def exercise_mask_data_1(space_group_info, n_sites=100):
from cctbx import maptbx
from cctbx.masks import vdw_radii_from_xray_structure
for d_min in [1, 1.5, 2.1]:
for resolution_factor in [1. / 2, 1. / 3, 1. / 4, 1. / 5]:
xrs = random_structure.xray_structure(
space_group_info=space_group_info,
elements=(("O", "N", "C") * (n_sites // 3 + 1))[:n_sites],
volume_per_atom=30,
min_distance=1)
atom_radii = vdw_radii_from_xray_structure(xray_structure=xrs)
asu_mask = masks.atom_mask(unit_cell=xrs.unit_cell(),
group=xrs.space_group(),
resolution=d_min,
grid_step_factor=resolution_factor,
solvent_radius=1.0,
shrink_truncation_radius=1.0)
asu_mask.compute(xrs.sites_frac(), atom_radii)
mask_data = asu_mask.mask_data_whole_uc()
assert flex.min(mask_data) == 0.0
# It's not just 0 and 1 ...
assert flex.max(mask_data) == xrs.space_group().order_z()
# In fact, it is a mixture ...
if 0: # XXX this will rightfully crash
mask_data_ = mask_data / xrs.space_group().order_z()
s0 = mask_data_ < 0.5
s1 = mask_data_ > 0.5
if (mask_data_.size() != s0.count(True) + s1.count(True)):
for d in mask_data_:
if (d != 0 and d != 1):
print(d, xrs.space_group().order_z())
assert mask_data_.size(
) == s0.count(True) + s1.count(True), [
mask_data_.size() - (s0.count(True) + s1.count(True))
]
if (
0
): # XXX This would crash with the message: "... The grid is not ..."
cr_gr = maptbx.crystal_gridding(
unit_cell=xrs.unit_cell(),
d_min=d_min,
resolution_factor=resolution_factor)
asu_mask = masks.atom_mask(unit_cell=xrs.unit_cell(),
space_group=xrs.space_group(),
gridding_n_real=cr_gr.n_real(),
solvent_radius=1.0,
shrink_truncation_radius=1.0)
asu_mask.compute(xrs.sites_frac(), atom_radii)
def exercise_mask_data_1(space_group_info, n_sites=100):
from cctbx import maptbx
from cctbx.masks import vdw_radii_from_xray_structure
for d_min in [1, 1.5, 2.1]:
for resolution_factor in [1./2, 1./3, 1./4, 1./5]:
xrs = random_structure.xray_structure(
space_group_info=space_group_info,
elements=(("O","N","C")*(n_sites//3+1))[:n_sites],
volume_per_atom=30,
min_distance=1)
atom_radii = vdw_radii_from_xray_structure(xray_structure = xrs)
asu_mask = masks.atom_mask(
unit_cell = xrs.unit_cell(),
group = xrs.space_group(),
resolution = d_min,
grid_step_factor = resolution_factor,
solvent_radius = 1.0,
shrink_truncation_radius = 1.0)
asu_mask.compute(xrs.sites_frac(), atom_radii)
mask_data = asu_mask.mask_data_whole_uc()
assert flex.min(mask_data) == 0.0
# It's not just 0 and 1 ...
assert flex.max(mask_data) == xrs.space_group().order_z()
# In fact, it is a mixture ...
if 0: # XXX this will rightfully crash
mask_data_ = mask_data / xrs.space_group().order_z()
s0 = mask_data_ < 0.5
s1 = mask_data_ > 0.5
if(mask_data_.size() != s0.count(True)+s1.count(True)):
for d in mask_data_:
if(d != 0 and d != 1): print d, xrs.space_group().order_z()
assert mask_data_.size() == s0.count(True)+s1.count(True), [
mask_data_.size()-(s0.count(True)+s1.count(True))]
if(0): # XXX This would crash with the message: "... The grid is not ..."
