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Commit b8f168eb authored by JonStargaryen's avatar JonStargaryen
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iterators

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src/mol-io/writer/mol2/encoder.ts
+ 221
− 144
View file @ b8f168eb
...@@ -9,12 +9,12 @@ import { LigandEncoder } from '../ligand-encoder'; ...@@ -9,12 +9,12 @@ import { LigandEncoder } from '../ligand-encoder';
import { StringBuilder } from '../../../mol-util'; import { StringBuilder } from '../../../mol-util';
import { getCategoryInstanceData } from '../cif/encoder/util'; import { getCategoryInstanceData } from '../cif/encoder/util';
import { BondType } from '../../../mol-model/structure/model/types'; 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 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'; // 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(' '); 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 BondMap = Map<string, { order: number, flags: number }>;
// specification: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf // specification: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
export class Mol2Encoder extends LigandEncoder { export class Mol2Encoder extends LigandEncoder {
...@@ -50,8 +50,7 @@ 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 = this.mapToSybyl(label_atom_id1, atom1.type_symbol, bondMap);
const sybyl = '?';
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 ${name} 0.000\n`); StringBuilder.writeSafe(a, `${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 { ...@@ -62,146 +61,224 @@ export class Mol2Encoder extends LigandEncoder {
StringBuilder.writeSafe(this.out, `@<TRIPOS>SUBSTRUCTURE\n1 ${name} 1\n`); StringBuilder.writeSafe(this.out, `@<TRIPOS>SUBSTRUCTURE\n1 ${name} 1\n`);
} }
// private toArray(map: Map<string, { order: number, flags: number }>): BondData[] { private count<K, V>(map: Map<K, V>, predicate: (k: K, v: V) => boolean): number {
// const array: BondData[] = []; let count = 0;
// map.forEach((v, k) => array.push({ label_atom_id: k, order: v.order, aromatic: BondType.is(BondType.Flag.Aromatic, v.flags) })); const iter = map.entries();
// return array; 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 // see https://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html
// cannot account for covalently bound amino acids etc // cannot account for covalently bound amino acids etc
// private mapToSybyl(label_atom_id: string, type_symbol: string, bondMap: ComponentBond.Entry) { private mapToSybyl(label_atom_id1: string, type_symbol1: string, bondMap: ComponentBond.Entry) {
// const partialBondMap = bondMap.map.get(label_atom_id)!; // TODO if altLoc: 'Du' // 1.1
// const bond = this.toArray(partialBondMap); // TODO if end of polymeric bond: 'Du' // 1.2
if (type_symbol1 === 'D') return 'H'; // 1.3
// const num_bond = bond.length; if (type_symbol1 === 'P') return 'P.3'; // 1.4, 4mpo/ligand?encoding=mol2&auth_seq_id=203 (PO4)
// const nonmet = bond.filter(b => this.isNonMetalBond(b)); if (type_symbol1 === 'Co' || type_symbol1 === 'Ru') return type_symbol1 + '.oh'; // 1.5
// const num_nonmet = nonmet.length;
// const arom = bond.filter(e => e.aromatic); const bonds = bondMap.map.get(label_atom_id1)!;
// const num_arom = arom.length; const numBonds = bonds.size;
// // TODO if altLoc: 'Du' // 1.1 if (type_symbol1 === 'Ti' || type_symbol1 === 'Cr') { // 1.10
// // TODO if end of polymeric bond: 'Du' // 1.2 return type_symbol1 + (numBonds <= 4 ? '.th' : '.oh'); // 1.10.1 & 1.10.2
// 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_symbol1 === 'C') { // 1.6
// if (type_symbol === 'Co' || type_symbol === 'Ru') return type_symbol + '.oh'; // 1.5 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 (type_symbol === 'C') { // 1.6 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 (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 (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 (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 ((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)
// 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) return 'C.2'; // 1.6.5
// 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
// } // most of the time, bonds will equal non-metal bonds
// if (type_symbol === 'O') { // 1.7 const nonmets = this.count(bonds, (k, _v) => this.isNonMetalBond(k)) === bonds.size ? bonds : this.extractNonmets(bonds);
