class jade.basic.structure.BioPose.BioPose(path, model_num=0)

Bases: object

This is my biopython meta class. Because biopython’s interface kinda sucks. This is a little cleaner.

The other way is to sublclass each Biopython class structure, which I’m not ready to do.

Right now, you need a path as I don’t know how we would use this from sequence, etc as you do in Rosetta. :path: Is a path to an RCSB file. PDB (.pdb), mmCIF(.cif), and gzipped (.gz) versions.

atom(atom_name, resnum, chain_id, icode=' ', alt=' ', model_num=0)

Get a Bio Atom of the stored structure

Parameters:

• atom_name – str
• resnum – int
• chain_id – str
• icode – str
• alt – str
• model_num – int

Return type:

bio.PDB.Atom.Atom

atoms(resnum, chain_id, icode=' ', alt=' ', model_num=0)

Get a list of Bio Atoms :param resnum: int :param chain_id: str :param icode: str :param alt: str :param model_num: int :rtype: list[bio.PDB.Atom.Atom]

chain(chain_id, model_num=0)

Get a Bio Chain of the stored structure :param chain_id: str :param model_num: int :rtype: bio.PDB.Chain.Chain

chains(model_num=0)

Get a list of Bio Chains :param model_num: int :rtype: list[bio.PDB.Chain.Chain

connected_to_next(resi, peptide_bond_distance_cutoff=1.8)

connected_to_previous(resi, peptide_bond_distance_cutoff=1.8)

get_chain_ids(model_num)

Get all chain IDS for a model. :param model_num: int :rtype: list[str]

get_chain_length(chain_id, model_num=0)

Get the number of AA in a chain - Not including alternate res locations :param chain_id: str :rtype: int

get_sequence(chain_id, model_num=0)

Get a sequence of a chain - Not including alternate res locations

Parameters:

• chain_id – str
• model_num – int

Return type:

str

load_from_file(path)

Load a file from PDB or mmCIF. .gz is supported.

Parameters:path – Path to PDB or mmCIF file Return type:tuple(bio.PDB.Structure.Structure, dict)

model(model_num=0)

Get a Bio Model of the stored structure :param id: int :rtype: bio.PDB.Model.Model

omega(i, rosetta_definitions=True)

Get the Omega Angle of i in radians Omega is defined as the dihedral angle between the peptide bond of i and i + 1, as in Rosetta. If rosetta_definitions are False, omega is then treated as being between i and i -1

Parameters:

• i – int
• reverse_rosetta_definitions – bool

Return type:

float

pdbinfo()

phi(i)

Get the Phi Angle of i in radians

Parameters:i – int Return type:float

psi(i)

Get the Psi Angle of i in radians

Parameters:i – int Return type:float

reload_from_file(path, model_num=0)

Reload a BioPose from a file path. :param path: str :param model_num: int :return:

res_bond_distance(resi)

Get the stored bond distances between residue and residue+1 :param res: int :rtype: float

residue(resnum, chain_id, icode=' ', alt=' ', model_num=0)

Get a Bio Residue of the stored structure. Adds a chain_id attribute.

Parameters:

• resnum – int
• chain_id – str
• icode – str
• alt – str
• model_num – int

Return type:

bio.PDB.Residue.Residue

residues(chain_id, model_num=0, include_alt=False)

Get residues, including or not including residues with alternate location codes - which can be a PITA Adds chain_id attribute to residue.

Parameters:

• chain_id – str
• model_num – int
• include_alt – bool

Return type:

list[bio.PDB.Residue.Residue]

resnum(pdb_num, chain, icode=' ')

structure()

Get the Bio Structure stored in this class. :rtype: bio.PDB.Structure.Structure

total_residue()

jade.basic.structure.BioPose.test_dihedrals(pose)

Simple Test for Dihedral output

Parameters:pose – BioPose Return type:bool

jade.basic.structure.BioPose.test_pdbinfo(pose)

Simple Test for pdbinfo output. :param pose: BioPose :rtype: bool