cr_gr = maptbx.crystal_gridding(
unit_cell = xrs.unit_cell(),
d_min = d_min,
resolution_factor = resolution_factor)
asu_mask = masks.atom_mask(
unit_cell = xrs.unit_cell(),
space_group = xrs.space_group(),
gridding_n_real = cr_gr.n_real(),
solvent_radius = 1.0,
shrink_truncation_radius = 1.0)
asu_mask.compute(xrs.sites_frac(), atom_radii)
def exercise_mask_data_2(space_group_info,
n_sites=100,
d_min=2.0,
resolution_factor=1. / 4):
from cctbx import maptbx
from cctbx.masks import vdw_radii_from_xray_structure
for yn2 in [0, 1]:
for yn in [0, 1]:
xrs = random_structure.xray_structure(
space_group_info=space_group_info,
elements=(("O", "N", "C") * (n_sites // 3 + 1))[:n_sites],
volume_per_atom=50,
min_distance=1.5)
xrs.shake_sites_in_place(mean_distance=10)
if (yn2): xrs = xrs.expand_to_p1(sites_mod_positive=True)
atom_radii = vdw_radii_from_xray_structure(xray_structure=xrs)
asu_mask = masks.atom_mask(unit_cell=xrs.unit_cell(),
group=xrs.space_group(),
resolution=d_min,
grid_step_factor=resolution_factor,
solvent_radius=1.0,
shrink_truncation_radius=1.0)
asu_mask.compute(xrs.sites_frac(), atom_radii)
mask_data = asu_mask.mask_data_whole_uc()
#
xrs_p1 = xrs.expand_to_p1(sites_mod_positive=True)
for site_frac in xrs_p1.sites_frac():
mv = mask_data.value_at_closest_grid_point(site_frac)
assert mv == 0
#
mask_data = mask_data / xrs.space_group().order_z()
if (yn == 1):
mask_data = maptbx.copy(mask_data,
flex.grid(mask_data.focus()))
#
for site_frac in xrs_p1.sites_frac():
mv = mask_data.value_at_closest_grid_point(site_frac)
assert mv == 0
#
fc = xrs.structure_factors(d_min=d_min).f_calc()
f_mask_1 = fc.set().array(
data=asu_mask.structure_factors(fc.indices()))
f_mask_2 = f_mask_1.structure_factors_from_map(
map=mask_data,
use_scale=True,
anomalous_flag=False,
use_sg=True)
fm1 = abs(f_mask_1).data()
fm2 = abs(f_mask_2).data()
r = flex.sum(flex.abs(fm1 - fm2)) / flex.sum(fm1 + fm2)
assert approx_equal(r, 0.0)
def exercise_mask_data_2(space_group_info, n_sites=100, d_min=2.0,
resolution_factor=1./4):
from cctbx import maptbx
from cctbx.masks import vdw_radii_from_xray_structure
for yn2 in [0,1]:
for yn in [0,1]:
xrs = random_structure.xray_structure(
space_group_info=space_group_info,
elements=(("O","N","C")*(n_sites//3+1))[:n_sites],
volume_per_atom=50,
min_distance=1.5)
xrs.shake_sites_in_place(mean_distance=10)
if(yn2): xrs = xrs.expand_to_p1(sites_mod_positive=True)
atom_radii = vdw_radii_from_xray_structure(xray_structure = xrs)
asu_mask = masks.atom_mask(
unit_cell = xrs.unit_cell(),
group = xrs.space_group(),
resolution = d_min,
grid_step_factor = resolution_factor,
solvent_radius = 1.0,
shrink_truncation_radius = 1.0)
asu_mask.compute(xrs.sites_frac(), atom_radii)
mask_data = asu_mask.mask_data_whole_uc()
#
xrs_p1 = xrs.expand_to_p1(sites_mod_positive=True)
for site_frac in xrs_p1.sites_frac():
mv = mask_data.value_at_closest_grid_point(site_frac)
assert mv == 0
#
mask_data = mask_data / xrs.space_group().order_z()
if(yn == 1):
mask_data = maptbx.copy(mask_data, flex.grid(mask_data.focus()))
#
for site_frac in xrs_p1.sites_frac():
mv = mask_data.value_at_closest_grid_point(site_frac)
assert mv == 0
#
fc = xrs.structure_factors(d_min = d_min).f_calc()
