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@@ -9,10 +9,14 @@ import { LigandEncoder } from '../ligand-encoder';
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import { StringBuilder } from '../../../mol-util';
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import { getCategoryInstanceData } from '../cif/encoder/util';
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import { BondType } from '../../../mol-model/structure/model/types';
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+import { ComponentBond } from '../../../mol-model-formats/structure/property/bonds/chem_comp';
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+
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+// type MOL_TYPE = 'SMALL' | 'BIOPOLYMER' | 'PROTEIN' | 'NUCLEIC_ACID' | 'SACCHARIDE';
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+// type CHARGE_TYPE = 'NO_CHARGES' | 'DEL_RE' | 'GASTEIGER' | 'GAST_HUCK' | 'HUCKEL' | 'PULLMAN' | 'GAUSS80_CHARGES' | 'AMPAC_CHARGES' | 'MULLIKEN_CHARGES' | 'DICT_ CHARGES' | 'MMFF94_CHARGES' | 'USER_CHARGES';
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+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(' ');
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+type BondMap = Map<string, { order: number, flags: number }>;
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// specification: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
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-// TODO amide (and real sp/sp2/sp3) support for bonds and SYBYL atom types: see https://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html
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-// TODO support charges
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export class Mol2Encoder extends LigandEncoder {
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private out: StringBuilder;
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@@ -25,36 +29,258 @@ export class Mol2Encoder extends LigandEncoder {
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const name = this.getName(instance, source);
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StringBuilder.writeSafe(this.builder, `# Name: ${name}\n# Created by ${this.encoder}\n\n`);
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- const bondMap = this.componentData.entries.get(name)!;
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+ const bondMap = this.componentBondData.entries.get(name)!;
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let bondCount = 0;
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const atoms = this.getAtoms(instance, source);
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StringBuilder.writeSafe(a, '@<TRIPOS>ATOM\n');
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StringBuilder.writeSafe(b, '@<TRIPOS>BOND\n');
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- for (let i1 = 0, il = atoms.length; i1 < il; i1++) {
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- const atom = atoms[i1];
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-
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- let aromatic = false;
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- bondMap.map.get(atom.label_atom_id)!.forEach((v, k) => {
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- const i2 = atoms.findIndex(e => e.label_atom_id === k);
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- const label2 = this.getLabel(k);
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- if (i1 < i2 && atoms.findIndex(e => e.label_atom_id === k) > -1 && !this.skipHydrogen(label2)) {
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- const { order, flags } = v;
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- const ar = flags === BondType.Flag.Aromatic;
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- if (ar) aromatic = true;
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+ atoms.forEach((atom1, label_atom_id1) => {
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+ const { index: i1 } = atom1;
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+ bondMap.map.get(label_atom_id1)!.forEach((bond, label_atom_id2) => {
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+ const atom2 = atoms.get(label_atom_id2);
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+ if (!atom2) return;
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+
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+ const { index: i2, type_symbol: type_symbol2 } = atom2;
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+ if (i1 < i2 && !this.skipHydrogen(type_symbol2)) {
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+ const { order, flags } = bond;
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+ const ar = BondType.is(BondType.Flag.Aromatic, flags);
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StringBuilder.writeSafe(b, `${++bondCount} ${i1 + 1} ${i2 + 1} ${ar ? 'ar' : order}`);
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StringBuilder.newline(b);
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}
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});
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- const sub = aromatic ? '.ar' : '';
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- StringBuilder.writeSafe(a, `${i1 + 1} ${atom.type_symbol} ${atom.Cartn_x.toFixed(3)} ${atom.Cartn_y.toFixed(3)} ${atom.Cartn_z.toFixed(3)} ${atom.type_symbol}${sub} 1 ${name} 0.000\n`);
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- }
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+ const sybyl = this.mapToSybyl(label_atom_id1, atom1.type_symbol, bondMap);
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+ StringBuilder.writeSafe(a, `${i1 + 1} ${label_atom_id1} ${atom1.Cartn_x.toFixed(3)} ${atom1.Cartn_y.toFixed(3)} ${atom1.Cartn_z.toFixed(3)} ${sybyl} 1 ${name} 0.000\n`);
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+ });
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- StringBuilder.writeSafe(this.out, `@<TRIPOS>MOLECULE\n${name}\n${atoms.length} ${bondCount} 0 0 0\nSMALL\nNO_CHARGES\n\n`);
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+ // could write something like 'SMALL\nNO_CHARGES', for now let's write **** indicating non-optional, yet missing, string values
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+ StringBuilder.writeSafe(this.out, `@<TRIPOS>MOLECULE\n${name}\n${atoms.size} ${bondCount} 1\n****\n****\n\n`);
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StringBuilder.writeSafe(this.out, StringBuilder.getString(a));
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StringBuilder.writeSafe(this.out, StringBuilder.getString(b));
