openchemlib-utils - npm Package Compare versions

Comparing version 5.17.0 to 5.18.0

lib-esm/topic/getCanonizedHoseCodes.d.ts

@@ -1,4 +0,3 @@
-import { HoseCodesOptions } from './HoseCodesOptions.js';
 import { TopicMolecule } from './TopicMolecule.js';
-export declare function getCanonizedHoseCodes(diaMol: TopicMolecule, options?: HoseCodesOptions): any[];
+export declare function getCanonizedHoseCodes(topicMolecule: TopicMolecule): any[];
 //# sourceMappingURL=getCanonizedHoseCodes.d.ts.map

lib-esm/topic/getCanonizedHoseCodes.js

 import { getHoseCodesForAtomsInternal } from '../hose/getHoseCodesForAtomsInternal.js';
 import { tagAtom } from '../util/tagAtom';
-export function getCanonizedHoseCodes(diaMol, options = {}) {
-    const heterotopicSymmetryRanks = diaMol.heterotopicSymmetryRanks;
-    const moleculeWithH = diaMol.moleculeWithH;
-    const finalRanks = diaMol.finalRanks;
+export function getCanonizedHoseCodes(topicMolecule) {
+    const options = topicMolecule.options;
+    const heterotopicSymmetryRanks = topicMolecule.heterotopicSymmetryRanks;
+    const moleculeWithH = topicMolecule.moleculeWithH;
+    const finalRanks = topicMolecule.finalRanks;
     const canonizedHoseCodes = new Array(moleculeWithH.getAllAtoms());
-    moleculeWithH.ensureHelperArrays(diaMol.molecule.getOCL().Molecule.cHelperSymmetryStereoHeterotopicity);
+    moleculeWithH.ensureHelperArrays(topicMolecule.molecule.getOCL().Molecule
+        .cHelperSymmetryStereoHeterotopicity);
     const cache = {};
-    for (let i = 0; i < diaMol.moleculeWithH.getAllAtoms(); i++) {
+    for (let i = 0; i < topicMolecule.moleculeWithH.getAllAtoms(); i++) {
         const rank = heterotopicSymmetryRanks[i];
@@ -16,3 +18,3 @@ if (rank && cache[rank]) {
         }
-        const tempMolecule = diaMol.moleculeWithH.getCompactCopy();
+        const tempMolecule = topicMolecule.moleculeWithH.getCompactCopy();
         tagAtom(tempMolecule, i);
@@ -19,0 +21,0 @@ const hoses = getHoseCodesForAtomsInternal(tempMolecule, options);

lib-esm/topic/TopicMolecule.d.ts

 import type { Molecule } from 'openchemlib';
+import { HoseCodesOptions } from './HoseCodesOptions.js';
 interface ToMolfileOptions {
@@ -13,4 +14,5 @@ version?: 2 | 3;
     idCode: string;
+    options: HoseCodesOptions;
     private cache;
-    constructor(molecule: Molecule);
+    constructor(molecule: Molecule, options?: HoseCodesOptions);
     ensureMapNo(): void;
@@ -17,0 +19,0 @@ toMolfile(options?: ToMolfileOptions): string;

lib-esm/topic/TopicMolecule.js

@@ -13,4 +13,5 @@ import { getConnectivityMatrix } from '../util/getConnectivityMatrix.js';
 export class TopicMolecule {
-    constructor(molecule) {
+    constructor(molecule, options = {}) {
         this.originalMolecule = molecule;
+        this.options = options;
         this.idCode = molecule.getIDCode();
@@ -17,0 +18,0 @@ this.molecule = this.originalMolecule.getCompactCopy();

lib/topic/getCanonizedHoseCodes.d.ts

@@ -1,4 +0,3 @@
-import { HoseCodesOptions } from './HoseCodesOptions.js';
 import { TopicMolecule } from './TopicMolecule.js';
-export declare function getCanonizedHoseCodes(diaMol: TopicMolecule, options?: HoseCodesOptions): any[];
+export declare function getCanonizedHoseCodes(topicMolecule: TopicMolecule): any[];
 //# sourceMappingURL=getCanonizedHoseCodes.d.ts.map

lib/topic/getCanonizedHoseCodes.js

@@ -6,10 +6,12 @@ "use strict";
 const tagAtom_1 = require("../util/tagAtom");
-function getCanonizedHoseCodes(diaMol, options = {}) {
-    const heterotopicSymmetryRanks = diaMol.heterotopicSymmetryRanks;
-    const moleculeWithH = diaMol.moleculeWithH;
-    const finalRanks = diaMol.finalRanks;
+function getCanonizedHoseCodes(topicMolecule) {
+    const options = topicMolecule.options;
+    const heterotopicSymmetryRanks = topicMolecule.heterotopicSymmetryRanks;
+    const moleculeWithH = topicMolecule.moleculeWithH;
+    const finalRanks = topicMolecule.finalRanks;
     const canonizedHoseCodes = new Array(moleculeWithH.getAllAtoms());
-    moleculeWithH.ensureHelperArrays(diaMol.molecule.getOCL().Molecule.cHelperSymmetryStereoHeterotopicity);
+    moleculeWithH.ensureHelperArrays(topicMolecule.molecule.getOCL().Molecule
+        .cHelperSymmetryStereoHeterotopicity);
     const cache = {};
-    for (let i = 0; i < diaMol.moleculeWithH.getAllAtoms(); i++) {
+    for (let i = 0; i < topicMolecule.moleculeWithH.getAllAtoms(); i++) {
         const rank = heterotopicSymmetryRanks[i];
@@ -20,3 +22,3 @@ if (rank && cache[rank]) {
         }
-        const tempMolecule = diaMol.moleculeWithH.getCompactCopy();
+        const tempMolecule = topicMolecule.moleculeWithH.getCompactCopy();
         (0, tagAtom_1.tagAtom)(tempMolecule, i);
@@ -23,0 +25,0 @@ const hoses = (0, getHoseCodesForAtomsInternal_js_1.getHoseCodesForAtomsInternal)(tempMolecule, options);

