remove all hydrogens of template residue SMILES to prevent crashes

stefdoerr · stefdoerr · commit 5ec65da20d29 · 2026-04-02T17:53:40.000+03:00
diff --git a/moleculekit/rdkittools.py b/moleculekit/rdkittools.py
@@ -306,6 +306,7 @@ def template_residue_from_smiles(
         sanitize=False, kekulize=False, assignStereo=False, _logger=_logger
     )
     rmol_smi = Chem.MolFromSmiles(smiles, sanitize=sanitizeSmiles)
+    rmol_smi = Chem.RemoveAllHs(rmol_smi)
     Chem.Kekulize(rmol_smi)
 
     res = rdFMCS.FindMCS(

Original file line number	Diff line number	Diff line change
`@@ -306,6 +306,7 @@ def template_residue_from_smiles(`
`306`	`306`	`sanitize=False, kekulize=False, assignStereo=False, _logger=_logger`
`307`	`307`	`)`
`308`	`308`	`rmol_smi = Chem.MolFromSmiles(smiles, sanitize=sanitizeSmiles)`
	`309`	`+ rmol_smi = Chem.RemoveAllHs(rmol_smi)`
`309`	`310`	`Chem.Kekulize(rmol_smi)`
`310`	`311`
`311`	`312`	`res = rdFMCS.FindMCS(`