def run(args, out=sys.stdout):
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="model",
map_file_def="map",
usage_string="""\
em_rscc.py model.pdb map.ccp4
%s""" % __doc__)
params = cmdline.work.extract()
assert (not None in [params.model, params.map])
pdb_in = cmdline.get_file(params.model).file_object
m = cmdline.get_file(params.map).file_object
print >> out, "Input electron density map:"
print >> out, "m.all() :", m.data.all()
print >> out, "m.focus() :", m.data.focus()
print >> out, "m.origin():", m.data.origin()
print >> out, "m.nd() :", m.data.nd()
print >> out, "m.size() :", m.data.size()
print >> out, "m.focus_size_1d():", m.data.focus_size_1d()
print >> out, "m.is_0_based() :", m.data.is_0_based()
print >> out, "map: min/max/mean:", flex.min(m.data), flex.max(
m.data), flex.mean(m.data)
print >> out, "unit cell:", m.unit_cell_parameters
symm = crystal.symmetry(space_group_symbol="P1",
unit_cell=m.unit_cell_parameters)
xrs = pdb_in.input.xray_structure_simple(crystal_symmetry=symm)
print >> out, "Setting up electron scattering table (d_min=%g)" % params.d_min
xrs.scattering_type_registry(d_min=params.d_min, table="electron")
fc = xrs.structure_factors(d_min=params.d_min).f_calc()
cg = maptbx.crystal_gridding(unit_cell=symm.unit_cell(),
space_group_info=symm.space_group_info(),
pre_determined_n_real=m.data.all())
fc_map = fc.fft_map(
crystal_gridding=cg).apply_sigma_scaling().real_map_unpadded()
assert (fc_map.all() == fc_map.focus() == m.data.all())
em_data = m.data.as_double()
unit_cell_for_interpolation = m.grid_unit_cell()
frac_matrix = unit_cell_for_interpolation.fractionalization_matrix()
sites_cart = xrs.sites_cart()
sites_frac = xrs.sites_frac()
print >> out, "PER-RESIDUE CORRELATION:"
for chain in pdb_in.hierarchy.only_model().chains():
for residue_group in chain.residue_groups():
i_seqs = residue_group.atoms().extract_i_seq()
values_em = flex.double()
values_fc = flex.double()
for i_seq in i_seqs:
rho_em = maptbx.non_crystallographic_eight_point_interpolation(
map=em_data,
gridding_matrix=frac_matrix,
site_cart=sites_cart[i_seq])
rho_fc = fc_map.eight_point_interpolation(sites_frac[i_seq])
values_em.append(rho_em)
values_fc.append(rho_fc)
cc = flex.linear_correlation(x=values_em,
y=values_fc).coefficient()
print >> out, residue_group.id_str(), cc
def get_density_at_position(position, frac_matrix, mapdata):
"""generic function for computing the density at a single point"""
# raise Sorry if the position doesn't appear to be within the bounds of the map.
# this may mean the user supplied a model that was not centered in the map.
try:
density = non_crystallographic_eight_point_interpolation(
map=mapdata, gridding_matrix=frac_matrix, site_cart=position)
except RuntimeError as e:
raise Sorry("Could not compute map density at the requested position. "+\
"Please check that model is entirely within map bounds.")
return density
def sample_angle (
i_seqs,
sites_cart,
map_coeffs,
real_map,
sigma,
angle_start,
params,
unit_cell=None) :
frac_matrix = None
if (unit_cell is None) :
assert (map_coeffs is not None)
unit_cell = map_coeffs.unit_cell()
frac_matrix = unit_cell.fractionalization_matrix()
assert (params.sampling_method != "direct") or (map_coeffs is not None)
from cctbx import maptbx
from scitbx.matrix import rotate_point_around_axis
point = rotate_point_around_axis(
axis_point_1=sites_cart[1],
axis_point_2=sites_cart[2],
point=sites_cart[3],
angle=-angle_start,
deg=True)
