feat: support pasting chemical group

package.json

@@ -81,6 +81,7 @@
     "d3-zoom": "^3.0.0",
     "dlv": "^1.1.3",
     "eventemitter3": "^5.0.4",
+    "expand-chemical-groups": "^1.0.0",
     "fifo-logger": "^2.0.1",
     "file-collection": "^6.7.0",
     "file-saver": "^2.0.5",

src/component/panels/MoleculesPanel/MoleculePanelHeader.tsx

@@ -251,7 +251,7 @@ export default function MoleculePanelHeader(props: MoleculePanelHeaderProps) {
   }
 
   /**
-   * The moleecule pasted could be SMILES, molfile or SDF
+   * The molecule pasted could be SMILES, molfile, SDF or chemical groups
    * @param text - text from clipboard
    * @returns
    */
@@ -430,9 +430,10 @@ export default function MoleculePanelHeader(props: MoleculePanelHeaderProps) {
           />
         )}
         <Toolbar.Item
-          tooltip="Paste SMILES or molfile"
+          tooltip="Paste SMILES, molfile or chemical groups"
           icon={<FaPaste />}
           onClick={handlePasteMoleculeAction}
+          data-testid="paste-molecule-action"
         />
         {renderSource === 'moleculePanel' && (
           <Toolbar.Item
@@ -502,7 +503,7 @@ export default function MoleculePanelHeader(props: MoleculePanelHeaderProps) {
         onDismiss={cleanShouldFallback}
         onReadText={handlePasteMolecule}
         text={text}
-        label="Enter here a molfile or SMILES"
+        label="Enter here a molfile, SMILES or chemical groups (e.g. HAlaGlyOH)"
       />
     </PanelHeader>
   );

src/data/molecules/Molecule.ts

@@ -1,4 +1,5 @@
 import type { MoleculeView, StateMolecule } from '@zakodium/nmrium-core';
+import { expandChemicalGroups } from 'expand-chemical-groups';
 import { Molecule } from 'openchemlib';
 
 import getAtomsFromMF from '../utilities/getAtomsFromMF.js';
@@ -36,17 +37,37 @@ type InitializeMoleculeOptions = { text: string } & Omit<
   'molfile'
 >;
 
+export const parseErrorMessage =
+  'Failed to parse SMILES, molfile or chemical groups. Please paste a valid format';
+
+function parseMoleculeText(text: string): Molecule {
+  const moleculeText = text.trim();
+  if (!moleculeText) {
+    throw new Error(parseErrorMessage);
+  }
+
+  if (/v[23]000/i.test(text)) {
+    return Molecule.fromMolfile(text);
+  }
+
+  try {
+    return Molecule.fromSmiles(moleculeText);
+  } catch {
+    // fallback to expanding chemical groups if SMILES parsing fails
+    // for example HAlaGlyOH, BocAlaOH ...etc.
+    // TODO a way to check if the text is a valid chemical group instead of fallback if can not read as SMILES
+    return expandChemicalGroups(moleculeText);
+  }
+}
+
 export function initMolecule(
   options: InitializeMoleculeOptions,
 ): StateMoleculeExtended {
   const { id = crypto.randomUUID(), label = 'p#', text, selector } = options;
+  const molecule = parseMoleculeText(text);
 
-  const molecule = Molecule.fromText(text);
-
-  if (!molecule) {
-    throw new Error(
-      'Failed to parse SMILES or molfile. Please paste a valid format',
-    );
+  if (molecule.getAllAtoms() === 0) {
+    throw new Error(parseErrorMessage);
   }
   const molfile = molecule.toMolfileV3();
   const mfInfo = molecule.getMolecularFormula();

src/data/molecules/MoleculeManager.ts

@@ -3,7 +3,9 @@ import { readSDF } from '@zakodium/nmrium-core-plugins';
 import { Molecule } from 'openchemlib';
 
 import type { StateMoleculeExtended } from './Molecule.js';
-import { initMolecule } from './Molecule.js';
+import { initMolecule, parseErrorMessage } from './Molecule.js';
+
+export { parseErrorMessage } from './Molecule.js';
 
 //TODO: Move molecule initialization to nmrium-core and log an error if the molecule cannot be parsed.
 export function fromJSON(
@@ -105,9 +107,6 @@ function getLabelNumber(reserveNumbers: number[]): number {
   return 1;
 }
 
-export const parseErrorMessage =
-  'Failed to parse SMILES or molfile. Please paste a valid format';
-
 function validateMolecules(molecules: StateMolecule[]) {
   if (!molecules?.length) {
     throw new Error(parseErrorMessage);
@@ -132,10 +131,8 @@ function validateMolecules(molecules: StateMolecule[]) {
 }
 
 /**
- * We will extract the molecule(s) from the text.
- * Because a molfile is actually a SDF we can just call 'readSDF' method
- * @param text - text containing one or several molecules in SMILES, molfile or SDF format
- * @returns
+ * Read SDF records and validate their structures.
+ * @param text - SDF content
  */
 
 function parseSDF(text: string) {
@@ -148,12 +145,17 @@ function parseSDF(text: string) {
   }
 }
 
+/**
+ * Parse SDF records or a single molfile, SMILES or chemical-group.
+ * @param text - Pasted structure text
+ */
 export function getMolecules(text?: string) {
   if (!text?.trim()) {
     throw new Error(parseErrorMessage);
   }
 
-  const isSDF = /v[23]000/i.test(text);
+  // identifies an SDF file by checking for the presence of the '$$$$' separator
+  const isSDF = text.includes('$$$$');
 
   return isSDF ? parseSDF(text) : [initMolecule({ text })];
 }

test-e2e/panels/structures.test.ts

@@ -408,9 +408,9 @@ test('molecules 1H spectrum', async ({ page, browserName }) => {
   if (browserName !== 'webkit') {
     await test.step('Check copy as molfile V3 or V2 and paste', async () => {
       await clickExportMenuOption(nmrium, 'text=Copy as molfile V3');
-      await nmrium.clickToolByTitle('Paste SMILES or molfile');
+      await nmrium.page.getByTestId('paste-molecule-action').click();
       await clickExportMenuOption(nmrium, 'text=Copy as molfile V2');
-      await nmrium.clickToolByTitle('Paste SMILES or molfile');
+      await nmrium.page.getByTestId('paste-molecule-action').click();
 
       await expect(
         nmrium.page.locator('_react=MoleculePanel >> text=5 / 5'),