When I have a Boron atom in a compound I am not able to get a MMFF94
forcefield
(RDKit 2014_03_1). Is this an issue with the MMFF94 forcefield
specification or with the implementation of it in RDKit?
The following code reproduces this problem.
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
def emin(smiles):
mol = Chem.MolFromSmiles(smiles) # no problem mol
mol_h = AllChem.AddHs(mol) # always add Hs
conformer_ids = AllChem.EmbedMultipleConfs(mol_h, numConfs = 5)
prop = AllChem.MMFFGetMoleculeProperties(mol_h, mmffVariant="MMFF94")
for conf_id in conformer_ids:
ff = AllChem.MMFFGetMoleculeForceField(mol_h, prop, conf_id)
print ff # for boron none
emin("CCC(C)(C)C") # works
emin("BCC(C)(C)C") # doesnt work
Output:
jp@jp-Galago-UltraPro:~/tmp$ ./emin.py
<rdkit.ForceField.rdForceField.ForceField object at 0x7fcb96e72ec0>
<rdkit.ForceField.rdForceField.ForceField object at 0x7fcb96e72e50>
<rdkit.ForceField.rdForceField.ForceField object at 0x7fcb96e72f30>
<rdkit.ForceField.rdForceField.ForceField object at 0x7fcb96e72ec0>
<rdkit.ForceField.rdForceField.ForceField object at 0x7fcb96e72e50>
None
None
None
None
None
Any ideas what is going on in the Boron-containing case?
-
Jean-Paul Ebejer
Early Stage Researcher
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