deepfold.relax.cleanup

Cleans up a PDB file using pdbfixer in preparation for OpenMM simulations.

fix_pdb uses a third-party tool. We also support fixing some additional edge cases like removing chains of length one (see clean_structure).

Functions

clean_structure(pdb_structure, alterations_info)	Applies additional fixes to an OpenMM structure, to handle edge cases.
fix_pdb(pdbfile, alterations_info)	Apply pdbfixer to the contents of a PDB file; return a PDB string result.