def parse_pdb(inital_model_directory, xtal, db_dict):
if os.path.isfile(os.path.join(inital_model_directory, xtal,
'refine.pdb')):
db_dict['RefinementPDB_latest'] = os.path.realpath(
os.path.join(inital_model_directory, xtal, 'refine.pdb'))
pdb = parse().PDBheader(
os.path.join(inital_model_directory, xtal, 'refine.pdb'))
db_dict['RefinementRcryst'] = pdb['Rcryst']
db_dict['RefinementRcrystTraficLight'] = pdb['RcrystTL']
db_dict['RefinementRfree'] = pdb['Rfree']
db_dict['RefinementRfreeTraficLight'] = pdb['RfreeTL']
db_dict['RefinementRmsdBonds'] = pdb['rmsdBonds']
db_dict['RefinementRmsdBondsTL'] = pdb['rmsdBondsTL']
db_dict['RefinementRmsdAngles'] = pdb['rmsdAngles']
db_dict['RefinementRmsdAnglesTL'] = pdb['rmsdAnglesTL']
db_dict['RefinementSpaceGroup'] = pdb['SpaceGroup']
db_dict['RefinementResolution'] = pdb['ResolutionHigh']
db_dict['RefinementResolutionTL'] = pdb['ResolutionColor']
db_dict['RefinementStatus'] = 'finished'
else:
db_dict['RefinementStatus'] = 'failed'
if os.path.isfile(
os.path.join(inital_model_directory, xtal, 'refine.bound.pdb')):
db_dict['RefinementBoundConformation'] = os.path.realpath(
os.path.join(inital_model_directory, xtal, 'refine.bound.pdb'))
elif os.path.isfile(
os.path.join(inital_model_directory, xtal,
'refine.split.bound-state.pdb')):
db_dict['RefinementBoundConformation'] = os.path.realpath(
os.path.join(inital_model_directory, xtal,
'refine.split.bound-state.pdb'))
return db_dict
def select_dataset_with_lowest_Rfree(panddaDir,datasetListwithoutEvent):
datasetList=[]
lowestRfree=''
for dataset in datasetListwithoutEvent:
if os.path.isfile(os.path.join(panddaDir,'processed_datasets',dataset,dataset+'-pandda-input.pdb')):
stats=parse().PDBheader(os.path.join(panddaDir,'processed_datasets',dataset,dataset+'-pandda-input.pdb'))
Rfree=stats['Rfree']
try:
print dataset,Rfree,stats['ResolutionHigh']
datasetList.append([dataset,float(Rfree)])
except ValueError:
pass
if datasetList:
lowestRfree=min(datasetList,key=lambda x: x[1])[0]
return lowestRfree
def parse_pdb(inital_model_directory,xtal,db_dict):
if os.path.isfile(os.path.join(inital_model_directory,xtal,'refine.pdb')):
db_dict['RefinementPDB_latest']=os.path.realpath(os.path.join(inital_model_directory,xtal,'refine.pdb'))
pdb=parse().PDBheader(os.path.join(inital_model_directory,xtal,'refine.pdb'))
db_dict['RefinementRcryst'] = pdb['Rcryst']
db_dict['RefinementRcrystTraficLight'] = pdb['RcrystTL']
db_dict['RefinementRfree']= pdb['Rfree']
db_dict['RefinementRfreeTraficLight'] = pdb['RfreeTL']
db_dict['RefinementRmsdBonds'] = pdb['rmsdBonds']
db_dict['RefinementRmsdBondsTL'] = pdb['rmsdBondsTL']
db_dict['RefinementRmsdAngles'] = pdb['rmsdAngles']
db_dict['RefinementRmsdAnglesTL'] = pdb['rmsdAnglesTL']
db_dict['RefinementSpaceGroup'] = pdb['SpaceGroup']
db_dict['RefinementResolution'] = pdb['ResolutionHigh']
db_dict['RefinementResolutionTL'] = pdb['ResolutionColor']
db_dict['RefinementStatus'] = 'finished'
else:
db_dict['RefinementStatus'] = 'failed'
if os.path.isfile(os.path.join(inital_model_directory,xtal,'refine.bound.pdb')):
db_dict['RefinementBoundConformation']=os.path.realpath(os.path.join(inital_model_directory,xtal,'refine.bound.pdb'))
return db_dict
'dimple.pdb')):
db_dict = {}
db_dict['DimplePathToPDB'] = os.path.join(inital_model_directory, xtal,
'dimple.pdb')
dimple_ran_successfully = False
if os.path.isfile(
os.path.join(inital_model_directory, xtal, 'dimple.mtz')):
db_dict['DimplePathToMTZ'] = os.path.join(inital_model_directory,
xtal, 'dimple.mtz')
dimple_ran_successfully = True
db_dict['DataProcessingDimpleSuccessful'] = 'True'
db_dict['DimpleStatus'] = 'finished'
if not dimple_ran_successfully:
db_dict['DataProcessingDimpleSuccessful'] = 'False'
db_dict['DimpleStatus'] = 'failed'
pdb = parse().PDBheader(
os.path.join(inital_model_directory, xtal, 'dimple.pdb'))
db_dict['DimpleRcryst'] = pdb['Rcryst']
db_dict['DimpleRfree'] = pdb['Rfree']
db_dict['RefinementOutcome'] = '1 - Analysis Pending'
db_dict['RefinementSpaceGroup'] = pdb['SpaceGroup']
# if not os.path.isfile(xtal+'.free.mtz'):
# os.chdir(os.path.join(inital_model_directory,xtal))
# os.system('/bin/rm '+xtal+'.free.mtz')
# if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz')):
# os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz'),xtal+'.free.mtz')
# db_dict['RefinementMTZfree']=xtal+'.free.mtz'
# elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz')):
# os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz'),xtal+'.free.mtz')
# db_dict['RefinementMTZfree']=xtal+'.free.mtz'
# setting free.mtz file
inital_model_directory=sys.argv[3]
db=XChemDB.data_source(db_file)
if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple.pdb')):
db_dict={}
db_dict['DimplePathToPDB']=os.path.join(inital_model_directory,xtal,'dimple.pdb')
dimple_ran_successfully=False
if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple.mtz')):
db_dict['DimplePathToMTZ']=os.path.join(inital_model_directory,xtal,'dimple.mtz')
dimple_ran_successfully=True
db_dict['DataProcessingDimpleSuccessful']='True'
db_dict['DimpleStatus'] = 'finished'
if not dimple_ran_successfully:
db_dict['DataProcessingDimpleSuccessful']='False'
db_dict['DimpleStatus'] = 'failed'
pdb=parse().PDBheader(os.path.join(inital_model_directory,xtal,'dimple.pdb'))
db_dict['DimpleRcryst']=pdb['Rcryst']
db_dict['DimpleRfree']=pdb['Rfree']
db_dict['RefinementOutcome']='1 - Analysis Pending'
db_dict['RefinementSpaceGroup']=pdb['SpaceGroup']
if not os.path.isfile(xtal+'.free.mtz'):
os.chdir(os.path.join(inital_model_directory,xtal))
os.system('/bin/rm '+xtal+'.free.mtz')
if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz')):
os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz'),xtal+'.free.mtz')
db_dict['RefinementMTZfree']=xtal+'.free.mtz'
elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz')):
os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz'),xtal+'.free.mtz')
db_dict['RefinementMTZfree']=xtal+'.free.mtz'
# if no refinement was carried out yet, then we also want to link the dimple files to refine.pdb/refine.log