pyKVFinder.read_pdb

pyKVFinder.read_pdb(fn: str | Path, vdw: Dict[str, Dict[str, float]] | None = None, model: int | None = None) → ndarray[source]

Reads PDB file into numpy.ndarrays.

Parameters:

  • fn (Union[str, pathlib.Path]) – A path to PDB file.

  • vdw (Dict[str, Dict[str, float]], optional) – A dictionary containing radii values, by default None. If None, use output of read_vdw().

  • model (int, optional) – The model number of a multi-model PDB file, by default None. If None, keep atoms from all models.

Returns:

atomic – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates and radius) for each atom.

Return type:

numpy.ndarray

Raises:

TypeError – fn must be a string or a pathlib.Path.

Note

The van der Waals radii file defines the radius values for each atom by residue and when not defined, it uses a generic value based on the atom type. The function by default loads the built-in van der Waals radii file: vdw.dat.

See also

read_vdw, read_xyz, get_vertices, get_vertices_from_file, detect, constitutional, hydropathy

Example

With the vdW radii dictionary loaded with read_vdw, we can read a target PDB file into Numpy array (atomic data):

>>> import os
>>> import pyKVFinder
>>> from pyKVFinder import read_pdb
>>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
>>> atomic = read_pdb(pdb)
>>> atomic
array([['13', 'E', 'GLU', ..., '-15.642', '-14.858', '1.824'],
   ['13', 'E', 'GLU', ..., '-14.62', '-15.897', '1.908'],
   ['13', 'E', 'GLU', ..., '-13.357', '-15.508', '1.908'],
   ...,
   ['350', 'E', 'PHE', ..., '18.878', '-9.885', '1.908'],
   ['350', 'E', 'PHE', ..., '17.624', '-9.558', '1.908'],
   ['350', 'E', 'PHE', ..., '19.234', '-13.442', '1.69']],
  dtype='<U32')

Warning

The function takes the built-in dictionary when the vdw argument is not specified. If you wish to use a custom van der Waals radii file, you must read it with read_vdw as shown earlier and pass it as read_pdb(pdb, vdw=vdw).