def fibRename(request, chosenPDB):
#get run number
runnum=tagOutput(request)
#get chosenPDB name
name = removePath(chosenPDB)
name = name[:-4]
#add Rosettas silly suffix
suffix = '_0001.pdb'
PathtofibrilPDB = 'RUN' + runnum + '_' + name + suffix
return PathtofibrilPDB
def UsedParam(Qobject6): #inputed object containing the chosen run number
#special path for fibPDB output
makestring = str(Qobject6.fibrilPDB)
FIBspecialPath = '/media/' + makestring[25:]
#special path for LL output
makestring2 = str(Qobject6.LLoutputPic)
LLspecialPath = '/media/' + makestring2[25:]
#make dictionary of used parameters from the Results object
used = {'ID': str(Qobject6.mostRes),
'Run date': str(Qobject6.timestamp),
'PDB': removePath(str(Qobject6.PDBused)),
'Optional_exp_layerlines': removePath(str(Qobject6.experimentalData)),
'Intensity file' : removePath(str(Qobject6.intensity)),
'Turns': str(Qobject6.turns),
'Units' : str(Qobject6.units),
'Rise' : str(Qobject6.rise),
'Resolution (L)': str(Qobject6.rescutL),
'Resolution (H)' : str(Qobject6.rescutH),
'fibPDB' : FIBspecialPath,
'LLoutput' : LLspecialPath,
'Handedness': str(Qobject6.LorR)}
if Qobject6.jobname != ' ':
used['jobname'] = str(Qobject6.jobname)
if Qobject6.bfactor != 20.0:
used['Bfactor'] = str(Qobject6.bfactor)
if Qobject6.bfactorSolv != 400:
used['BfactorSolv'] = str(Qobject6.bfactorSolv)
if Qobject6.bfactorSolvK != 0.4:
used['BfactorSolvK'] = str(Qobject6.bfactorSolvK)
if Qobject6.qfhtK1 != 2.0:
used['qfhtK1'] = str(Qobject6.qfhtK1)
if Qobject6.qfhtK2 != 2.2:
used['qfhtK2'] = str(Qobject6.qfhtK2)
if Qobject6.scscaling != 0.92:
used['sc_scaling'] = str(Qobject6.scscaling)
if Qobject6.gridR != 256:
used['gridR'] = str(Qobject6.gridR)
if Qobject6.gridZ != 128:
used['gridZ'] = str(Qobject6.gridZ)
if Qobject6.gridPhi != 128:
used['gridPhi'] = str(Qobject6.gridPhi)
if Qobject6.R_step != 0.001:
used['R_step'] = str(Qobject6.R_step)
if Qobject6.layer_lines != 20:
used['layer_lines'] = str(Qobject6.layer_lines)
if Qobject6.experimentalData != 'none chosen':
used['Chi-square'] = str(Qobject6.chisq)
#make parameters.txt for email/download
ParamUsedFile(Qobject6, used)
#make 'CurrentLoaded.txt' with the 'used' dictionary so data can be displayed in other renders
thefile = PathMaker(Qobject6.username, 'CurrentLoaded.txt')
fout = open(thefile, 'w')
json.dump(used, fout)
fout.close()
#include most recent newrundict.txt, so it can be displayed during page refresh
rundict=getRunDict(Qobject6.username)
used['ToBeRunHTML'] = rundict
#for display on mainpage
return used
def toberun(object):
username = object.username #need name for finding correct user dir
#open newrundict.txt, open the dictionary
import json
thefile = PathMaker(username, 'newrundict.txt')
try:
FHin = open(thefile, 'r')
except:
newrundict(username) #if you cant open above, just make new file in user's dir and month with default settings
FHin = open(thefile, 'r') #now open the new file
#take out the dict
theDict = json.load(FHin)
#open the object, take out whats needed
#PDBdown
if hasattr(object, 'PDBdown'):
key = 'PDB'
value= str(object.PDBdown)
value = removePath(value) #extra path removal bit, so just file name is seen
theDict[key]=value
#PDBup
if hasattr(object, 'PDBup'):
key = 'PDB'
value= str(object.PDBup)
value = removePath(value) #extra path removal bit, so just file name is seen
theDict[key]=value
#Experimental
if hasattr(object, 'EXPupload'):
key = 'Optional_exp_layerlines'
value= str(object.EXPupload)
value = removePath(value) #extra path removal bit, so just file name is seen
theDict[key]=value
#parameters
if hasattr(object, 'jobname') and str(object.jobname) != ' ':
key = 'jobname'
value= str(object.jobname)
theDict[key]=value
if hasattr(object, 'turns'):
key = 'turns'
value= str(object.turns)
theDict[key]=value
if hasattr(object, 'units'):
key = 'units'
value= str(object.units)
theDict[key]=value
if hasattr(object, 'rise'):
key = 'rise'
value= str(object.rise)
theDict[key]=value
if hasattr(object, 'rescutH'):
key = 'resolution (H)'
value= str(object.rescutH)
theDict[key]=value
if hasattr(object, 'rescutL'):
key = 'resolution (L)'
value= str(object.rescutL)
theDict[key]=value
if hasattr(object, 'LorR'):
key = 'handedness'
value= str(object.LorR)
theDict[key]=value
#extra parameters (these should be added to dict only if not default vals)
if hasattr(object, 'rfactor') and str(object.rfactor) != 'False':
key = 'rfactor'
value= str(object.rfactor)
theDict[key]=value
if hasattr(object, 'bfactor') and str(object.bfactor) != '20.0':
key = 'bfactor'
value= str(object.bfactor)
theDict[key]=value
if hasattr(object, 'bfactorSolv') and str(object.bfactorSolv) != '400.0':
key = 'bfactorSolv'
value= str(object.bfactorSolv)
theDict[key]=value
if hasattr(object, 'bfactorSolvK') and str(object.bfactorSolvK) != '0.4':
key = 'bfactorSolvK'
value= str(object.bfactorSolvK)
theDict[key]=value
if hasattr(object, 'qfhtK1') and str(object.qfhtK1) != '2.0':
key = 'qfhtK1'
value= str(object.qfhtK1)
theDict[key]=value
if hasattr(object, 'qfhtK2') and str(object.qfhtK2) != '2.2':
key = 'qfhtK2'
value= str(object.qfhtK2)
theDict[key]=value
if hasattr(object, 'scscaling') and str(object.scscaling) != '0.92':
key = 'scscaling'
value= str(object.scscaling)
theDict[key]=value
if hasattr(object, 'gridR') and str(object.gridR) != '256':
key = 'gridR'
value= str(object.gridR)
theDict[key]=value
if hasattr(object, 'gridZ') and str(object.gridZ) != '128':
key = 'gridZ'
value= str(object.gridZ)
theDict[key]=value
if hasattr(object, 'gridPhi') and str(object.gridPhi) != '128':
key = 'gridPhi'
value= str(object.gridPhi)
theDict[key]=value
if hasattr(object, 'R_step') and str(object.R_step) != '0.001':
key = 'R_step'
value= str(object.R_step)
theDict[key]=value
if hasattr(object, 'layer_lines') and str(object.layer_lines) != '20':
key = 'layer_lines'
value= str(object.layer_lines)
theDict[key]=value
#save the dict to the file and close
fout = open(thefile, 'w')
json.dump(theDict,fout)
FHin.close()
fout.close()
#return saved dictionary
return theDict
