Merge pull request #79 from molssi-seamm/dev

Bugfix: creating H2 from SMILES failed
molssi-seamm · Aug 5, 2024 · 8a53509 · 8a53509
2 parents 9c5a57e + a6e2958
commit 8a53509
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -1,6 +1,10 @@
 =======
 History
 =======
+2024.8.5 -- Bugfix: creating H2 from SMILES failed
+    * Fixed bug where creating molecules consisting of just hydrogen failed because
+      RDKit by default ignores all hydrogens when reorienting the molecule.
+
 2024.6.21 -- Switching default for SMILES to RDKit rather than OpenBabel
     * RDKit seems more robust, and also the atom typing uses RDkit, so compatibility is
       important.

diff --git a/molsystem/smiles.py b/molsystem/smiles.py
@@ -142,7 +142,7 @@ def from_smiles(self, smiles, name=None, reorient=True, rdkit=True):
         if reorient:
             rdkMol = self.to_RDKMol()
             rdkConf = rdkMol.GetConformers()[0]
-            Chem.rdMolTransforms.CanonicalizeConformer(rdkConf)
+            Chem.rdMolTransforms.CanonicalizeConformer(rdkConf, ignoreHs=False)
             self.from_RDKMol(rdkMol)
 
         if name is not None: