Wednesday, 12 February 2020

Guess bond order in Rdkit by number of bound atoms

Some compChem/Biochem programs do not care about bond order and strip them, which is rather frustrating. Pre-made Rosetta params files for some non-canonical amino acids in the database folder are a classic example.
There is no single magic mol.CorrectBondOrder() command in Rdkit, but luckily there are some tricks that can be done. Here I will discuss finding out using the number of bound atoms.