feat: add changeCustomLabelPosition method on Molecule instance

__tests__/__snapshots__/library.test.ts.snap

@@ -70,6 +70,7 @@ exports[`class prototypes > prototype properties of Molecule 1`] = `
   "changeAtom",
   "changeAtomCharge",
   "changeBond",
+  "changeCustomLabelPosition",
   "clear",
   "convertStereoBondsToSingleBonds",
   "copyAtom",

lib/extend/appendChangeCustomLabelPosition.js

@@ -0,0 +1,52 @@
+/**
+ * Append the method changeCustomLabelPosition to the Molecule class in order
+ * to change the position of custom labels according to the provided option
+ * - 'superscript' will add a ] at the beginning of the custom label
+ * - 'normal' will remove a leading ] if present
+ * - 'auto' will set the label as superscript for non-carbon atoms and normal for carbon atoms
+ * @param {*} Molecule
+ */
+export function appendChangeCustomLabelPosition(Molecule) {
+  Molecule.prototype.changeCustomLabelPosition =
+    function changeCustomLabelPosition(customLabelPosition) {
+      switch (customLabelPosition) {
+        case 'superscript':
+          for (let i = 0; i < this.getAllAtoms(); i++) {
+            const customLabel = this.getAtomCustomLabel(i);
+            if (customLabel && !customLabel.startsWith(']')) {
+              this.setAtomCustomLabel(i, `]${customLabel}`);
+            }
+          }
+          break;
+        case 'normal':
+          for (let i = 0; i < this.getAllAtoms(); i++) {
+            const customLabel = this.getAtomCustomLabel(i);
+            if (customLabel?.startsWith(']')) {
+              this.setAtomCustomLabel(i, customLabel.slice(1));
+            }
+          }
+          break;
+        case 'auto':
+          for (let i = 0; i < this.getAllAtoms(); i++) {
+            const customLabel = this.getAtomCustomLabel(i);
+            if (customLabel) {
+              const atomLabel = this.getAtomLabel(i);
+              if (atomLabel === 'C') {
+                // normal
+                if (customLabel.startsWith(']')) {
+                  this.setAtomCustomLabel(i, customLabel.slice(1));
+                }
+              } else if (!customLabel.startsWith(']')) {
+                this.setAtomCustomLabel(i, `]${customLabel}`);
+              }
+            }
+          }
+          break;
+        case undefined:
+          // nothing to do
+          break;
+        default:
+          break;
+      }
+    };
+}

lib/extend/extendFromMolfile.js

@@ -1,5 +1,3 @@
-import { changeMolfileCustomLabelPosition } from './utils/changeMolfileCustomLabelPosition.js';
-
 export function extendFromMolfile(Molecule) {
   const _fromMolfile = Molecule.fromMolfile;
   Molecule.fromMolfile = function fromMolfile(molfile, options = {}) {
@@ -52,7 +50,7 @@ export function extendFromMolfile(Molecule) {
         }
       }
     }
-    changeMolfileCustomLabelPosition(molecule, customLabelPosition);
+    molecule.changeCustomLabelPosition(customLabelPosition);
     return molecule;
   };
 }

lib/extend/extendToMolfile.js

@@ -1,5 +1,3 @@
-import { changeMolfileCustomLabelPosition } from './utils/changeMolfileCustomLabelPosition.js';
-
 const CUSTOM_ATOMS_LABELS_TAGS = [
   'M  STY',
   'M  SLB',
@@ -23,7 +21,7 @@ export function extendToMolfile(Molecule) {
       customLabelPosition,
       removeCustomAtomLabels = false,
     } = options;
-    changeMolfileCustomLabelPosition(molecule, customLabelPosition);
+    molecule.changeCustomLabelPosition(customLabelPosition);
 
     const molfile = _toMolfile.call(molecule);
 

lib/extend/index.js

@@ -1,3 +1,4 @@
+import { appendChangeCustomLabelPosition } from './appendChangeCustomLabelPosition.js';
 import { appendGetNextCustomAtomLabel } from './appendGetNextCustomAtomLabel.js';
 import { extendFromMolfile } from './extendFromMolfile.js';
 import { extendToMolfile } from './extendToMolfile.js';
@@ -29,10 +30,11 @@ export function extendOCL(OCL) {
       options.funcTol,
     );
   };
+  appendChangeCustomLabelPosition(Molecule);
+  appendGetNextCustomAtomLabel(Molecule);
   extendFromMolfile(Molecule);
   extendToMolfile(Molecule);
   extendToRxn(Reaction, Molecule);
-  appendGetNextCustomAtomLabel(Molecule);
 
   function parseMoleculeFromText(text) {
     // Empty input

lib/index.d.ts

@@ -36,6 +36,8 @@ export interface MoleculeFromSmilesOptions {
   noStereo?: boolean;
 }
 
+type CustomLabelPosition = 'normal' | 'superscript' | 'auto' | undefined;
+
 interface FromMolfileOptions {
   /**
    * If set to 'superscript', it will add a ']' at the beginning of the custom label to be
@@ -46,7 +48,7 @@ interface FromMolfileOptions {
    * Default: undefined (keep as is)
    * @default undefined
    */
-  customLabelPosition?: 'normal' | 'superscript' | 'auto' | undefined;
+  customLabelPosition?: CustomLabelPosition;
 }
 
 interface ToMolfileOptions {
@@ -67,7 +69,7 @@ interface ToMolfileOptions {
    * Default: undefined (keep as is)
    * @default undefined
    */
-  customLabelPosition?: 'normal' | 'superscript' | 'auto' | undefined;
+  customLabelPosition?: CustomLabelPosition;
   /**
    * Remove custom atom labels
    * @default false
@@ -769,6 +771,14 @@ export declare class Molecule {
    */
   addSubstituent(substituent: Molecule, connectionAtom: number): number[];
 
+  /**
+   * Change the position of custom labels according to the provided option
+   * - 'superscript' will add a ] at the beginning of the custom label
+   * - 'normal' will remove a leading ] if present
+   * - 'auto' will set the label as superscript for non-carbon atoms and normal for carbon atoms
+   */
+  changeCustomLabelPosition(position?: CustomLabelPosition): string;
+
   /**
    * Copies this molecule including parity settings, if valid. The original
    * content of destMol is replaced. Helper arrays are not copied and need to be