diff --git a/src/mol-io/writer/mol2/encoder.ts b/src/mol-io/writer/mol2/encoder.ts
index 936a496eab289580b4a48296bd0f2f9b6213d7bf..a5c5eccf1af8adbeb1e1fd8ba85ea741f781ed05 100644
--- a/src/mol-io/writer/mol2/encoder.ts
+++ b/src/mol-io/writer/mol2/encoder.ts
@@ -9,12 +9,12 @@ import { LigandEncoder } from '../ligand-encoder';
import { StringBuilder } from '../../../mol-util';
import { getCategoryInstanceData } from '../cif/encoder/util';
import { BondType } from '../../../mol-model/structure/model/types';
-// import { ComponentBond } from '../../../mol-model-formats/structure/property/bonds/comp';
+import { ComponentBond } from '../../../mol-model-formats/structure/property/bonds/comp';
-// // 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(' ');
-// type BondData = { label_atom_id: string, order: number, aromatic: boolean };
+// 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(' ');
+type BondMap = Map<string, { order: number, flags: number }>;
// specification: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
export class Mol2Encoder extends LigandEncoder {
@@ -50,8 +50,7 @@ export class Mol2Encoder extends LigandEncoder {
}
});
- // const sybyl = this.mapToSybyl(label_atom_id1, atom1.type_symbol, bondMap);
- const sybyl = '?';
+ const sybyl = this.mapToSybyl(label_atom_id1, atom1.type_symbol, bondMap);
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`);
});
@@ -62,146 +61,224 @@ export class Mol2Encoder extends LigandEncoder {
StringBuilder.writeSafe(this.out, `@<TRIPOS>SUBSTRUCTURE\n1 ${name} 1\n`);
}
- // private toArray(map: Map<string, { order: number, flags: number }>): BondData[] {
- // const array: BondData[] = [];
- // map.forEach((v, k) => array.push({ label_atom_id: k, order: v.order, aromatic: BondType.is(BondType.Flag.Aromatic, v.flags) }));
- // return array;
- // }
+ private count<K, V>(map: Map<K, V>, predicate: (k: K, v: V) => boolean): number {
+ let count = 0;
+ const iter = map.entries();
+ let result = iter.next();
+ while (!result.done) {
+ if (predicate(result.value[0], result.value[1])) {
+ count++;
+ }
+ result = iter.next();
+ }
+ return count;
+ }
+
+ private orderSum(map: BondMap): number {
+ let sum = 0;
+ const iter = map.values();
+ let result = iter.next();
+ while (!result.done) {
+ sum += result.value.order;
+ result = iter.next();
+ }
+ return sum;
+ }
+
+ private isNonMetalBond(label_atom_id: string): boolean {
+ return NON_METAL_ATOMS.some(a => label_atom_id.startsWith(a));
+ }
+
+ private extractNonmets(map: BondMap): BondMap {
+ const ret = new Map<string, { order: number, flags: number }>();
+ const iter = map.entries();
+ let result = iter.next();
+ while (!result.done) {
+ const [k, v] = result.value;
+ if (NON_METAL_ATOMS.some(a => k.startsWith(a))) {
+ 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
- // private mapToSybyl(label_atom_id: string, type_symbol: string, bondMap: ComponentBond.Entry) {
- // const partialBondMap = bondMap.map.get(label_atom_id)!;
- // const bond = this.toArray(partialBondMap);
-
- // const num_bond = bond.length;
- // const nonmet = bond.filter(b => this.isNonMetalBond(b));
- // const num_nonmet = nonmet.length;
- // const arom = bond.filter(e => e.aromatic);
- // const num_arom = arom.length;
-
- // // TODO if altLoc: 'Du' // 1.1
- // // TODO if end of polymeric bond: 'Du' // 1.2
- // if (type_symbol === 'D') return 'H'; // 1.3
- // if (type_symbol === 'P') return 'P.3'; // 1.4, 4mpo/ligand?encoding=mol2&auth_seq_id=203 (PO4)
- // if (type_symbol === 'Co' || type_symbol === 'Ru') return type_symbol + '.oh'; // 1.5
- // if (type_symbol === 'C') { // 1.6
- // if (num_bond >= 4 && bond.every(b => b.order === 1)) return 'C.3'; // 1.6.1, 3rga/ligand?encoding=mol2&auth_seq_id=307 (MOH)
- // if (num_bond === 3 && this.isCat(label_atom_id, bond, 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 (num_bond >= 2 && num_arom >= 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 ((num_bond === 1 || num_bond === 2) && bond.filter(b => b.order === 3).length === 1) 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
- // }
- // if (type_symbol === 'O') { // 1.7
- // if (num_nonmet === 1) { // 1.7.1
