From fbe3171d64ed82a2eef5cd5d4243f0e691e07b3e Mon Sep 17 00:00:00 2001 From: Michael Taylor Date: Tue, 23 Jan 2024 08:13:21 -0700 Subject: [PATCH] Fix symmetry to use Z. --- architector/io_symmetry.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/architector/io_symmetry.py b/architector/io_symmetry.py index 6571bdb..c1decd7 100644 --- 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.