molstar
Version:
A comprehensive macromolecular library.
86 lines (85 loc) • 3.55 kB
JavaScript
;
/**
* Copyright (c) 2020 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 Sebastian Bittrich <sebastian.bittrich@rcsb.org>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.ComponentAtom = void 0;
const cif_1 = require("../../../../mol-io/writer/cif");
const db_1 = require("../../../../mol-data/db");
const property_1 = require("../../common/property");
const ccd_1 = require("../../../../mol-io/reader/cif/schema/ccd");
var ComponentAtom;
(function (ComponentAtom) {
ComponentAtom.Descriptor = {
name: 'chem_comp_atom',
cifExport: {
prefix: '',
categories: [{
name: 'chem_comp_atom',
instance(ctx) {
const p = ComponentAtom.Provider.get(ctx.firstModel);
if (!p)
return cif_1.CifWriter.Category.Empty;
const chem_comp_atom = p.data;
if (!chem_comp_atom)
return cif_1.CifWriter.Category.Empty;
const comp_names = ctx.structures[0].uniqueResidueNames;
const { comp_id, _rowCount } = chem_comp_atom;
const indices = [];
for (let i = 0; i < _rowCount; i++) {
if (comp_names.has(comp_id.value(i)))
indices[indices.length] = i;
}
return cif_1.CifWriter.Category.ofTable(chem_comp_atom, indices);
}
}]
}
};
ComponentAtom.Provider = property_1.FormatPropertyProvider.create(ComponentAtom.Descriptor);
function chemCompAtomFromTable(model, table) {
return db_1.Table.pick(table, ccd_1.CCD_Schema.chem_comp_atom, (i) => {
return model.properties.chemicalComponentMap.has(table.comp_id.value(i));
});
}
ComponentAtom.chemCompAtomFromTable = chemCompAtomFromTable;
function getEntriesFromChemCompAtom(data) {
const entries = new Map();
function addEntry(id) {
// weird behavior when 'PRO' is requested - will report a single bond between N and H because a later operation would override real content
if (entries.has(id)) {
return entries.get(id);
}
const e = new Entry(id);
entries.set(id, e);
return e;
}
const { comp_id, atom_id, charge, pdbx_stereo_config, _rowCount } = data;
let entry = addEntry(comp_id.value(0));
for (let i = 0; i < _rowCount; i++) {
const name = atom_id.value(i);
const id = comp_id.value(i);
const ch = charge.value(i);
const stereo = pdbx_stereo_config.value(i);
if (entry.id !== id) {
entry = addEntry(id);
}
entry.add(name, ch, stereo);
}
return entries;
}
ComponentAtom.getEntriesFromChemCompAtom = getEntriesFromChemCompAtom;
class Entry {
add(a, charge, stereo_config) {
this.map.set(a, { charge, stereo_config });
}
constructor(id) {
this.id = id;
this.map = new Map();
}
}
ComponentAtom.Entry = Entry;
})(ComponentAtom || (exports.ComponentAtom = ComponentAtom = {}));