# TODO: present option to have point (sites_cart[3]) be generated based on idealized geometry.
n_degrees = 0
densities = []
while (n_degrees < 360) :
point = rotate_point_around_axis(
axis_point_1=sites_cart[1],
axis_point_2=sites_cart[2],
point=point,
angle=params.sampling_angle,
deg=True)
point_frac = unit_cell.fractionalize(site_cart=point)
if (params.sampling_method == "spline") and (map_coeffs is not None) :
rho = real_map.tricubic_interpolation(point_frac)
elif (params.sampling_method == "linear") or (map_coeffs is None) :
if (map_coeffs is None) :
rho = maptbx.non_crystallographic_eight_point_interpolation(
map=real_map,
gridding_matrix=frac_matrix,
site_cart=point)
#allow_out_of_bounds=True)
else :
rho = real_map.eight_point_interpolation(point_frac)
else :
rho = map_coeffs.direct_summation_at_point(
site_frac=point_frac,
sigma=sigma).real
densities.append(rho)
n_degrees += params.sampling_angle
#print densities
return densities
def exercise_non_crystallographic_eight_point_interpolation():
unit_cell=130.45,130.245,288.405,90,90,120
unit_cell_gridding_n=144,144,360
grid_cell=uctbx.unit_cell((130.45/144,130.245/144,388.405/360,90,90,120))
grid_mat = grid_cell.fractionalization_matrix()
map = test_map.deep_copy()
map.resize(flex.grid((-1,-2,-1),(3,3,5)))
for site_cart,expected_result in ([(0.468661,-1.549268,3.352108),-0.333095],
[(0.624992,1.553980,1.205578),-0.187556],
[(0.278175,0.968454,2.578265),-0.375068],
[(0.265198,-1.476055,0.704381),-0.147061],
[(1.296042,0.002101,3.459270),-0.304401],
[(0.296189,-1.346603,2.935777),-0.296395],
[(0.551586,-1.284371,3.202145),-0.363263],
[(0.856542,-0.782700,-0.985020),-0.106925],
[(0.154407,1.078936,-0.917551),-0.151128]):
assert approx_equal(maptbx.non_crystallographic_eight_point_interpolation(
map=map,
gridding_matrix=grid_mat,
site_cart=site_cart,
allow_out_of_bounds=False,
out_of_bounds_substitute_value=0), expected_result)
for x in range(0,2):
for y in range(-1,2):
for z in range(0,4):
assert approx_equal(
maptbx.non_crystallographic_eight_point_interpolation(
map,
grid_mat,
grid_cell.orthogonalize((x,y,z))), map[x,y,z])
try:
val = maptbx.non_crystallographic_eight_point_interpolation(
map, grid_mat, (5,5,5))
except RuntimeError as e:
assert str(e) == \
"cctbx Error: non_crystallographic_eight_point_interpolation:" \
" point required for interpolation is out of bounds."
else: raise Exception_expected
assert approx_equal(maptbx.non_crystallographic_eight_point_interpolation(
map, grid_mat, (5,5,5), True, -123), -123)
def sample_angle(i_seqs,
sites_cart,
map_coeffs,
real_map,
difference_map,
sigma,
angle_start,
params,
sampling_method="linear",
unit_cell=None):
"""
Given a set of four sites defining a rotatable dihedral angle, sample the
density at the fourth site in small angular increments.
returns: a tuple of lists containing the sampled density values (floats) for
the primary map and optional difference map.
