Beispiel #1
0
def startpKa():
    """
        Function for starting pKa script from the command line.

        Returns
            protein:    The protein object as generated by PDB2PQR
            routines:   The routines object as generated by PDB2PQR
            forcefield: The forcefield object as generated by PDB2PQR
    """
    print
    print 'PDB2PQR pKa calculations'
    print

    parser = optparse.OptionParser()

    ##
    ## set optparse options
    ##
    parser.add_option(
        '-v','--verbose',
        dest='verbose',
        action="store_true",
        default=False,
        )
    parser.add_option(
        '--pdie',
        dest='pdie',
        default=8,
        type='int',
        help='<protein dielectric constant>',
        )
    parser.add_option(
        '--sdie',
        dest='sdie',
        default=80,
        type='int',
        help='<solvent dielectric constant>',
        )
    parser.add_option(
        '--ff',
        dest='ff',
        type='choice',
        default='parse',
        choices=("amber","AMBER","charmm","CHARMM","parse","PARSE",),
        help='<force field (amber, charmm, parse)>',
        )
    parser.add_option(
        '--resume',
        dest='resume',
        action="store_true",
        default=False,
        help='resume run from saved state.',
        )
    parser.add_option(
        '--ligand',
        dest='ligand',
        type='str',
        help='<ligand in MOL2 format>',
        )
    parser.add_option(
        '--maps',
        dest='maps',
        default=None,
        type='int',
        help='<1 for using provided 3D maps; 2 for genereting new maps>',
        )
    parser.add_option(
        '--xdiel',
        dest='xdiel',
        default=None,
        type='str',
        help='<xdiel maps>',
        )
    parser.add_option(
        '--ydiel',
        dest='ydiel',
        default=None,
        type='str',
        help='<ydiel maps>',
        )
    parser.add_option(
        '--zdiel',
        dest='zdiel',
        default=None,
        type='str',
        help='<zdiel maps>',
        )
    parser.add_option(
        '--kappa',
        dest='kappa',
        default=None,
        type='str',
        help='<ion-accessibility map>',
        )
    parser.add_option(
        '--smooth',
        dest='sd',
        default=None,
        type='float',
        help='<st.dev [A] of Gaussian smooting of 3D maps at the boundary, bandthwith=3 st.dev>',
        )
    #
    # Cut off energy for calculating non-charged-charged interaction energies
    #
    parser.add_option('--pairene',dest='pairene',type='float',default=1.0,
                      help='Cutoff energy in kT for calculating non charged-charged interaction energies. Default: %default')
    #
    # Options for doing partial calculations
    #
    parser.add_option('--res_energy',
                      dest='desolvation_res',
                      default=[],
                      action='append',
                      type='string',
                      help='Calculate desolvation energy and interaction energy for this residue in its default protonation state. Protonation states can be specified with the --protonation_state argument')
    parser.add_option('--PS_file',dest='PS_file',default='',type='string',action='store',help='Set protonation states according to the pdb2pka protonation state file (option --PS_file)')
    (options,args,) = parser.parse_args()

    ##
    ## parse optparse options
    ##
    ff = options.ff.lower()
    pdie = options.pdie
    verbose = options.verbose
    sdie = options.sdie
    maps = options.maps
    xdiel = options.xdiel
    ydiel = options.ydiel
    zdiel = options.zdiel
    kappa = options.kappa
    sd = options.sd

    #
    # Find the PDB file
    #
    if len(args) != 2:
        parser.error("Usage: pka.py [options] <pdbfile> <output directory>\n")
    input_path = args[0]
    output_path = args[1]

    ligand = None
    if options.ligand is not None:
        try:
            ligand = open(options.ligand, 'rU')
        except IOError:
            print 'Unable to find ligand file %s! Skipping...' % options.ligand

