def exercise_with_tst_input_map_2(use_mrcfile=None,file_name=None):
if not file_name:
file_name = libtbx.env.under_dist(
module_name="iotbx",
path="ccp4_map/ccp4_20_21_22_to_30_40_50.ccp4")
print("\nTesting read of input map with offset origin and axis order 3 1 2 "+\
"\n and use_mrcfile=",use_mrcfile)
if use_mrcfile:
m = mrcfile.map_reader(file_name=file_name,verbose=True)
else:
m = iotbx.ccp4_map.map_reader(file_name=file_name)
print(m.unit_cell_grid,m.map_data().origin(),m.map_data().all(),m.unit_cell().parameters(), end=' ')
assert m.unit_cell_grid == (55, 59, 61)
assert approx_equal(m.unit_cell().parameters(),
(24.53101921081543, 24.61971664428711, 26.457056045532227,
90.0, 90.0, 90.0))
assert m.map_data().origin() == (20, 21, 22)
assert m.map_data().all() == (11, 20, 29)
def exercise_with_tst_input_map(use_mrcfile=None,file_name=None):
if not file_name:
file_name = libtbx.env.under_dist(
module_name="iotbx",
path="ccp4_map/tst_input.map")
print("\nTesting read of input map with axis order 3 1 2 "+\
"\n and use_mrcfile=",use_mrcfile)
if use_mrcfile:
m = mrcfile.map_reader(file_name=file_name,verbose=True)
for label in m.labels: print(label)
else:
m = iotbx.ccp4_map.map_reader(file_name=file_name)
assert approx_equal(m.header_min, -0.422722190619)
assert approx_equal(m.header_max, 0.335603952408)
assert approx_equal(m.header_mean, 0)
assert approx_equal(m.header_rms, 0.140116646886)
assert m.unit_cell_grid == (16, 8, 16)
assert approx_equal(m.unit_cell().parameters(), (
82.095001220703125, 37.453998565673828, 69.636001586914062,
90.0, 101.47599792480469, 90.0))
assert m.unit_cell_crystal_symmetry().space_group_number()==5
assert m.map_data().origin() == (0, 0, 0)
assert m.map_data().all() == (16, 8, 16)
assert approx_equal(m.pixel_sizes(),(5.130937576293945, 4.6817498207092285, 4.352250099182129))
assert not m.map_data().is_padded()
out = StringIO()
m.show_summary(out=out)
assert ("map cell grid: (16, 8, 16)" in out.getvalue())
uc = m.unit_cell_crystal_symmetry().unit_cell()
assert approx_equal(m.unit_cell().parameters(), m.unit_cell().parameters())
assert approx_equal(m.grid_unit_cell().parameters(),
(5.13094, 4.68175, 4.35225, 90, 101.476, 90))
# Read and write map with offset
print("\nReading and writing map with origin not at zero, use_mrcfile=",use_mrcfile)
from scitbx.array_family.flex import grid
from scitbx.array_family import flex
from cctbx import uctbx, sgtbx
real_map=m.map_data().as_double()
grid_start=(5,5,5)
grid_end=(9,10,11)
if use_mrcfile:
iotbx.mrcfile.write_ccp4_map(
file_name="shifted_map.mrc",
unit_cell=uctbx.unit_cell(m.unit_cell().parameters()),
space_group=sgtbx.space_group_info("P1").group(),
gridding_first=grid_start,
gridding_last=grid_end,
map_data=real_map,
labels=flex.std_string(["iotbx.ccp4_map.tst"]),
verbose=True)
m = mrcfile.map_reader(file_name='shifted_map.mrc',verbose=True)
else:
iotbx.ccp4_map.write_ccp4_map(
file_name="shifted_map.ccp4",
unit_cell=uctbx.unit_cell(m.unit_cell().parameters()),
space_group=sgtbx.space_group_info("P1").group(),
gridding_first=grid_start,
gridding_last=grid_end,
map_data=real_map,
labels=flex.std_string(["iotbx.ccp4_map.tst"]))
m = iotbx.ccp4_map.map_reader(file_name='shifted_map.ccp4')
print(m.map_data().origin(),m.map_data().all())
print("GRID:",m.unit_cell_grid)
assert m.unit_cell_grid == (16, 8, 16)
assert approx_equal(m.unit_cell().parameters(), (
82.095001220703125, 37.453998565673828, 69.636001586914062,
90.0, 101.47599792480469, 90.0))
assert m.unit_cell_crystal_symmetry().space_group_number()== 1
print(m.map_data().origin(),m.map_data().all())
assert m.map_data().origin() == (5,5,5)
assert m.map_data().all() == (5,6,7)