def new_reflections_from_reflections_at_res(reflections: Reflections,
resolution: float,
) -> Reflections:
new_hkl_info = clipper_python.HKL_info(reflections.hkl_info.spacegroup,
reflections.hkl_info.cell,
clipper_python.Resolution(resolution),
True,
)
# new_hkl_data = clipper_python.data32.HKL_data_F_phi_float(new_hkl_info)
new_hkl_data = clipper_python.HKL_data_F_phi(new_hkl_info)
index = new_hkl_info.first
print(index)
while not index.last():
try:
new_hkl_data[index.hkl] = reflections.hkl_data[index.hkl]
except:
pass
index.next()
return Reflections(new_hkl_info,
new_hkl_data,
)
def xmap_from_path(
path,
structure_factors,
) -> MCDXMap:
mtz_file = clipper_python.CCP4MTZfile()
mtz_file.open_read(str(path))
hkl_info = clipper_python.HKL_info()
mtz_file.import_hkl_info(hkl_info)
# hkl_data = clipper_python.HKL_data_F_phi(hkl_info)
hkl_data = clipper_python.data32.HKL_data_F_phi_float(hkl_info)
# mtz_file.import_hkl_data(hkl_data,
# "*/*/[{}]".format(structure_factors),
# )
mtz_file.import_hkl_data(hkl_data, "*/*/[2FOFCWT,PH2FOFCWT]")
mtz_file.close_read()
spacegroup = hkl_info.spacegroup
cell = hkl_info.cell
resolution = hkl_info.resolution
hkl_data = hkl_data
return MCDXMap.xmap_from_clipper_res(spacegroup, cell, resolution,
hkl_data)
def load_mtz(mtz_path):
mtz = clipper.CCP4MTZfile()
mtz.open_read(mtz_path)
hkl_info = clipper.HKL_info()
hkl_data = clipper.data32.HKL_data_F_phi_float(hkl_info)
mtz.import_hkl_info(hkl_info)
mtz.import_hkl_data(hkl_data, "*/*/[FWT,PHWT]")
mtz.close_read()
return hkl_info, hkl_data
def __setstate__(self, state):
spacegroup = spacegroup_from_state(state["spacegroup"])
cell = cell_from_state(state["cell"])
resolution = resolution_from_state(state["resolution"])
self.hkl_info = clipper_python.HKL_info(spacegroup,
cell,
resolution,
)
self.hkl_data = clipper_python.HKL_data_F_phi(self.hkl_info)
# print(state["data"])
# print(np.std(state["data"]))
self.hkl_data._getDataNumpy(state["data"])
def reflections_from_mtz(mtz_file: MTZFile) -> Reflections:
mtz_file.mtz.open_read(str(mtz_file.path))
hkl_info = clipper_python.HKL_info()
mtz_file.mtz.import_hkl_info(hkl_info)
hkl_data = clipper_python.HKL_data_F_phi(hkl_info)
# hkl_data = clipper_python.data32.HKL_data_F_phi_float(hkl_info)
mtz_file.mtz.import_hkl_data(hkl_data, "*/*/[FWT,PHWT]")
mtz_file.mtz.close_read()
return Reflections(hkl_info,
hkl_data,
)
def __setstate__(self, state):
spacegroup = spacegroup_from_state(state["spacegroup"])
cell = cell_from_state(state["cell"])
resolution = resolution_from_state(state["resolution"])
self.hkl_info = clipper_python.HKL_info(
spacegroup,
cell,
resolution,
True,
)
self.hkl_data = clipper_python.data32.HKL_data_F_phi_float(
self.hkl_info)
# print(state["data"])
# print(np.std(state["data"]))
self.hkl_data.set_data(
state["data"][0],
state["data"][1],
)
def new_reflections_from_reflections(reflections: Reflections) -> Reflections:
new_hkl_info = clipper_python.HKL_info(reflections.hkl_info.spacegroup,
reflections.hkl_info.cell,
reflections.hkl_info.resolution,
True,
)
new_hkl_data = clipper_python.HKL_data_F_phi(reflections.hkl_data)
# new_hkl_data = clipper_python.data32.HKL_data_F_phi_float(reflections.hkl_data)
old_hkl_array, old_data_array = reflections.hkl_data.data
new_hkl_data.set_data(old_hkl_array,
old_data_array,
)
return Reflections(new_hkl_info,
new_hkl_data,
)