#4878 – Replace of Linking nodes

epam · Aug 5, 2024 · fe6a743 · fe6a743
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commit fe6a743
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Showing 17 changed files with 136 additions and 36 deletions.
diff --git a/...s-when-3f720--a-CHEM-on-canvas-while-Bond-tool-is-selected-1-chromium-linux.png b/...s-when-3f720--a-CHEM-on-canvas-while-Bond-tool-is-selected-1-chromium-linux.png
diff --git a/...s-when-989f0-a-CHEM-on-canvas-while-Erase-tool-is-selected-1-chromium-linux.png b/...s-when-989f0-a-CHEM-on-canvas-while-Erase-tool-is-selected-1-chromium-linux.png
diff --git a/...s-when-c6566-EM-on-canvas-while-Selection-tool-is-selected-1-chromium-linux.png b/...s-when-c6566-EM-on-canvas-while-Selection-tool-is-selected-1-chromium-linux.png
diff --git a/...ots/RNA-Library-Base-preview-window-when-hovered-on-canvas-1-chromium-linux.png b/...ots/RNA-Library-Base-preview-window-when-hovered-on-canvas-1-chromium-linux.png
diff --git a/...snapshots/RNA-Library-Move-Bases-on-canvas-to-new-position-1-chromium-linux.png b/...snapshots/RNA-Library-Move-Bases-on-canvas-to-new-position-1-chromium-linux.png
diff --git a/...hots/RNA-Library-Move-Phosphates-on-canvas-to-new-position-1-chromium-linux.png b/...hots/RNA-Library-Move-Phosphates-on-canvas-to-new-position-1-chromium-linux.png
diff --git a/...NA-Library-Phosphate-preview-window-when-hovered-on-canvas-1-chromium-linux.png b/...NA-Library-Phosphate-preview-window-when-hovered-on-canvas-1-chromium-linux.png
diff --git a/...-selected-by-selection-tool-CHEM-to-new-position-on-canvas-1-chromium-linux.png b/...-selected-by-selection-tool-CHEM-to-new-position-on-canvas-1-chromium-linux.png
diff --git a/...builde-be9b3-ed-monomers-switches-RNA-Builder-to-edit-mode-1-chromium-linux.png b/...builde-be9b3-ed-monomers-switches-RNA-Builder-to-edit-mode-1-chromium-linux.png
diff --git a/...-nucle-3234e-dify-sugar-and-phosphate-as-it-one-nucleotide-4-chromium-linux.png b/...-nucle-3234e-dify-sugar-and-phosphate-as-it-one-nucleotide-4-chromium-linux.png
diff --git a/...t-nucle-403dc-hosphate-nucleoside-should-become-nucleotide-4-chromium-linux.png b/...t-nucle-403dc-hosphate-nucleoside-should-become-nucleotide-4-chromium-linux.png
diff --git a/...edit-in-RNA-Builder-Select-one-nucleotide-and-modify-sugar-2-chromium-linux.png b/...edit-in-RNA-Builder-Select-one-nucleotide-and-modify-sugar-2-chromium-linux.png
diff --git a/...edit-in-RNA-Builder-Select-one-nucleotide-and-modify-sugar-3-chromium-linux.png b/...edit-in-RNA-Builder-Select-one-nucleotide-and-modify-sugar-3-chromium-linux.png
diff --git a/...edit-in-RNA-Builder-Select-one-nucleotide-and-modify-sugar-5-chromium-linux.png b/...edit-in-RNA-Builder-Select-one-nucleotide-and-modify-sugar-5-chromium-linux.png
diff --git a/...mode.spec.ts-snapshots/Sequence-Mode-Select-drop-down-menu-1-chromium-linux.png b/...mode.spec.ts-snapshots/Sequence-Mode-Select-drop-down-menu-1-chromium-linux.png
diff --git a/packages/ketcher-core/src/application/editor/modes/SequenceMode.ts b/packages/ketcher-core/src/application/editor/modes/SequenceMode.ts
@@ -1070,28 +1070,78 @@ export class SequenceMode extends BaseMode {
           selectionRange[0].nodeIndexOverall - 1,
         );
 
