Esempio n. 1
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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))
Esempio n. 2
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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']
Esempio n. 3
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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")