Wednesday, 18 March 2020

Atom names purely in RDKit

For some applications, such as PyMOL scripts or Rosetta, atom names are really important, say CA is the standard name for the α-carbon. Example uses of atom names in Rosetta/pyrosetta include setting constraints, using a params file for a custom ligand and so forth. However, RDKit is a bit of a nuisance with atom names as it is not a central feature, but a feature added for PDB files that is not too well documented.