feat: provide coordinates in idcode

cheminfo · Oct 15, 2024 · f609534 · f609534
1 parent a099f97
commit f609534
Showing 1 changed file with 34 additions and 6 deletions.
diff --git a/lib/canvas_editor/init/canvas_editor_element.js b/lib/canvas_editor/init/canvas_editor_element.js
@@ -72,7 +72,7 @@ function initCanvasEditorElement(CanvasEditor, Molecule, ReactionEncoder) {
      */
     setMolecule(molecule) {
       this.fragment = molecule.isFragment();
-      this.idcode = molecule.getIDCode();
+      this.idcode = `${molecule.getIDCode()} ${molecule.getIDCoordinates()}`;
 
       this.#editor.setMolecule(molecule);
     }
@@ -91,7 +91,13 @@ function initCanvasEditorElement(CanvasEditor, Molecule, ReactionEncoder) {
      */
     setReaction(reaction) {
       this.fragment = reaction.isFragment();
-      this.idcode = ReactionEncoder.encode(reaction);
+      this.idcode = ReactionEncoder.encode(
+        reaction,
+        true,
+        ReactionEncoder.INCLUDE_MAPPING |
+          ReactionEncoder.INCLUDE_COORDS |
+          ReactionEncoder.RETAIN_REACTANT_AND_PRODUCT_ORDER,
+      );
 
       this.#editor.setReaction(reaction);
     }
@@ -146,11 +152,27 @@ function initCanvasEditorElement(CanvasEditor, Molecule, ReactionEncoder) {
       }
     }
 
+    /**
+     * @param {string} idcodeAndCoordinates
+     */
+    #moleculeFromIdCode(idcodeAndCoordinates) {
+      const index = idcodeAndCoordinates.indexOf(' ');
+
+      if (index === -1) {
+        return Molecule.fromIDCode(idcodeAndCoordinates);
+      }
+
+      const idcode = idcodeAndCoordinates.slice(0, index);
+      const coordinates = idcodeAndCoordinates.slice(index + 1);
+
+      return Molecule.fromIDCode(idcode, coordinates);
+    }
+
     /**
      * @this {CanvasEditorElement}
      */
     #initMolecule() {
-      const molecule = Molecule.fromIDCode(this.idcode);
+      const molecule = this.#moleculeFromIdCode(this.idcode);
       molecule.setFragment(this.fragment);
 
       this.#editor.setMolecule(molecule);
@@ -160,7 +182,7 @@ function initCanvasEditorElement(CanvasEditor, Molecule, ReactionEncoder) {
      * @this {CanvasEditorElement}
      */
     #initReaction() {
-      const reaction = ReactionEncoder.decode(this.idcode);
+      const reaction = ReactionEncoder.decode(this.idcode, true);
       reaction.setFragment(this.fragment);
 
       this.#editor.setReaction(reaction);
@@ -198,13 +220,19 @@ function initCanvasEditorElement(CanvasEditor, Molecule, ReactionEncoder) {
         switch (this.mode) {
           case CanvasEditorElement.MODE.MOLECULE: {
             const molecule = this.getMolecule();
-            this.idcode = molecule.getIDCode();
+            this.idcode = `${molecule.getIDCode()} ${molecule.getIDCoordinates()}`;
             this.fragment = molecule.isFragment();
             break;
           }
           case CanvasEditorElement.MODE.REACTION: {
             const reaction = this.getReaction();
-            this.idcode = ReactionEncoder.encode(reaction);
+            this.idcode = ReactionEncoder.encode(
+              reaction,
+              true,
+              ReactionEncoder.INCLUDE_MAPPING |
+                ReactionEncoder.INCLUDE_COORDS |
+                ReactionEncoder.RETAIN_REACTANT_AND_PRODUCT_ORDER,
+            );
             this.fragment = reaction.isFragment();
             break;
           }