def show_characteristics(self, out):
from mmtbx.scaling import printed_output
if out is None:
out = sys.stdout
if not isinstance(out, printed_output):
out = printed_output(out)
out.show_paragraph_header("\nDataset characteristics:")
out.show_preformatted_text(
"""\
Target anomalous signal: %(target_s_ano)7.1f
Residues: %(residues)d
Chain-type: %(chain_type)s
Solvent_fraction: %(solvent_fraction)7.2f
Atoms: %(natoms)d
Anomalously-scattering atom: %(atom_type)s
Wavelength: %(wavelength)7.4f A
Sites: %(nsites)d
f-double-prime: %(fpp)7.2f
Resolution: %(resolution)5.1f A
B-value for anomalously-scattering atoms: %(b_value_anomalous)4.0f
"""
% self.__dict__
)
if self.atom_type:
t = self.atom_type
else:
t = "-"
contribution = self.fpp * math.sqrt(self.nsites)
out.show_preformatted_text(
"""\
Target anomalous scatterer:
Atom: %2s f": %4.2f n:%5.0f rmsF:%7.1f rmsF/rms(Total F) (%%):%5.1f"""
% (t, self.fpp, self.nsites, contribution, 100.0 * math.sqrt(self.fa2))
)
if self.noise_table_rows:
out.show_preformatted_text(
"""\
Other anomalous scatterers in the structure:"""
)
for row in self.noise_table_rows:
out.show_preformatted_text(' Atom: %2s f": %4.2f n:%5.0f rmsF:%7.1f' % tuple(row))
fa = 100.0 * math.sqrt(self.fa2)
fb = 100.0 * math.sqrt(self.fb2)
fab = math.sqrt(self.fa2 / (self.fa2 + self.fb2))
out.show_preformatted_text(
"""\
Normalized anomalous scattering:
From target anomalous atoms rms(x**2)/rms(F**2): %7.2f
From other anomalous atoms rms(e**2)/rms(F**2): %7.2f
Correlation of useful to total anomalous scattering: %4.2f
"""
% (fa, fb, fab)
)
def show_characteristics(self, out):
from mmtbx.scaling import printed_output
if out is None:
out=sys.stdout
if (not isinstance(out, printed_output)):
out = printed_output(out)
out.show_paragraph_header(
"\nDataset characteristics:")
out.show_preformatted_text("""\
Target anomalous signal: %(target_s_ano)7.1f
Residues: %(residues)d
Chain-type: %(chain_type)s
Solvent_fraction: %(solvent_fraction)7.2f
Atoms: %(natoms)d
Anomalously-scattering atom: %(atom_type)s
Wavelength: %(wavelength)7.4f A
Sites: %(nsites)d
f-double-prime: %(fpp)7.2f
Resolution: %(resolution)5.1f A
B-value for anomalously-scattering atoms: %(b_value_anomalous)4.0f
""" % self.__dict__)
if self.atom_type:
t=self.atom_type
else:
t='-'
contribution=self.fpp*math.sqrt(self.nsites)
out.show_preformatted_text("""\
Target anomalous scatterer:
Atom: %2s f": %4.2f n:%5.0f rmsF:%7.1f rmsF/rms(Total F) (%%):%5.1f""" %(
t,self.fpp,self.nsites,contribution,100.*math.sqrt(self.fa2)))
if self.noise_table_rows:
out.show_preformatted_text("""\
Other anomalous scatterers in the structure:""")
for row in self.noise_table_rows :
out.show_preformatted_text(
' Atom: %2s f": %4.2f n:%5.0f rmsF:%7.1f' %tuple(row))
fa=100.*math.sqrt(self.fa2)
fb=100.*math.sqrt(self.fb2)
fab=math.sqrt(self.fa2/(self.fa2+self.fb2))
out.show_preformatted_text("""\
Normalized anomalous scattering:
From target anomalous atoms rms(x**2)/rms(F**2): %7.2f
From other anomalous atoms rms(e**2)/rms(F**2): %7.2f
Correlation of useful to total anomalous scattering: %4.2f
""" % (fa,fb,fab))
def xtriage_report(self):
xtriage_success = []
xtriage_warnings = []
xtriage_danger = []
s = StringIO()
pout = printed_output(out=s)
from mmtbx.scaling.xtriage import xtriage_analyses
from mmtbx.scaling.xtriage import master_params as xtriage_master_params
xtriage_params = xtriage_master_params.fetch(sources=[]).extract()
xtriage_params.scaling.input.xray_data.skip_sanity_checks = True
xanalysis = xtriage_analyses(
miller_obs=self.merged_intensities,
unmerged_obs=self.intensities,
text_out=pout,
params=xtriage_params,
)
if self.report_dir is not None:
with open(os.path.join(self.report_dir, "xtriage.log"), "wb") as f:
f.write(s.getvalue())
xia2.Handlers.Files.FileHandler.record_log_file(
"Xtriage", os.path.join(self.report_dir, "xtriage.log"))
xs = StringIO()
xout = xtriage_output(xs)
xanalysis.show(out=xout)
xout.flush()
sub_header_to_out = xout._sub_header_to_out
issues = xanalysis.summarize_issues()
# issues.show()
for level, text, sub_header in issues._issues:
summary = sub_header_to_out.get(sub_header, StringIO()).getvalue()
d = {
"level": level,
"text": text,
"summary": summary,
"header": sub_header
}
if level == 0:
xtriage_success.append(d)
elif level == 1:
xtriage_warnings.append(d)
elif level == 2:
xtriage_danger.append(d)
self._xanalysis = xanalysis
return xtriage_success, xtriage_warnings, xtriage_danger
def xtriage_report(self):
xtriage_success = []
xtriage_warnings = []
xtriage_danger = []
s = StringIO()
pout = printed_output(out=s)
from mmtbx.scaling.xtriage import xtriage_analyses
from mmtbx.scaling.xtriage import master_params as xtriage_master_params
xtriage_params = xtriage_master_params.fetch(sources=[]).extract()
xtriage_params.scaling.input.xray_data.skip_sanity_checks = True
xanalysis = xtriage_analyses(
miller_obs=self.merged_intensities,
unmerged_obs=self.intensities,
text_out=pout,
params=xtriage_params,
)
with open(os.path.join(self.report_dir, 'xtriage.log'), 'wb') as f:
f.write(s.getvalue())
xia2.Handlers.Files.FileHandler.record_log_file(
'Xtriage', os.path.join(self.report_dir, 'xtriage.log'))
xs = StringIO()
xout = xtriage_output(xs)
xanalysis.show(out=xout)
xout.flush()
sub_header_to_out = xout._sub_header_to_out
issues = xanalysis.summarize_issues()
#issues.show()
for level, text, sub_header in issues._issues:
summary = sub_header_to_out.get(sub_header, StringIO()).getvalue()
summary = summary.replace('<', '<').replace('>', '>')
d = {
'level': level,
'text': text,
'summary': summary,
'header': sub_header,
}
if level == 0: xtriage_success.append(d)
elif level == 1: xtriage_warnings.append(d)
elif level == 2: xtriage_danger.append(d)
self._xanalysis = xanalysis
return xtriage_success, xtriage_warnings, xtriage_danger