def parse(self):
self.names = []
self.adp_frac = {}
self.adp_error_frac = {}
self.adp_cart = {}
self.adp_error_cart = {}
self.frac = {}
self.cart = {}
self.element = {}
self.cif = CIF(self.filename)
self.cell = self.cif.cell
self.T = value(self.cif['_diffrn_ambient_temperature'])
for atomname, values in self.cif.positions.items():
self.names.append(atomname)
self.frac[atomname] = values['frac']
self.cart[atomname] = frac2cart(values['frac'], self.cell)
self.element[atomname] = values['element']
if atomname in self.cif.atoms.keys():
self.adp_frac[atomname] = self.cif.atoms[atomname]['adp']
self.adp_error_frac[atomname] = self.cif.atoms[atomname]['adp_error']
self.adp_cart[atomname] = frac2cart_ADP(self.cif.atoms[atomname]['adp'], self.cell)
try:
self.adp_error_cart[atomname] = frac2cart_ADP(self.cif.atoms[atomname]['adp_error'], self.cell)
except TypeError:
self.adp_error_cart[atomname] = None
else:
self.adp_error_frac[atomname] = None
self.adp_frac[atomname] = None
self.adp_error_cart[atomname] = None
self.adp_cart[atomname] = None
def __add__(self, atom):
new_atom = copy(atom)
oldfrac = new_atom.get_frac()
newfrac = dot(oldfrac, self.matrix) + self.trans
newfrac = array(*newfrac[0,].tolist())
new_atom.set_frac(newfrac.flatten().tolist())
newcart = frac2cart(newfrac, atom.molecule.get_cell())
new_atom.cart = newcart
new_atom.set_name(new_atom.get_name() + '_' + str(self.ID))
try:
old_adp = ADP_to_matrix(new_atom.adp['cart_meas'])
new_adp = dot(self.matrix.transpose(), old_adp)
new_adp = dot(new_adp, self.matrix)
new_adp = ADP_to_XD_list(new_adp)
new_atom.adp['cart_meas'] = new_adp
new_adp_frac = frac2cart_ADP(new_adp, atom.molecule.get_cell())
new_atom.adp['frac_meas'] = new_adp_frac
except ADPDataError:
pass
return new_atom
def run(self):
super(Frac2Cart, self).run()
self._Cart(frac2cart(self._Position, self._Cell))
def set_frac(self, frac):
self.frac = frac
self.cart = frac2cart(frac, self.molecule.get_cell())
def get_cart(self):
if self.cart is None:
self.cart = frac2cart(self.frac, self.cell)
return self.cart
def get_cart(self):
return frac2cart(self.frac, self.cell)