molstar
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A comprehensive macromolecular library.
337 lines (336 loc) • 17 kB
JavaScript
;
/**
* 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.Mol2Encoder = void 0;
const ligand_encoder_1 = require("../ligand-encoder");
const mol_util_1 = require("../../../mol-util");
const util_1 = require("../cif/encoder/util");
const types_1 = require("../../../mol-model/structure/model/types");
// type MOL_TYPE = 'SMALL' | 'BIOPOLYMER' | 'PROTEIN' | 'NUCLEIC_ACID' | 'SACCHARIDE';
// type CHARGE_TYPE = 'NO_CHARGES' | 'DEL_RE' | 'GASTEIGER' | 'GAST_HUCK' | 'HUCKEL' | 'PULLMAN' | 'GAUSS80_CHARGES' | 'AMPAC_CHARGES' | 'MULLIKEN_CHARGES' | 'DICT_ CHARGES' | 'MMFF94_CHARGES' | 'USER_CHARGES';
const NON_METAL_ATOMS = 'H D B C N O F Si P S Cl As Se Br Te I At He Ne Ar Kr Xe Rn'.split(' ');
// specification: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
class Mol2Encoder extends ligand_encoder_1.LigandEncoder {
_writeCategory(category, context) {
const a = mol_util_1.StringBuilder.create();
const b = mol_util_1.StringBuilder.create();
const { instance, source } = (0, util_1.getCategoryInstanceData)(category, context);
// write header
const name = this.getName(instance, source);
mol_util_1.StringBuilder.writeSafe(this.builder, `# Name: ${name}\n# Created by ${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;
const atoms = this.getAtoms(instance, source, atomMap.map);
mol_util_1.StringBuilder.writeSafe(a, '@<TRIPOS>ATOM\n');
mol_util_1.StringBuilder.writeSafe(b, '@<TRIPOS>BOND\n');
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 ${name}`);
}
}
if (bondMap === null || bondMap === void 0 ? void 0 : bondMap.map) {
bondMap.map.get(label_atom_id1).forEach((bond, label_atom_id2) => {
const atom2 = atoms.get(label_atom_id2);
if (!atom2)
return;
const { index: i2 } = atom2;
if (i1 < i2) {
const { order, flags } = bond;
const ar = types_1.BondType.is(types_1.BondType.Flag.Aromatic, flags);
mol_util_1.StringBuilder.writeSafe(b, `${++bondCount} ${i1 + 1} ${i2 + 1} ${ar ? 'ar' : order}`);
mol_util_1.StringBuilder.newline(b);
}
});
}
const sybyl = (bondMap === null || bondMap === void 0 ? void 0 : bondMap.map) ? this.mapToSybyl(label_atom_id1, type_symbol1, bondMap) : type_symbol1;
mol_util_1.StringBuilder.writeSafe(a, `${i1 + 1} ${label_atom_id1} ${atom1.Cartn_x.toFixed(3)} ${atom1.Cartn_y.toFixed(3)} ${atom1.Cartn_z.toFixed(3)} ${sybyl} 1 ${name} 0.000\n`);
atomCount++;
});
// could write something like 'SMALL\nNO_CHARGES', for now let's write **** indicating non-optional, yet missing, string values
mol_util_1.StringBuilder.writeSafe(this.out, `@<TRIPOS>MOLECULE\n${name}\n${atomCount} ${bondCount} 1\n****\n****\n\n`);
mol_util_1.StringBuilder.writeSafe(this.out, mol_util_1.StringBuilder.getString(a));
mol_util_1.StringBuilder.writeSafe(this.out, mol_util_1.StringBuilder.getString(b));
mol_util_1.StringBuilder.writeSafe(this.out, `@<TRIPOS>SUBSTRUCTURE\n1 ${name} 1\n`);
}
count(map, ctx, predicate) {
let count = 0;
const iter = map.entries();
let result = iter.next();
while (!result.done) {
if (predicate(result.value[0], result.value[1], ctx)) {
count++;
