def test_value_grid(self):
#path = full_path('5wkd_phases.mtz.gz')
path = full_path('5e5z.mtz')
mtz = gemmi.read_mtz_file(path)
size = mtz.get_size_for_hkl()
if numpy is None:
return
asu = gemmi.ReciprocalAsu(mtz.spacegroup)
mtz_data = numpy.array(mtz, copy=False)
fp_idx = mtz.column_labels().index('FP')
fp_map = {}
for row in mtz_data:
fp_map[tuple(row[0:3])] = row[fp_idx]
for order in (gemmi.AxisOrder.XYZ, gemmi.AxisOrder.ZYX):
for half_l in (True, False):
grid = mtz.get_value_on_grid('FP',
size,
half_l=half_l,
order=order)
counter = 0
for point in grid:
hkl = grid.to_hkl(point)
value = fp_map.get(tuple(hkl))
if asu.is_in(hkl):
if value is not None:
self.assertTrue(point.value == value
or (numpy.isnan(point.value)
and numpy.isnan(value)))
counter += 1
else:
self.assertEqual(point.value, 0.)
else:
self.assertIsNone(value)
self.assertEqual(counter, mtz_data.shape[0])
def test_reciprocal_asu_checker(self):
sg = gemmi.SpaceGroup('I 1 2 1')
checker = gemmi.ReciprocalAsu(sg)
self.assertTrue(checker.is_in([-5, 5, 1]))
self.assertFalse(checker.is_in([5, 5, -1]))
def phase_graft(
initial_mtz_path,
event_mtz_path,
out_path,
):
print(
"\tGrafting phases from {} to {}".format(
str(event_mtz_path),
str(initial_mtz_path),
), )
initial_mtz = gemmi.read_mtz_file(str(initial_mtz_path))
# print("\tInitial mtz spacegroup: {}".format(initial_mtz.spacegroup))
event_mtz = gemmi.read_mtz_file(str(event_mtz_path))
# print("\tEvent mtz spacegroup: {}".format(event_mtz.spacegroup))
initial_mtz_data = np.array(initial_mtz, copy=False)
# print("\tShape of initial array is {}".format(initial_mtz_data.shape))
event_mtz_data = np.array(event_mtz, copy=False)
# print("\tShape of event array is {}".format(event_mtz_data.shape))
initial_reflections: Reflections = Reflections.from_array(initial_mtz_data)
event_reflections: Reflections = Reflections.from_array(event_mtz_data)
initial_asu = gemmi.ReciprocalAsu(initial_mtz.spacegroup)
operations = initial_mtz.spacegroup.operations()
initial_mtz_fwt_index = initial_mtz.column_labels().index("FWT")
event_mtz_fwt_index = event_mtz.column_labels().index("FWT")
initial_mtz_phwt_index = initial_mtz.column_labels().index("PHWT")
event_mtz_phwt_index = event_mtz.column_labels().index("PHWT")
fom_index = initial_mtz.column_labels().index("FOM")
initial_mtz_fo_index = initial_mtz.column_labels().index("F")
initial_mtz_fc_index = initial_mtz.column_labels().index("FC")
initial_mtz_phc_index = initial_mtz.column_labels().index("PHIC")
initial_mtz_r_index = initial_mtz.column_labels().index("FreeR_flag")
initial_mtz_ls_fc_all_index = initial_mtz.column_labels().index(
"FC_ALL_LS")
initial_mtz_ls_phc_all_index = initial_mtz.column_labels().index(
"PHIC_ALL_LS")
initial_mtz_fc_all_index = initial_mtz.column_labels().index("FC_ALL")
initial_mtz_phc_all_index = initial_mtz.column_labels().index("PHIC_ALL")
initial_mtz_delfwt_index = initial_mtz.column_labels().index("DELFWT")
initial_mtz_phdelwt_index = initial_mtz.column_labels().index("PHDELWT")
initial_mtz_sigf_index = initial_mtz.column_labels().index("SIGF")
print("\tBeginning graft...")
new_reflections = {}
for hkl in event_reflections:
event_reflection = event_reflections[hkl]
asu_hkl = HKL.from_list(initial_asu.to_asu(
hkl.to_list(),
operations,
))
# print("\t\tasu reflection is {}".format(asu_hkl))
if asu_hkl.is_000():
# print("\t\t\tReflection 000 {}".format(event_reflection))
data = np.zeros(
len(list(initial_reflections.reflections.values())[0].data))
# print("\t\t\t{}".format(data.shape))
new_reflection = Reflection(hkl, data)
else:
initial_reflection: Reflection = initial_reflections[asu_hkl]
new_reflection = Reflection(hkl, np.copy(initial_reflection.data))
new_reflection.data[initial_mtz_fwt_index -
3] = event_reflection.data[event_mtz_fwt_index - 3]
new_reflection.data[initial_mtz_phwt_index -
3] = event_reflection.data[event_mtz_phwt_index -
3]
# new_reflection.data[initial_mtz_fo_index - 3] = 0.0
# new_reflection.data[initial_mtz_fc_index - 3] = 0.0
# new_reflection.data[initial_mtz_phc_index - 3] = 0.0
# new_reflection.data[fom_index - 3] = 0.0
# new_reflection.data[initial_mtz_r_index - 3] = 0.0
#
# new_reflection.data[initial_mtz_ls_fc_all_index - 3] = 0.0
# new_reflection.data[initial_mtz_ls_phc_all_index - 3] = 0.0
# new_reflection.data[initial_mtz_fc_all_index - 3] = 0.0
# new_reflection.data[initial_mtz_phc_all_index - 3] = 0.0
# new_reflection.data[initial_mtz_delfwt_index - 3] = 0.0
# new_reflection.data[initial_mtz_phdelwt_index - 3] = 0.0
#
# new_reflection.data[initial_mtz_sigf_index - 3] = 0.0
# event_reflection = event_reflections[hkl]
#
# asu_hkl = HKL.from_list(initial_asu.to_asu(hkl.to_list(), operations, ))
# if asu_hkl.is_000():
# print("\t\t{}".format([hkl, asu_hkl]))
#
# print("#### zeros array, normal array")
# print(np.zeros(len(list(initial_reflections.reflections.values())[0].data)).shape)
# print(list(initial_reflections.reflections.values())[0].data.shape)
#
# data = np.zeros(len(list(initial_reflections.reflections.values())[0].data))
# new_reflection = Reflection(hkl, data)
#
# new_reflection.data[initial_mtz_fwt_index - 3] = event_reflection.data[event_mtz_fwt_index - 3]
# new_reflection.data[initial_mtz_phwt_index - 3] = event_reflection.data[event_mtz_phwt_index - 3]
new_reflections[hkl] = new_reflection
print("\tFinished iterating reflections")
new_array = Reflections(new_reflections).to_array()
# print("\tShape of new array is {}".format(new_array.shape))
initial_mtz.spacegroup = event_mtz.spacegroup
initial_mtz.set_data(new_array)
np.core.arrayprint._line_width = 240
# print([initial_mtz_fwt_index, initial_mtz_phwt_index, event_mtz_fwt_index, event_mtz_phwt_index])
# print(new_array.shape)
# print(new_array[-5:-1,:])
# print(np.array(initial_mtz)[-5:-1,:])
# print(np.array(event_mtz)[-5:-1,:])
print("\tWriting new reflections to {}".format(str(out_path)))
initial_mtz.write_to_file(str(out_path))