jade.basic.structure.util.atomic_distance(res1, res2, res1_atom_name, res2_atom_name)

Return the atomic distance between two arbitrary Bio residues and two arbitrary atom names. :param res1: Bio.PDB.Residue.Residue :param res2: Bio.PDB.Residue.Residue :param res1_atom_name: str :param res2_atom_name: str :rtype: float

jade.basic.structure.util.get_biopython_structure(path, model_id=None)

jade.basic.structure.util.get_chain_length(bio_chain)

jade.basic.structure.util.get_num_biochains(model)

jade.basic.structure.util.get_seq_from_biochain(bio_chain)

jade.basic.structure.util.get_seq_from_biostructure(structure, chain_id)

jade.basic.structure.util.has_id(model, id)

Returns true or false if the model has the chain. Because biopython is not updating it’s index that has_id is using. WTF.

jade.basic.structure.util.peptide_bond_distance(res1, res2)

Return the bond distance between two residues using Numpy array math. :param res1: Bio.PDB.Residue.Residue :param res2: Bio.PDB.Residue.Residue :rtype: float