openchemlib-utils - npm Package Compare versions

Comparing version 6.4.0 to 6.4.1

lib-esm/topic/getCanonizedDiaIDs.d.ts

@@ -0,3 +1,8 @@
+import { Logger } from 'cheminfo-types';
 import { TopicMolecule } from './TopicMolecule.js';
-export declare function getCanonizedDiaIDs(diaMol: TopicMolecule): any[];
+export interface GetCanonizedDiaIDsOptions {
+    maxNbAtoms: number;
+    logger: Omit<Logger, 'child' | 'fatal'>;
+}
+export declare function getCanonizedDiaIDs(diaMol: TopicMolecule, options: GetCanonizedDiaIDsOptions): any[];
 //# sourceMappingURL=getCanonizedDiaIDs.d.ts.map

lib-esm/topic/getCanonizedDiaIDs.js

 import { makeRacemic } from '../util/makeRacemic.js';
 import { tagAtom } from '../util/tagAtom';
-export function getCanonizedDiaIDs(diaMol) {
+export function getCanonizedDiaIDs(diaMol, options) {
+    const { logger, maxNbAtoms } = options;
+    const moleculeWithH = diaMol.moleculeWithH;
+    if (moleculeWithH.getAllAtoms() > maxNbAtoms) {
+        logger.warn(`too many atoms to evaluate heterotopic chiral bonds: ${moleculeWithH.getAllAtoms()} > ${maxNbAtoms}`);
+        return [];
+    }
     const heterotopicSymmetryRanks = diaMol.heterotopicSymmetryRanks;
-    const moleculeWithH = diaMol.moleculeWithH;
     const finalRanks = diaMol.finalRanks;
@@ -7,0 +12,0 @@ const canonizedDiaIDs = new Array(moleculeWithH.getAllAtoms());

lib-esm/topic/TopicMolecule.d.ts

@@ -89,3 +89,3 @@ import { Logger } from 'cheminfo-types';
      */
-    get diaIDs(): string[] | undefined;
+    get diaIDs(): string[];
     /**
@@ -92,0 +92,0 @@ * We return the atomIDs corresponding to the specified diaID as well has the attached hydrogens or heavy atoms

lib-esm/topic/TopicMolecule.js

@@ -176,10 +176,10 @@ import { getHoseCodesForAtomsAsFragments } from '../hose/getHoseCodesForAtomsInternal.js';
             return this.cache.diaIDs;
+        const diaIDs = [];
         if (this.moleculeWithH.getAllAtoms() > this.options.maxNbAtoms) {
             this.options.logger.warn(`too many atoms to evaluate heterotopicity: ${this.moleculeWithH.getAllAtoms()} > ${this.options.maxNbAtoms}`);
-            this.cache.diaIDs = undefined;
-            return undefined;
         }
-        const diaIDs = [];
-        for (let i = 0; i < this.moleculeWithH.getAllAtoms(); i++) {
-            diaIDs.push(this.canonizedDiaIDs[this.finalRanks[i]]);
+        else {
+            for (let i = 0; i < this.moleculeWithH.getAllAtoms(); i++) {
+                diaIDs.push(this.canonizedDiaIDs[this.finalRanks[i]]);
+            }
         }
@@ -215,3 +215,6 @@ this.cache.diaIDs = diaIDs;
             return this.cache.canonizedDiaIDs;
-        this.cache.canonizedDiaIDs = getCanonizedDiaIDs(this);
+        this.cache.canonizedDiaIDs = getCanonizedDiaIDs(this, {
+            maxNbAtoms: this.options.maxNbAtoms,
+            logger: this.options.logger,
+        });
         return this.cache.canonizedDiaIDs;
@@ -233,4 +236,5 @@ }
     get diaIDsAndInfo() {
-        if (this.cache.diaIDsAndInfo)
+        if (this.cache.diaIDsAndInfo) {
             return this.cache.diaIDsAndInfo;
+        }
         this.cache.diaIDsAndInfo = getDiaIDsAndInfo(this, this.canonizedDiaIDs);
@@ -237,0 +241,0 @@ return this.cache.diaIDsAndInfo;

