molstar
Version:
A comprehensive macromolecular library.
244 lines (243 loc) • 10.9 kB
JavaScript
/**
* Copyright (c) 2017-2025 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>
*/
import { CifWriter } from '../../../mol-io/writer/cif';
import { _atom_site } from './categories/atom_site';
var CifCategory = CifWriter.Category;
import { _struct_conf, _struct_sheet_range } from './categories/secondary-structure';
import { _chem_comp, _chem_comp_bond, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './categories/misc';
import { getUniqueEntityIndicesFromStructures, copy_mmCif_category, copy_source_mmCifCategory } from './categories/utils';
import { _struct_asym, _entity_poly, _entity_poly_seq } from './categories/sequence';
import { CustomPropertyDescriptor } from '../../custom-property';
import { atom_site_operator_mapping } from './categories/atom_site_operator_mapping';
import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
import { molstar_bond_site } from './categories/molstar_bond_site';
export var CifExportContext;
(function (CifExportContext) {
function create(structures) {
const structureArray = Array.isArray(structures) ? structures : [structures];
return {
structures: structureArray,
firstModel: structureArray[0].model,
cache: Object.create(null)
};
}
CifExportContext.create = create;
})(CifExportContext || (CifExportContext = {}));
const _entity = {
name: 'entity',
instance({ structures }) {
const indices = getUniqueEntityIndicesFromStructures(structures);
return CifCategory.ofTable(structures[0].model.entities.data, indices);
}
};
function isWithoutSymmetry(structure) {
return structure.units.every(u => u.conformation.operator.isIdentity);
}
function isWithoutOperator(structure) {
return isWithoutSymmetry(structure) && structure.units.every(u => !u.conformation.operator.assembly && !u.conformation.operator.suffix);
}
const Categories = (options) => [
// Basics
copy_mmCif_category('entry'),
copy_mmCif_category('exptl'),
_entity,
// Symmetry
copy_mmCif_category('cell', isWithoutSymmetry),
copy_mmCif_category('symmetry', isWithoutSymmetry),
// Assemblies
copy_mmCif_category('pdbx_struct_assembly', isWithoutOperator),
copy_mmCif_category('pdbx_struct_assembly_gen', isWithoutOperator),
copy_mmCif_category('pdbx_struct_oper_list', isWithoutOperator),
// Secondary structure
_struct_conf,
_struct_sheet_range,
// Sequence
_struct_asym,
_entity_poly,
_entity_poly_seq,
// Branch
copy_mmCif_category('pdbx_entity_branch'),
copy_mmCif_category('pdbx_entity_branch_link'),
copy_mmCif_category('pdbx_branch_scheme'),
// Struct conn
copy_mmCif_category('struct_conn'),
// Misc
_chem_comp,
_chem_comp_bond,
_pdbx_chem_comp_identifier,
copy_mmCif_category('atom_sites'),
_pdbx_nonpoly_scheme,
// Atoms
_atom_site({ keepId: options === null || options === void 0 ? void 0 : options.keepAtomSiteId }),
];
var _Filters;
(function (_Filters) {
_Filters.AtomSitePositionsFieldNames = new Set(['id', 'Cartn_x', 'Cartn_y', 'Cartn_z']);
})(_Filters || (_Filters = {}));
export const mmCIF_Export_Filters = {
onlyPositions: {
includeCategory(name) { return name === 'atom_site'; },
includeField(cat, field) { return _Filters.AtomSitePositionsFieldNames.has(field); }
}
};
function getCustomPropCategories(customProp, ctx, params) {
var _a;
if (!customProp.cifExport || customProp.cifExport.categories.length === 0)
return [];
const prefix = customProp.cifExport.prefix;
const cats = customProp.cifExport.categories;
let propCtx = ctx;
if (customProp.cifExport.context) {
const propId = CustomPropertyDescriptor.getUUID(customProp);
if (ctx.cache[propId + '__ctx'])
propCtx = ctx.cache[propId + '__ctx'];
else {
propCtx = customProp.cifExport.context(ctx) || ctx;
ctx.cache[propId + '__ctx'] = propCtx;
}
}
const ret = [];
for (const cat of cats) {
if ((_a = params === null || params === void 0 ? void 0 : params.skipCategoryNames) === null || _a === void 0 ? void 0 : _a.has(cat.name))
continue;
if ((params === null || params === void 0 ? void 0 : params.includedCategoryNames) && !params.includedCategoryNames.has(cat.name))
continue;
if (cat.name.indexOf(prefix) !== 0)
throw new Error(`Custom category '${cat.name}' name must start with prefix '${prefix}.'`);
ret.push([cat, propCtx]);
}
return ret;
}
/** Doesn't start a data block */
export function encode_mmCIF_categories(encoder, structures, params) {
const first = Array.isArray(structures) ? structures[0] : structures;
const models = first.models;
if (models.length !== 1)
throw new Error('Can\'t export stucture composed from multiple models.');
const ctx = (params === null || params === void 0 ? void 0 : params.exportCtx) || CifExportContext.create(structures);
if ((params === null || params === void 0 ? void 0 : params.copyAllCategories) && MmcifFormat.is(models[0].sourceData)) {
