molstar
Version:
A comprehensive macromolecular library.
119 lines (118 loc) • 4.75 kB
JavaScript
;
/**
* Copyright (c) 2017-2022 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.ComponentBond = void 0;
const types_1 = require("../../../../mol-model/structure/model/types");
const mmcif_1 = require("../../../../mol-io/reader/cif/schema/mmcif");
const cif_1 = require("../../../../mol-io/writer/cif");
const db_1 = require("../../../../mol-data/db");
const property_1 = require("../../common/property");
var ComponentBond;
(function (ComponentBond) {
ComponentBond.Descriptor = {
name: 'chem_comp_bond',
cifExport: {
prefix: '',
categories: [{
name: 'chem_comp_bond',
instance(ctx) {
const p = ComponentBond.Provider.get(ctx.firstModel);
if (!p)
return cif_1.CifWriter.Category.Empty;
const chem_comp_bond = p.data;
if (!chem_comp_bond)
return cif_1.CifWriter.Category.Empty;
const comp_names = ctx.structures[0].uniqueResidueNames;
const { comp_id, _rowCount } = chem_comp_bond;
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_bond, indices);
}
}]
}
};
ComponentBond.Provider = property_1.FormatPropertyProvider.create(ComponentBond.Descriptor);
function chemCompBondFromTable(model, table) {
return db_1.Table.pick(table, mmcif_1.mmCIF_Schema.chem_comp_bond, (i) => {
return model.properties.chemicalComponentMap.has(table.comp_id.value(i));
});
}
ComponentBond.chemCompBondFromTable = chemCompBondFromTable;
function getEntriesFromChemCompBond(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_1, atom_id_2, value_order, pdbx_aromatic_flag, _rowCount, pdbx_ordinal } = data;
let entry = addEntry(comp_id.value(0));
for (let i = 0; i < _rowCount; i++) {
const id = comp_id.value(i);
const nameA = atom_id_1.value(i);
const nameB = atom_id_2.value(i);
const order = value_order.value(i);
const aromatic = pdbx_aromatic_flag.value(i) === 'y';
const key = pdbx_ordinal.value(i);
if (entry.id !== id) {
entry = addEntry(id);
}
let flags = types_1.BondType.Flag.Covalent;
let ord = 1;
if (aromatic)
flags |= types_1.BondType.Flag.Aromatic;
switch (order.toLowerCase()) {
case 'delo':
flags |= types_1.BondType.Flag.Aromatic;
break;
case 'doub':
ord = 2;
break;
case 'trip':
ord = 3;
break;
case 'quad':
ord = 4;
break;
}
entry.add(nameA, nameB, ord, flags, key);
}
return entries;
}
ComponentBond.getEntriesFromChemCompBond = getEntriesFromChemCompBond;
class Entry {
add(a, b, order, flags, key, swap = true) {
const e = this.map.get(a);
if (e !== void 0) {
const f = e.get(b);
if (f === void 0) {
e.set(b, { order, flags, key });
}
}
else {
const map = new Map();
map.set(b, { order, flags, key });
this.map.set(a, map);
}
if (swap)
this.add(b, a, order, flags, key, false);
}
constructor(id) {
this.id = id;
this.map = new Map();
}
}
ComponentBond.Entry = Entry;
})(ComponentBond || (exports.ComponentBond = ComponentBond = {}));