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 _parse_atoms(self):
self.cart = {}
self.frac = {}
self.adp_cart = {}
self.adp_frac = {}
self.adp_iso_frac = {}
self.element = {}
self.names = []
for name, atom in self.atoms.items():
atom.parse()
atom.build()
self.cart[name] = atom.get_cart()
self.frac[name] = atom.get_frac()
adp = atom.get_adp_frac()
if len(adp) == 6:
self.adp_frac[name] = adp
self.adp_cart[name] = frac2cart_ADP(adp, self.cell)
else:
self.adp_frac[name] = None
self.adp_cart[name] = None
self.adp_iso_frac[name] = adp
self.names.append(name)
self.element[name] = atom.get_element()
# if self.bedeInstructions or self.loneInstructions:
# self.buildConnectionTable()
for name, atom in self.atoms.items():
self.findBEDEInstructions(name, atom)
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 get_adp_cart(self):
adp = [self.adp_frac[0], self.adp_frac[1], self.adp_frac[2],
self.adp_frac[5], self.adp_frac[4], self.adp_frac[3]]
return frac2cart_ADP(adp, self.cell)
def get_adp_cart(self):
return frac2cart_ADP(self.adp_frac, self.cell)
