def from_hdf5(cls, grp):
'''Construct a Symmetry object from a HDF5 group'''
return cls(
grp['name'][()],
grp['generators'][:],
grp['fracs'][:],
grp['numbers'][:],
Cell.from_hdf5(grp['cell']),
grp['labels'][:],
)
def load_cif(filename, lf):
'''Load a CIF file
**Arguments:**
filename
The name of an existing CIF file
lf
An instance of the LinalgFactory class. (Ignored here)
**Returns** a dictionary with: ``title``, ``coordinates``, ``numbers``,
``symmetry``, ``links``, ``cell``.
'''
title, fields = _load_cif_low(filename)
name = fields.get('symmetry_Int_Tables_number', 'None')
generators = [equiv_pos_to_generator(s) for s in fields['symmetry_equiv_pos_as_xyz']]
x = fields['atom_site_fract_x'].reshape(-1, 1)
y = fields['atom_site_fract_y'].reshape(-1, 1)
z = fields['atom_site_fract_z'].reshape(-1, 1)
prim_fracs = np.hstack((x, y, z))
prim_numbers = np.array([periodic[symbol].number for symbol in fields['atom_site_type_symbol']])
lengths = np.array([fields['cell_length_a'], fields['cell_length_b'], fields['cell_length_c']])*angstrom
angles = np.array([fields['cell_angle_alpha'], fields['cell_angle_beta'], fields['cell_angle_gamma']])*deg
cell = Cell.from_parameters(lengths, angles)
prim_labels = fields['atom_site_label']
symmetry = Symmetry(name, generators, prim_fracs, prim_numbers, cell, prim_labels)
coordinates, numbers, links = symmetry.generate()
return {
'title': title,
'coordinates': coordinates,
'numbers': numbers,
'symmetry': symmetry,
'links': links,
'cell': cell,
}
