openchemlib-utils - npm Package Compare versions

Comparing version 5.19.1 to 5.20.0

lib-esm/misc/getNMRHints.js

@@ -57,3 +57,3 @@ // this page allows to debug the hints: https://my.cheminfo.org/?viewURL=https%3A%2F%2Fmyviews.cheminfo.org%2Fdb%2Fvisualizer%2Fentry%2F108024089da99d0cb70a57724486d0c6%2Fview.json
         idCode: 'eMB@HRZCBKSFXXJt{?Y@',
-        message: 'You should consider an thiol.',
+        message: 'You should consider a thiol.',
     },
@@ -60,0 +60,0 @@ {

lib-esm/topic/getMoleculeWithH.d.ts

 import type { Molecule } from 'openchemlib';
+export interface GetMoleculeWithHOptions {
+    /**
+     * @default 250
+     * Maximum number of atoms with hydrogens
+     */
+    maxNbAtoms?: number;
+}
 /**
@@ -7,3 +14,3 @@ * Expand all the implicit hydrogens and ensure chiral bonds on heterotopic bonds
  */
-export declare function getMoleculeWithH(molecule: Molecule): Molecule;
+export declare function getMoleculeWithH(molecule: Molecule, options?: GetMoleculeWithHOptions): Molecule;
 //# sourceMappingURL=getMoleculeWithH.d.ts.map

lib-esm/topic/getMoleculeWithH.js

 import { ensureHeterotopicChiralBonds } from '../diastereotopic/ensureHeterotopicChiralBonds.js';
-const MAX_NB_ATOMS = 250;
 /**
@@ -8,7 +7,8 @@ * Expand all the implicit hydrogens and ensure chiral bonds on heterotopic bonds
  */
-export function getMoleculeWithH(molecule) {
+export function getMoleculeWithH(molecule, options = {}) {
+    const { maxNbAtoms = 250 } = options;
     const moleculeWithH = molecule.getCompactCopy();
     moleculeWithH.addImplicitHydrogens();
-    if (moleculeWithH.getAllAtoms() > MAX_NB_ATOMS) {
-        throw new Error(`too many atoms to add hydrogens: ${moleculeWithH.getAllAtoms()} > ${MAX_NB_ATOMS}`);
+    if (moleculeWithH.getAllAtoms() > maxNbAtoms) {
+        throw new Error(`too many atoms to add hydrogens: ${moleculeWithH.getAllAtoms()} > ${maxNbAtoms}`);
     }
@@ -15,0 +15,0 @@ ensureHeterotopicChiralBonds(moleculeWithH);

lib-esm/topic/TopicMolecule.d.ts

 import type { Molecule } from 'openchemlib';
 import { AtomPath } from '../path/getAllAtomsPaths.js';
 import { HoseCodesOptions } from './HoseCodesOptions.js';
+import { GetMoleculeWithHOptions } from './getMoleculeWithH';
 interface ToMolfileOptions {
     version?: 2 | 3;
 }
-interface TopicMoleculeOptions extends HoseCodesOptions {
+interface TopicMoleculeOptions extends HoseCodesOptions, GetMoleculeWithHOptions {
     /**
@@ -13,2 +14,3 @@ * The maximum path length to consider when calculating the paths between atoms
     maxPathLength?: number;
+    maxNbAtoms?: number;
 }
@@ -15,0 +17,0 @@ type TopicMoleculeInternalOptions = Omit<TopicMoleculeOptions, 'maxPathLength'> & Required<Pick<TopicMoleculeOptions, 'maxPathLength'>>;

lib-esm/topic/TopicMolecule.js

@@ -158,3 +158,5 @@ import { getAllAtomsPaths } from '../path/getAllAtomsPaths.js';
             return this.cache.moleculeWithH;
-        this.cache.moleculeWithH = getMoleculeWithH(this.molecule);
+        this.cache.moleculeWithH = getMoleculeWithH(this.molecule, {
+            maxNbAtoms: this.options.maxNbAtoms,
+        });
         return this.cache.moleculeWithH;
@@ -161,0 +163,0 @@ }

lib/misc/getNMRHints.js

@@ -60,3 +60,3 @@ "use strict";
         idCode: 'eMB@HRZCBKSFXXJt{?Y@',
-        message: 'You should consider an thiol.',
+        message: 'You should consider a thiol.',
     },
@@ -63,0 +63,0 @@ {

lib/topic/getMoleculeWithH.d.ts

 import type { Molecule } from 'openchemlib';
+export interface GetMoleculeWithHOptions {
+    /**
+     * @default 250
+     * Maximum number of atoms with hydrogens
+     */
+    maxNbAtoms?: number;
+}
 /**
@@ -7,3 +14,3 @@ * Expand all the implicit hydrogens and ensure chiral bonds on heterotopic bonds
  */
-export declare function getMoleculeWithH(molecule: Molecule): Molecule;
+export declare function getMoleculeWithH(molecule: Molecule, options?: GetMoleculeWithHOptions): Molecule;
 //# sourceMappingURL=getMoleculeWithH.d.ts.map