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- StringBuilder.writeSafe(this.out, `@<TRIPOS>SUBSTRUCTURE\n${name} ${name} 1\n`);
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+ StringBuilder.writeSafe(this.out, `@<TRIPOS>SUBSTRUCTURE\n1 ${name} 1\n`);
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+ }
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+
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+ private count<K, V, C>(map: Map<K, V>, ctx: C, predicate: (k: K, v: V, ctx: C) => boolean): number {
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+ let count = 0;
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+ const iter = map.entries();
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+ let result = iter.next();
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+ while (!result.done) {
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+ if (predicate(result.value[0], result.value[1], ctx)) {
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+ count++;
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+ }
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+ result = iter.next();
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+ }
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+ return count;
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+ }
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+
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+ private orderSum(map: BondMap): number {
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+ let sum = 0;
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+ const iter = map.values();
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+ let result = iter.next();
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+ while (!result.done) {
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+ sum += result.value.order;
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+ result = iter.next();
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+ }
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+ return sum;
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+ }
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+
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+ private isNonMetalBond(label_atom_id: string): boolean {
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+ for (const a of NON_METAL_ATOMS) {
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+ if (label_atom_id.startsWith(a)) return true;
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+ }
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+ return false;
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+ }
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+
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+ private extractNonmets(map: BondMap): BondMap {
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+ const ret = new Map<string, { order: number, flags: number }>();
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+ const iter = map.entries();
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+ let result = iter.next();
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+ while (!result.done) {
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+ const [k, v] = result.value;
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+ if (this.isNonMetalBond(k)) {
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+ ret.set(k, v);
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+ }
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+ result = iter.next();
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+ }
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+ return ret;
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+ }
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+
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+ // see https://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html
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+ // cannot account for covalently bound amino acids etc
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+ private mapToSybyl(label_atom_id1: string, type_symbol1: string, bondMap: ComponentBond.Entry) {
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+ // TODO if altLoc: 'Du' // 1.1
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+ // TODO if end of polymeric bond: 'Du' // 1.2
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+ if (type_symbol1 === 'D') return 'H'; // 1.3
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+ if (type_symbol1 === 'P') return 'P.3'; // 1.4, 4mpo/ligand?encoding=mol2&auth_seq_id=203 (PO4)
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+ if (type_symbol1 === 'Co' || type_symbol1 === 'Ru') return type_symbol1 + '.oh'; // 1.5
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+
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+ const bonds = bondMap.map.get(label_atom_id1)!;
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+ const numBonds = bonds.size;
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+
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+ if (type_symbol1 === 'Ti' || type_symbol1 === 'Cr') { // 1.10
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+ return type_symbol1 + (numBonds <= 4 ? '.th' : '.oh'); // 1.10.1 & 1.10.2
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+ }
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+ if (type_symbol1 === 'C') { // 1.6
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+ 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)
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+ 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)
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+ if (numBonds >= 2 && this.count(bonds, this, (_k, v) => BondType.is(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)
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+ 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)
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+ return 'C.2'; // 1.6.5
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+ }
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+
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+ // most of the time, bonds will equal non-metal bonds
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+ const nonmets = this.count(bonds, this, (k, _v, ctx) => ctx.isNonMetalBond(k)) === bonds.size ? bonds : this.extractNonmets(bonds);
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+ const numNonmets = nonmets.size;
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+
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+ if (type_symbol1 === 'O') { // 1.7