- // if (this.isOC(nonmet[0], bondMap)) return 'O.co2'; // 1.7.1.1, 4h2v/ligand?encoding=mol2&auth_seq_id=403 (ACT)
- // if (this.isOP(nonmet[0], bondMap)) return 'O.co2'; // 1.7.1.2, 4mpo/ligand?encoding=mol2&auth_seq_id=203 (PO4)
- // }
- // if (num_nonmet >= 2 && bond.every(b => b.order === 1)) 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_symbol === 'N') { // 1.8
- // if (num_nonmet === 4 && bond.every(b => b.order === 1)) return 'N.4'; // 1.8.1, 4ikf/ligand?encoding=mol2&auth_seq_id=403 (NH4)
- // if (num_bond >= 2 && num_arom === 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 (num_nonmet === 1 && nonmet.some(b => b.order === 3)) return 'N.1'; // 1.8.3, 3i04/ligand?encoding=mol2&auth_asym_id=C&auth_seq_id=900 (CYN)
- // if (num_nonmet === 2 && (nonmet[0].order + nonmet[1].order === 4)) return 'N.1'; // 1.8.4, 3sbr/ligand?encoding=mol2&auth_seq_id=640&auth_asym_id=D (N2O)
- // if (num_nonmet === 3 && this.hasCOCS(nonmet, bondMap)) return 'N.am'; // 1.8.5, 3zfz/ligand?encoding=mol2&auth_seq_id=1669 (1W8)
- // if (num_nonmet === 3) { // 1.8.6
- // if (nonmet.filter(b => b.order > 1).length === 1) return 'N.pl3'; // 1.8.6.1, 4hon/ligand?encoding=mol2&auth_seq_id=407 (NO3)
- // if (nonmet.every(b => b.order === 1)) {
- // if (this.isNpl3(nonmet, 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_symbol === 'S') { // 1.9
- // if (num_nonmet === 3 && this.countOfOxygenWithSingleNonmet(nonmet, bondMap) === 1) return 'S.o'; // 1.9.1, 4i03/ligand?encoding=mol2&auth_seq_id=312 (DMS)
- // if (num_nonmet === 4 && this.countOfOxygenWithSingleNonmet(nonmet, bondMap) === 2) return 'S.o2'; // 1.9.2, 1udt/ligand?encoding=mol2&auth_seq_id=1000 (VIA)
- // if (num_nonmet >= 2 && bond.every(b => b.order === 1)) return 'S.3'; // 1.9.3, 3zfz/ligand?encoding=mol2&auth_seq_id=1669 (1W8)
- // return 'S.2'; // 1.9.4, 4gpc/ligand?encoding=mol2&auth_seq_id=902 (SO4)
- // }
- // if (type_symbol === 'Ti' || type_symbol === 'Cr') { // 1.10
- // return type_symbol + (num_bond <= 4 ? '.th' : '.oh'); // 1.10.1 & 1.10.2
- // }
- // return type_symbol; // 1.11
- // }
-
- // private isNonMetalBond(b: BondData): boolean {
- // // would be nice to have type_symbol here...
- // return NON_METAL_ATOMS.some(a => this.getLabel(b.label_atom_id).startsWith(a));
- // }
-
- // // 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
- // // TODO cannot check accurately for 2nd criterion without coordinates
- // private isNpl3(nonmet: BondData[], bondMap: ComponentBond.Entry): boolean {
- // for (let i = 0, il = nonmet.length; i < il; i++) {
- // const consumed = nonmet[i];
- // // determine index that fulfills 1st criterion
- // if (this.toArray(bondMap.map.get(consumed.label_atom_id)!).some(b => b.order > 1 || b.aromatic)) {
- // if (nonmet.filter(b => b !== consumed).filter(b => this.getLabel(b.label_atom_id).startsWith('H')).length === 1) return true; // 1.8.6.2.1
- // if (nonmet.filter(b => b !== consumed).every(b => !this.getLabel(b.label_atom_id).startsWith('H'))) return true; // 1.8.6.2.2
- // }
- // }
- // 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
- // private isOC(nonmet: BondData, bondMap: ComponentBond.Entry): boolean {
- // if (!this.getLabel(nonmet.label_atom_id).startsWith('C')) return false;
- // const carbonBonds = this.toArray(bondMap.map.get(nonmet.label_atom_id)!);
- // if (carbonBonds.length !== 3) return false;
- // return carbonBonds.filter(b => this.getLabel(b.label_atom_id).startsWith('O') &&
- // this.toArray(bondMap.map.get(b.label_atom_id)!).filter(ob => this.isNonMetalBond(ob)).length === 1).length === 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
- // private isOP(nonmet: BondData, bondMap: ComponentBond.Entry): boolean {
- // if (!this.getLabel(nonmet.label_atom_id).startsWith('P')) return false;
- // const phosphorusBonds = this.toArray(bondMap.map.get(nonmet.label_atom_id)!);
- // if (phosphorusBonds.length < 2) return false;
- // return phosphorusBonds.filter(b => this.getLabel(b.label_atom_id).startsWith('O') &&
- // this.toArray(bondMap.map.get(b.label_atom_id)!).filter(ob => this.isNonMetalBond(ob)).length === 1).length >= 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.
