molstar
Version:
A comprehensive macromolecular library.
117 lines (116 loc) • 4.95 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>
*/
import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
import { CifWriter } from '../../../../mol-io/writer/cif';
import { Table } from '../../../../mol-data/db';
import { FormatPropertyProvider } from '../../common/property';
export var ComponentBond;
(function (ComponentBond) {
ComponentBond.Descriptor = {
name: 'chem_comp_bond',
cifExport: {
prefix: '',
categories: [{
name: 'chem_comp_bond',
instance: function (ctx) {
var p = ComponentBond.Provider.get(ctx.firstModel);
if (!p)
return CifWriter.Category.Empty;
var chem_comp_bond = p.data;
if (!chem_comp_bond)
return CifWriter.Category.Empty;
var comp_names = ctx.structures[0].uniqueResidueNames;
var comp_id = chem_comp_bond.comp_id, _rowCount = chem_comp_bond._rowCount;
var indices = [];
for (var i = 0; i < _rowCount; i++) {
if (comp_names.has(comp_id.value(i)))
indices[indices.length] = i;
}
return CifWriter.Category.ofTable(chem_comp_bond, indices);
}
}]
}
};
ComponentBond.Provider = FormatPropertyProvider.create(ComponentBond.Descriptor);
function chemCompBondFromTable(model, table) {
return Table.pick(table, mmCIF_Schema.chem_comp_bond, function (i) {
return model.properties.chemicalComponentMap.has(table.comp_id.value(i));
});
}
ComponentBond.chemCompBondFromTable = chemCompBondFromTable;
function getEntriesFromChemCompBond(data) {
var 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);
var e = new Entry(id);
entries.set(id, e);
return e;
}
var comp_id = data.comp_id, atom_id_1 = data.atom_id_1, atom_id_2 = data.atom_id_2, value_order = data.value_order, pdbx_aromatic_flag = data.pdbx_aromatic_flag, _rowCount = data._rowCount, pdbx_ordinal = data.pdbx_ordinal;
var entry = addEntry(comp_id.value(0));
for (var i = 0; i < _rowCount; i++) {
var id = comp_id.value(i);
var nameA = atom_id_1.value(i);
var nameB = atom_id_2.value(i);
var order = value_order.value(i);
var aromatic = pdbx_aromatic_flag.value(i) === 'y';
var key = pdbx_ordinal.value(i);
if (entry.id !== id) {
entry = addEntry(id);
}
var flags = 1 /* BondType.Flag.Covalent */;
var ord = 1;
if (aromatic)
flags |= 16 /* BondType.Flag.Aromatic */;
switch (order.toLowerCase()) {
case 'delo':
flags |= 16 /* 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;
var Entry = /** @class */ (function () {
function Entry(id) {
this.id = id;
this.map = new Map();
}
Entry.prototype.add = function (a, b, order, flags, key, swap) {
if (swap === void 0) { swap = true; }
var e = this.map.get(a);
if (e !== void 0) {
var f = e.get(b);
if (f === void 0) {
e.set(b, { order: order, flags: flags, key: key });
}
}
else {
var map = new Map();
map.set(b, { order: order, flags: flags, key: key });
this.map.set(a, map);
}
if (swap)
this.add(b, a, order, flags, key, false);
};
return Entry;
}());
ComponentBond.Entry = Entry;
})(ComponentBond || (ComponentBond = {}));