def exercise_around_model():
from cctbx.maptbx.box import make_list_symmetric
a = [3, 4, 5, 3, 9, 1, 6, 3, 2, 5, 6, 6]
new_a = make_list_symmetric(a)
from scitbx.array_family import flex
aa = flex.double(a)
new_aa = flex.double(new_a)
assert (aa.size(), new_aa.size()) == (12, 12)
assert aa.min_max_mean().mean == new_aa.min_max_mean().mean
print(a, new_a)
a = [3, 4, 5, 3, 8, 1, 6, 7, 3, 2, 5, 6, 6]
new_a = make_list_symmetric(a)
from scitbx.array_family import flex
aa = flex.double(a)
new_aa = flex.double(new_a)
print(a, new_a)
assert (aa.size(), new_aa.size()) == (13, 13)
assert aa.min_max_mean().mean == new_aa.min_max_mean().mean
mam = get_random_structure_and_map(use_static_structure=True)
map_data_orig = mam.mm.map_data().deep_copy()
sites_frac_orig = mam.model.get_sites_frac().deep_copy()
sites_cart_orig = mam.model.get_sites_cart().deep_copy()
cs_orig = mam.model.crystal_symmetry()
box = cctbx.maptbx.box.around_model(map_manager=mam.mm,
model=mam.model.deep_copy(),
box_cushion=10,
wrapping=True)
new_mm1 = box.map_manager()
new_mm2 = box.apply_to_map(map_manager=mam.mm.deep_copy())
assert approx_equal(new_mm1.map_data(), new_mm2.map_data())
new_model1 = box.model()
new_model2 = box.apply_to_model(model=mam.model.deep_copy())
assert new_model1.crystal_symmetry().is_similar_symmetry(
new_model2.crystal_symmetry())
assert new_model1.crystal_symmetry().is_similar_symmetry(
box.crystal_symmetry)
assert approx_equal(new_model1.get_sites_cart()[0],
(19.705233333333336, 15.631525, 13.5040625))
# make sure things did change
assert new_mm2.map_data().size() != map_data_orig.size()
# make sure things are changed in-place and are therefore different from start
assert box.map_manager().map_data().size() != map_data_orig.size()
assert box.model().get_sites_frac() != sites_frac_orig
assert box.model().get_sites_cart() != sites_cart_orig
assert (not cs_orig.is_similar_symmetry(box.model().crystal_symmetry()))
# make sure box, model and map_manager remember original crystal symmetry
assert cs_orig.is_similar_symmetry(
box.map_manager().unit_cell_crystal_symmetry())
assert cs_orig.is_similar_symmetry(
box.map_manager().unit_cell_crystal_symmetry())
assert approx_equal(
box.model().shift_cart(),
[5.229233333333334, 5.061524999999999, 5.162062499999999])
assert box.model().unit_cell_crystal_symmetry().is_similar_symmetry(
cs_orig)
assert (not box.model().crystal_symmetry().is_similar_symmetry(cs_orig))
assert approx_equal(
box.model()._figure_out_hierarchy_to_output(
do_not_shift_back=False).atoms().extract_xyz()[0],
(14.476, 10.57, 8.342))
# make sure we can stack shifts
sel = box.model().selection("resseq 219:219")
m_small = box.model().select(selection=sel)
assert approx_equal(box.model().shift_cart(), m_small.shift_cart())
# Now box again:
small_box = cctbx.maptbx.box.around_model(map_manager=mam.mm,
model=mam.model.deep_copy(),
box_cushion=5,
wrapping=True)
