def retrieveAtomList():
et = eTrack()
et.runPipeline('n','n','y','n','e_Track_inputfile_TRAP.txt')
doses = [1.31,3.88,6.45,9.02,11.58,14.15,16.72,19.29,21.86,24.98,33.01,40.86,48.89,56.75,64.78,72.63]
atomList = processedAtomList(et.PDBmulti,10,doses[1:10])
atomList.processAtomList()
return atomList
os.makedirs(projectName)
# prepare maps for eTrack pipeline
runOverVDWRs(projectName)
for r in np.arange(0.5,2.5,0.5):
# make sure correct directory is present
runDirectory = '{}/eTrackReadyFiles_{}'.format(projectName,VDWR)
if not os.path.exists(runDirectory):
print 'Directory not found --> unable to continue'
sys.exit()
# write suitable eTrack input script
writeInputFile(runDirectory)
# run eTrack pipeline now
eT = eTrack()
eT.runPipeline('y','y','n','n',inputfilename)
# make a working directory for post processing analysis (whatever that may be)
workDirectoryName = projectName+'/Results'
if not os.path.exists(workDirectoryName):
os.makedirs(workDirectoryName)
for datasetNum in range(2,11):
fileName = ('/13830_TRAPRNAdamage{}_data.pkl'.format(datasetNum)).split('.')[0]
oldPlace = runDirectory+fileName+'.pkl'
newPlace = workDirectoryName+fileName+'_VDWR'+r+'.pkl'
os.rename(oldPlace,newPlace)
