def correct(self, orientation):
if self.flag == None: raise # no correction necessary
from scitbx import matrix
M1 = matrix.sqr(self.flag['trans'])
corrected = orientation.change_basis(M1.transpose().elems)
unit_cell_too_small(corrected.unit_cell(), cutoff=100.)
return corrected
def correct(self, orientation):
if self.flag is None:
raise RuntimeError("no correction necessary")
M1 = scitbx.matrix.sqr(self.flag['trans'])
corrected = orientation.change_basis(M1.transpose().elems)
unit_cell_too_small(corrected.unit_cell(), cutoff=100.)
return corrected
def correct(experiments, reflections, assign_indices, threshold=0.9):
assert len(experiments.crystals()) == 1
while True:
sel = reflections["miller_index"] != (0, 0, 0)
if sel.count(True) == 0:
break
T = detect(reflections["miller_index"].select(sel),
threshold=threshold)
if T is None:
break
crystal_model = experiments.crystals()[0]
direct_matrix = scitbx.matrix.sqr(crystal_model.get_A()).inverse()
M = T.inverse().transpose()
new_direct_matrix = M * direct_matrix
crystal_model.set_A(new_direct_matrix.inverse())
unit_cell_too_small(crystal_model.get_unit_cell())
cb_op = crystal_model.get_unit_cell(
).change_of_basis_op_to_niggli_cell()
crystal_model.update(crystal_model.change_basis(cb_op))
reflections["id"] = flex.int(len(reflections), -1)
reflections.unset_flags(flex.bool(len(reflections), True),
reflections.flags.indexed)
assign_indices(reflections, experiments)
def correct(self,orientation): if self.flag==None: raise # no correction necessary from scitbx import matrix M1 = matrix.sqr(self.flag['trans']) corrected = orientation.change_basis(M1.transpose().elems) unit_cell_too_small(corrected.unit_cell(),cutoff = 100.) return corrected
def correct(self,orientation): print "before", orientation.unit_cell(),orientation.unit_cell().volume() print [float(i) for i in self.cb_op.elems] corrected = orientation.change_basis([float(i) for i in self.cb_op.elems]) print "after", corrected.unit_cell(),orientation.unit_cell().volume() unit_cell_too_small(corrected.unit_cell(),cutoff=25.) return corrected
def __init__(self,ai,combo,cutoff=unphysical_cell_cutoff_small_molecule_regime): self.ai = ai self.combo = combo self.cutoff = cutoff solns=[ai[combo[i]] for i in [0,1,2]] self.setA(solns) unit_cell_too_small(ai.getOrientation().unit_cell(),cutoff=self.cutoff) ai.niggli() # reduce cell
def __init__(self,ai,combo,cutoff=unphysical_cell_cutoff_small_molecule_regime): self.ai = ai self.combo = combo self.cutoff = cutoff solns=[ai[combo[i]] for i in [0,1,2]] self.setA(solns) unit_cell_too_small(ai.getOrientation().unit_cell(),cutoff=self.cutoff) ai.niggli() # reduce cell
def rwgk_niggli(UC,epsilon=None,cutoff=100.):
'''Reference:
R.W. Grosse-Kunstleve, N.K. Sauter and P.D. Adams.
Numerically stable algorithms for the computation of reduced unit cells.
Acta Cryst. A60, 1-6 (2004)
'''
if isinstance(UC,unit_cell):
#return UC.niggli_cell(epsilon)
return fast_minimum_reduction(UC).as_unit_cell()
elif isinstance(UC,crystal_orientation.crystal_orientation):
uc = UC.unit_cell()
unit_cell_too_small(uc,cutoff=cutoff)
#R = uc.niggli_reduction(epsilon)
R = fast_minimum_reduction(uc)
#minimum reduction gets r_inv as a tuple instead of scitbx.matrix
rinverse = matrix.sqr( R.r_inv() )
#NIG = R.as_unit_cell().parameters()
#MIN = fast_minimum_reduction(uc).as_unit_cell().parameters()
return UC.change_basis(rinverse.transpose().inverse().elems)
#print "transformation",invS.transpose().elems,{True:"is",False:"not"}[idx_possible],"possible"
if idx_possible:
print "There are systematic absences. Applying transformation",invS.transpose().elems
self.cb_op = invS.transpose().inverse() # not sure if transpose.inverse or just inverse
self.flag = True
return 1
return 0
def correct(self,orientation):
print "before", orientation.unit_cell(),orientation.unit_cell().volume()
print [float(i) for i in self.cb_op.elems]
corrected = orientation.change_basis([float(i) for i in self.cb_op.elems])
print "after", corrected.unit_cell(),orientation.unit_cell().volume()
unit_cell_too_small(corrected.unit_cell(),cutoff=25.)
return corrected
class FewSpots(exceptions.Exception): pass
class SolutionTracker:
def __init__(self):
self.all_solutions=[]
self.volume_filtered=[]
def append(self,item):
item['serial']=len(self.all_solutions)
self.all_solutions.append(item)
self.update_analysis()
def update_analysis(self):
self.best_likelihood = max([i['model_likelihood'] for i in self.all_solutions])
self.close_solutions = [