"""
frac_matrix = None
if (unit_cell is None):
assert (map_coeffs is not None)
unit_cell = map_coeffs.unit_cell()
frac_matrix = unit_cell.fractionalization_matrix()
assert (sampling_method != "direct") or (map_coeffs is not None)
from cctbx import maptbx
from scitbx.matrix import rotate_point_around_axis
point = rotate_point_around_axis(axis_point_1=sites_cart[1],
axis_point_2=sites_cart[2],
point=sites_cart[3],
angle=-angle_start,
deg=True)
# TODO: present option to have point (sites_cart[3]) be generated based on
# idealized geometry.
n_degrees = 0
densities = []
difference_densities = []
while (n_degrees < 360):
point = rotate_point_around_axis(axis_point_1=sites_cart[1],
axis_point_2=sites_cart[2],
point=point,
angle=params.sampling_angle,
deg=True)
point_frac = unit_cell.fractionalize(site_cart=point)
rho = rho_fofc = None
if (sampling_method == "spline") and (map_coeffs is not None):
rho = real_map.tricubic_interpolation(point_frac)
if (difference_map is not None):
rho_fofc = difference_map.tricubic_interpolation(point_frac)
elif (sampling_method == "linear") or (map_coeffs is None):
if (map_coeffs is None):
rho = maptbx.non_crystallographic_eight_point_interpolation(
map=real_map, gridding_matrix=frac_matrix, site_cart=point)
#allow_out_of_bounds=True)
else:
rho = real_map.eight_point_interpolation(point_frac)
if (difference_map is not None):
rho_fofc = difference_map.eight_point_interpolation(
point_frac)
else:
rho = map_coeffs.direct_summation_at_point(site_frac=point_frac,
sigma=sigma).real
densities.append(rho)
if (rho_fofc is not None):
difference_densities.append(rho_fofc)
n_degrees += params.sampling_angle
#print densities
return densities, difference_densities
def sample_angle (
i_seqs,
sites_cart,
map_coeffs,
real_map,
difference_map,
sigma,
angle_start,
params,
sampling_method="linear",
unit_cell=None) :
"""
Given a set of four sites defining a rotatable dihedral angle, sample the
density at the fourth site in small angular increments.
returns: a tuple of lists containing the sampled density values (floats) for
the primary map and optional difference map.
"""
frac_matrix = None
if (unit_cell is None) :
assert (map_coeffs is not None)
unit_cell = map_coeffs.unit_cell()
frac_matrix = unit_cell.fractionalization_matrix()
assert (sampling_method != "direct") or (map_coeffs is not None)
from cctbx import maptbx
from scitbx.matrix import rotate_point_around_axis
point = rotate_point_around_axis(
axis_point_1=sites_cart[1],
axis_point_2=sites_cart[2],
point=sites_cart[3],
angle=-angle_start,
deg=True)
# TODO: present option to have point (sites_cart[3]) be generated based on
# idealized geometry.
n_degrees = 0
densities = []
difference_densities = []
while (n_degrees < 360) :
point = rotate_point_around_axis(
axis_point_1=sites_cart[1],
axis_point_2=sites_cart[2],
point=point,
angle=params.sampling_angle,
deg=True)
point_frac = unit_cell.fractionalize(site_cart=point)
rho = rho_fofc = None
if (sampling_method == "spline") and (map_coeffs is not None) :
rho = real_map.tricubic_interpolation(point_frac)
if (difference_map is not None) :
rho_fofc = difference_map.tricubic_interpolation(point_frac)
elif (sampling_method == "linear") or (map_coeffs is None) :
if (map_coeffs is None) :
rho = maptbx.non_crystallographic_eight_point_interpolation(
map=real_map,
gridding_matrix=frac_matrix,
site_cart=point)
#allow_out_of_bounds=True)
else :
rho = real_map.eight_point_interpolation(point_frac)
if (difference_map is not None) :
rho_fofc = difference_map.eight_point_interpolation(point_frac)
else :
rho = map_coeffs.direct_summation_at_point(
site_frac=point_frac,
sigma=sigma).real
densities.append(rho)
if (rho_fofc is not None) :
difference_densities.append(rho_fofc)
n_degrees += params.sampling_angle
#print densities
return densities, difference_densities
for y in range(-1,2):
for z in range(0,4):
assert approx_equal(
maptbx.non_crystallographic_eight_point_interpolation(
map,
grid_mat,
grid_cell.orthogonalize((x,y,z))), map[x,y,z])
try:
val = maptbx.non_crystallographic_eight_point_interpolation(
map, grid_mat, (5,5,5))
except RuntimeError, e:
assert str(e) == \
"cctbx Error: non_crystallographic_eight_point_interpolation:" \
" point required for interpolation is out of bounds."
