def run():
try:
reflection_file_converter.run(args=sys.argv[1:])
except RuntimeError, e:
print e
def exercise_Compute_phifom_from_abcd_interface(args):
miller_arrays = reflection_file_converter.run(
args=args, simply_return_all_miller_arrays=True)
complex_input = None
for miller_array in miller_arrays:
if (miller_array.is_complex_array()):
complex_input = miller_array
break
if (complex_input is not None):
print("complex_input.info():", complex_input.info())
fom_input = None
for miller_array in miller_arrays:
if (miller_array.is_real_array()
and miller_array.info().lower().find("fom")):
fom_input = miller_array
break
if (fom_input is not None):
print("fom_input.info():", fom_input.info())
for miller_array in miller_arrays:
if (isinstance(miller_array.data(), flex.hendrickson_lattman)):
print("Hendrickson-Lattman coefficients:", miller_array.info())
n_bad_figures_of_merit = 0
n_bad_phases = 0
if (miller_array.anomalous_flag()):
print("Clipper cannot currently handle anomalous arrays" \
+ " with Hendrickson-Lattman coefficients.")
continue
phi_fom = clipper.Compute_phifom_from_abcd_interface(
unit_cell=miller_array.unit_cell(),
space_group=miller_array.space_group(),
miller_indices=miller_array.indices(),
phase_probabilities=miller_array.data())
phi_clipper = phi_fom.centroid_phases() * 180 / math.pi
fom_clipper = phi_fom.figures_of_merit()
fom_deltas = fom_input.data() - fom_clipper
if (fom_input is not None):
perm = flex.sort_permutation(flex.abs(fom_deltas),
reverse=True)
fom_deltas_sorted = fom_deltas.select(perm)
fom_clipper_sorted = fom_clipper.select(perm)
fom_input_sorted = fom_input.data().select(perm)
pp_sorted = miller_array.data().select(perm)
indices_sorted = miller_array.indices().select(perm)
centric_flags_sorted = fom_input.centric_flags().data().select(
perm)
print("FOM comparison")
for f, i, c, d, p, ix in zip(centric_flags_sorted,
fom_input_sorted,
fom_clipper_sorted,
fom_deltas_sorted, pp_sorted,
indices_sorted):
print(f, "%.3f %.3f %.3f" % (i, c, d), end=' ')
if (abs(d) > 0.01):
print("LOOK", "%.2f %.2f %.2f %.2f" % p, ix, end=' ')
n_bad_figures_of_merit += 1
print()
print()
if (complex_input is not None):
phi_input = complex_input.phases(deg=True).data()
phi_deltas = flex.double()
for phi1, phi2 in zip(phi_input, phi_clipper):
phi_deltas.append(
scitbx.math.signed_phase_error(phi1, phi2, deg=True))
perm = flex.sort_permutation(flex.abs(phi_deltas),
reverse=True)
phi_deltas_sorted = phi_deltas.select(perm)
phi_clipper_sorted = phi_clipper.select(perm)
phi_input_sorted = phi_input.select(perm)
pp_sorted = miller_array.data().select(perm)
indices_sorted = miller_array.indices().select(perm)
centric_flags_sorted = complex_input.centric_flags().data(
).select(perm)
fom_clipper_sorted = fom_clipper.select(perm)
print("PHI comparison")
for f, i, c, d, m, p, ix in zip(centric_flags_sorted,
phi_input_sorted,
phi_clipper_sorted,
phi_deltas_sorted,
fom_clipper_sorted, pp_sorted,
indices_sorted):
if (m < 0.01): continue
print(f, "%.3f %.3f %.3f" % (i, c, d), end=' ')
if (abs(d) > 3 and (max(p) < 1000 or abs(d) > 10)):
print("LOOK",
"%.2f %.2f %.2f %.2f" % p,
"fom=%.3f" % m,
ix,
end=' ')
n_bad_phases += 1
print()
print()
assert n_bad_figures_of_merit == 0
assert n_bad_phases == 0
def run():
try:
reflection_file_converter.run(args=sys.argv[1:])
except RuntimeError, e:
print e
def exercise_Compute_phifom_from_abcd_interface(args):
miller_arrays = reflection_file_converter.run(
args=args, simply_return_all_miller_arrays=True)
complex_input = None
for miller_array in miller_arrays:
if (miller_array.is_complex_array()):
complex_input = miller_array
break
if (complex_input is not None):
print "complex_input.info():", complex_input.info()
fom_input = None
for miller_array in miller_arrays:
if (miller_array.is_real_array()
and miller_array.info().lower().find("fom")):
fom_input = miller_array
break
if (fom_input is not None):
print "fom_input.info():", fom_input.info()
for miller_array in miller_arrays:
if (isinstance(miller_array.data(), flex.hendrickson_lattman)):
print "Hendrickson-Lattman coefficients:", miller_array.info()
n_bad_figures_of_merit = 0
n_bad_phases = 0
if (miller_array.anomalous_flag()):
print "Clipper cannot currently handle anomalous arrays" \
+ " with Hendrickson-Lattman coefficients."
