def simple(fmodel, pdb_hierarchy, params=None, log=None, show_results=False):
if (params is None): params = master_params().extract()
if (log is None): log = sys.stdout
crystal_gridding = None
unit_cell = None
d_min = 1.0
map_1 = None
map_2 = None
# compute map_1 and map_2 if given F_obs (fmodel exists)
if ((params.map_file_name is None)
and (params.map_coefficients_file_name is None)
and (fmodel is not None)):
e_map_obj = fmodel.electron_density_map()
coeffs_2 = e_map_obj.map_coefficients(
map_type=params.map_2.type,
fill_missing=params.map_2.fill_missing_reflections,
isotropize=params.map_2.isotropize)
fft_map_2 = coeffs_2.fft_map(
resolution_factor=params.resolution_factor)
crystal_gridding = fft_map_2
fft_map_2.apply_sigma_scaling()
map_2 = fft_map_2.real_map_unpadded()
coeffs_1 = e_map_obj.map_coefficients(
map_type=params.map_1.type,
fill_missing=params.map_1.fill_missing_reflections,
isotropize=params.map_1.isotropize)
fft_map_1 = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=coeffs_1)
fft_map_1.apply_sigma_scaling()
map_1 = fft_map_1.real_map_unpadded()
unit_cell = fmodel.xray_structure.unit_cell()
d_min = fmodel.f_obs().d_min()
# or read map coefficents
elif (params.map_coefficients_file_name is not None):
map_handle = any_file(params.map_coefficients_file_name)
crystal_symmetry = get_crystal_symmetry(map_handle)
unit_cell = crystal_symmetry.unit_cell()
d_min = get_d_min(map_handle)
crystal_gridding = maptbx.crystal_gridding(
crystal_symmetry.unit_cell(),
d_min=d_min,
resolution_factor=params.resolution_factor,
space_group_info=crystal_symmetry.space_group_info())
coeffs_2 = map_handle.file_server.get_miller_array(
params.map_coefficients_label)
fft_map_2 = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=coeffs_2)
fft_map_2.apply_sigma_scaling()
map_2 = fft_map_2.real_map_unpadded()
# or read CCP4 map
else:
map_handle = any_file(params.map_file_name)
unit_cell = map_handle.file_object.unit_cell()
sg_info = space_group_info(map_handle.file_object.space_group_number)
n_real = map_handle.file_object.unit_cell_grid
crystal_gridding = maptbx.crystal_gridding(
unit_cell, space_group_info=sg_info, pre_determined_n_real=n_real)
map_2 = map_handle.file_object.map_data()
# check for origin shift
# modified from phenix.command_line.real_space_refine
# plan to centralize functionality in another location
# -------------------------------------------------------------------------
shift_manager = mmtbx.utils.shift_origin(
map_data=map_2,
pdb_hierarchy=pdb_hierarchy,
crystal_symmetry=map_handle.crystal_symmetry())
if (shift_manager.shift_cart is not None):
print("Map origin is not at (0,0,0): shifting the map and model.",
file=log)
pdb_hierarchy = shift_manager.pdb_hierarchy
map_2 = shift_manager.map_data
# -------------------------------------------------------------------------
# compute map_1 (Fc) if given a map (fmodel does not exist)
if (map_1 is None):
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=crystal_gridding.crystal_symmetry())
fft_map_1 = compute_map_from_model(d_min,
None,
xray_structure,
crystal_gridding=crystal_gridding)
fft_map_1.apply_sigma_scaling()
map_1 = fft_map_1.real_map_unpadded()
# compute cc
assert ((map_1 is not None) and (map_2 is not None))
broadcast(m="Map correlation and map values", log=log)
overall_cc = flex.linear_correlation(x=map_1.as_1d(),
y=map_2.as_1d()).coefficient()
print(" Overall map cc(%s,%s): %6.4f" %
(params.map_1.type, params.map_2.type, overall_cc),
file=log)
detail, atom_radius = params.detail, params.atom_radius
detail, atom_radius = set_detail_level_and_radius(detail=detail,
atom_radius=atom_radius,
d_min=d_min)
use_hydrogens = params.use_hydrogens
if (use_hydrogens is None):
if (params.scattering_table == "neutron" or d_min <= 1.2):
use_hydrogens = True
else:
use_hydrogens = False
hydrogen_atom_radius = params.hydrogen_atom_radius
if (hydrogen_atom_radius is None):
if (params.scattering_table == "neutron"):
hydrogen_atom_radius = atom_radius
else:
hydrogen_atom_radius = 1
results = compute(pdb_hierarchy=pdb_hierarchy,
unit_cell=unit_cell,
