Is RDKit correctly assigning connectivities from ligand PDBs?

[martimunicoy]

We should double check some of the "known tricky" cases below:

• Tertiary nitrogens like NH4
• Carboxylic acids
• Carboxylates

[martimunicoy]

I analyzed three different compounds:

• Ammonium, [NH4+]
• Malonate, O=C([O-])CC(O)=O
• Trimethylglycine, C[N+](C)(C)CC(=O)[O-]

When representing RDKit's structures obtained from PDB files (with connectivity) and SMILES, the same connectivity is observed in each pair. The results are displayed in the following example. So, apparently, RDKit is able to assign the right connectivity in both cases (only when the PDB file that is read contains information about the connectivity).