# Make sure nothing was zeroed out in this map (wrapping = True)
assert new_mm1.map_data().as_1d().count(0) == 0
# Now without wrapping...
box = cctbx.maptbx.box.around_model(map_manager=mam.mm,
model=mam.model.deep_copy(),
box_cushion=10,
wrapping=False)
# make sure things are changed in-place and are therefore different from start
assert box.map_manager().map_data().size() != map_data_orig.size()
assert box.model().get_sites_frac() != sites_frac_orig
assert box.model().get_sites_cart() != sites_cart_orig
assert (not cs_orig.is_similar_symmetry(box.model().crystal_symmetry()))
# make sure box, model and map_manager remember original crystal symmetry
assert cs_orig.is_similar_symmetry(
box.model().unit_cell_crystal_symmetry())
assert cs_orig.is_similar_symmetry(
box.map_manager().unit_cell_crystal_symmetry())
assert box.map_manager().map_data().as_1d().count(0) == 81264
# Now specify bounds directly
new_box = cctbx.maptbx.box.with_bounds(map_manager=mam.mm.deep_copy(),
lower_bounds=(-7, -7, -7),
upper_bounds=(37, 47, 39),
wrapping=False)
new_model = new_box.apply_to_model(mam.model.deep_copy())
# make sure things are changed in-place and are therefore different from start
assert new_box.map_manager().map_data().size() != map_data_orig.size()
assert new_model.get_sites_frac() != sites_frac_orig
assert new_model.get_sites_cart() != sites_cart_orig
assert (not cs_orig.is_similar_symmetry(new_model.crystal_symmetry()))
# make sure box, model and map_manager remember original crystal symmetry
assert cs_orig.is_similar_symmetry(
box.model().unit_cell_crystal_symmetry())
assert cs_orig.is_similar_symmetry(
box.map_manager().unit_cell_crystal_symmetry())
assert box.map_manager().map_data().as_1d().count(0) == 81264
# Now specify bounds directly and init with model
box = cctbx.maptbx.box.with_bounds(map_manager=mam.mm.deep_copy(),
lower_bounds=(-7, -7, -7),
upper_bounds=(37, 47, 39),
wrapping=False,
model=mam.model.deep_copy())
new_model = box.model()
# make sure things are changed in-place and are therefore different from start
assert box.map_manager().map_data().size() != map_data_orig.size()
assert new_model.get_sites_frac() != sites_frac_orig
assert new_model.get_sites_cart() != sites_cart_orig
assert (not cs_orig.is_similar_symmetry(new_model.crystal_symmetry()))
# make sure box, model and map_manager remember original crystal symmetry
assert cs_orig.is_similar_symmetry(
box.model().unit_cell_crystal_symmetry())
assert cs_orig.is_similar_symmetry(
box.map_manager().unit_cell_crystal_symmetry())
assert box.map_manager().map_data().as_1d().count(0) == 81264
# Extract using around_unique
data_dir = os.path.dirname(os.path.abspath(__file__))
data_ccp4 = os.path.join(data_dir, 'data', 'D7.ccp4')
data_ncs = os.path.join(data_dir, 'data', 'D7.ncs_spec')
data_seq = os.path.join(data_dir, 'data', 'D7.seq')
dm = DataManager(['real_map', 'phil', 'ncs_spec', 'sequence'])
dm.process_real_map_file(data_ccp4)
mm = dm.get_real_map(data_ccp4)
dm.process_ncs_spec_file(data_ncs)
ncs_obj = dm.get_ncs_spec(data_ncs)
dm.process_sequence_file(data_seq)
sequence = dm.get_sequence(data_seq)
sequence_as_text = sequence[0].sequence
map_model_mgr = map_model_manager(map_manager=mm, ncs_object=ncs_obj)
mm = map_model_mgr.map_manager()
mm.show_summary()
box = cctbx.maptbx.box.around_unique(
map_manager=mm.deep_copy(),
resolution=3,
box_cushion=1,
sequence=sequence_as_text,
soft_mask=True,
wrapping=False,
)
box.map_manager().write_map('new_box.ccp4')
# run again from map_manager
map_model_mgr.box_all_maps_around_unique_and_shift_origin(
resolution=3,
box_cushion=1,
sequence=sequence_as_text,
soft_mask=True,
)
# Get bounds around density
box = cctbx.maptbx.box.around_density(map_manager=mam.mm.deep_copy(),
wrapping=False)
# Create a mask
mm = mam.mm.deep_copy()
mm.create_mask_around_density(
resolution=3,
molecular_mass=2100,
sequence="GAVAGA",
solvent_content=0.5,
)
mask_mm = mm.get_mask_as_map_manager()
assert approx_equal(
(mask_mm.map_data().count(0), mask_mm.map_data().count(1),
mask_mm.map_data().size()), (19184, 19216, 38400))
# Box around the mask
box = cctbx.maptbx.box.around_mask(
map_manager=mam.mm.deep_copy(),
mask_as_map_manager=mask_mm,
wrapping=False,
)
assert (box.gridding_first, box.gridding_last) == ([0, 0, 0], [29, 39, 31])
# Box around the mask with cubic box
box = cctbx.maptbx.box.around_mask(
map_manager=mam.mm.deep_copy(),
mask_as_map_manager=mask_mm,
use_cubic_boxing=True,
wrapping=False,
)
assert (box.gridding_first, box.gridding_last) == ([1, 6, 2], [30, 35, 31])