}
result = iter.next();
}
return count;
}
orderSum(map) {
let sum = 0;
const iter = map.values();
let result = iter.next();
while (!result.done) {
sum += result.value.order;
result = iter.next();
}
return sum;
}
isNonMetalBond(label_atom_id) {
for (const a of NON_METAL_ATOMS) {
if (label_atom_id.startsWith(a))
return true;
}
return false;
}
extractNonmets(map) {
const ret = new Map();
const iter = map.entries();
let result = iter.next();
while (!result.done) {
const [k, v] = result.value;
if (this.isNonMetalBond(k)) {
ret.set(k, v);
}
result = iter.next();
}
return ret;
}
// see https://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html
// cannot account for covalently bound amino acids etc
mapToSybyl(label_atom_id1, type_symbol1, bondMap) {
// TODO if altLoc: 'Du' // 1.1
// TODO if end of polymeric bond: 'Du' // 1.2
if (type_symbol1 === 'D')
return 'H'; // 1.3
if (type_symbol1 === 'P')
return 'P.3'; // 1.4, 4mpo/ligand?encoding=mol2&auth_seq_id=203 (PO4)
if (type_symbol1 === 'Co' || type_symbol1 === 'Ru')
return type_symbol1 + '.oh'; // 1.5
const bonds = bondMap.map.get(label_atom_id1);
const numBonds = bonds.size;
if (type_symbol1 === 'Ti' || type_symbol1 === 'Cr') { // 1.10
return type_symbol1 + (numBonds <= 4 ? '.th' : '.oh'); // 1.10.1 & 1.10.2
}
if (type_symbol1 === 'C') { // 1.6
if (numBonds >= 4 && this.count(bonds, this, (_k, v) => v.order === 1) >= 4)
return 'C.3'; // 1.6.1, 3rga/ligand?encoding=mol2&auth_seq_id=307 (MOH)
if (numBonds === 3 && this.isCat(bonds, bondMap))
return 'C.cat'; // 1.6.2, 1acj/ligand?encoding=mol2&auth_seq_id=44 (ARG), 5vjb/ligand?encoding=mol2&auth_seq_id=101 (GAI)
if (numBonds >= 2 && this.count(bonds, this, (_k, v) => types_1.BondType.is(types_1.BondType.Flag.Aromatic, v.flags)) >= 2)
return 'C.ar'; // 1.6.3, 1acj/ligand?encoding=mol2&auth_seq_id=30 (PHE), 1acj/ligand?encoding=mol2&auth_seq_id=63 (TYR), 1acj/ligand?encoding=mol2&auth_seq_id=84 (TRP), 1acj/ligand?encoding=mol2&auth_seq_id=999 (THA)
if ((numBonds === 1 || numBonds === 2) && this.count(bonds, this, (_k, v) => v.order === 3))
return 'C.1'; // 1.6.4, 3i04/ligand?encoding=mol2&auth_asym_id=C&auth_seq_id=900 (CYN)
return 'C.2'; // 1.6.5
}
// most of the time, bonds will equal non-metal bonds
const nonmets = this.count(bonds, this, (k, _v, ctx) => ctx.isNonMetalBond(k)) === bonds.size ? bonds : this.extractNonmets(bonds);
const numNonmets = nonmets.size;
if (type_symbol1 === 'O') { // 1.7
if (numNonmets === 1) { // 1.7.1
if (this.isOC(nonmets, bondMap))
return 'O.co2'; // 1.7.1.1, 4h2v/ligand?encoding=mol2&auth_seq_id=403 (ACT)
if (this.isOP(nonmets, bondMap))
return 'O.co2'; // 1.7.1.2, 4mpo/ligand?encoding=mol2&auth_seq_id=203 (PO4)
}
if (numNonmets >= 2 && this.count(bonds, this, (_k, v) => v.order === 1) === bonds.size)
return 'O.3'; // 1.7.2, 1acj/ligand?encoding=mol2&auth_seq_id=601 (HOH), 3rga/ligand?encoding=mol2&auth_seq_id=307 (MOH)
return 'O.2'; // 1.7.3, 1acj/ligand?encoding=mol2&auth_seq_id=4 (SER)
}
if (type_symbol1 === 'N') { // 1.8
if (numNonmets === 4 && this.count(nonmets, this, (_k, v) => v.order === 1) === 4)
return 'N.4'; // 1.8.1, 4ikf/ligand?encoding=mol2&auth_seq_id=403 (NH4)
