def run_validation(self) :
rsc = rscc_utils.get_rscc_diff(
pdb_file=self.pdb_file,
reflection_file=self.hklmtz_file,
high_resolution=self.high_resolution)
# self.mdb_residues have MDBRes.get_residue_key() keys and values are lists
# of MDBAtom[s].
self.mdb_residues = {}
atomd = None
broadcastdetail = True
for i, result_ in enumerate(rsc) :
resd = {'pdb_id' : self.pdb_code,
'model_id' : None,
'chain_id' : result_.chain_id,
'icode' : result_.ins_code,
'resseq' : result_.res_num,
'altloc' : result_.alt_loc,
'resname' : result_.res_name}
if 'residue' in dir(result_) :
if broadcastdetail :
utils.broadcast('detail : residue')
broadcastdetail = False
detail = 'residue'
elif 'atom' in dir(result_) :
if broadcastdetail :
utils.broadcast('detail : atom')
broadcastdetail = False
detail = 'atom'
# map_value_1 = Fc
# map_value_2 = 2mFo-DFc
# map_value_3 = mFo-DFc
atomd = {'name':result_.atom.name,
'adp':result_.atom.b,
'xyz':result_.atom.xyz,
'rscc':result_.cc,
'twoFo_DFc_value':result_.map_value_2,
'Fo_DFc_value':result_.map_value_3,
'occ':result_.atom.occ}
else :
raise RuntimeError("Could not resolve detail")
MDBRes = mdb_utils.MDBResidue(**resd)
reskey = MDBRes.get_residue_key()
if reskey not in self.mdb_residues.keys() :
#self.mdb_residues[reskey] = MDBRes
self.mdb_residues[reskey] = []
if detail == 'atom' :
#self.mdb_residues[reskey].deposit_atom(mdb_utils.MDBAtom(**atomd))
self.mdb_residues[reskey].append(atomd)
def get_rscc_diff(pdb_file,reflection_file,high_resolution,log=None) :
if not log : log = sys.stderr
print >> log, '*' * 20 + ' rscc ' + '*' * 20
print >> log, 'pdb file : %s' % pdb_file
print >> log, 'hkl mtz : %s' % reflection_file
print >> log, 'high_resolution : %.2f' % high_resolution
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
inputs = mmtbx.utils.process_command_line_args([pdb_file,reflection_file])
# try to get data labels
data_labels = get_data_labels(reflection_file)
parameters = mmtbx.utils.data_and_flags_master_params().extract()
parameters.force_anomalous_flag_to_be_equal_to = False
if data_labels : parameters.labels = [data_labels]
if high_resolution : parameters.high_resolution = high_resolution
data_and_flags = mmtbx.utils.determine_data_and_flags(
reflection_file_server = inputs.get_reflection_file_server(),
keep_going = True, # don't stop if free flags are not present
parameters = parameters,
log = StringIO())
f_obs = data_and_flags.f_obs
r_free_flags = data_and_flags.f_obs.array(
data = flex.bool(data_and_flags.f_obs.size(), False))
pdb_lines = excise_unk_get_lines(inputs.pdb_file_names[0])
xrs = iotbx.pdb.input(
lines = pdb_lines).xray_structure_simple()
#file_name=inputs.pdb_file_names[0]).xray_structure_simple()
fmodel = mmtbx.utils.fmodel_simple(
f_obs=f_obs,
r_free_flags=r_free_flags,
scattering_table="n_gaussian",
xray_structures=[xrs],
bulk_solvent_correction=True,
skip_twin_detection=True)
e_map_obj = fmodel.electron_density_map()
coeffs_1 = e_map_obj.map_coefficients(
map_type = 'Fc',
fill_missing = False,
isotropize = False)
coeffs_2 = e_map_obj.map_coefficients(
map_type = '2mFo-DFc',
fill_missing = True,
isotropize = True)
coeffs_3 = e_map_obj.map_coefficients(
map_type = 'mFo-DFc',
fill_missing = False,
isotropize = True)
# compute maps
fft_map_1 = coeffs_1.fft_map(resolution_factor = 1./4)
fft_map_1.apply_sigma_scaling()
map_1 = fft_map_1.real_map_unpadded()
fft_map_2 = miller.fft_map(
crystal_gridding = fft_map_1,
fourier_coefficients = coeffs_2)
fft_map_2.apply_sigma_scaling()
map_2 = fft_map_2.real_map_unpadded()
fft_map_3 = miller.fft_map(
crystal_gridding = fft_map_1,
fourier_coefficients = coeffs_3)
fft_map_3.apply_sigma_scaling()
map_3 = fft_map_3.real_map_unpadded()
# compute cc
utils.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"%('Fc','2mFo-DFc',overall_cc)
detail='atom'
atom_radius = set_radius(d_min=fmodel.f_obs().d_min())
print >> sys.stderr, 'radius : %.3f' % atom_radius
results = compute(
pdb_hierarchy = hierarchy,
unit_cell = fmodel.xray_structure.unit_cell(),
map_1 = map_1,
map_2 = map_2,
map_3 = map_3,
detail = detail,
atom_radius = atom_radius)
return results
