Protein structure manipulation — pbxplore.structure

Constants

• PDB_EXTENSIONS

  list of file extensions corresponding to PDB files

• PDBx_EXTENSIONS

  list of file extensions corresponding to PDBx/mmCIF files

Functions

pbxplore.structure.chains_from_files(path_list)

pbxplore.structure.chains_from_trajectory(trajectory, topology)

Objects

class pbxplore.structure.structure.Chain

Class to handle PDB chain

get_phi_psi_angles()

Compute phi and psi angles.

Returns:phi_psi_angles – Dict with residue number (int) as keys and a {'phi' : (float), 'psi' : (float)} dictionnary as values. Return type:dict Raises:FloatingPointError – If the computation of angles produces NaN. Generally, it means there is some problem with the residue coordinates.

Examples

>>> lines = ("ATOM    840  C   ARG B  11      22.955  23.561  -4.012  1.00 28.07           C  ",
...          "ATOM    849  N   SER B  12      22.623  24.218  -2.883  1.00 24.77           N  ",
...          "ATOM    850  CA  SER B  12      22.385  23.396  -1.637  1.00 21.99           C  ",
...          "ATOM    851  C   SER B  12      21.150  24.066  -0.947  1.00 32.67           C  ",
...          "ATOM    855  N   ILE B  13      20.421  23.341  -0.088  1.00 30.25           N  ")
>>>
>>> import pbxplore as pbx
>>> ch = pbx.structure.structure.Chain()
>>> for line in lines:
...     at = pbx.structure.structure.Atom()
...     at.read_from_PDB(line)
...     ch.add_atom(at)
...
>>> print(ch.get_phi_psi_angles())
{11: {'phi': None, 'psi': None}, 12: {'phi': -139.77684605036447, 'psi': 157.94348570201197}, 13: {'phi': None, 'psi': None}}

class pbxplore.structure.structure.Atom(ident=0, name=None, resname=None, chain=None, resid=0, x=0.0, y=0.0, z=0.0, model=None)

Class for atoms in PDB or PDBx/mmCIF format.

class pbxplore.structure.PDB.PDB(name)

Class to read PDB files.

Exceptions

exception pbxplore.structure.structure.ChainError

Exeption class for the Chain class

exception pbxplore.structure.structure.AtomError

Exeption class for the Atom class.