asymIds.value(i));
}
atom_site = (0, atom_site_1.getAtomSite)(atomSite);
if (!isPdbqt)
delete atom_site.partial_charge;
if (conectRange) {
helperCategories.push((0, conect_1.parseConect)(lines, conectRange[0], conectRange[1], atom_site));
}
categories = {
entity: cif_1.CifCategory.ofTable('entity', entityBuilder.getEntityTable()),
chem_comp: cif_1.CifCategory.ofTable('chem_comp', componentBuilder.getChemCompTable()),
atom_site: cif_1.CifCategory.ofFields('atom_site', atom_site),
atom_site_anisotrop: cif_1.CifCategory.ofFields('atom_site_anisotrop', (0, anisotropic_1.getAnisotropic)(anisotropic))
};
for (_a = 0, helperCategories_1 = helperCategories; _a < helperCategories_1.length; _a++) {
c = helperCategories_1[_a];
categories[c.name] = c;
}
return [2 /*return*/, {
header: pdb.id || 'PDB',
categoryNames: Object.keys(categories),
categories: categories
}];
});
});
}
exports.pdbToMmCif = pdbToMmCif;
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