Exemplo n.º 1
0
        'ARG',
        'ARG',
        'ASP',
        'LYS'
    ]  # mutations in chain B

    mutscan = DirectedMutagenesis(pdb=pdbfile,
                                  pdb2pqr_exe=path_pdb2pqr,
                                  apbs_exe=path_apbs,
                                  coulomb_exe=path_coulomb,
                                  jobname=jobname,
                                  selstr=selstr,
                                  target=target,
                                  mutation=mutation,
                                  minim=True)

    mutscan.run()
    # mutscan.run_parallel(6) # Uncomment to run in parallel on 6 threads
    # mutscan.run_parallel()  # Uncomment to run on half of available threads

    mutscan.viewLogs()
    mutscan.writeLogs(filename="mutscan_logs.txt")

    plotScan(mutscan, filename='directedmutagenesis.png')

    mut_ids = mutscan.getMutids()
    energies = mutscan.ddGa_rel()

    mutscan.summary(filename='mutscan_summary.txt')

    writePDB(mutscan, filename='mutscan.ddGa.pdb')
Exemplo n.º 2
0
    alascan = Alascan(pdb=pdbfile,
                      pdb2pqr_exe=path_pdb2pqr,
                      apbs_exe=path_apbs,
                      coulomb_exe=path_coulomb,
                      jobname=jobname,
                      selstr=selstr,
                      minim=False)
    # alascan = Alascan(pdb=pdbfile, jobname=jobname, selstr=selstr)

    alascan.run()
    # alascan.run_parallel(6) # Uncomment to run in parallel on 6 threads
    # alascan.run_parallel()  # Uncomment to run on half of available threads

    alascan.viewLogs()
    alascan.writeLogs(filename="alascan_logs.txt")

    plotScan(alascan, filename='alascan.png')

    try:
        plotNetwork(alascan, filename='network.png')
    except:
        print 'Skipping plotNetwork example!'

    mut_ids = alascan.getMutids()
    energies = alascan.ddGa_rel()

    alascan.summary(filename='alascan_summary.txt')

    writePDB(alascan, filename='alascan.ddGa.pdb')
path_pdb2pqr = "C:\\PDB2PQR\\pdb2pqr-windows-bin64-2.0.0\\pdb2pqr.exe"

jobname = "mutscan"
pdbfile = "barnase_barstar.pdb"

selstr = ["chain A", "chain B"]

target = ["resnum 27", "resnum 27", "resnum 73", "resnum 73", "resnum 142", "resnum 142", "resnum 145", "resnum 145"]
mutation = ["ALA", "ASP", "ALA", "LYS", "ALA", "LYS", "ALA", "LYS"]

mutscan = DirectedMutagenesis(
    pdbfile,
    target,
    mutation,
    path_pdb2pqr,
    path_apbs,
    coulomb_exe=path_coul,
    selstr=selstr,
    jobname=jobname,
    grid=1,
    ion=0.150,
    pdie=20.0,
    sdie=78.54,
    ff="parse",
    cfac=1.5,
    dx=False,
)
mutscan.run_parallel()
p.dump(mutscan, open(jobname + ".p", "wb"))
plotScan(mutscan, filename=jobname + ".png")