pyKVFinder.read_xyz

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

Reads XYZ file into numpy.ndarrays.

Parameters:

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

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

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_pdb, get_vertices, get_vertices_from_file, detect, constitutional, hydropathy

Example

With the vdW radii dictionary loaded with pyKVFinder.read_vdw, we can read a target XYZ file into Numpy arrays (atomic information and atomic coordinates):

>>> import os
>>> import pyKVFinder
>>> from pyKVFinder import read_xyz
>>> xyz = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.xyz')
>>> atomic = read_xyz(xyz)
>>> atominfo
array([['1', 'A', 'UNK', ..., '-15.642', '-14.858', '1.97'],
   ['2', 'A', 'UNK', ..., '-14.62', '-15.897', '1.66'],
   ['3', 'A', 'UNK', ..., '-13.357', '-15.508', '1.66'],
   ...,
   ['2790', 'A', 'UNK', ..., '18.878', '-9.885', '1.66'],
   ['2791', 'A', 'UNK', ..., '17.624001', '-9.558', '1.66'],
   ['2792', 'A', 'UNK', ..., '19.233999', '-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_xyz(xyz, vdw=vdw).