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+ if (numNonmets === 1) { // 1.7.1
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+ if (this.isOC(nonmets, bondMap)) return 'O.co2'; // 1.7.1.1, 4h2v/ligand?encoding=mol2&auth_seq_id=403 (ACT)
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+ if (this.isOP(nonmets, bondMap)) return 'O.co2'; // 1.7.1.2, 4mpo/ligand?encoding=mol2&auth_seq_id=203 (PO4)
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+ }
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+ 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)
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+ return 'O.2'; // 1.7.3, 1acj/ligand?encoding=mol2&auth_seq_id=4 (SER)
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+ }
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+ if (type_symbol1 === 'N') { // 1.8
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+ 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)
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+ if (numBonds >= 2 && this.count(bonds, this, (_k, v) => BondType.is(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)
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+ 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)
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+ 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)
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+ if (numNonmets === 3 && this.hasCOCS(nonmets, bondMap)) return 'N.am'; // 1.8.5, 3zfz/ligand?encoding=mol2&auth_seq_id=1669 (1W8)
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+ if (numNonmets === 3) { // 1.8.6
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+ 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)
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+ if (this.count(nonmets, this, (_k, v) => v.order === 1) === 3) {
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+ 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)
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+ }
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+ return 'N.3';
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+ }
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+ return 'N.2'; // 1.8.7, 1acj/ligand?encoding=mol2&auth_seq_id=4 (SER)
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+ }
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+ if (type_symbol1 === 'S') { // 1.9
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+ if (numNonmets === 3 && this.countOfOxygenWithSingleNonmet(nonmets, bondMap) === 1) return 'S.o'; // 1.9.1, 4i03/ligand?encoding=mol2&auth_seq_id=312 (DMS)
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+ if (numNonmets === 4 && this.countOfOxygenWithSingleNonmet(nonmets, bondMap) === 2) return 'S.o2'; // 1.9.2, 1udt/ligand?encoding=mol2&auth_seq_id=1000 (VIA)
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+ 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)
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+ return 'S.2'; // 1.9.4
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+ }
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+ return type_symbol1; // 1.11
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+ }
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+
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+ // 1.8.6.2.1: If one single bond is to an atom that forms a bond of type double, triple, aromatic or
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+ // delocalised .AND. one other single bond is to H then atom_type is N.pl3
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+ // 1.8.6.2.2: If one single bond is to an atom that forms a bond of type double, triple, aromatic or
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+ // 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
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+ // TODO cannot check accurately for delocalized bonds
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+ private isNpl3(nonmets: BondMap, bondMap: ComponentBond.Entry): boolean {
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+ const iter = nonmets.keys();
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+ let result = iter.next();
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+ while (!result.done) {
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+ const label_atom_id = result.value;
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+ const adjacentBonds = bondMap.map.get(label_atom_id)!;
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+ if (this.count(adjacentBonds, this, (_k, v) => v.order > 1 || BondType.is(BondType.Flag.Aromatic, v.flags))) {
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+ // TODO check accurately for 2nd criterion with coordinates
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+ return true;
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+ }
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+ result = iter.next();
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+ }
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+ return false;
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+ }
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+
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+ // If bond is to carbon .AND. carbon forms a total of 3 bonds, 2 of which are to an oxygen
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+ // forming only 1 non-metal bond then atom_type is O.co2
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+ private isOC(nonmets: BondMap, bondMap: ComponentBond.Entry): boolean {
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+ const nonmet = nonmets.entries().next()!.value as [string, { order: number, flags: number }];
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+ if (!nonmet[0].startsWith('C')) return false;
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+ const carbonBonds = bondMap.map.get(nonmet[0])!;
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+ if (carbonBonds.size !== 3) return false;
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+
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+ let count = 0;
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+ const iter = carbonBonds.keys();
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+ let result = iter.next();
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+ while (!result.done) {
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+ const label_atom_id = result.value;
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+ if (label_atom_id.startsWith('O')) {