lib/topic/getMoleculeWithH.js

@@ -5,3 +5,2 @@ "use strict";
 const ensureHeterotopicChiralBonds_js_1 = require("../diastereotopic/ensureHeterotopicChiralBonds.js");
-const MAX_NB_ATOMS = 250;
 /**
@@ -12,7 +11,8 @@ * Expand all the implicit hydrogens and ensure chiral bonds on heterotopic bonds
  */
-function getMoleculeWithH(molecule) {
+function getMoleculeWithH(molecule, options = {}) {
+    const { maxNbAtoms = 250 } = options;
     const moleculeWithH = molecule.getCompactCopy();
     moleculeWithH.addImplicitHydrogens();
-    if (moleculeWithH.getAllAtoms() > MAX_NB_ATOMS) {
-        throw new Error(`too many atoms to add hydrogens: ${moleculeWithH.getAllAtoms()} > ${MAX_NB_ATOMS}`);
+    if (moleculeWithH.getAllAtoms() > maxNbAtoms) {
+        throw new Error(`too many atoms to add hydrogens: ${moleculeWithH.getAllAtoms()} > ${maxNbAtoms}`);
     }
@@ -19,0 +19,0 @@ (0, ensureHeterotopicChiralBonds_js_1.ensureHeterotopicChiralBonds)(moleculeWithH);

lib/topic/TopicMolecule.d.ts

 import type { Molecule } from 'openchemlib';
 import { AtomPath } from '../path/getAllAtomsPaths.js';
 import { HoseCodesOptions } from './HoseCodesOptions.js';
+import { GetMoleculeWithHOptions } from './getMoleculeWithH';
 interface ToMolfileOptions {
     version?: 2 | 3;
 }
-interface TopicMoleculeOptions extends HoseCodesOptions {
+interface TopicMoleculeOptions extends HoseCodesOptions, GetMoleculeWithHOptions {
     /**
@@ -13,2 +14,3 @@ * The maximum path length to consider when calculating the paths between atoms
     maxPathLength?: number;
+    maxNbAtoms?: number;
 }
@@ -15,0 +17,0 @@ type TopicMoleculeInternalOptions = Omit<TopicMoleculeOptions, 'maxPathLength'> & Required<Pick<TopicMoleculeOptions, 'maxPathLength'>>;

lib/topic/TopicMolecule.js

@@ -161,3 +161,5 @@ "use strict";
             return this.cache.moleculeWithH;
-        this.cache.moleculeWithH = (0, getMoleculeWithH_1.getMoleculeWithH)(this.molecule);
+        this.cache.moleculeWithH = (0, getMoleculeWithH_1.getMoleculeWithH)(this.molecule, {
+            maxNbAtoms: this.options.maxNbAtoms,
+        });
         return this.cache.moleculeWithH;
@@ -164,0 +166,0 @@ }

package.json

 {
   "name": "openchemlib-utils",
-  "version": "5.19.1",
+  "version": "5.20.0",
   "description": "Various utilities that extends openchemlib-js like HOSE codes or diastereotopic IDs",
@@ -5,0 +5,0 @@ "main": "./lib/index.js",

src/misc/getNMRHints.js

@@ -60,3 +60,3 @@ // this page allows to debug the hints: https://my.cheminfo.org/?viewURL=https%3A%2F%2Fmyviews.cheminfo.org%2Fdb%2Fvisualizer%2Fentry%2F108024089da99d0cb70a57724486d0c6%2Fview.json
     idCode: 'eMB@HRZCBKSFXXJt{?Y@',
-    message: 'You should consider an thiol.',
+    message: 'You should consider a thiol.',
   },
@@ -63,0 +63,0 @@ {

src/topic/getMoleculeWithH.ts

@@ -5,3 +5,9 @@ import type { Molecule } from 'openchemlib';
 
-const MAX_NB_ATOMS = 250;
+export interface GetMoleculeWithHOptions {
+  /**
+   * @default 250
+   * Maximum number of atoms with hydrogens
+   */
+  maxNbAtoms?: number;
+}
 
@@ -13,8 +19,12 @@ /**
  */
-export function getMoleculeWithH(molecule: Molecule) {
+export function getMoleculeWithH(
+  molecule: Molecule,
+  options: GetMoleculeWithHOptions = {},
+) {
+  const { maxNbAtoms = 250 } = options;
   const moleculeWithH = molecule.getCompactCopy();
   moleculeWithH.addImplicitHydrogens();
-  if (moleculeWithH.getAllAtoms() > MAX_NB_ATOMS) {
+  if (moleculeWithH.getAllAtoms() > maxNbAtoms) {
     throw new Error(
-      `too many atoms to add hydrogens: ${moleculeWithH.getAllAtoms()} > ${MAX_NB_ATOMS}`,
+      `too many atoms to add hydrogens: ${moleculeWithH.getAllAtoms()} > ${maxNbAtoms}`,
     );
@@ -21,0 +31,0 @@ }

src/topic/TopicMolecule.ts

@@ -15,3 +15,3 @@ import type { Molecule } from 'openchemlib';
 } from './getHeterotopicSymmetryRanks';
-import { getMoleculeWithH } from './getMoleculeWithH';
+import { getMoleculeWithH, GetMoleculeWithHOptions } from './getMoleculeWithH';
 import { getXMolecule } from './getXMolecule';
@@ -23,3 +23,5 @@
 
-interface TopicMoleculeOptions extends HoseCodesOptions {
+interface TopicMoleculeOptions
+  extends HoseCodesOptions,
+    GetMoleculeWithHOptions {
   /**
@@ -30,2 +32,3 @@ * The maximum path length to consider when calculating the paths between atoms
   maxPathLength?: number;
+  maxNbAtoms?: number;
 }
@@ -245,3 +248,5 @@
     if (this.cache.moleculeWithH) return this.cache.moleculeWithH;
-    this.cache.moleculeWithH = getMoleculeWithH(this.molecule);
+    this.cache.moleculeWithH = getMoleculeWithH(this.molecule, {
+      maxNbAtoms: this.options.maxNbAtoms,
+    });
     return this.cache.moleculeWithH;
@@ -248,0 +253,0 @@ }

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Improved metrics

Total package byte prevSize

1130553

increased by0.15%

Lines of code

17033

increased by0.22%

No dependency changes