-        selectionRange.forEach((nodeSelection) => {
-          if (nodeSelection.node instanceof LinkerSequenceNode) {
-            editor.events.openConfirmationDialog.dispatch({
-              confirmationText:
-                'Symbol @ can represent multiple monomers, all of them are going to be deleted. Do you want to proceed?',
-              onConfirm: () =>
-                this.replaceSelectionWithMonomer(
+        if (
+          selectionRange.some(
+            (nodeSelection) => nodeSelection.node instanceof LinkerSequenceNode,
+          )
+        ) {
+          editor.events.openConfirmationDialog.dispatch({
+            confirmationText:
+              'Symbol @ can represent multiple monomers, all of them are going to be deleted. Do you want to proceed?',
+            onConfirm: () => {
+              selectionRange.forEach((nodeSelection) => {
+                previousReplacedNode = this.replaceSelectionWithMonomer(
                   monomerItem,
                   nodeSelection,
                   modelChanges,
                   previousReplacedNode,
-                ),
-            });
-          } else {
+                );
+              });
+
+              modelChanges.addOperation(new ReinitializeModeOperation());
+              editor.renderersContainer.update(modelChanges);
+              SequenceRenderer.moveCaretForward();
+              history.update(modelChanges);
+            },
+          });
+        } else if (
+          selectionRange.some(
+            (nodeSelection) =>
+              nodeSelection.node.monomer.sideConnections.length !== 0 &&
+              Object.values(
+                nodeSelection.node.monomer.attachmentPointsToBonds,
+              ).reduce((count, ap) => {
+                if (ap) {
+                  count++;
+                }
+                return count;
+              }, 0) > (monomerItem.attachmentPoints?.length ?? 0),
+          )
+        ) {
+          editor.events.openConfirmationDialog.dispatch({
+            confirmationText:
+              'Side chain connections will be deleted during replacement. Do you want to proceed?',
+            onConfirm: () => {
+              selectionRange.forEach((nodeSelection) => {
+                previousReplacedNode = this.replaceSelectionWithMonomer(
+                  monomerItem,
+                  nodeSelection,
+                  modelChanges,
+                  previousReplacedNode,
+                );
+              });
+
+              modelChanges.addOperation(new ReinitializeModeOperation());
+              editor.renderersContainer.update(modelChanges);
+              SequenceRenderer.moveCaretForward();
+              history.update(modelChanges);
+            },
+          });
+        } else {
+          selectionRange.forEach((nodeSelection) => {
             previousReplacedNode = this.replaceSelectionWithMonomer(
               monomerItem,
               nodeSelection,
               modelChanges,
               previousReplacedNode,
             );
-          }
-        });
+          });
+
+          modelChanges.addOperation(new ReinitializeModeOperation());
+          editor.renderersContainer.update(modelChanges);
+          SequenceRenderer.moveCaretForward();
+          history.update(modelChanges);
+        }
       });
     } else {
       const newNodePosition = this.getNewNodePosition();
@@ -1107,12 +1157,12 @@ export class SequenceMode extends BaseMode {
       modelChanges.merge(
         this.insertNewSequenceFragment(newMonomerSequenceNode),
       );
-    }
 
-    modelChanges.addOperation(new ReinitializeModeOperation());
-    editor.renderersContainer.update(modelChanges);
-    SequenceRenderer.moveCaretForward();
-    history.update(modelChanges);
+      modelChanges.addOperation(new ReinitializeModeOperation());
+      editor.renderersContainer.update(modelChanges);
+      SequenceRenderer.moveCaretForward();
+      history.update(modelChanges);
+    }
   }
 
   private replaceSelectionWithPreset(
@@ -1195,14 +1245,70 @@ export class SequenceMode extends BaseMode {
           selectionRange[0].nodeIndexOverall - 1,
         );
 