- // private isCat(root: string, bond: BondData[], bondMap: ComponentBond.Entry): boolean {
- // if (bond.some(b => !this.getLabel(b.label_atom_id).startsWith('N'))) return false;
- // const nitrogenBonds = bond.map(b => b.label_atom_id).map(label_atom_id => this.toArray(bondMap.map.get(label_atom_id)!));
-
- // // ensure no cycles
- // const all = [];
- // const unique = new Set();
- // nitrogenBonds.forEach(a => a.map(b => b.label_atom_id).filter(lai => lai !== root).forEach(lai => { all.push(lai); unique.add(lai); }));
- // if (all.length !== unique.size) return false;
-
- // return nitrogenBonds.every(a => a.length >= 2 && a.every(b => b.label_atom_id !== 'O'));
- // }
-
- // private countOfOxygenWithSingleNonmet(nonmet: BondData[], bondMap: ComponentBond.Entry): number {
- // return nonmet.map(b => b.label_atom_id)
- // .filter(label_atom_id => this.getLabel(label_atom_id).startsWith('O'))
- // .map(label_atom_id => this.toArray(bondMap.map.get(label_atom_id)!)
- // .filter(b => this.isNonMetalBond(b)).length === 1)
- // .length;
- // }
-
- // // If num_nonmet .eq. 3 .AND. one bond is to C=O or C=S then atom_type is N.am
- // private hasCOCS(nonmet: BondData[], bondMap: ComponentBond.Entry): boolean {
- // return nonmet.map(b => b.label_atom_id)
- // .filter(label_atom_id => this.getLabel(label_atom_id).startsWith('C'))
- // .filter(label_atom_id => this.toArray(bondMap.map.get(label_atom_id)!)
- // .filter(b => b.order === 2)
- // .filter(b => this.getLabel(b.label_atom_id).startsWith('O') || this.getLabel(b.label_atom_id).startsWith('S')))
- // .length === 1;
- // }
+ private mapToSybyl(label_atom_id1: string, type_symbol1: string, bondMap: ComponentBond.Entry) {
+ // 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, (_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, (_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)
+ if ((numBonds === 1 || numBonds === 2) && this.count(bonds, (_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, (k, _v) => this.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, (_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, (_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, (_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)
+ if (numNonmets === 1 && this.count(nonmets, (_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, (_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, (_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, (_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
+ private isNpl3(nonmets: BondMap, bondMap: ComponentBond.Entry): boolean {
+ 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, (_k, v) => v.order > 1 || BondType.is(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
+ private isOC(nonmets: BondMap, bondMap: ComponentBond.Entry): boolean {
+ const nonmet = nonmets.entries().next()!.value as [string, { order: number, flags: number }];
+ 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, (k, _v) => this.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
+ private isOP(nonmets: BondMap, bondMap: ComponentBond.Entry): boolean {
+ const nonmet = nonmets.entries().next()!.value as [string, { order: number, flags: number }];
+ 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, (k, _v) => this.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.
+ private isCat(currentBondMap: BondMap, bondMap: ComponentBond.Entry): boolean {
+ 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;
+ }
+
+ private countOfOxygenWithSingleNonmet(nonmets: BondMap, bondMap: ComponentBond.Entry): number {
+ 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, (k, _v) => this.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
+ private hasCOCS(nonmets: BondMap, bondMap: ComponentBond.Entry): boolean {
+ 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, (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) {
const { instance, source } = getCategoryInstanceData(category, context);