Bio.PDB.Structure module

The structure class, representing a macromolecular structure.

class Bio.PDB.Structure.Structure(id)

Bases: Bio.PDB.Entity.Entity

The Structure class contains a collection of Model instances.

__init__(self, id)

Initialize the class.

__repr__(self)

Return the structure identifier.

get_models(self)

Return models.

get_chains(self)

Return chains from models.

get_residues(self)

Return residues from chains.

get_atoms(self)

Return atoms from residue.

atom_to_internal_coordinates(self, verbose: bool = False) → None

Create/update internal coordinates from Atom X,Y,Z coordinates.

Internal coordinates are bond length, angle and dihedral angles.

Parameters

bool (verbose) – default False describe runtime problems

internal_to_atom_coordinates(self, verbose: bool = False) → None

Create/update atom coordinates from internal coordinates.

Parameters

bool (verbose) – default False describe runtime problems

Raises

Exception – if any chain does not have .pic attribute