def load_from_xdict(args):
"""
Create a crystal object from a dictionary.
The input dictionary must have all used fields or key errors will result.
"""
#print args
sites = [
Site(label=a['name'], abc=a['abc'], occupancy=a['occupancy'])
for a in args['sites']
]
# Lattice and SpaceGroup could be initialized from dict or Lattice/SpaceGroup objects
# right not crystal is initialized by dict
lattice = Lattice(args['lattice']['a'], args['lattice']['b'],
args['lattice']['c'], args['lattice']['alpha'],
args['lattice']['beta'], args['lattice']['gamma'])
# self.cctbx_name = args["space_group"]["cctbx_name"]
# name should be of the type : "P m m n :2"
cctbx_name = args['space_group']['cctbx_name']
space_group = SpaceGroup(cctbx_name)
# necessary data from db
transforms = args.get('transforms', [])
crystal = Crystal(sites=sites,
lattice=lattice,
space_group=space_group,
transforms=transforms)
return crystal
def test_symmetry_error(self):
space_group = SpaceGroup('F d d 2')
lattice = Lattice(4.0, 5.0, 6.0, 88.0, 91.0, 95.0)
sites = []
sites.append(Site(label="Li", abc=(0.25, 0.0, 0.0), occupancy=0.80))
#crystal = Crystal(sites=sites, space_group=space_group, lattice=lattice)
pass
def __init__(self,
space_group=SpaceGroup('P 1'),
lattice=Lattice(1.0, 1.0, 1.0, 90.0, 90.0, 90.0),
sites=[]):
"""
Crystal object.
Functions as a wrapper to a cctbx xray.structure object,
but adds additional variables and functionality.
Core object of this package.
Input:
SpaceGroup space_group space group for the current crystal
List of Site objects sites List of Site objects.
Warning:
'crystal_structure' must be given,
or 'space_group', 'lattice', and 'sites' must be given,
or creation of the crystal will fail.
"""
try:
crystal_symmetry = crystal.symmetry(
unit_cell=str(lattice),
space_group_symbol=space_group.cctbx_name)
except Exception as e:
raise SymmetryError(
"SpaceGroup {s} is incompatible with Lattice -> {l} cctbx error {e}"
.format(l=str(lattice), s=SpaceGroup.cctbx_name, e=e))
scatterers = flex.xray_scatterer()
for i, site in enumerate(sites):
# the element name can be pulled from scatterer via the s.element_symbol() method (if it's an element!!!)
# example: 'atom-b-12',or 'vacancy-c-3'
# we need to set the scattering_type so we can freely use the label to store metadata
#scattering_type = something
#scatterers.append(xray.scatterer(label=atom.name, site=tuple(atom.abc), occupancy=atom.occupancy), scattering_type=atom.name)
#Method #2
# explicitly add metadata to _meta
st_temp, dash, num = site.label.partition("-")
if dash == "-":
k = site.label
else:
k = "-".join([site.label, str(i)])
# problems here not sure what's up
k = str(k)
# print "label = ", k, ' type of label = ', type(k)
# print "site = ", tuple(site.abc)
# print "occupancy = ", site.occupancy
scatterers.append(
xray.scatterer(label=k,
site=tuple(site.abc),
occupancy=site.occupancy))
# Test for coherency of Lattice and SpaceGroup
self.crystal_structure = xray.structure(
crystal_symmetry=crystal_symmetry, scatterers=scatterers)
def space_group(self):
""" Return the space group of the crystal. """
sgt = self.crystal_structure.space_group().type()
symbol = sgt.lookup_symbol()
name = ''
if re.search(r'\(', symbol):
name = symbol.split("(")[0].rstrip()
else:
name = symbol
return SpaceGroup(name)
def setUp(self):
self.cif_file_names = [
os.path.abspath(file_name)
for file_name in glob.glob(os.path.join(TEST_FILES, 'cifs/*.cif'))
]
space_group = SpaceGroup('C 1 2/m 1')
lattice = Lattice(4.0, 5.0, 6.0, 90.0, 109.10, 90.0)
sites = []
sites.append(Site(label="Li", abc=(0.25, 0.0, 0.0), occupancy=0.80))
sites.append(Site(label="Mn", abc=(0.25, 0.0, 0.0), occupancy=0.20))
sites.append(Site(label="O", abc=(0.5, 0.5, 0.5)))
self.crystal = Crystal(sites=sites,
space_group=space_group,
lattice=lattice)
def from_crystal_structure(crystal_structure):
c = Crystal(space_group=SpaceGroup('P1'))
c.crystal_structure = crystal_structure
return c
def setUp(self):
"""docstring for setUp"""
cctbx_names = ["P m m n :1", "P 1", "C 1 2/m 1"]
self.space_groups = [SpaceGroup(name) for name in cctbx_names]