#
# IF you are about to change this - THINK TWICE!
#
from libtbx.introspection import getfullargspec
r = getfullargspec(cctbx.maptbx.box.around_model.__init__)
assert r.args == [
'self', 'map_manager', 'model', 'box_cushion', 'wrapping',
'model_can_be_outside_bounds', 'stay_inside_current_map',
'use_cubic_boxing', 'require_match_unit_cell_crystal_symmetry', 'log'
], r.args
r = getfullargspec(cctbx.maptbx.box.with_bounds.__init__)
assert r.args == [
'self', 'map_manager', 'lower_bounds', 'upper_bounds', 'model',
'wrapping', 'model_can_be_outside_bounds', 'stay_inside_current_map',
'use_cubic_boxing', 'log'
], r.args
print("OK")
def exercise_around_model():
mam = get_random_structure_and_map(use_static_structure=True)
map_data_orig = mam.mm.map_data().deep_copy()
sites_frac_orig = mam.model.get_sites_frac().deep_copy()
sites_cart_orig = mam.model.get_sites_cart().deep_copy()
cs_orig = mam.model.crystal_symmetry()
box = cctbx.maptbx.box.around_model(map_manager=mam.mm,
model=mam.model.deep_copy(),
cushion=10,
wrapping=True)
new_mm1 = box.map_manager
new_mm2 = box.apply_to_map(map_manager=mam.mm.deep_copy())
assert approx_equal(new_mm1.map_data(), new_mm2.map_data())
new_model1 = box.model
new_model2 = box.apply_to_model(model=mam.model.deep_copy())
assert new_model1.crystal_symmetry().is_similar_symmetry(
new_model2.crystal_symmetry())
assert new_model1.crystal_symmetry().is_similar_symmetry(
box.crystal_symmetry)
assert approx_equal(new_model1.get_sites_cart()[0],
(19.705233333333336, 15.631525, 13.5040625))
# make sure things did change
assert new_mm2.map_data().size() != map_data_orig.size()
# make sure things are changed in-place and are therefore different from start
assert box.map_manager.map_data().size() != map_data_orig.size()
assert box.model.get_sites_frac() != sites_frac_orig
assert box.model.get_sites_cart() != sites_cart_orig
assert (not cs_orig.is_similar_symmetry(box.model.crystal_symmetry()))
# make sure box, model and map_manager remember original crystal symmetry
assert cs_orig.is_similar_symmetry(box.original_crystal_symmetry)
assert cs_orig.is_similar_symmetry(
box.map_manager.original_unit_cell_crystal_symmetry)
assert approx_equal(
box.model.get_shift_manager().shift_cart,
[5.229233333333334, 5.061524999999999, 5.162062499999999])
assert box.model.get_shift_manager(
).shifted_crystal_symmetry.is_similar_symmetry(
box.model.crystal_symmetry())
assert box.model.get_shift_manager(
).original_crystal_symmetry.is_similar_symmetry(cs_orig)
assert (not box.model.get_shift_manager().shifted_crystal_symmetry.
is_similar_symmetry(cs_orig))
assert approx_equal(
box.model._figure_out_hierarchy_to_output(
do_not_shift_back=False).atoms().extract_xyz()[0],
(14.476, 10.57, 8.342))
# make sure we can stack shifts
sel = box.model.selection("resseq 219:219")
m_small = box.model.select(selection=sel)
# Just until deep_copy() deep-copies shift_manager...
m_small._shift_manager = m_small.get_shift_manager().deep_copy()
assert approx_equal(box.model.get_shift_manager().shift_cart,
m_small.get_shift_manager().shift_cart)
assert not (box.model.get_shift_manager() is m_small.get_shift_manager())
# Now box again:
small_box = cctbx.maptbx.box.around_model(map_manager=mam.mm,
model=m_small,
cushion=5,
wrapping=True)
