AutoModel.guess_atom_types() — automatically assign CHARMM atom types

guess_atom_types()

When using BLK residues to represent ligands or other non-standard residues as rigid bodies (see Section 5.2.1) all atoms in these residues are assigned the CHARMM ‘undf’ type, which behaves similarly to carbon or nitrogen. This can lead to inaccurate soft-sphere or Lennard-Jones interactions for hydrogens or metal ions. This function will attempt to assign suitable CHARMM atom types to all residues without defined topology (usually BLK residues) in the model. To use it, call it from AutoModel.special_patches(). Any atom type assignments are shown in the log file, which should be carefully inspected for mistakes. It calls AutoModel.guess_atom_type() for each atom, so its guesses can be improved by overriding that function.