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+ const adjacentBonds = bondMap.map.get(label_atom_id)!;
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+ if (this.count(adjacentBonds, this, (k, _v, ctx) => ctx.isNonMetalBond(k)) === 1) count++;
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+ }
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+ result = iter.next();
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+ }
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+ return count === 2;
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+ }
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+
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+ // If bond is to phosphorus .AND. phosphorus forms at least 2 bonds to an oxygen forming
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+ // only 1 non-metal bond then atom_type is O.co2
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+ private isOP(nonmets: BondMap, bondMap: ComponentBond.Entry): boolean {
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+ const nonmet = nonmets.entries().next()!.value as [string, { order: number, flags: number }];
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+ if (!nonmet[0].startsWith('P')) return false;
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+ const phosphorusBonds = bondMap.map.get(nonmet[0])!;
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+ if (phosphorusBonds.size < 2) return false;
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+
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+ let count = 0;
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+ const iter = phosphorusBonds.keys();
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+ let result = iter.next();
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+ while (!result.done) {
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+ const label_atom_id = result.value;
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+ if (label_atom_id.startsWith('O')) {
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+ const adjacentBonds = bondMap.map.get(label_atom_id)!;
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+ if (this.count(adjacentBonds, this, (k, _v, ctx) => ctx.isNonMetalBond(k)) === 1) count++;
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+ }
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+ result = iter.next();
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+ }
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+ return count >= 2;
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+ }
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+
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+ // If num_bond .eq. 3 .AND. all bonds are acyclic .AND. all bonds are to nitrogen .AND. each
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+ // nitrogen forms bonds to 2 other atoms both of which are not oxygen then atom_type is C.cat.
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+ private isCat(currentBondMap: BondMap, bondMap: ComponentBond.Entry): boolean {
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+ const iter1 = currentBondMap.keys();
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+ let result1 = iter1.next();
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+ while (!result1.done) {
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+ const label_atom_id = result1.value;
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+ if (!label_atom_id.startsWith('N')) return false;
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+
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+ const adjacentBonds = bondMap.map.get(label_atom_id)!;
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+ if (adjacentBonds.size < 2) return false;
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+
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+ const iter2 = adjacentBonds.keys();
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+ let result2 = iter2.next();
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+ while (!result2.done) {
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+ if (result2.value.startsWith('O')) return false;
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+ result2 = iter2.next();
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+ }
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+ result1 = iter1.next();
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+ }
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+ // TODO ensure no cycles
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+ return true;
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+ }
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+
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+ private countOfOxygenWithSingleNonmet(nonmets: BondMap, bondMap: ComponentBond.Entry): number {
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+ let count = 0;
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+ const iter = nonmets.keys();
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+ let result = iter.next();
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+ while (!result.done) {
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+ const label_atom_id = result.value;
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+ if (label_atom_id.startsWith('O')) {
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+ const adjacentBonds = bondMap.map.get(label_atom_id)!;
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+ if (this.count(adjacentBonds, this, (k, _v, ctx) => ctx.isNonMetalBond(k))) count++;
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+ }
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+ result = iter.next();
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+ }
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+ return count;
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+ }
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+
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+ // If num_nonmet .eq. 3 .AND. one bond is to C=O or C=S then atom_type is N.am
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+ private hasCOCS(nonmets: BondMap, bondMap: ComponentBond.Entry): boolean {
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+ const iter = nonmets.keys();
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+ let result = iter.next();
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+ 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;
|
|
|
}
|
|
|
|
|
|
protected writeFullCategory<Ctx>(sb: StringBuilder, category: Category<Ctx>, context?: Ctx) {
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David Sehnal