# Make sure nothing was zeroed out in this map (wrapping=True)
assert new_mm1.map_data().as_1d().count(0) == 0
# Now without wrapping...
box = cctbx.maptbx.box.around_model(map_manager=mam.mm,
model=mam.model.deep_copy(),
cushion=10,
wrapping=False)
# make sure things are changed in-place and are therefore different from start
assert box.map_manager.map_data().size() != map_data_orig.size()
assert box.model.get_sites_frac() != sites_frac_orig
assert box.model.get_sites_cart() != sites_cart_orig
assert (not cs_orig.is_similar_symmetry(box.model.crystal_symmetry()))
# make sure box, model and map_manager remember original crystal symmetry
assert cs_orig.is_similar_symmetry(box.original_crystal_symmetry)
assert cs_orig.is_similar_symmetry(
box.map_manager.original_unit_cell_crystal_symmetry)
assert box.map_manager.map_data().as_1d().count(0) == 81264
# Now specify bounds directly
box = cctbx.maptbx.box.with_bounds(map_manager=mam.mm.deep_copy(),
lower_bounds=(-7, -7, -7),
upper_bounds=(37, 47, 39),
wrapping=False)
new_model = box.apply_to_model(mam.model.deep_copy())
# make sure things are changed in-place and are therefore different from start
assert box.map_manager.map_data().size() != map_data_orig.size()
assert new_model.get_sites_frac() != sites_frac_orig
assert new_model.get_sites_cart() != sites_cart_orig
assert (not cs_orig.is_similar_symmetry(new_model.crystal_symmetry()))
# make sure box, model and map_manager remember original crystal symmetry
assert cs_orig.is_similar_symmetry(box.original_crystal_symmetry)
assert cs_orig.is_similar_symmetry(
box.map_manager.original_unit_cell_crystal_symmetry)
assert box.map_manager.map_data().as_1d().count(0) == 81264
# Now specify bounds directly and init with model
box = cctbx.maptbx.box.with_bounds(map_manager=mam.mm.deep_copy(),
lower_bounds=(-7, -7, -7),
upper_bounds=(37, 47, 39),
wrapping=False,
model=mam.model.deep_copy())
new_model = box.model
# make sure things are changed in-place and are therefore different from start
assert box.map_manager.map_data().size() != map_data_orig.size()
assert new_model.get_sites_frac() != sites_frac_orig
assert new_model.get_sites_cart() != sites_cart_orig
assert (not cs_orig.is_similar_symmetry(new_model.crystal_symmetry()))
# make sure box, model and map_manager remember original crystal symmetry
assert cs_orig.is_similar_symmetry(box.original_crystal_symmetry)
assert cs_orig.is_similar_symmetry(
box.map_manager.original_unit_cell_crystal_symmetry)
assert box.map_manager.map_data().as_1d().count(0) == 81264
# Extract using extract_unique
data_dir = os.path.dirname(os.path.abspath(__file__))
data_ccp4 = os.path.join(data_dir, 'data', 'D7.ccp4')
data_ncs = os.path.join(data_dir, 'data', 'D7.ncs_spec')
data_seq = os.path.join(data_dir, 'data', 'D7.seq')
dm = DataManager(['real_map', 'phil', 'ncs_spec', 'sequence'])
dm.process_real_map_file(data_ccp4)
mm = dm.get_real_map(data_ccp4)
dm.process_ncs_spec_file(data_ncs)
ncs_obj = dm.get_ncs_spec(data_ncs)
dm.process_sequence_file(data_seq)
sequence = dm.get_sequence(data_seq)
sequence_as_text = sequence[0].sequence
mm.show_summary()
box = cctbx.maptbx.box.extract_unique(
map_manager=mm.deep_copy(),
resolution=3,
box_buffer=1,
sequence=sequence_as_text,
ncs_object=ncs_obj,
wrapping=False,
)
box.map_manager.write_map('new_box.ccp4')
# Get bounds around density
box = cctbx.maptbx.box.around_density(map_manager=mam.mm.deep_copy(),
wrapping=False)
#
# IF you are about to change this - THINK TWICE!
#
import inspect
r = inspect.getargspec(cctbx.maptbx.box.around_model.__init__)
assert r.args == [
'self', 'map_manager', 'model', 'cushion', 'wrapping', 'log'
], r.args
r = inspect.getargspec(cctbx.maptbx.box.with_bounds.__init__)
assert r.args == [
'self', 'map_manager', 'lower_bounds', 'upper_bounds', 'wrapping',
'model', 'log'
], r.args