'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')
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")