Fix incorrect CIP values for some aromatic atropisomers (rdkit#7957)

e-kwsm · Nov 9, 2024 · 57a9d29 · 57a9d29
1 parent 75e8858
commit 57a9d29
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Showing 6 changed files with 266 additions and 70 deletions.
diff --git a/Code/GraphMol/CIPLabeler/Node.cpp b/Code/GraphMol/CIPLabeler/Node.cpp
@@ -91,6 +91,8 @@ bool Node::isSet(int mask) const { return mask & d_flags; }
 
 bool Node::isDuplicate() const { return d_flags & DUPLICATE; }
 
+bool Node::isDuplicateOrH() const { return d_flags & DUPLICATE_OR_H; }
+
 bool Node::isTerminal() const {
   return d_visit.empty() || (isExpanded() && d_edges.size() == 1);
 }

diff --git a/Code/GraphMol/CIPLabeler/Node.h b/Code/GraphMol/CIPLabeler/Node.h
@@ -46,14 +46,22 @@ class Node {
   /**
    * Mask to check if a node is duplicated.
    */
-  static const int DUPLICATE = 0x6;
+
+  static const int DUPLICATE = RING_DUPLICATE | BOND_DUPLICATE;
 
   /**
    * Node was created for an implicit hydrogen,
    * the 'atom' value will be null.
    */
   static const int IMPL_HYDROGEN = 0x8;
 
+  /**
+   * Mask to check if a node is duplicated or created for an implicit H (not a
+   * primary node).
+   */
+  static const int DUPLICATE_OR_H =
+      RING_DUPLICATE | BOND_DUPLICATE | IMPL_HYDROGEN;
+
   Node() = delete;
   Node(const Node &) = delete;
   Node &operator=(const Node &) = delete;
@@ -81,6 +89,8 @@ class Node {
 
   bool isDuplicate() const;
 
+  bool isDuplicateOrH() const;
+
   bool isTerminal() const;
 
   bool isExpanded() const;