if (numBonds >= 2 && this.count(bonds, this, (_k, v) => types_1.BondType.is(types_1.BondType.Flag.Aromatic, v.flags)) >= 2)
return 'N.ar'; // 1.8.2, 1acj/ligand?encoding=mol2&auth_seq_id=84 (TRP), 1acj/ligand?encoding=mol2&auth_seq_id=999 (THA)
if (numNonmets === 1 && this.count(nonmets, this, (_k, v) => v.order === 3))
return 'N.1'; // 1.8.3, 3i04/ligand?encoding=mol2&auth_asym_id=C&auth_seq_id=900 (CYN)
if (numNonmets === 2 && this.orderSum(nonmets) === 4)
return 'N.1'; // 1.8.4, 3sbr/ligand?encoding=mol2&auth_seq_id=640&auth_asym_id=D (N2O)
if (numNonmets === 3 && this.hasCOCS(nonmets, bondMap))
return 'N.am'; // 1.8.5, 3zfz/ligand?encoding=mol2&auth_seq_id=1669 (1W8)
if (numNonmets === 3) { // 1.8.6
if (this.count(nonmets, this, (_k, v) => v.order > 1) === 1)
return 'N.pl3'; // 1.8.6.1, 4hon/ligand?encoding=mol2&auth_seq_id=407 (NO3)
if (this.count(nonmets, this, (_k, v) => v.order === 1) === 3) {
if (this.isNpl3(nonmets, bondMap))
return 'N.pl3'; // 1.8.6.1.1 & 1.8.6.1.2, 1acj/ligand?encoding=mol2&auth_seq_id=44 (ARG), 5vjb/ligand?encoding=mol2&auth_seq_id=101 (GAI)
}
return 'N.3';
}
return 'N.2'; // 1.8.7, 1acj/ligand?encoding=mol2&auth_seq_id=4 (SER)
}
if (type_symbol1 === 'S') { // 1.9
if (numNonmets === 3 && this.countOfOxygenWithSingleNonmet(nonmets, bondMap) === 1)
return 'S.o'; // 1.9.1, 4i03/ligand?encoding=mol2&auth_seq_id=312 (DMS)
if (numNonmets === 4 && this.countOfOxygenWithSingleNonmet(nonmets, bondMap) === 2)
return 'S.o2'; // 1.9.2, 1udt/ligand?encoding=mol2&auth_seq_id=1000 (VIA)
if (numNonmets >= 2 && this.count(bonds, this, (_k, v) => v.order === 1) >= 2)
return 'S.3'; // 1.9.3, 3zfz/ligand?encoding=mol2&auth_seq_id=1669 (1W8), 4gpc/ligand?encoding=mol2&auth_seq_id=902 (SO4)
return 'S.2'; // 1.9.4
}
return type_symbol1; // 1.11
}
// 1.8.6.2.1: If one single bond is to an atom that forms a bond of type double, triple, aromatic or
// delocalised .AND. one other single bond is to H then atom_type is N.pl3
// 1.8.6.2.2: If one single bond is to an atom that forms a bond of type double, triple, aromatic or
// delocalised .AND. neither of the other single bonds are to H .AND. sum_of_angles around N .ge. 350 deg then atom_type is N.pl3
// TODO cannot check accurately for delocalized bonds
isNpl3(nonmets, bondMap) {
const iter = nonmets.keys();
let result = iter.next();
while (!result.done) {
const label_atom_id = result.value;
const adjacentBonds = bondMap.map.get(label_atom_id);
if (this.count(adjacentBonds, this, (_k, v) => v.order > 1 || types_1.BondType.is(types_1.BondType.Flag.Aromatic, v.flags))) {
// TODO check accurately for 2nd criterion with coordinates
return true;
}
result = iter.next();
}
return false;
}
// If bond is to carbon .AND. carbon forms a total of 3 bonds, 2 of which are to an oxygen
// forming only 1 non-metal bond then atom_type is O.co2
isOC(nonmets, bondMap) {
const nonmet = nonmets.entries().next().value;
if (!nonmet[0].startsWith('C'))
return false;
const carbonBonds = bondMap.map.get(nonmet[0]);
if (carbonBonds.size !== 3)
return false;
let count = 0;
const iter = carbonBonds.keys();
let result = iter.next();
while (!result.done) {
