def mergeProteinAndMembranePdb(file,fileToMerge):
'''
Merges all amino acid lines in file with non protein atoms in filetoMerge
the box size of fileToMerge is kept and the boxsize of file is discarded
'''
boxSize = pdb_util.findPDBBoxSize(fileToMerge)
lines = pdb_util.findAllNonProtein(fileToMerge)
toMerge = pdb_util.findAllAminoAcidLines(file)
#backup the file
versionFile(file)
# #write new file
with open(file,"w") as f:
str = boxSize.strip() +'\n' + toMerge.strip() +'\n'+ lines.strip()
f.write(str)
logCommand("Merged the non Amino acid lines of %s with all the atoms in %s"%(file,fileToMerge))
with open(confFile,"w") as f:
f.write(proteinString)
# if args.mutatations:
# #TODO set correct filenames
# args = ['Scwrl4','-i',confFile,'-o','confs/test.pdb']
# md_tools.executeCommand(args)
# args = ['Scwrl4','-i','confs/test.pdb','-o',confFile,'-s',scrwl_sequence_file]
# md_tools.executeCommand(args)
# index = index+1
md_tools.pdb2gmx(confFile,"-ff amber99sb-ildn -vsite hydrogens -water tip3p -ignh -o %s"%confFile)
#TODO grep the last line to get charge imbalances
boxSize= pdb_util.findPDBBoxSize(frame)
nonProteinString = pdb_util.findAllNonProtein(frame)
proteinString = pdb_util.findAllAminoAcidLines(confFile)
with open(confFile,"w") as f:
f.write(boxSize)
f.write("\n")
f.write(proteinString)
f.write(nonProteinString)
membrane.injectLinesIntoTop("topol.top")
md_tools.updateMembraneCount("POPC",confFile,"topol.top",fileType="pdb")
md_tools.updateWaterAndIonCount(confFile,"topol.top")
md_tools.cleanupBackups()