def fft_test(self, data, f, phi, size, order=gemmi.AxisOrder.XYZ):
if numpy is None:
return
self.assertTrue(data.data_fits_into(size))
grid_full = data.get_f_phi_on_grid(f, phi, size, half_l=False, order=order)
self.assertEqual(grid_full.axis_order, order)
array_full = numpy.array(grid_full, copy=False)
map1 = gemmi.transform_f_phi_grid_to_map(grid_full)
self.assertEqual(map1.axis_order, order)
map2 = numpy.fft.ifftn(array_full.conj())
map2 = numpy.real(map2) * (map2.size / grid_full.unit_cell.volume)
compare_maps(self, map1, map2, atol=6e-7)
map3 = data.transform_f_phi_to_map(f, phi, size, order=order)
compare_maps(self, map1, map3, atol=6e-7)
grid2 = gemmi.transform_map_to_f_phi(map1, half_l=False)
self.assertFalse(grid2.half_l)
self.assertEqual(grid2.axis_order, order)
compare_maps(self, grid2, array_full, atol=1e-4)
if grid2.axis_order != gemmi.AxisOrder.ZYX:
compare_asu_data(self, grid2.prepare_asu_data(), data, f, phi)
grid_half = data.get_f_phi_on_grid(f, phi, size, half_l=True, order=order)
if order == gemmi.AxisOrder.ZYX: # half_l+ZYX not supported yet
return
grid3 = gemmi.transform_map_to_f_phi(map1, half_l=True)
self.assertTrue(grid3.half_l)
self.assertEqual(grid3.axis_order, order)
compare_maps(self, grid3, grid_half, atol=1e-4)
compare_asu_data(self, grid3.prepare_asu_data(), data, f, phi)
def main():
config = Config.from_config()
m = gemmi.read_ccp4_map(str(config.xmap_in))
print(dir(m))
# m.spacegroup = gemmi.find_spacegroup_by_name('P1')
print(m.grid.spacegroup)
m.grid.spacegroup = gemmi.find_spacegroup_by_name('P1')
print(m.grid.spacegroup)
m.setup()
print(m.grid.spacegroup)
m.grid.spacegroup = gemmi.find_spacegroup_by_name('P1')
print(m.grid.spacegroup)
sf = gemmi.transform_map_to_f_phi(m.grid, half_l=True)
print(sf.spacegroup)
# data = sf
print(dir(sf))
data = sf.prepare_asu_data(dmin=config.resolution, with_000=True)
mtz = gemmi.Mtz(with_base=True)
# mtz = gemmi.Mtz()
print(dir(mtz))
mtz.spacegroup = sf.spacegroup
# mtz.spacegroup = gemmi.find_spacegroup_by_name('P1')
# mtz.set_cell_for_all(sf.unit_cell)
mtz.cell = sf.unit_cell
mtz.add_dataset('unknown')
mtz.add_column('FWT', 'F')
mtz.add_column('PHWT', 'P')
mtz.set_data(data)
mtz.write_to_file(str(config.mtz_out))
def fft_test(self, data, f, phi, size):
if numpy is None:
return
grid_full = data.get_f_phi_on_grid(f, phi, size, half_l=False)
array_full = numpy.array(grid_full, copy=False)
map1 = gemmi.transform_f_phi_grid_to_map(grid_full)
map2 = numpy.fft.ifftn(array_full.conj())
map2 = numpy.real(map2) * (map2.size / grid_full.unit_cell.volume)
compare_maps(self, map1, map2, atol=6e-7)
map3 = data.transform_f_phi_to_map(f, phi, size)
compare_maps(self, map1, map3, atol=6e-7)
grid2 = gemmi.transform_map_to_f_phi(map1, half_l=False)
compare_maps(self, grid2, array_full, atol=1e-4)
grid_half = data.get_f_phi_on_grid(f, phi, size, half_l=True)
grid3 = gemmi.transform_map_to_f_phi(map1, half_l=True)
compare_maps(self, grid3, grid_half, atol=1e-4)
#!/usr/bin/env python
# Convert CCP4 map to map coefficients in MTZ
import sys
import gemmi
RESOLUTION_LIMIT = 1.5 # set 0 for no limit
if len(sys.argv) != 3:
sys.exit('Usage: map2mtz.py input.ccp4 output.mtz')
m = gemmi.read_ccp4_map(sys.argv[1])
m.setup()
sf = gemmi.transform_map_to_f_phi(m.grid, half_l=True)
data = sf.prepare_asu_data(dmin=RESOLUTION_LIMIT)
mtz = gemmi.Mtz(with_base=True)
mtz.spacegroup = sf.spacegroup
mtz.set_cell_for_all(sf.unit_cell)
mtz.add_dataset('unknown')
mtz.add_column('FWT', 'F')
mtz.add_column('PHWT', 'P')
mtz.set_data(data)
mtz.write_to_file(sys.argv[2])
