"""
Functions for manipulating pdb files.
"""
[docs]def open_pdb(file_location):
"""Open and read coordinates and atom symbols from a pdb file.
The pdb file must specify the atom elements in the last column, and follow
the conventions outlined in the PDB format specification.
Parameters
----------
file_location : str
The location of the pdb file to read in.
Returns
-------
coords : np.ndarray
The coordinates of the pdb file.
symbols : list
The atomic symbols of the pdb file.
"""
with open(file_location) as f:
data = f.readlines()
coordinates = []
symbols = []
for line in data:
if "ATOM" in line[0:6] or "HETATM" in line[0:6]:
symbols.append(line[76:79].strip())
atom_coords = [float(x) for x in line[30:55].split()]
coordinates.append(atom_coords)
coords = np.array(coordinates)
symbols = np.array(symbols)
return symbols, coords