def from_tprfile(tprfile, index_file=None):
"""
Load atoms from a compiled tpr file.
Args:
tprile (str): Filename of the tpr file
index_file (opt.): Index file that should be loaded alongside.
Returns:
AtomSubset: All atoms in tprfile
"""
tpr = TPXReader(tprfile)
if index_file is not None:
indices = load_indices(index_file)
else:
indices = None
return Atoms(tpr.atoms, indices=indices, charges=tpr.charge, masses=tpr.mass).subset()
def from_grofile(grofile, index_file=None):
"""
Load atoms from a GROMACS coordinate file.
Args:
grofile (str): Filename of the grofile
index_file (str, optional): Filename of the gromacs indexfile
Returns:
AtomSubset: All atoms in grofile
"""
indices = None
if index_file is not None:
indices = load_indices(index_file)
t = np.genfromtxt(grofile, skip_header=2, delimiter=(5, 5, 5), dtype='U8', autostrip=True, skip_footer=1)
return Atoms(t, indices).subset()