// if (num_nonmet === 1) { // 1.7.1 const numNonmets = nonmets.size;
// 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 (type_symbol1 === 'O') { // 1.7
// } if (numNonmets === 1) { // 1.7.1
// 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) if (this.isOC(nonmets, bondMap)) return 'O.co2'; // 1.7.1.1, 4h2v/ligand?encoding=mol2&auth_seq_id=403 (ACT)
// return 'O.2'; // 1.7.3, 1acj/ligand?encoding=mol2&auth_seq_id=4 (SER) if (this.isOP(nonmets, bondMap)) return 'O.co2'; // 1.7.1.2, 4mpo/ligand?encoding=mol2&auth_seq_id=203 (PO4)
// } }
// if (type_symbol === 'N') { // 1.8 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)
// 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) return 'O.2'; // 1.7.3, 1acj/ligand?encoding=mol2&auth_seq_id=4 (SER)
// 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 (type_symbol1 === 'N') { // 1.8
// 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 (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 (num_nonmet === 3 && this.hasCOCS(nonmet, bondMap)) return 'N.am'; // 1.8.5, 3zfz/ligand?encoding=mol2&auth_seq_id=1669 (1W8) 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 (num_nonmet === 3) { // 1.8.6 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 (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 (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 (nonmet.every(b => b.order === 1)) { if (numNonmets === 3 && this.hasCOCS(nonmets, bondMap)) return 'N.am'; // 1.8.5, 3zfz/ligand?encoding=mol2&auth_seq_id=1669 (1W8)
// 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) 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)
// return 'N.3'; 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.2'; // 1.8.7, 1acj/ligand?encoding=mol2&auth_seq_id=4 (SER) }
// } return 'N.3';
// 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) return 'N.2'; // 1.8.7, 1acj/ligand?encoding=mol2&auth_seq_id=4 (SER)
// 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) if (type_symbol1 === 'S') { // 1.9
// return 'S.2'; // 1.9.4, 4gpc/ligand?encoding=mol2&auth_seq_id=902 (SO4) 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 (type_symbol === 'Ti' || type_symbol === 'Cr') { // 1.10 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 type_symbol + (num_bond <= 4 ? '.th' : '.oh'); // 1.10.1 & 1.10.2 return 'S.2'; // 1.9.4
// } }
// return type_symbol; // 1.11 return type_symbol1; // 1.11
// } }
// private isNonMetalBond(b: BondData): boolean { // 1.8.6.2.1: If one single bond is to an atom that forms a bond of type double, triple, aromatic or
// // would be nice to have type_symbol here... // delocalised .AND. one other single bond is to H then atom_type is N.pl3
// return NON_METAL_ATOMS.some(a => this.getLabel(b.label_atom_id).startsWith(a)); // 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
// // 1.8.6.2.1: If one single bond is to an atom that forms a bond of type double, triple, aromatic or private isNpl3(nonmets: BondMap, bondMap: ComponentBond.Entry): boolean {
// // delocalised .AND. one other single bond is to H then atom_type is N.pl3 const iter = nonmets.keys();
// // 1.8.6.2.2: If one single bond is to an atom that forms a bond of type double, triple, aromatic or let result = iter.next();
// // 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 while (!result.done) {
// // TODO cannot check accurately for delocalized bonds const label_atom_id = result.value;
// // TODO cannot check accurately for 2nd criterion without coordinates const adjacentBonds = bondMap.map.get(label_atom_id)!;
// private isNpl3(nonmet: BondData[], bondMap: ComponentBond.Entry): boolean { if (this.count(adjacentBonds, (_k, v) => v.order > 1 || BondType.is(BondType.Flag.Aromatic, v.flags))) {
// for (let i = 0, il = nonmet.length; i < il; i++) { // TODO check accurately for 2nd criterion with coordinates
// const consumed = nonmet[i]; return true;
// // determine index that fulfills 1st criterion }
// if (this.toArray(bondMap.map.get(consumed.label_atom_id)!).some(b => b.order > 1 || b.aromatic)) { result = iter.next();
// 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;
// } }
// }
// 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 {
// // If bond is to carbon .AND. carbon forms a total of 3 bonds, 2 of which are to an oxygen const nonmet = nonmets.entries().next()!.value as [string, { order: number, flags: number }];
// // forming only 1 non-metal bond then atom_type is O.co2 if (!nonmet[0].startsWith('C')) return false;