    #Set up the protien object
    #In the standalone version of pdb2pka this is redundent but needed so we emulate the
    #interface needed by pdb2pqr

    pdbfile = getPDBFile(input_path)
    pdblist, errlist = readPDB(pdbfile)
    if len(errlist) != 0 and verbose:
        print "Warning: %s is a non-standard PDB file.\n" %input_path
        print errlist
    #
    # Read the definition file
    #
    myDefinition = Definition()
    #
    #
    # Choose whether to include the ligand or not
    #
    # Add the ligand to the pdb2pqr arrays
    #
    if ligand is None:
        myProtein = Protein(pdblist, myDefinition)
    else:
        from pdb2pka.ligandclean import ligff
        myProtein, _, _ = ligff.initialize(myDefinition, ligand, pdblist, verbose)

    #
    # Call the pre_init function
    #
    return pre_init(protein=myProtein,
                    output_dir=output_path,
                    ff=ff,
                    verbose=verbose,
                    pdie=pdie,
                    sdie=sdie,
                    maps=maps,
                    xdiel=xdiel,
                    ydiel=ydiel,
                    zdiel=zdiel,
                    kappa=kappa,
                    sd=sd,
                    ligand=ligand),options
Beispiel #2
0
def startpKa():
    """
        Function for starting pKa script from the command line.

        Returns
            protein:    The protein object as generated by PDB2PQR
            routines:   The routines object as generated by PDB2PQR
            forcefield: The forcefield object as generated by PDB2PQR
    """
    print
    print 'PDB2PQR pKa calculations'
    print

    parser = optparse.OptionParser()

    ##
    ## set optparse options
    ##
    parser.add_option(
        '-v',
        '--verbose',
        dest='verbose',
        action="store_true",
        default=False,
    )
    parser.add_option(
        '--pdie',
        dest='pdie',
        default=8,
        type='int',
        help='<protein dielectric constant>',
    )
    parser.add_option(
        '--sdie',
        dest='sdie',
        default=80,
        type='int',
        help='<solvent dielectric constant>',
    )
    parser.add_option(
        '--ff',
        dest='ff',
        type='choice',
        default='parse',
        choices=(
            "amber",
            "AMBER",
            "charmm",
            "CHARMM",
            "parse",
            "PARSE",
        ),
        help='<force field (amber, charmm, parse)>',
    )
    parser.add_option(
        '--resume',
        dest='resume',
        action="store_true",
        default=False,
        help='resume run from saved state.',
    )
    parser.add_option(
        '--ligand',
        dest='ligand',
        type='str',
        help='<ligand in MOL2 format>',
    )
    parser.add_option(
        '--maps',
        dest='maps',
        default=None,
        type='int',
        help='<1 for using provided 3D maps; 2 for genereting new maps>',
    )
    parser.add_option(
        '--xdiel',
        dest='xdiel',
        default=None,
        type='str',
        help='<xdiel maps>',
    )
    parser.add_option(
        '--ydiel',
        dest='ydiel',
        default=None,
        type='str',
        help='<ydiel maps>',
    )
    parser.add_option(
        '--zdiel',
        dest='zdiel',
        default=None,
        type='str',
        help='<zdiel maps>',
    )
    parser.add_option(
        '--kappa',
        dest='kappa',
        default=None,
        type='str',
        help='<ion-accessibility map>',
    )
    parser.add_option(
        '--smooth',
        dest='sd',
        default=None,
        type='float',
        help=
        '<st.dev [A] of Gaussian smooting of 3D maps at the boundary, bandthwith=3 st.dev>',
    )
    #
    # Cut off energy for calculating non-charged-charged interaction energies
    #
    parser.add_option(
        '--pairene',
        dest='pairene',
        type='float',
        default=1.0,
        help=
        'Cutoff energy in kT for calculating non charged-charged interaction energies. Default: %default'
    )
    #
    # Options for doing partial calculations
    #
    parser.add_option(
        '--res_energy',
        dest='desolvation_res',
        default=[],
        action='append',
        type='string',
        help=
        'Calculate desolvation energy and interaction energy for this residue in its default protonation state. Protonation states can be specified with the --protonation_state argument'
    )
    parser.add_option(
        '--PS_file',
        dest='PS_file',
        default='',
        type='string',
        action='store',
        help=
        'Set protonation states according to the pdb2pka protonation state file (option --PS_file)'
    )
    (
        options,
        args,
    ) = parser.parse_args()