f_mask_1 = fc.set().array(data = asu_mask.structure_factors(fc.indices()))
f_mask_2 = f_mask_1.structure_factors_from_map(map=mask_data,
use_scale = True, anomalous_flag = False, use_sg = True)
fm1 = abs(f_mask_1).data()
fm2 = abs(f_mask_2).data()
r = flex.sum( flex.abs( fm1 - fm2 ) ) / flex.sum( fm1 + fm2 )
assert approx_equal(r, 0.0)
def compare_masks(struc, opts):
tolerance = opts.tolerance
resolution = opts.resolution
solvent_radius = opts.solvent_radius
shrink_radius = opts.shrink_radius
verbose = opts.verbose
cout.truncate(0)
time_p1 = 0.0
time_asu = 0.0
time_orig = 0.0
params = masks.mask_master_params.extract()
params.ignore_hydrogens = False
params.ignore_zero_occupancy_atoms = False
params.solvent_radius = solvent_radius
params.shrink_truncation_radius = shrink_radius
fc = struc.structure_factors(d_min = resolution).f_calc()
while fc.data().size() <= 3 :
resolution /= 1.2
assert resolution > 1.0E-3
fc = struc.structure_factors( d_min = resolution).f_calc()
print >>cout, "Resolution= ", resolution, " solvent radius= ", \
solvent_radius, " shrink radius= ", shrink_radius, " Tolerance= ", \
tolerance, " Number of reflection= ", fc.data().size()
struc.show_summary(cout)
group = struc.space_group()
print >>cout, "Cell volume= ", struc.unit_cell().volume(), \
" Group order= ", group.order_z(), " p= ", group.order_p()
print >>cout, "Hall symbol: ", group.type().hall_symbol()
#check_group(group)
tb = time.time()
asu_mask = masks.atom_mask(
unit_cell = struc.unit_cell(),
group = struc.space_group(),
resolution = fc.d_min(),
grid_step_factor = params.grid_step_factor,
solvent_radius = params.solvent_radius,
shrink_truncation_radius = params.shrink_truncation_radius )
te = time.time()
time_asu += (te-tb)
grid = asu_mask.grid_size()
print >>cout, "asu mask grid = ", grid
zero_test(asu_mask, fc, tolerance = tolerance)
radii = get_radii(struc)
assert len(radii) == len(struc.sites_frac())
tb = time.time()
asu_mask.compute( struc.sites_frac(), radii )
te = time.time()
time_asu += (te-tb)
print >>cout, " n asu atoms= ", asu_mask.n_asu_atoms(), \
" has-enclosed= ", asu_mask.debug_has_enclosed_box
tb = time.time()
fm_asu = asu_mask.structure_factors( fc.indices() )
fm_asu = fc.set().array( data = fm_asu )
te = time.time()
time_asu_sf = te-tb
time_asu += (te-tb)
# save files
if not opts.save_files is None:
tmp_file = open(opts.save_files + ".pdb", "w")
print >>tmp_file, struc.as_pdb_file()
tmp_file.close()
asu_mask.xplor_write_map(opts.save_files + "_mask.map")
asu_mask.xplor_write_map(opts.save_files + "_inverted_mask.map", 1, True)
# also save structure factors
import iotbx.mtz
mtzo = iotbx.mtz.object()
mtzo.set_title("mask test")
mtzo.add_history(line="start")
mtzo.set_space_group_info(fm_asu.space_group_info())
mtzo.set_hkl_base(fm_asu.unit_cell())
crystal = mtzo.add_crystal(
name="mask_test_crystal",
project_name="mask_test_project",
unit_cell=fm_asu.unit_cell())
dataset = crystal.add_dataset(
name="mask_test_dataset",
wavelength=1)
assert dataset.add_miller_array(
miller_array=fm_asu,
column_root_label="F",
#column_types=column_types
) is dataset
mtzo.add_history(line="done")
mtzo.write(opts.save_files + "_sf.mtz")
#
# ========= old mask =============
#
tb = time.time()
struc_p1 = struc.expand_to_p1()
te = time.time()
