def run(self):
sqlite = (
'select'
' CrystalName,'
' PANDDA_site_event_map,'
' PANDDA_site_ligand_resname,'
' PANDDA_site_ligand_chain,'
' PANDDA_site_ligand_sequence_number,'
' PANDDA_site_ligand_altLoc '
'from panddaTable '
'where PANDDA_site_event_map not like "event%"'
)
query=self.db.execute_statement(sqlite)
progress_step=1
if len(query) != 0:
progress_step=100/float(len(query))
else:
progress_step=1
progress=0
self.emit(QtCore.SIGNAL('update_progress_bar'), progress)
for item in query:
xtalID=str(item[0])
event_map=str(item[1])
resname=str(item[2])
chainID=str(item[3])
resseq=str(item[4])
altLoc=str(item[5])
if os.path.isfile(os.path.join(self.initial_model_directory,xtalID,'refine.pdb')):
os.chdir(os.path.join(self.initial_model_directory,xtalID))
self.Logfile.insert('extracting ligand (%s,%s,%s,%s) from refine.pdb' %(str(resname),str(chainID),str(resseq),str(altLoc)))
XChemUtils.pdbtools('refine.pdb').save_specific_ligands_to_pdb(resname,chainID,resseq,altLoc)
if os.path.isfile('ligand_%s_%s_%s_%s.pdb' %(str(resname),str(chainID),str(resseq),str(altLoc))):
ligand_pdb='ligand_%s_%s_%s_%s.pdb' %(str(resname),str(chainID),str(resseq),str(altLoc))
print os.path.join(self.initial_model_directory,xtalID,ligand_pdb)
else:
self.Logfile.insert('could not extract ligand; trying next...')
continue
else:
self.Logfile.insert('directory: '+os.path.join(self.initial_model_directory,xtalID)+' -> cannot find refine.pdb; trying next')
continue
if os.path.isfile(os.path.join(self.initial_model_directory,xtalID,'refine.mtz')):
resolution=XChemUtils.mtztools(os.path.join(self.initial_model_directory,xtalID,'refine.mtz')).get_high_resolution_from_mtz()
else:
self.Logfile.insert('directory: '+os.path.join(self.initial_model_directory,xtalID)+' -> cannot find refine.mtz; trying next')
continue
convert_event_map_to_SF(self.initial_model_directory,xtalID,event_map,ligand_pdb,self.xce_logfile,self.datasource,resolution).run()
progress += progress_step
self.emit(QtCore.SIGNAL('update_progress_bar'), progress)
def calculate_electron_density_map(self,mtzin):
missing_columns=False
column_dict=XChemUtils.mtztools(mtzin).get_all_columns_as_dict()
if 'FWT' in column_dict['F'] and 'PHWT' in column_dict['PHS']:
labin=' labin F1=FWT PHI=PHWT\n'
elif '2FOFCWT' in column_dict['F'] and 'PH2FOFCWT' in column_dict['PHS']:
labin=' labin F1=2FOFCWT PHI=PH2FOFCWT\n'
else:
missing_columns=True
if not missing_columns:
os.chdir(os.path.join(self.project_directory,self.xtalID))
cmd = (
'fft hklin '+mtzin+' mapout 2fofc.map << EOF\n'
+labin+
'EOF\n'
)
self.Logfile.insert('calculating 2fofc map from '+mtzin)
os.system(cmd)
else:
self.Logfile.insert('cannot calculate 2fofc.map; missing map coefficients')