    ##
    ## parse optparse options
    ##
    ff = options.ff.lower()
    pdie = options.pdie
    verbose = options.verbose
    sdie = options.sdie
    maps = options.maps
    xdiel = options.xdiel
    ydiel = options.ydiel
    zdiel = options.zdiel
    kappa = options.kappa
    sd = options.sd

    #
    # Find the PDB file
    #
    if len(args) != 2:
        parser.error("Usage: pka.py [options] <pdbfile> <output directory>\n")
    input_path = args[0]
    output_path = args[1]

    ligand = None
    if options.ligand is not None:
        try:
            ligand = open(options.ligand, 'rU')
        except IOError:
            print 'Unable to find ligand file %s! Skipping...' % options.ligand

    #Set up the protien object
    #In the standalone version of pdb2pka this is redundent but needed so we emulate the
    #interface needed by pdb2pqr

    pdbfile = getPDBFile(input_path)
    pdblist, errlist = readPDB(pdbfile)
    if len(errlist) != 0 and verbose:
        print "Warning: %s is a non-standard PDB file.\n" % input_path
        print errlist
    #
    # Read the definition file
    #
    myDefinition = Definition()
    #
    #
    # Choose whether to include the ligand or not
    #
    # Add the ligand to the pdb2pqr arrays
    #
    if ligand is None:
        myProtein = Protein(pdblist, myDefinition)
    else:
        from pdb2pka.ligandclean import ligff
        myProtein, _, _ = ligff.initialize(myDefinition, ligand, pdblist,
                                           verbose)

    #
    # Call the pre_init function
    #
    return pre_init(protein=myProtein,
                    output_dir=output_path,
                    ff=ff,
                    verbose=verbose,
                    pdie=pdie,
                    sdie=sdie,
                    maps=maps,
                    xdiel=xdiel,
                    ydiel=ydiel,
                    zdiel=zdiel,
                    kappa=kappa,
                    sd=sd,
                    ligand=ligand), options
Beispiel #3
0
def pre_init(original_pdb_list=None,
             output_dir=None,
             ff=None,
             verbose=False,
             pdie=8.0,
             sdie=80,
             maps=None,
             xdiel=None,
             ydiel=None,
             zdiel=None,
             kappa=None,
             sd=None,
             ligand=None):
    """This function cleans the PDB and prepares the APBS input file

    Prepares the output folder."""

    #prepare the output directory

    output_dir = os.path.abspath(output_dir)

    try:
        os.makedirs(output_dir)
    except OSError:
        if not os.path.isdir(output_dir):
            raise ValueError('Target directory is a file! Aborting.')

    workspace_dir = os.path.join(output_dir,'workspace')

    try:
        os.makedirs(workspace_dir)
    except OSError:
        if not os.path.isdir(output_dir):
            raise ValueError('Target directory is a file! Aborting.')

    #
    # remove hydrogen atoms
    #

    working_pdb_filename = os.path.join(workspace_dir,'working.pdb')

    pka_help.dump_protein_no_hydrogens(original_pdb_list, working_pdb_filename)
    #
    # Get the PDBfile
    #
    pdbfile = getPDBFile(working_pdb_filename)
    pdblist, errlist = readPDB(pdbfile)