const label_atom_id = result.value;
if (label_atom_id.startsWith('O')) {
const adjacentBonds = bondMap.map.get(label_atom_id);
if (this.count(adjacentBonds, this, (k, _v, ctx) => ctx.isNonMetalBond(k)) === 1)
count++;
}
result = iter.next();
}
return count === 2;
}
// If bond is to phosphorus .AND. phosphorus forms at least 2 bonds to an oxygen forming
// only 1 non-metal bond then atom_type is O.co2
isOP(nonmets, bondMap) {
const nonmet = nonmets.entries().next().value;
if (!nonmet[0].startsWith('P'))
return false;
const phosphorusBonds = bondMap.map.get(nonmet[0]);
if (phosphorusBonds.size < 2)
return false;
let count = 0;
const iter = phosphorusBonds.keys();
let result = iter.next();
while (!result.done) {
const label_atom_id = result.value;
if (label_atom_id.startsWith('O')) {
const adjacentBonds = bondMap.map.get(label_atom_id);
if (this.count(adjacentBonds, this, (k, _v, ctx) => ctx.isNonMetalBond(k)) === 1)
count++;
}
result = iter.next();
}
return count >= 2;
}
// If num_bond .eq. 3 .AND. all bonds are acyclic .AND. all bonds are to nitrogen .AND. each
// nitrogen forms bonds to 2 other atoms both of which are not oxygen then atom_type is C.cat.
isCat(currentBondMap, bondMap) {
const iter1 = currentBondMap.keys();
let result1 = iter1.next();
while (!result1.done) {
const label_atom_id = result1.value;
if (!label_atom_id.startsWith('N'))
return false;
const adjacentBonds = bondMap.map.get(label_atom_id);
if (adjacentBonds.size < 2)
return false;
const iter2 = adjacentBonds.keys();
let result2 = iter2.next();
while (!result2.done) {
if (result2.value.startsWith('O'))
return false;
result2 = iter2.next();
}
result1 = iter1.next();
}
// TODO ensure no cycles
return true;
}
countOfOxygenWithSingleNonmet(nonmets, bondMap) {
let count = 0;
const iter = nonmets.keys();
let result = iter.next();
while (!result.done) {
const label_atom_id = result.value;
if (label_atom_id.startsWith('O')) {
const adjacentBonds = bondMap.map.get(label_atom_id);
if (this.count(adjacentBonds, this, (k, _v, ctx) => ctx.isNonMetalBond(k)))
count++;
}
result = iter.next();
}
return count;
}
// If num_nonmet .eq. 3 .AND. one bond is to C=O or C=S then atom_type is N.am
hasCOCS(nonmets, bondMap) {
const iter = nonmets.keys();
let result = iter.next();
while (!result.done) {
const label_atom_id = result.value;
if (label_atom_id.startsWith('C')) {
const adjacentBonds = bondMap.map.get(label_atom_id);
if (this.count(adjacentBonds, this, (k, v) => k.startsWith('O') || k.startsWith('S') && v.order === 2))
return true;
}
result = iter.next();
}
return false;
}
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}: `);
const val = f.value(key, data, 0);
mol_util_1.StringBuilder.writeSafe(sb, val);
mol_util_1.StringBuilder.newline(sb);
}
mol_util_1.StringBuilder.newline(sb);
}
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));
}
mol_util_1.StringBuilder.writeSafe(this.builder, mol_util_1.StringBuilder.getString(this.out));
this.encoded = true;
}
constructor(encoder, metaInformation, hydrogens) {
super(encoder, metaInformation, hydrogens);
this.out = mol_util_1.StringBuilder.create();
}
}
exports.Mol2Encoder = Mol2Encoder;