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))
parser.add_argument("--confs",default ="/Users/iman/nethome/iman/Projects/EGFR/EGFR_WT/sim_frames/*pdb",
help="starting configurations to use, can use glob pattern ex:*pdb")
args = parser.parse_args()
frames = glob.glob(args.confs)
frames.sort()
scrwl_sequence_file = "scrwl_sequence.txt"
index = 0
membrane.copyItpFiles()
for frame in frames:
proteinString = md_tools.strip_vsites(pdb_util.findAllAminoAcidLines(frame))
#proteinString = pdb_util.findAllAminoAcidLines(frame)
#All files will have the same sequence so we only need to do this once
if(os.path.isfile(scrwl_sequence_file)==False and args.mutations):
sequence = md_tools.generateOneLetterSequence(proteinString,args.mutations)
f= open(scrwl_sequence_file,"w")
f.write(sequence)
confFile = "%s/conf_%s.pdb"%(util.ProjectDirectories.CONF_DIR,index)
with open(confFile,"w") as f:
f.write(proteinString)
# if args.mutatations:
# #TODO set correct filenames
# args = ['Scwrl4','-i',confFile,'-o','confs/test.pdb']
files = glob.glob(path)
files = sorted_nicely(set(files))
index=0
# proteinFileName = "conf%s.pdb"
#we just prefix the regular filename of the starting file with conf
proteinFileName = "conf_%s"
for system in files:
currentProtein = proteinFileName%os.path.basename(system)
#we only want to do pdb2gmx on the protein not the rest of the stuff
str = findAllAminoAcidLines(system)
str = strip_vsites(str)
with open(currentProtein,"w") as f:
f.write(str)
#FIXME awful and hacky and not general
if(os.path.isfile("../mutate.pml")):
mutateAbsPath = os.path.abspath("../mutate.pml")
os.system("cp %s protein.pdb"%currentProtein)
print "Mutating!"
cmd = "/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -c ../mutate.pml"
os.system(cmd)
logCommand(cmd)
os.system("cp protein_mutated.pdb %s"%currentProtein)
print "Done mutating"
logCommand("Mutated protein using the file mutate.pml in root project dir")