    if verbose:
        print "Beginning PDB2PKA...\n"
    #
    # Read the definition file
    #
    myDefinition = Definition()
    ligand_titratable_groups=None
    #
    #
    # Choose whether to include the ligand or not
    #
    # Add the ligand to the pdb2pqr arrays
    #
    Lig=None
    if ligand is None:
        myProtein = Protein(pdblist, myDefinition)
    else:
        from pdb2pka.ligandclean import ligff
        myProtein, myDefinition, Lig = ligff.initialize(myDefinition, ligand, pdblist, verbose)
    #
    # =======================================================================
    #
    # We have identified the structural elements, now contiue with the setup
    #
    # Print something for some reason?
    #
    if verbose:
        print "Created protein object -"
        print "\tNumber of residues in protein: %s" % myProtein.numResidues()
        print "\tNumber of atoms in protein   : %s" % myProtein.numAtoms()
    #
    # Set up all other routines
    #
    myRoutines = Routines(myProtein, verbose) #myDefinition)
    myRoutines.updateResidueTypes()
    myRoutines.updateSSbridges()
    myRoutines.updateBonds()
    myRoutines.setTermini()
    myRoutines.updateInternalBonds()

    myRoutines.applyNameScheme(Forcefield(ff, myDefinition, None))
    myRoutines.findMissingHeavy()
    myRoutines.addHydrogens()
    myRoutines.debumpProtein()

    #myRoutines.randomizeWaters()
    myProtein.reSerialize()
    #
    # Inject the information on hydrogen conformations in the HYDROGENS.DAT arrays
    # We get this information from ligand_titratable_groups
    #
    from src.hydrogens import hydrogenRoutines
    myRoutines.updateInternalBonds()
    myRoutines.calculateDihedralAngles()
    myhydRoutines = hydrogenRoutines(myRoutines)
    #
    # Here we should inject the info!!
    #
    myhydRoutines.setOptimizeableHydrogens()
    myhydRoutines.initializeFullOptimization()
    myhydRoutines.optimizeHydrogens()
    myhydRoutines.cleanup()
    myRoutines.setStates()

    #
    # Choose the correct forcefield
    #
    myForcefield = Forcefield(ff, myDefinition, None)
    if Lig:
        hitlist, misslist = myRoutines.applyForcefield(myForcefield)
        #
        # Can we get charges for the ligand?
        #
        templist=[]
        ligsuccess=False
        for residue in myProtein.getResidues():
            if isinstance(residue, LIG):
                templist = []
                Lig.make_up2date(residue)
                net_charge=0.0
                print 'Ligand',residue
                print 'Atom\tCharge\tRadius'
                for atom in residue.getAtoms():
                    if atom.mol2charge:
                        atom.ffcharge=atom.mol2charge
                    else:
                        atom.ffcharge = Lig.ligand_props[atom.name]["charge"]
                    #
                    # Find the net charge
                    #
                    net_charge=net_charge+atom.ffcharge
                    #
                    # Assign radius
                    #
                    atom.radius = Lig.ligand_props[atom.name]["radius"]
                    print '%s\t%6.4f\t%6.4f' %(atom.name,atom.ffcharge,atom.radius)
                    if atom in misslist:
                        misslist.pop(misslist.index(atom))
                        templist.append(atom)
                    #
                    # Store the charge and radius in the atom instance for later use
                    # This really should be done in a nicer way, but this will do for now
                    #
                    atom.secret_radius=atom.radius
                    atom.secret_charge=atom.ffcharge
                    #
                    #

                charge = residue.getCharge()
                if abs(charge - round(charge)) > 0.01:
                    # Ligand parameterization failed
                    myProtein.residues.remove(residue)
                    raise Exception('Non-integer charge on ligand: %8.5f' %charge)
                else:
                    ligsuccess = 1
                    # Mark these atoms as hits
                    hitlist = hitlist + templist
                #
                # Print the net charge
                #
                print 'Net charge for ligand %s is: %5.3f' %(residue.name,net_charge)
        #
        # Temporary fix; if ligand was successful, pull all ligands from misslist
        # Not sure if this is needed at all here ...? (Jens wrote this)
        #
        if ligsuccess:
            templist = misslist[:]
            for atom in templist:
                if isinstance(atom.residue, Amino) or isinstance(atom.residue, Nucleic):
                    continue
                misslist.remove(atom)

