feat: remap existing assignments when molecule is edited (#2779)

Closes: #1329
cheminfo · Dec 1, 2023 · 840c3e5 · 840c3e5
1 parent 683e511
commit 840c3e5
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Showing 7 changed files with 1,459 additions and 22 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -90,7 +90,7 @@
     "nmredata": "^0.9.7",
     "numeral": "^2.0.6",
     "openchemlib": "^8.7.1",
-    "openchemlib-utils": "^5.4.0",
+    "openchemlib-utils": "^5.6.0",
     "papaparse": "^5.4.1",
     "re-resizable": "6.9.11",
     "react-d3-utils": "^1.0.0",

diff --git a/src/component/modal/MoleculeStructureEditorModal.tsx b/src/component/modal/MoleculeStructureEditorModal.tsx
@@ -1,5 +1,7 @@
 /** @jsxImportSource @emotion/react */
-import { useState, useEffect, useCallback } from 'react';
+import { Molecule } from 'openchemlib/full';
+import { TopicMolecule } from 'openchemlib-utils';
+import { useState, useEffect, useCallback, useMemo } from 'react';
 import { StructureEditor, IStructureEditorProps } from 'react-ocl/full';
 import { ConfirmModal, Modal, useOnOff } from 'react-science/ui';
 
@@ -23,15 +25,28 @@ function MoleculeStructureEditorModal(
     isOpen = false,
   } = props;
 
+  const initialMolfile = selectedMolecule?.molfile;
+  const initialEnhancedMolfile = useMemo(() => {
+    if (!initialMolfile) {
+      return null;
+    }
+    // Add mapNo to molfile, so we can remap diaIDs after edition.
+    const molecule = Molecule.fromMolfile(initialMolfile);
+    const topicMolecule = new TopicMolecule(molecule);
+    topicMolecule.ensureMapNo();
+    const newMolfile = topicMolecule.toMolfile({ version: 3 });
+    return { molfile: newMolfile, topicMolecule };
+  }, [initialMolfile]);
+
   const [molfile, setMolfile] = useState<string | null>(null);
   const dispatch = useDispatch();
   useEffect(() => {
-    if (selectedMolecule) {
-      setMolfile(selectedMolecule.molfile);
+    if (initialEnhancedMolfile) {
+      setMolfile(initialEnhancedMolfile.molfile);
     } else {
       setMolfile(null);
     }
-  }, [selectedMolecule]);
+  }, [initialEnhancedMolfile]);
 
   const cb = useCallback<Exclude<IStructureEditorProps['onChange'], undefined>>(
     (newMolfile, molecule) => {
@@ -50,14 +65,18 @@ function MoleculeStructureEditorModal(
 
   const handleSave = useCallback(() => {
     if (molfile) {
-      if (selectedMolecule) {
+      if (selectedMolecule && initialEnhancedMolfile) {
         const { id, label } = selectedMolecule;
+        const editedMolecule = Molecule.fromMolfile(molfile);
+        const mappings =
+          initialEnhancedMolfile.topicMolecule.getDiaIDsMapping(editedMolecule);
         dispatch({
           type: 'SET_MOLECULE',
           payload: {
             molfile,
             id,
             label,
+            mappings,
           },
         });
         onClose('replace');
@@ -72,7 +91,14 @@ function MoleculeStructureEditorModal(
         onClose('new');
       }
     }
-  }, [molfile, selectedMolecule, dispatch, floatMoleculeOnSave, onClose]);
+  }, [
+    molfile,
+    selectedMolecule,
+    initialEnhancedMolfile,
+    dispatch,
+    floatMoleculeOnSave,
+    onClose,
+  ]);
 
   return (
     <ConfirmModal
@@ -85,7 +111,7 @@ function MoleculeStructureEditorModal(
     >
       <Modal.Body>
         <StructureEditor
-          initialMolfile={selectedMolecule?.molfile}
+          initialMolfile={initialEnhancedMolfile?.molfile}
           svgMenu
           fragment={false}
           onChange={cb}
@@ -115,5 +141,3 @@ export function useMoleculeEditor(floatMoleculeOnSave = false) {
   );
   return { modal, openMoleculeEditor };
 }
-
-export default MoleculeStructureEditorModal;
diff --git a/src/component/reducer/actions/MoleculeActions.ts b/src/component/reducer/actions/MoleculeActions.ts
@@ -2,7 +2,7 @@ import { Logger } from 'cheminfo-types';
 import { FifoLogger } from 'fifo-logger';
 import { Draft } from 'immer';
 import OCL from 'openchemlib/full';
-import { nbLabileH, getAtoms } from 'openchemlib-utils';
+import { nbLabileH, getAtoms, TopicMolecule } from 'openchemlib-utils';
 
 import {
   PredictedSpectraResult,
@@ -25,6 +25,7 @@ import { ActionType } from '../types/ActionType';
 import { unlinkRange } from './RangesActions';
 import { setActiveTab } from './ToolsActions';
 import { unlinkZone } from './ZonesActions';
+import { deepReplaceDiaIDs } from './utilities/deepReplaceDiaIDs';
 
 interface AddMoleculeProps {
   molfile: string;
@@ -35,7 +36,12 @@ type AddMoleculesAction = ActionType<
   'ADD_MOLECULES',
   { molecules: StateMolecule[] }
 >;
-type SetMoleculeAction = ActionType<'SET_MOLECULE', Required<StateMolecule>>;
+type SetMoleculeAction = ActionType<
+  'SET_MOLECULE',
+  Required<StateMolecule> & {
+    mappings?: ReturnType<TopicMolecule['getDiaIDsMapping']>;
+  }
+>;
 type DeleteMoleculeAction = ActionType<
   'DELETE_MOLECULE',
   { id: string; assignmentData: AssignmentContext }
@@ -108,8 +114,8 @@ function handleAddMolecules(draft: Draft<State>, action: AddMoleculesAction) {
   }
 }
 
-function setMolecule(draft: Draft<State>, props: Required<StateMolecule>) {
-  const { id, label, molfile } = props;
+function setMolecule(draft: Draft<State>, props: SetMoleculeAction['payload']) {
+  const { id, label, molfile, mappings } = props;
   MoleculeManager.setMolfile(draft.molecules, {
     id,
     label,
@@ -121,6 +127,10 @@ function setMolecule(draft: Draft<State>, props: Required<StateMolecule>) {
    */
   const index = draft.molecules.findIndex((molecule) => molecule.id === id);
 
+  if (mappings) {
+    deepReplaceDiaIDs(draft, mappings);
+  }
+
   changeSpectraRelativeSum(
     draft,
     id,
@@ -328,8 +338,7 @@ function getFloatingMoleculeInitialPosition(id: string, draft: Draft<State>) {
   const rows = Math.floor(height / baseHeight);
   const moleculeKeys = Object.keys(molecules);
 
-  let index = 0;
-
+  let index: number;
   if (!molecules[id]) {
     index = moleculeKeys.length - 1;
   } else {