-        selectionRange.forEach((nodeSelection) => {
-          previousReplacedNode = this.replaceSelectionWithPreset(
-            preset,
-            nodeSelection,
-            modelChanges,
-            previousReplacedNode,
-          );
-        });
+        if (
+          selectionRange.some(
+            (nodeSelection) => nodeSelection.node instanceof LinkerSequenceNode,
+          )
+        ) {
+          editor.events.openConfirmationDialog.dispatch({
+            confirmationText:
+              'Symbol @ can represent multiple monomers, all of them are going to be deleted. Do you want to proceed?',
+            onConfirm: () => {
+              selectionRange.forEach((nodeSelection) => {
+                previousReplacedNode = this.replaceSelectionWithPreset(
+                  preset,
+                  nodeSelection,
+                  modelChanges,
+                  previousReplacedNode,
+                );
+              });
+
+              modelChanges.addOperation(new ReinitializeModeOperation());
+              editor.renderersContainer.update(modelChanges);
+              SequenceRenderer.moveCaretForward();
+              history.update(modelChanges);
+            },
+          });
+        } else if (
+          selectionRange.some(
+            (nodeSelection) =>
+              nodeSelection.node.monomer.sideConnections.length !== 0,
+          )
+        ) {
+          editor.events.openConfirmationDialog.dispatch({
+            confirmationText:
+              'Side chain connections will be deleted during replacement. Do you want to proceed?',
+            onConfirm: () => {
+              selectionRange.forEach((nodeSelection) => {
+                previousReplacedNode = this.replaceSelectionWithPreset(
+                  preset,
+                  nodeSelection,
+                  modelChanges,
+                  previousReplacedNode,
+                );
+              });
+
+              modelChanges.addOperation(new ReinitializeModeOperation());
+              editor.renderersContainer.update(modelChanges);
+              SequenceRenderer.moveCaretForward();
+              history.update(modelChanges);
+            },
+          });
+        } else {
+          selectionRange.forEach((nodeSelection) => {
+            previousReplacedNode = this.replaceSelectionWithPreset(
+              preset,
+              nodeSelection,
+              modelChanges,
+              previousReplacedNode,
+            );
+          });
+
+          modelChanges.addOperation(new ReinitializeModeOperation());
+          editor.renderersContainer.update(modelChanges);
+          SequenceRenderer.moveCaretForward();
+          history.update(modelChanges);
+        }
       });
     } else {
       const newNodePosition = this.getNewNodePosition();
@@ -1246,12 +1352,12 @@ export class SequenceMode extends BaseMode {
       }
 
       modelChanges.merge(this.insertNewSequenceFragment(newPresetNode));
-    }
 
-    modelChanges.addOperation(new ReinitializeModeOperation());
-    editor.renderersContainer.update(modelChanges);
-    SequenceRenderer.moveCaretForward();
-    history.update(modelChanges);
+      modelChanges.addOperation(new ReinitializeModeOperation());
+      editor.renderersContainer.update(modelChanges);
+      SequenceRenderer.moveCaretForward();
+      history.update(modelChanges);
+    }
   }
 
   private insertNewSequenceItem(editor: CoreEditor, enteredSymbol: string) {

diff --git a/packages/ketcher-macromolecules/src/components/monomerLibrary/MonomerLibrary.tsx b/packages/ketcher-macromolecules/src/components/monomerLibrary/MonomerLibrary.tsx
@@ -40,12 +40,6 @@ const COPY = '_Copy';
 const MonomerLibrary = () => {
   const presetsRef = useRef<IRnaPreset[]>([]);
   const dispatch = useAppDispatch();
-  // const layoutMode = useLayoutMode();
-  // const isSequenceEditInRNABuilderMode = props?.isSequenceEditInRNABuilderMode;
-  // const isSequenceMode = layoutMode === 'sequence-layout-mode';
-  // const isDisabledTabs = isSequenceMode;
-  // const isDisabledTabsPanels =
-  //   isSequenceMode && !isSequenceEditInRNABuilderMode;
 
   useEffect(() => {
     dispatch(setSearchFilter(''));