lib/topic/TopicMolecule.d.ts

 import type { Molecule } from 'openchemlib';
+import { HoseCodesOptions } from './HoseCodesOptions.js';
 interface ToMolfileOptions {
@@ -13,4 +14,5 @@ version?: 2 | 3;
     idCode: string;
+    options: HoseCodesOptions;
     private cache;
-    constructor(molecule: Molecule);
+    constructor(molecule: Molecule, options?: HoseCodesOptions);
     ensureMapNo(): void;
@@ -17,0 +19,0 @@ toMolfile(options?: ToMolfileOptions): string;

lib/topic/TopicMolecule.js

@@ -16,4 +16,5 @@ "use strict";
 class TopicMolecule {
-    constructor(molecule) {
+    constructor(molecule, options = {}) {
         this.originalMolecule = molecule;
+        this.options = options;
         this.idCode = molecule.getIDCode();
@@ -20,0 +21,0 @@ this.molecule = this.originalMolecule.getCompactCopy();

package.json

 {
   "name": "openchemlib-utils",
-  "version": "5.17.0",
+  "version": "5.18.0",
   "description": "Various utilities that extends openchemlib-js like HOSE codes or diastereotopic IDs",
@@ -5,0 +5,0 @@ "main": "./lib/index.js",

src/topic/getCanonizedHoseCodes.ts

 import { getHoseCodesForAtomsInternal } from '../hose/getHoseCodesForAtomsInternal.js';
 import { tagAtom } from '../util/tagAtom';
 
-import { HoseCodesOptions } from './HoseCodesOptions.js';
 import { TopicMolecule } from './TopicMolecule.js';
 
-export function getCanonizedHoseCodes(
-  diaMol: TopicMolecule,
-  options: HoseCodesOptions = {},
-) {
-  const heterotopicSymmetryRanks = diaMol.heterotopicSymmetryRanks;
-  const moleculeWithH = diaMol.moleculeWithH;
-  const finalRanks = diaMol.finalRanks;
+export function getCanonizedHoseCodes(topicMolecule: TopicMolecule) {
+  const options = topicMolecule.options;
+  const heterotopicSymmetryRanks = topicMolecule.heterotopicSymmetryRanks;
+  const moleculeWithH = topicMolecule.moleculeWithH;
+  const finalRanks = topicMolecule.finalRanks;
   const canonizedHoseCodes = new Array(moleculeWithH.getAllAtoms());
   moleculeWithH.ensureHelperArrays(
-    diaMol.molecule.getOCL().Molecule.cHelperSymmetryStereoHeterotopicity,
+    topicMolecule.molecule.getOCL().Molecule
+      .cHelperSymmetryStereoHeterotopicity,
   );
   const cache: Record<string, any> = {};
-  for (let i = 0; i < diaMol.moleculeWithH.getAllAtoms(); i++) {
+  for (let i = 0; i < topicMolecule.moleculeWithH.getAllAtoms(); i++) {
     const rank = heterotopicSymmetryRanks[i];
@@ -25,3 +23,3 @@ if (rank && cache[rank]) {
     }
-    const tempMolecule = diaMol.moleculeWithH.getCompactCopy();
+    const tempMolecule = topicMolecule.moleculeWithH.getCompactCopy();
     tagAtom(tempMolecule, i);
@@ -28,0 +26,0 @@ const hoses = getHoseCodesForAtomsInternal(tempMolecule, options);

src/topic/TopicMolecule.ts

@@ -5,2 +5,3 @@ import type { Molecule } from 'openchemlib';
 
+import { HoseCodesOptions } from './HoseCodesOptions.js';
 import { getCanonizedDiaIDs } from './getCanonizedDiaIDs';
@@ -28,7 +29,9 @@ import { getCanonizedHoseCodes } from './getCanonizedHoseCodes';
   idCode: string;
+  options: HoseCodesOptions;
 
   private cache: any;
 
-  constructor(molecule: Molecule) {
+  constructor(molecule: Molecule, options: HoseCodesOptions = {}) {
     this.originalMolecule = molecule;
+    this.options = options;
     this.idCode = molecule.getIDCode();
@@ -35,0 +38,0 @@ this.molecule = this.originalMolecule.getCompactCopy();

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Improved metrics

Total package byte prevSize

1096819

increased by0.06%

Lines of code

16468

increased by0.05%

No dependency changes