choppa.utils

Functions

biopython_to_mda(BP_complex)	Converts a biopython protein object to an MDAnalysis one.
get_contacts_mda(complex[, bigcutoff, ...])	Use MDAnalysis to generate a dictionary of distance endpoint xyz coordinates between atoms in the ligand and protein residues.
get_ligand_resnames_from_pdb_str(PDB_str[, ...])	Uses MDAnalysis to figure out what residue names the ligand(s) in the protein PDB (str) has/have.
get_pdb_components(PDB_str[, remove_solvent])	Split a protein-ligand pdb into protein and ligand components :param PDB_str: :return:
process_ligand(ligand)	Add bond orders to a pdb ligand in an MDA universe object.
process_protein(protein)	Returns the string for the protein in an MDA universe object.
sdf_str_from_pdb(pdb_str)	Convert a PDB string to an SDF string using RDKit.
show_contacts(pymol_instance, ...[, bigcutoff])	Heavily reduced PyMOL plugin that provides show_contacts command and GUI for highlighting good and bad polar contacts.
split_pdb_str(PDB_str)	From a PDB string, gets the string for the protein and (if present) the ligand SDF (with guessed bond orders).