fft_n_real=map_1.focus(),
fft_m_real=map_1.all(),
map_1=map_1,
map_2=map_2,
detail=detail,
atom_radius=atom_radius,
use_hydrogens=use_hydrogens,
hydrogen_atom_radius=hydrogen_atom_radius)
if (show_results):
show(log=log, results=results, params=params, detail=detail)
return overall_cc, results
def simple(fmodel, pdb_hierarchy, params=None, log=None, show_results=False):
if(params is None): params = master_params().extract()
if(log is None): log = sys.stdout
crystal_gridding = None
unit_cell = None
d_min = 1.0
map_1 = None
map_2 = None
# compute map_1 and map_2 if given F_obs (fmodel exists)
if ( (params.map_file_name is None) and
(params.map_coefficients_file_name is None) and
(fmodel is not None) ):
e_map_obj = fmodel.electron_density_map()
coeffs_2 = e_map_obj.map_coefficients(
map_type = params.map_2.type,
fill_missing = params.map_2.fill_missing_reflections,
isotropize = params.map_2.isotropize)
fft_map_2 = coeffs_2.fft_map(resolution_factor = params.resolution_factor)
crystal_gridding = fft_map_2
fft_map_2.apply_sigma_scaling()
map_2 = fft_map_2.real_map_unpadded()
coeffs_1 = e_map_obj.map_coefficients(
map_type = params.map_1.type,
fill_missing = params.map_1.fill_missing_reflections,
isotropize = params.map_1.isotropize)
fft_map_1 = miller.fft_map(crystal_gridding = crystal_gridding,
fourier_coefficients = coeffs_1)
fft_map_1.apply_sigma_scaling()
map_1 = fft_map_1.real_map_unpadded()
unit_cell = fmodel.xray_structure.unit_cell()
d_min = fmodel.f_obs().d_min()
# or read map coefficents
elif (params.map_coefficients_file_name is not None):
map_handle = any_file(params.map_coefficients_file_name)
crystal_symmetry = get_crystal_symmetry(map_handle)
unit_cell = crystal_symmetry.unit_cell()
d_min = get_d_min(map_handle)
crystal_gridding = maptbx.crystal_gridding(
crystal_symmetry.unit_cell(), d_min=d_min,
resolution_factor=params.resolution_factor,
space_group_info=crystal_symmetry.space_group_info())
coeffs_2 = map_handle.file_server.get_miller_array(
params.map_coefficients_label)
fft_map_2 = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=coeffs_2)
fft_map_2.apply_sigma_scaling()
map_2 = fft_map_2.real_map_unpadded()
# or read CCP4 map
else:
map_handle = any_file(params.map_file_name)
unit_cell = map_handle.file_object.unit_cell()
sg_info = space_group_info(map_handle.file_object.space_group_number)
n_real = map_handle.file_object.unit_cell_grid
crystal_gridding = maptbx.crystal_gridding(
unit_cell, space_group_info=sg_info, pre_determined_n_real=n_real)
map_2 = map_handle.file_object.map_data()
# compute map_1 (Fc) if given a map (fmodel does not exist)
if (map_1 is None):
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=crystal_gridding.crystal_symmetry())
fft_map_1 = compute_map_from_model(d_min, None, xray_structure,
crystal_gridding=crystal_gridding)
fft_map_1.apply_sigma_scaling()
map_1 = fft_map_1.real_map_unpadded()
# compute cc
assert ( (map_1 is not None) and (map_2 is not None) )
broadcast(m="Map correlation and map values", log=log)
overall_cc = flex.linear_correlation(x = map_1.as_1d(),
y = map_2.as_1d()).coefficient()
print >> log, " Overall map cc(%s,%s): %6.4f"%(params.map_1.type,
params.map_2.type, overall_cc)
detail, atom_radius = params.detail, params.atom_radius
detail, atom_radius = set_detail_level_and_radius(
detail=detail, atom_radius=atom_radius, d_min=d_min)
use_hydrogens = params.use_hydrogens
if(use_hydrogens is None):
if(params.scattering_table == "neutron" or d_min <= 1.2):
use_hydrogens = True
else:
use_hydrogens = False
hydrogen_atom_radius = params.hydrogen_atom_radius
if(hydrogen_atom_radius is None):
if(params.scattering_table == "neutron"):
hydrogen_atom_radius = atom_radius
else:
hydrogen_atom_radius = 1
results = compute(
pdb_hierarchy = pdb_hierarchy,
unit_cell = unit_cell,
fft_n_real = map_1.focus(),
fft_m_real = map_1.all(),
map_1 = map_1,
map_2 = map_2,
detail = detail,
atom_radius = atom_radius,
use_hydrogens = use_hydrogens,
hydrogen_atom_radius = hydrogen_atom_radius)
if(show_results):
show(log=log, results=results, params=params, detail=detail)
return results