molstar
Version:
A comprehensive macromolecular library.
133 lines (132 loc) • 6.36 kB
JavaScript
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/**
* Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.MolEncoder = void 0;
const mol_util_1 = require("../../../mol-util");
const util_1 = require("../cif/encoder/util");
const ligand_encoder_1 = require("../ligand-encoder");
// specification: http://c4.cabrillo.edu/404/ctfile.pdf
// SDF wraps MOL and allows for multiple molecules per file as well as additional properties
class MolEncoder extends ligand_encoder_1.LigandEncoder {
_writeCategory(category, context) {
// use separate builder because we still need to write Counts and Bonds line
const ctab = mol_util_1.StringBuilder.create();
const bonds = mol_util_1.StringBuilder.create();
// write Atom block and gather data for Bonds and Charges
const { instance, source } = (0, util_1.getCategoryInstanceData)(category, context);
// write header
const name = this.getName(instance, source);
// 3rd lines must be present and can contain comments
mol_util_1.StringBuilder.writeSafe(this.builder, `${name}\n ${this.encoder}\n\n`);
const atomMap = this.componentAtomData.entries.get(name);
const bondMap = this.componentBondData.entries.get(name);
// happens for the unknown ligands (UNL)
if (!atomMap)
throw Error(`The Chemical Component Dictionary doesn't hold any atom data for ${name}`);
let atomCount = 0;
let bondCount = 0;
let chiral = false;
// traverse once to determine all actually present atoms
const atoms = this.getAtoms(instance, source, atomMap.map);
atoms.forEach((atom1, label_atom_id1) => {
const { index: i1, type_symbol: type_symbol1 } = atom1;
const atomMapData1 = atomMap.map.get(label_atom_id1);
if (!atomMapData1) {
if (this.isHydrogen(type_symbol1)) {
return;
}
else {
throw Error(`Unknown atom ${label_atom_id1} for component ${name}`);
}
}
const { charge, stereo_config } = atomMapData1;
mol_util_1.StringBuilder.writePadLeft(ctab, atom1.Cartn_x.toFixed(4), 10);
mol_util_1.StringBuilder.writePadLeft(ctab, atom1.Cartn_y.toFixed(4), 10);
mol_util_1.StringBuilder.writePadLeft(ctab, atom1.Cartn_z.toFixed(4), 10);
mol_util_1.StringBuilder.whitespace1(ctab);
mol_util_1.StringBuilder.writePadRight(ctab, atom1.type_symbol, 2);
mol_util_1.StringBuilder.writeSafe(ctab, ' 0');
mol_util_1.StringBuilder.writeIntegerPadLeft(ctab, this.mapCharge(charge), 3);
mol_util_1.StringBuilder.writeSafe(ctab, ' 0 0 0 0 0 0 0 0 0 0\n');
atomCount++;
if (stereo_config !== 'n')
chiral = true;
// no data for metal ions
if (!(bondMap === null || bondMap === void 0 ? void 0 : bondMap.map))
return;
bondMap.map.get(label_atom_id1).forEach((bond, label_atom_id2) => {
const atom2 = atoms.get(label_atom_id2);
if (!atom2)
return;
const { index: i2 } = atom2;
if (i1 < i2) {
const { order } = bond;
mol_util_1.StringBuilder.writeIntegerPadLeft(bonds, i1 + 1, 3);
mol_util_1.StringBuilder.writeIntegerPadLeft(bonds, i2 + 1, 3);
mol_util_1.StringBuilder.writeIntegerPadLeft(bonds, order, 3);
mol_util_1.StringBuilder.writeSafe(bonds, ' 0 0 0 0\n');
bondCount++;
}
});
});
// write counts line
mol_util_1.StringBuilder.writeIntegerPadLeft(this.builder, atomCount, 3);
mol_util_1.StringBuilder.writeIntegerPadLeft(this.builder, bondCount, 3);
mol_util_1.StringBuilder.writeSafe(this.builder, ` 0 0 ${chiral ? 1 : 0} 0 0 0 0 0 0\n`);
mol_util_1.StringBuilder.writeSafe(this.builder, mol_util_1.StringBuilder.getString(ctab));
mol_util_1.StringBuilder.writeSafe(this.builder, mol_util_1.StringBuilder.getString(bonds));
mol_util_1.StringBuilder.writeSafe(this.builder, 'M END\n');
}
mapCharge(raw) {
// 0 = uncharged or value other than these, 1 = +3, 2 = +2, 3 = +1, 4 = doublet radical, 5 = -1, 6 = -2, 7 = -3
switch (raw) {
case 3: return 1;
case 2: return 2;
case 1: return 3;
case -1: return 5;
case -2: return 6;
case -3: return 7;
default: return 0;
}
}
writeFullCategory(sb, category, context) {
const { instance, source } = (0, util_1.getCategoryInstanceData)(category, context);
const fields = instance.fields;
const src = source[0];
if (!src)
return;
const data = src.data;
const it = src.keys();
const key = it.move();
for (let _f = 0; _f < fields.length; _f++) {
const f = fields[_f];
mol_util_1.StringBuilder.writeSafe(sb, `> <${category.name}.${f.name}>\n`);
const val = f.value(key, data, 0);
mol_util_1.StringBuilder.writeSafe(sb, val);
mol_util_1.StringBuilder.writeSafe(sb, '\n\n');
}
}
encode() {
// write meta-information, do so after ctab
if (this.error || this.metaInformation) {
mol_util_1.StringBuilder.writeSafe(this.builder, mol_util_1.StringBuilder.getString(this.meta));
}
// terminate file (needed for SDF only)
if (!!this.terminator) {
mol_util_1.StringBuilder.writeSafe(this.builder, `${this.terminator}\n`);
}
this.encoded = true;
}
constructor(encoder, metaInformation, hydrogens, terminator = '') {
super(encoder, metaInformation, hydrogens);
this.terminator = terminator;
if (metaInformation && !terminator) {
throw new Error('meta-information cannot be written for MOL files');
}
}
}
exports.MolEncoder = MolEncoder;