lib/topic/getCanonizedDiaIDs.d.ts

@@ -0,3 +1,8 @@
+import { Logger } from 'cheminfo-types';
 import { TopicMolecule } from './TopicMolecule.js';
-export declare function getCanonizedDiaIDs(diaMol: TopicMolecule): any[];
+export interface GetCanonizedDiaIDsOptions {
+    maxNbAtoms: number;
+    logger: Omit<Logger, 'child' | 'fatal'>;
+}
+export declare function getCanonizedDiaIDs(diaMol: TopicMolecule, options: GetCanonizedDiaIDsOptions): any[];
 //# sourceMappingURL=getCanonizedDiaIDs.d.ts.map

lib/topic/getCanonizedDiaIDs.js

@@ -6,5 +6,10 @@ "use strict";
 const tagAtom_1 = require("../util/tagAtom");
-function getCanonizedDiaIDs(diaMol) {
+function getCanonizedDiaIDs(diaMol, options) {
+    const { logger, maxNbAtoms } = options;
+    const moleculeWithH = diaMol.moleculeWithH;
+    if (moleculeWithH.getAllAtoms() > maxNbAtoms) {
+        logger.warn(`too many atoms to evaluate heterotopic chiral bonds: ${moleculeWithH.getAllAtoms()} > ${maxNbAtoms}`);
+        return [];
+    }
     const heterotopicSymmetryRanks = diaMol.heterotopicSymmetryRanks;
-    const moleculeWithH = diaMol.moleculeWithH;
     const finalRanks = diaMol.finalRanks;
@@ -11,0 +16,0 @@ const canonizedDiaIDs = new Array(moleculeWithH.getAllAtoms());

lib/topic/TopicMolecule.d.ts

@@ -89,3 +89,3 @@ import { Logger } from 'cheminfo-types';
      */
-    get diaIDs(): string[] | undefined;
+    get diaIDs(): string[];
     /**
@@ -92,0 +92,0 @@ * We return the atomIDs corresponding to the specified diaID as well has the attached hydrogens or heavy atoms

lib/topic/TopicMolecule.js

@@ -180,10 +180,10 @@ "use strict";
             return this.cache.diaIDs;
+        const diaIDs = [];
         if (this.moleculeWithH.getAllAtoms() > this.options.maxNbAtoms) {
             this.options.logger.warn(`too many atoms to evaluate heterotopicity: ${this.moleculeWithH.getAllAtoms()} > ${this.options.maxNbAtoms}`);
-            this.cache.diaIDs = undefined;
-            return undefined;
         }
-        const diaIDs = [];
-        for (let i = 0; i < this.moleculeWithH.getAllAtoms(); i++) {
-            diaIDs.push(this.canonizedDiaIDs[this.finalRanks[i]]);
+        else {
+            for (let i = 0; i < this.moleculeWithH.getAllAtoms(); i++) {
+                diaIDs.push(this.canonizedDiaIDs[this.finalRanks[i]]);
+            }
         }
@@ -219,3 +219,6 @@ this.cache.diaIDs = diaIDs;
             return this.cache.canonizedDiaIDs;
-        this.cache.canonizedDiaIDs = (0, getCanonizedDiaIDs_1.getCanonizedDiaIDs)(this);
+        this.cache.canonizedDiaIDs = (0, getCanonizedDiaIDs_1.getCanonizedDiaIDs)(this, {
+            maxNbAtoms: this.options.maxNbAtoms,
+            logger: this.options.logger,
+        });
         return this.cache.canonizedDiaIDs;
@@ -237,4 +240,5 @@ }
     get diaIDsAndInfo() {
-        if (this.cache.diaIDsAndInfo)
+        if (this.cache.diaIDsAndInfo) {
             return this.cache.diaIDsAndInfo;
+        }
         this.cache.diaIDsAndInfo = (0, getDiaIDsAndInfo_1.getDiaIDsAndInfo)(this, this.canonizedDiaIDs);
@@ -241,0 +245,0 @@ return this.cache.diaIDsAndInfo;