encode_mmCIF_categories_copyAll(encoder, ctx, params);
}
else {
encode_mmCIF_categories_default(encoder, ctx, params);
}
}
function encode_mmCIF_categories_default(encoder, ctx, params) {
var _a, _b, _c;
for (const cat of Categories({
keepAtomSiteId: ((_a = params === null || params === void 0 ? void 0 : params.extensions) === null || _a === void 0 ? void 0 : _a.molstar_bond_site) || (params === null || params === void 0 ? void 0 : params.doNotReindexAtomSiteId)
})) {
if ((params === null || params === void 0 ? void 0 : params.skipCategoryNames) && (params === null || params === void 0 ? void 0 : params.skipCategoryNames.has(cat.name)))
continue;
if ((params === null || params === void 0 ? void 0 : params.includedCategoryNames) && !params.includedCategoryNames.has(cat.name))
continue;
encoder.writeCategory(cat, ctx);
}
if (!((_b = params === null || params === void 0 ? void 0 : params.skipCategoryNames) === null || _b === void 0 ? void 0 : _b.has('atom_site')) && encoder.isCategoryIncluded('atom_site')) {
const info = atom_site_operator_mapping(ctx);
if (info)
encoder.writeCategory(info[0], info[1], info[2]);
}
if ((_c = params === null || params === void 0 ? void 0 : params.extensions) === null || _c === void 0 ? void 0 : _c.molstar_bond_site) {
const info = molstar_bond_site(ctx);
if (info)
encoder.writeCategory(info[0], info[1], info[2]);
}
const _params = params || {};
for (const customProp of ctx.firstModel.customProperties.all) {
for (const [cat, propCtx] of getCustomPropCategories(customProp, ctx, _params)) {
encoder.writeCategory(cat, propCtx);
}
}
if (params === null || params === void 0 ? void 0 : params.customProperties) {
for (const customProp of params === null || params === void 0 ? void 0 : params.customProperties) {
for (const [cat, propCtx] of getCustomPropCategories(customProp, ctx, _params)) {
encoder.writeCategory(cat, propCtx);
}
}
}
for (const s of ctx.structures) {
if (!s.hasCustomProperties)
continue;
for (const customProp of s.customPropertyDescriptors.all) {
for (const [cat, propCtx] of getCustomPropCategories(customProp, ctx, _params)) {
encoder.writeCategory(cat, propCtx);
}
}
}
}
function encode_mmCIF_categories_copyAll(encoder, ctx, params) {
var _a, _b;
const providedCategories = new Map();
for (const cat of Categories({
keepAtomSiteId: ((_a = params === null || params === void 0 ? void 0 : params.extensions) === null || _a === void 0 ? void 0 : _a.molstar_bond_site) || (params === null || params === void 0 ? void 0 : params.doNotReindexAtomSiteId)
})) {
providedCategories.set(cat.name, [cat, ctx]);
}
const mapping = atom_site_operator_mapping(ctx);
if (mapping)
providedCategories.set(mapping[0].name, mapping);
const _params = params || {};
for (const customProp of ctx.firstModel.customProperties.all) {
for (const info of getCustomPropCategories(customProp, ctx, _params)) {
providedCategories.set(info[0].name, info);
}
}
if (params === null || params === void 0 ? void 0 : params.customProperties) {
for (const customProp of params === null || params === void 0 ? void 0 : params.customProperties) {
for (const info of getCustomPropCategories(customProp, ctx, _params)) {
providedCategories.set(info[0].name, info);
}
}
}
for (const s of ctx.structures) {
if (!s.hasCustomProperties)
continue;
for (const customProp of s.customPropertyDescriptors.all) {
for (const info of getCustomPropCategories(customProp, ctx)) {
providedCategories.set(info[0].name, info);
}
}
}
const handled = new Set();
const data = ctx.firstModel.sourceData.data;
for (const catName of data.frame.categoryNames) {
handled.add(catName);
if (providedCategories.has(catName)) {
const info = providedCategories.get(catName);
encoder.writeCategory(info[0], info[1], info[2]);
}
else {
if (data.db[catName]) {
const cat = copy_mmCif_category(catName);
encoder.writeCategory(cat, ctx);
}
else {
const cat = copy_source_mmCifCategory(encoder, ctx, data.frame.categories[catName]);
if (cat)
encoder.writeCategory(cat);
}
}
}
providedCategories.forEach((info, name) => {
if (!handled.has(name))
encoder.writeCategory(info[0], info[1], info[2]);
});
if ((_b = params === null || params === void 0 ? void 0 : params.extensions) === null || _b === void 0 ? void 0 : _b.molstar_bond_site) {
const info = molstar_bond_site(ctx);
if (info)
encoder.writeCategory(info[0], info[1], info[2]);
}
}
function to_mmCIF(name, structure, asBinary = false, params) {
var _a;
const enc = (_a = params === null || params === void 0 ? void 0 : params.encoder) !== null && _a !== void 0 ? _a : CifWriter.createEncoder({ binary: asBinary });
enc.startDataBlock(name);
encode_mmCIF_categories(enc, structure, params);
return enc.getData();
}
export { to_mmCIF };