continue
phi_fom = clipper.Compute_phifom_from_abcd_interface(
unit_cell=miller_array.unit_cell(),
space_group=miller_array.space_group(),
miller_indices=miller_array.indices(),
phase_probabilities=miller_array.data())
phi_clipper = phi_fom.centroid_phases()*180/math.pi
fom_clipper = phi_fom.figures_of_merit()
fom_deltas = fom_input.data() - fom_clipper
if (fom_input is not None):
perm = flex.sort_permutation(flex.abs(fom_deltas), reverse=True)
fom_deltas_sorted = fom_deltas.select(perm)
fom_clipper_sorted = fom_clipper.select(perm)
fom_input_sorted = fom_input.data().select(perm)
pp_sorted = miller_array.data().select(perm)
indices_sorted = miller_array.indices().select(perm)
centric_flags_sorted = fom_input.centric_flags().data().select(perm)
print "FOM comparison"
for f,i,c,d,p,ix in zip(centric_flags_sorted,
fom_input_sorted,
fom_clipper_sorted,
fom_deltas_sorted,
pp_sorted,
indices_sorted):
print f, "%.3f %.3f %.3f" % (i,c,d),
if (abs(d) > 0.01):
print "LOOK", "%.2f %.2f %.2f %.2f" % p, ix,
n_bad_figures_of_merit += 1
print
print
if (complex_input is not None):
phi_input = complex_input.phases(deg=True).data()
phi_deltas = flex.double()
for phi1,phi2 in zip(phi_input, phi_clipper):
phi_deltas.append(
scitbx.math.signed_phase_error(phi1, phi2, deg=True))
perm = flex.sort_permutation(flex.abs(phi_deltas), reverse=True)
phi_deltas_sorted = phi_deltas.select(perm)
phi_clipper_sorted = phi_clipper.select(perm)
phi_input_sorted = phi_input.select(perm)
pp_sorted = miller_array.data().select(perm)
indices_sorted = miller_array.indices().select(perm)
centric_flags_sorted =complex_input.centric_flags().data().select(perm)
fom_clipper_sorted = fom_clipper.select(perm)
print "PHI comparison"
for f,i,c,d,m,p,ix in zip(centric_flags_sorted,
phi_input_sorted,
phi_clipper_sorted,
phi_deltas_sorted,
fom_clipper_sorted,
pp_sorted,
indices_sorted):
if (m < 0.01): continue
print f, "%.3f %.3f %.3f" % (i,c,d),
if (abs(d) > 3 and (max(p) < 1000 or abs(d) > 10)):
print "LOOK", "%.2f %.2f %.2f %.2f" % p, "fom=%.3f" % m, ix,
n_bad_phases += 1
print
print
assert n_bad_figures_of_merit == 0
assert n_bad_phases == 0
