CXSMILES optimisation - don't create and swap a new Pseudo atom if th…

…e atom to set the label on is already a pseudo atom.
cdk · Feb 3, 2022 · 454fbe9 · 454fbe9
1 parent ade938a
commit 454fbe9
Showing 1 changed file with 12 additions and 5 deletions.
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java
@@ -497,7 +497,18 @@ private void assignCxSmilesInfo(IChemObjectBuilder bldr,
                     continue;
 
                 IAtom old = atoms.get(e.getKey());
-                IPseudoAtom pseudo = bldr.newInstance(IPseudoAtom.class);
+                IPseudoAtom pseudo;
+                if (old instanceof IPseudoAtom) {
+                    pseudo = (IPseudoAtom) old;
+                } else {
+                    // possibly a warning, is "CCO |$R$|" valid?
+                    pseudo = bldr.newInstance(IPseudoAtom.class);
+                    IAtomContainer mol = atomToMol.get(old);
+                    AtomContainerManipulator.replaceAtomByAtom(mol, old, pseudo);
+                    atomToMol.put(pseudo, mol);
+                    atoms.set(e.getKey(), mol.getAtom(old.getIndex()));
+                }
+
                 String val = e.getValue();
 
                 // specialised label handling
@@ -509,10 +520,6 @@ else if (val.startsWith("_AP")) // attachment point
                 pseudo.setLabel(val);
                 pseudo.setAtomicNumber(0);
                 pseudo.setImplicitHydrogenCount(0);
-                IAtomContainer mol = atomToMol.get(old);
-                AtomContainerManipulator.replaceAtomByAtom(mol, old, pseudo);
-                atomToMol.put(pseudo, mol);
-                atoms.set(e.getKey(), mol.getAtom(old.getIndex()));
             }
         }