// private isOC(nonmet: BondData, bondMap: ComponentBond.Entry): boolean { const carbonBonds = bondMap.map.get(nonmet[0])!;
// if (!this.getLabel(nonmet.label_atom_id).startsWith('C')) return false; if (carbonBonds.size !== 3) return false;
// const carbonBonds = this.toArray(bondMap.map.get(nonmet.label_atom_id)!);
// if (carbonBonds.length !== 3) return false; let count = 0;
// return carbonBonds.filter(b => this.getLabel(b.label_atom_id).startsWith('O') && const iter = carbonBonds.keys();
// this.toArray(bondMap.map.get(b.label_atom_id)!).filter(ob => this.isNonMetalBond(ob)).length === 1).length === 2; let result = iter.next();
// } while (!result.done) {
const label_atom_id = result.value;
// // If bond is to phosphorus .AND. phosphorus forms at least 2 bonds to an oxygen forming if (label_atom_id.startsWith('O')) {
// // only 1 non-metal bond then atom_type is O.co2 const adjacentBonds = bondMap.map.get(label_atom_id)!;
// private isOP(nonmet: BondData, bondMap: ComponentBond.Entry): boolean { if (this.count(adjacentBonds, (k, _v) => this.isNonMetalBond(k)) === 1) count++;
// if (!this.getLabel(nonmet.label_atom_id).startsWith('P')) return false; }
// const phosphorusBonds = this.toArray(bondMap.map.get(nonmet.label_atom_id)!); result = iter.next();
// if (phosphorusBonds.length < 2) return false; }
// return phosphorusBonds.filter(b => this.getLabel(b.label_atom_id).startsWith('O') && return count === 2;
// 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
// // If num_bond .eq. 3 .AND. all bonds are acyclic .AND. all bonds are to nitrogen .AND. each // only 1 non-metal bond then atom_type is O.co2
// // nitrogen forms bonds to 2 other atoms both of which are not oxygen then atom_type is C.cat. private isOP(nonmets: BondMap, bondMap: ComponentBond.Entry): boolean {
// private isCat(root: string, bond: BondData[], bondMap: ComponentBond.Entry): boolean { const nonmet = nonmets.entries().next()!.value as [string, { order: number, flags: number }];
// if (bond.some(b => !this.getLabel(b.label_atom_id).startsWith('N'))) return false; if (!nonmet[0].startsWith('P')) return false;
// const nitrogenBonds = bond.map(b => b.label_atom_id).map(label_atom_id => this.toArray(bondMap.map.get(label_atom_id)!)); const phosphorusBonds = bondMap.map.get(nonmet[0])!;
if (phosphorusBonds.size < 2) return false;
// // ensure no cycles
// const all = []; let count = 0;
// const unique = new Set(); const iter = phosphorusBonds.keys();
// nitrogenBonds.forEach(a => a.map(b => b.label_atom_id).filter(lai => lai !== root).forEach(lai => { all.push(lai); unique.add(lai); })); let result = iter.next();
// if (all.length !== unique.size) return false; while (!result.done) {
const label_atom_id = result.value;
// return nitrogenBonds.every(a => a.length >= 2 && a.every(b => b.label_atom_id !== 'O')); 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++;
// private countOfOxygenWithSingleNonmet(nonmet: BondData[], bondMap: ComponentBond.Entry): number { }
// return nonmet.map(b => b.label_atom_id) result = iter.next();
// .filter(label_atom_id => this.getLabel(label_atom_id).startsWith('O')) }
// .map(label_atom_id => this.toArray(bondMap.map.get(label_atom_id)!) return count >= 2;
// .filter(b => this.isNonMetalBond(b)).length === 1) }
// .length;
// } // 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.
// // If num_nonmet .eq. 3 .AND. one bond is to C=O or C=S then atom_type is N.am private isCat(currentBondMap: BondMap, bondMap: ComponentBond.Entry): boolean {
// private hasCOCS(nonmet: BondData[], bondMap: ComponentBond.Entry): boolean { const iter1 = currentBondMap.keys();
// return nonmet.map(b => b.label_atom_id) let result1 = iter1.next();
// .filter(label_atom_id => this.getLabel(label_atom_id).startsWith('C')) while (!result1.done) {
// .filter(label_atom_id => this.toArray(bondMap.map.get(label_atom_id)!) const label_atom_id = result1.value;
// .filter(b => b.order === 2) if (!label_atom_id.startsWith('N')) return false;
// .filter(b => this.getLabel(b.label_atom_id).startsWith('O') || this.getLabel(b.label_atom_id).startsWith('S')))
// .length === 1; 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) { protected writeFullCategory<Ctx>(sb: StringBuilder, category: Category<Ctx>, context?: Ctx) {
const { instance, source } = getCategoryInstanceData(category, context); const { instance, source } = getCategoryInstanceData(category, context);
......
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