package.json

 {
   "name": "openchemlib-utils",
-  "version": "6.4.0",
+  "version": "6.4.1",
   "description": "Various utilities that extends openchemlib-js like HOSE codes or diastereotopic IDs",
@@ -5,0 +5,0 @@ "main": "./lib/index.js",

src/topic/getCanonizedDiaIDs.ts

@@ -0,1 +1,3 @@
+import { Logger } from 'cheminfo-types';
+
 import { makeRacemic } from '../util/makeRacemic.js';
@@ -6,5 +8,20 @@ import { tagAtom } from '../util/tagAtom';
 
-export function getCanonizedDiaIDs(diaMol: TopicMolecule) {
+export interface GetCanonizedDiaIDsOptions {
+  maxNbAtoms: number;
+  logger: Omit<Logger, 'child' | 'fatal'>;
+}
+
+export function getCanonizedDiaIDs(
+  diaMol: TopicMolecule,
+  options: GetCanonizedDiaIDsOptions,
+) {
+  const { logger, maxNbAtoms } = options;
+  const moleculeWithH = diaMol.moleculeWithH;
+  if (moleculeWithH.getAllAtoms() > maxNbAtoms) {
+    logger.warn(
+      `too many atoms to evaluate heterotopic chiral bonds: ${moleculeWithH.getAllAtoms()} > ${maxNbAtoms}`,
+    );
+    return [];
+  }
   const heterotopicSymmetryRanks = diaMol.heterotopicSymmetryRanks;
-  const moleculeWithH = diaMol.moleculeWithH;
   const finalRanks = diaMol.finalRanks;
@@ -11,0 +28,0 @@ const canonizedDiaIDs = new Array(moleculeWithH.getAllAtoms());

src/topic/TopicMolecule.ts

@@ -291,4 +291,5 @@ import { Logger } from 'cheminfo-types';
    */
-  get diaIDs(): string[] | undefined {
+  get diaIDs(): string[] {
     if (this.cache.diaIDs) return this.cache.diaIDs;
+    const diaIDs = [];
     if (this.moleculeWithH.getAllAtoms() > this.options.maxNbAtoms) {
@@ -298,9 +299,7 @@ this.options.logger.warn(
       );
-      this.cache.diaIDs = undefined;
-      return undefined;
+    } else {
+      for (let i = 0; i < this.moleculeWithH.getAllAtoms(); i++) {
+        diaIDs.push(this.canonizedDiaIDs[this.finalRanks[i]]);
+      }
     }
-    const diaIDs = [];
-    for (let i = 0; i < this.moleculeWithH.getAllAtoms(); i++) {
-      diaIDs.push(this.canonizedDiaIDs[this.finalRanks[i]]);
-    }
     this.cache.diaIDs = diaIDs;
@@ -339,3 +338,6 @@ return diaIDs;
     if (this.cache.canonizedDiaIDs) return this.cache.canonizedDiaIDs;
-    this.cache.canonizedDiaIDs = getCanonizedDiaIDs(this);
+    this.cache.canonizedDiaIDs = getCanonizedDiaIDs(this, {
+      maxNbAtoms: this.options.maxNbAtoms,
+      logger: this.options.logger,
+    });
     return this.cache.canonizedDiaIDs;
@@ -360,3 +362,5 @@ }
   get diaIDsAndInfo(): DiaIDAndInfo[] {
-    if (this.cache.diaIDsAndInfo) return this.cache.diaIDsAndInfo;
+    if (this.cache.diaIDsAndInfo) {
+      return this.cache.diaIDsAndInfo;
+    }
     this.cache.diaIDsAndInfo = getDiaIDsAndInfo(this, this.canonizedDiaIDs);
@@ -363,0 +367,0 @@ return this.cache.diaIDsAndInfo;

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Improved metrics

Total package byte prevSize

1163092

increased by0.21%

Lines of code

17564

increased by0.27%

No dependency changes