feat: CT exports with alias atoms

Author: lpatiny

package-lock.json

@@ -92,7 +92,7 @@
     "nmr-processing": "^19.1.0",
     "numeral": "^2.0.6",
     "openchemlib": "^9.8.0",
-    "openchemlib-utils": "^8.3.1",
+    "openchemlib-utils": "^8.4.0",
     "papaparse": "^5.5.3",
     "react-d3-utils": "^3.1.2",
     "react-dropzone": "^14.3.8",

package.json

@@ -193,14 +193,20 @@ export default function MoleculePanelHeader(props: MoleculePanelHeaderProps) {
     [molecules, currentIndex, copyHandler, saveAsPNGHandler, saveAsSVGHandler],
   );
 
-  function handlePasteMolfileAction() {
+  function handlePasteMoleculeAction() {
     onClickPastMolecule?.();
-    void readText().then(handlePasteMolfile);
+    void readText().then(handlePasteMolecule);
   }
-  async function handlePasteMolfile(molfile: string | undefined) {
-    if (!molfile) return;
+
+  /**
+   * The moleecule pasted could be SMILES, molfile or SDF
+   * @param text - text from clipboard
+   * @returns
+   */
+  async function handlePasteMolecule(text: string | undefined) {
+    if (!text) return;
     try {
-      const molecules = getMolecules(molfile);
+      const molecules = getMolecules(text);
       dispatch({ type: 'ADD_MOLECULES', payload: { molecules } });
     } catch {
       toaster.show({
@@ -296,7 +302,7 @@ export default function MoleculePanelHeader(props: MoleculePanelHeaderProps) {
         <Toolbar.Item
           tooltip="Paste SMILES or molfile"
           icon={<FaPaste />}
-          onClick={handlePasteMolfileAction}
+          onClick={handlePasteMoleculeAction}
         />
         {renderSource === 'moleculePanel' && (
           <Toolbar.Item
@@ -350,7 +356,7 @@ export default function MoleculePanelHeader(props: MoleculePanelHeaderProps) {
       <ClipboardFallbackModal
         mode={shouldFallback}
         onDismiss={cleanShouldFallback}
-        onReadText={handlePasteMolfile}
+        onReadText={handlePasteMolecule}
         text={text}
         label="Molfile"
       />

src/component/panels/MoleculesPanel/MoleculePanelHeader.tsx

@@ -12,6 +12,7 @@ import {
 import { BlobWriter, TextReader, ZipWriter } from '@zip.js/zip.js';
 import fileSaver from 'file-saver';
 import * as OCL from 'openchemlib';
+import { toMolfile } from 'openchemlib-utils';
 
 import type { State } from '../component/reducer/Reducer.js';
 
@@ -204,8 +205,12 @@ export async function exportForCT(options: ExportForCTOptions) {
   const { molfile } = molecules[0];
   const molecule = OCL.Molecule.fromMolfile(molfile);
   const molFileName = molecule.getMolecularFormula().formula;
+  const ctMolfile = toMolfile(molecule, {
+    includeCustomAtomLabelsAsALines: true,
+    customLabelPosition: 'normal',
+  });
 
-  await zip.add(`${molFileName}.mol`, new TextReader(molecule.toMolfile()));
+  await zip.add(`${molFileName}.mol`, new TextReader(ctMolfile));
 
   const blob = await zip.close();
   fileSaver.saveAs(blob, `${name}.zip`);

src/data/SpectraManager.ts

@@ -98,6 +98,12 @@ function getLabelNumber(reserveNumbers: number[]): number {
   return 1;
 }
 
+/**
+ * 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
+ */
 export function getMolecules(text: string) {
   // parse SDF
   if (/v[23]000/i.test(text)) {