else: raise Exception_expected
assert approx_equal(maptbx.non_crystallographic_eight_point_interpolation(
map, grid_mat, (5,5,5), True, -123), -123)
def exercise_average_density():
map = test_map.deep_copy()
map.resize(flex.grid(4,5,6))
sites_frac = flex.vec3_double([
(-0.8492400683111605, 0.49159543530354166, 0.55624239788303198),
(0.10631567870879444, -0.38726326483005269, -0.13581656178827783),
(0.1895918946688977, -0.25027164520003642, -0.61981792226895172),
(-0.88980846616667897, -0.79492758628794169, 0.015347308715653485)])
unit_cell = uctbx.unit_cell((130,130,288,90,90,120))
densities = maptbx.average_densities(
unit_cell=unit_cell,
data=map,
sites_frac=sites_frac,
radius=5)
def run (args, out=sys.stdout) :
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="model",
map_file_def="map",
usage_string="""\
em_rscc.py model.pdb map.ccp4
%s""" % __doc__)
params = cmdline.work.extract()
assert (not None in [params.model, params.map])
pdb_in = cmdline.get_file(params.model).file_object
m = cmdline.get_file(params.map).file_object
print >> out, "Input electron density map:"
print >> out, "m.all() :", m.data.all()
print >> out, "m.focus() :", m.data.focus()
print >> out, "m.origin():", m.data.origin()
print >> out, "m.nd() :", m.data.nd()
print >> out, "m.size() :", m.data.size()
print >> out, "m.focus_size_1d():", m.data.focus_size_1d()
print >> out, "m.is_0_based() :", m.data.is_0_based()
print >> out, "map: min/max/mean:", flex.min(m.data), flex.max(m.data), flex.mean(m.data)
print >> out, "unit cell:", m.unit_cell_parameters
symm = crystal.symmetry(
space_group_symbol="P1",
unit_cell=m.unit_cell_parameters)
xrs = pdb_in.input.xray_structure_simple(crystal_symmetry=symm)
print >> out, "Setting up electron scattering table (d_min=%g)" % params.d_min
xrs.scattering_type_registry(
d_min=params.d_min,
table="electron")
fc = xrs.structure_factors(d_min=params.d_min).f_calc()
cg = maptbx.crystal_gridding(
unit_cell=symm.unit_cell(),
space_group_info=symm.space_group_info(),
pre_determined_n_real=m.data.all())
fc_map = fc.fft_map(
crystal_gridding=cg).apply_sigma_scaling().real_map_unpadded()
assert (fc_map.all() == fc_map.focus() == m.data.all())
em_data = m.data.as_double()
unit_cell_for_interpolation = m.grid_unit_cell()
frac_matrix = unit_cell_for_interpolation.fractionalization_matrix()
sites_cart = xrs.sites_cart()
sites_frac = xrs.sites_frac()
print >> out, "PER-RESIDUE CORRELATION:"
for chain in pdb_in.hierarchy.only_model().chains() :
for residue_group in chain.residue_groups() :
i_seqs = residue_group.atoms().extract_i_seq()
values_em = flex.double()
values_fc = flex.double()
for i_seq in i_seqs :
rho_em = maptbx.non_crystallographic_eight_point_interpolation(
map=em_data,
gridding_matrix=frac_matrix,
site_cart=sites_cart[i_seq])
rho_fc = fc_map.eight_point_interpolation(sites_frac[i_seq])
values_em.append(rho_em)
values_fc.append(rho_fc)
cc = flex.linear_correlation(x=values_em, y=values_fc).coefficient()
print >> out, residue_group.id_str(), cc
