Fix symmetry to use Z.

lanl · Jan 23, 2024 · fbe3171 · fbe3171
1 parent aca6b39
commit fbe3171
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/architector/io_symmetry.py b/architector/io_symmetry.py
@@ -341,7 +341,10 @@ class containing the core geometry information.
             raise ValueError('{} not in known ligTypes'.format(ligInput['ligType']))
         ligobmol = io_obabel.get_obmol_smiles(ligInput['smiles']) # Get obmol for each lig 
         lig_charges.append(ligobmol.GetTotalCharge()) # Calculate total charge.
-        lig_num_atoms.append(ligobmol.NumAtoms()) # Get number of atoms (estimate steric contribution)
+        lig_zs=[]
+        for atom in io_obabel.ob.OBMolAtomIter(ligobmol):
+            lig_zs.append(atom.GetAtomicNum())
+        lig_num_atoms.append(np.sum(lig_zs)) # Get sum of z of atoms (estimate steric contribution)
         selected_con_lists.append(possible_core_cons)
 
     # Re-order so highest denticity ligand is always placed first.