Thanks for your amazing work!
When handling ligand molecules with RDKit, discrepancies in bond types may arise, such as carbon atoms exhibiting pentavalency and nitrogen atoms displaying tetravalent. Why these errors happen and how to rectify them for accurate molecular processing?
The example reading code,:
mol = Chem.MolFromMolFile('2v5z_A_rec_2v5z_fad_lig_tt_min_0.sdf')
The sdf file is attached.
The log I got: "Explicit valence for atom # 13 C, 5, is greater than permitted"
Thanks for your amazing work! When handling ligand molecules with RDKit, discrepancies in bond types may arise, such as carbon atoms exhibiting pentavalency and nitrogen atoms displaying tetravalent. Why these errors happen and how to rectify them for accurate molecular processing?
The example reading code,: mol = Chem.MolFromMolFile('2v5z_A_rec_2v5z_fad_lig_tt_min_0.sdf')
The sdf file is attached.
The log I got: "Explicit valence for atom # 13 C, 5, is greater than permitted"
2v5z_A_rec_2v5z_fad_lig_tt_min_0.zip