time_p1_exp = (te-tb)
time_p1 += (te-tb)
fc_p1 = fc.deep_copy()
fc_p1 = fc_p1.customized_copy(crystal_symmetry = struc_p1.crystal_symmetry())
tb = time.time()
blk_p1 = masks.bulk_solvent(
xray_structure = struc_p1,
gridding_n_real = grid,
ignore_zero_occupancy_atoms = params.ignore_zero_occupancy_atoms,
ignore_hydrogen_atoms = params.ignore_hydrogens,
solvent_radius = params.solvent_radius,
shrink_truncation_radius = params.shrink_truncation_radius)
te = time.time()
time_p1_msk = (te-tb)
time_p1 += (te-tb)
tb = time.time()
fm_p1 = blk_p1.structure_factors( miller_set = fc_p1 )
te = time.time()
time_p1_sf = (te-tb)
time_p1 += (te-tb)
blk_p1.show_summary(cout)
### original mask
tb = time.time()
blk_o = masks.bulk_solvent(
xray_structure = struc,
gridding_n_real = grid,
ignore_zero_occupancy_atoms = params.ignore_zero_occupancy_atoms,
ignore_hydrogen_atoms = params.ignore_hydrogens,
solvent_radius = params.solvent_radius,
shrink_truncation_radius = params.shrink_truncation_radius)
te = time.time()
time_orig_msk = (te-tb)
time_orig += (te-tb)
tb = time.time()
fm_o = blk_o.structure_factors( miller_set = fc )
te = time.time()
time_orig_sf = (te-tb)
time_orig += (te-tb)
print >>cout, "Number of reflections ::: Fm asu = ", fm_asu.data().size(), \
"Fm P1 = ", fm_p1.data().size()
print >>cout, "Time ( ms ) P1= ", time_p1*1000.0, " orig= ", \
time_orig*1000.0, " asu= ", time_asu*1000.0
print >>cout, "Times ( ms ) mask_asu= ", asu_mask.debug_mask_asu_time, \
" atoms_to_asu= ", asu_mask.debug_atoms_to_asu_time, \
" accessible= ", asu_mask.debug_accessible_time, \
" contact= ", asu_mask.debug_contact_time, \
" Fc= ", time_asu_sf*1000.0, \
" fft= ", asu_mask.debug_fft_time
print >>cout, "Times ( ms ) orig: mask= ", time_orig_msk*1000.0, " Fc=", \
time_orig_sf*1000.0
print >>cout, "Times ( ms ) p1 : expand= ", time_p1_exp*1000.0, " mask= ", \
time_p1_msk*1000.0, " Fc=", time_p1_sf*1000.0
assert fm_asu.data().size() == fm_o.data().size()
t_v1 = asu_mask.contact_surface_fraction
t_v2 = blk_p1.contact_surface_fraction
t_v3 = max( abs(t_v1), abs(t_v2) )
if t_v3 > 1.0E-6:
t_v4 = abs( t_v1 - t_v2 ) / t_v3
else:
t_v4 = 0.0
if( t_v4>1.0E-6 ):
if not opts.failed_file is None:
tmp_file = open(opts.failed_file, "w")
print >>tmp_file, struc.as_pdb_file()
tmp_file.close()
raise "Not equal solvent volume"
assert approx_equal(
asu_mask.contact_surface_fraction, blk_p1.contact_surface_fraction)
assert approx_equal(
asu_mask.accessible_surface_fraction, blk_p1.accessible_surface_fraction)
assert is_below_limit(
value=asu_mask.accessible_surface_fraction,
limit=asu_mask.contact_surface_fraction)
n_compared = compare_fc(fm_asu, fm_p1, tolerance = tolerance)
assert n_compared == fm_asu.data().size(), \
"N compared refls: "+str(n_compared) + " != " + str(fm_asu.data().size())
assert n_compared >0
if verbose:
print cout.getvalue()
# test that second calculation will produce the same results
asu_mask.compute( struc.sites_frac(), radii )
fm_asu2 = asu_mask.structure_factors( fc.indices() )
fm_asu2 = fc.set().array( data = fm_asu2 )
n_compared = compare_fc(fm_asu, fm_asu2, tolerance = tolerance)
assert n_compared == fm_asu.data().size(), \
"N compared refls: "+str(n_compared) + " != " + str(fm_asu.data().size())
cout.truncate(0)