chisurf.fio.structure.coordinates module

Read PDB files.

PDB files contain atomic coordinates.

PDB

Author

Thomas-Otavio Peulen

Requirements

Revisions

Notes

The API is not stable yet and might change between revisions.

References

Examples

chisurf.fio.structure.coordinates.assign_element_to_atom_name(atom_name: 'str')

Tries to guess element from atom name if not recognised.

Parameters

atom_name (str) – string

Examples

>>> assign_element_to_atom_name('CA')
C

chisurf.fio.structure.coordinates.fetch_pdb(pdb_id: 'str', **kwargs)

chisurf.fio.structure.coordinates.fetch_pdb_string(pdb_id: 'str') → 'str'

Downloads from the RCSB a PDB file with the specified PDB-ID

Parameters

• pdb_id (str) – The PDB-ID that is downloaded

• get_binary – If get_binary is True a binary string is returned.

Return type

str

Returns

chisurf.fio.structure.coordinates.get_atom_index(atoms: 'np.array', chain_identifier: 'str', residue_seq_number: 'int', atom_name: 'str', residue_name: 'str', **kwargs)

Get the atom index by the the identifier

Parameters

• atoms (array) –

• chain_identifier (str) –

• residue_seq_number (int) –

• atom_name (str) –

• residue_name (str) –

• kwargs –

Returns

chisurf.fio.structure.coordinates.parse_string_pdb(string: 'str', assign_charge: 'bool' = False, verbose: 'bool' = False)

Parameters

• string (str) –

• assign_charge (bool) –

• verbose (bool) –

Returns

chisurf.fio.structure.coordinates.parse_string_pqr(string: 'str', verbose: 'bool' = False)

chisurf.fio.structure.coordinates.read(filename: 'str', assign_charge: 'bool' = False, verbose: 'bool' = False, **kwargs) → 'np.ndarray'

Open pdb_file and read each line into pdb (a list of lines)

Parameters

• filename (str) –

• assign_charge (bool) –

Return type

ndarray

Returns

numpy structured array containing the PDB info and VdW-radii and charges

Examples

>>> import chisurf.fio
>>> pdb_file = './test/data/atomic_coordinates/pdb_files/hGBP1_closed.pdb'
>>> pdb = chisurf.fio.structure.coordinates.read(pdb_file, verbose=True)
>>> pdb[:5]
array([ (0, ' ', 7, 'MET', 1, 'N', 'N', [72.739, -17.501, 8.879], 0.0, 1.65, 0.0, 14.0067),
       (1, ' ', 7, 'MET', 2, 'CA', 'C', [73.841, -17.042, 9.747], 0.0, 1.76, 0.0, 12.0107),
       (2, ' ', 7, 'MET', 3, 'C', 'C', [74.361, -18.178, 10.643], 0.0, 1.76, 0.0, 12.0107),
       (3, ' ', 7, 'MET', 4, 'O', 'O', [73.642, -18.708, 11.489], 0.0, 1.4, 0.0, 15.9994),
       (4, ' ', 7, 'MET', 5, 'CB', 'C', [73.384, -15.89, 10.649], 0.0, 1.76, 0.0, 12.0107)],
      dtype=[('i', '<i4'), ('chain', 'S1'), ('res_id', '<i4'), ('res_name', 'S5'), ('atom_id', '<i4'), ('atom_name', 'S5
'), ('element', 'S1'), ('xyz', '<f8', (3,)), ('charge', '<f8'), ('radius', '<f8'), ('bfactor', '<f8'), ('mass', '<f8')
])

chisurf.fio.structure.coordinates.read_xyz(filename: 'str') → 'np.array'

Return type

array

chisurf.fio.structure.coordinates.write_pdb(filename: 'str', atoms=None, append_model: 'bool' = False, append_coordinates: 'bool' = False, verbose: 'bool' = False)

Writes a structured numpy array containing the PDB-info to a PDB-file

If append_model and append_coordinates are False the file is overwritten. Otherwise the atomic-coordinates are appended to the existing file.

Parameters

• filename (str) – target-filename

• atoms – structured numpy array

• append_model (bool) – bool If True the atoms are appended as a new models

• append_coordinates (bool) – If True the coordinates are appended to the file

chisurf.fio.structure.coordinates.write_points(filename: 'str', points: 'np.ndarray', verbose: 'bool' = False, mode: 'str' = 'xyz', density: 'np.ndarray' = None)

Parameters

• filename (str) –

• points (ndarray) –

• verbose (bool) –

• mode (str) –

• density (Optional[ndarray]) –

Returns

chisurf.fio.structure.coordinates.write_xyz(filename: 'str', points: 'np.array', verbose: 'bool' = False)

Writes the points as xyz-format file. The xyz-format file can be opened and displayed for instance in PyMol

Parameters

• filename (str) – string

• points (array) – array

• verbose (bool) – bool