    if verbose:
        print "Created protein object (after processing myRoutines) -"
        print "\tNumber of residues in protein: %s" % myProtein.numResidues()
        print "\tNumber of atoms in protein   : %s" % myProtein.numAtoms()
    #
    # Create the APBS input file
    #
    import src.psize
    size=src.psize.Psize()

    method=""
    async=0
    split=0

    igen = inputgen_pKa.inputGen(working_pdb_filename)
    #
    # For convenience
    #
    igen.pdie = pdie
    print 'Setting protein dielectric constant to ',igen.pdie
    igen.sdie=sdie
    igen.maps=maps
    if maps==1:
        print "Using dielectric and mobile ion-accessibility function maps in PBE"
        if xdiel:
            igen.xdiel = xdiel
        else:
            raise PDB2PKAError('X dielectric map is missing')
        if ydiel:
            igen.ydiel = ydiel
        else:
            raise PDB2PKAError("Y dielectric map is missing\n")
        if zdiel:
            igen.zdiel = zdiel
        else:
            raise PDB2PKAError("Z dielectric map is missing\n")

        print 'Setting dielectric function maps: %s, %s, %s'%(igen.xdiel,igen.ydiel,igen.zdiel)

        if kappa:
            igen.kappa = kappa
        else:
            raise PDB2PKAError("Mobile ion-accessibility map is missing\n")

        print 'Setting mobile ion-accessibility function map to: ',igen.kappa

        if sd:
            xdiel_smooth, ydiel_smooth, zdiel_smooth = smooth(xdiel,ydiel,zdiel)
            igen.xdiel = xdiel_smooth
            igen.ydiel = ydiel_smooth
            igen.zdiel = zdiel_smooth
    #
    # Return all we need
    #
    return output_dir, myProtein, myRoutines, myForcefield,igen, ligand_titratable_groups, maps, sd
Beispiel #4
0
def pre_init(original_pdb_list=None,
             output_dir=None,
             ff=None,
             verbose=False,
             pdie=8.0,
             sdie=80,
             maps=None,
             xdiel=None,
             ydiel=None,
             zdiel=None,
             kappa=None,
             sd=None,
             ligand=None):
    """This function cleans the PDB and prepares the APBS input file

    Prepares the output folder."""

    #prepare the output directory

    output_dir = os.path.abspath(output_dir)

    try:
        os.makedirs(output_dir)
    except OSError:
        if not os.path.isdir(output_dir):
            raise ValueError('Target directory is a file! Aborting.')

    workspace_dir = os.path.join(output_dir, 'workspace')

    try:
        os.makedirs(workspace_dir)
    except OSError:
        if not os.path.isdir(output_dir):
            raise ValueError('Target directory is a file! Aborting.')

    #
    # remove hydrogen atoms
    #

    working_pdb_filename = os.path.join(workspace_dir, 'working.pdb')

    pka_help.dump_protein_no_hydrogens(original_pdb_list, working_pdb_filename)
    #
    # Get the PDBfile
    #
    pdbfile = getPDBFile(working_pdb_filename)
    pdblist, errlist = readPDB(pdbfile)

    if verbose:
        print "Beginning PDB2PKA...\n"
    #
    # Read the definition file
    #
    myDefinition = Definition()
    ligand_titratable_groups = None
    #
    #
    # Choose whether to include the ligand or not
    #
    # Add the ligand to the pdb2pqr arrays
    #
    Lig = None
    if ligand is None:
        myProtein = Protein(pdblist, myDefinition)
    else:
        from pdb2pka.ligandclean import ligff
        myProtein, myDefinition, Lig = ligff.initialize(
            myDefinition, ligand, pdblist, verbose)
    #
    # =======================================================================
    #
    # We have identified the structural elements, now contiue with the setup
    #
    # Print something for some reason?
    #
    if verbose:
        print "Created protein object -"
        print "\tNumber of residues in protein: %s" % myProtein.numResidues()
        print "\tNumber of atoms in protein   : %s" % myProtein.numAtoms()
    #
    # Set up all other routines
    #
    myRoutines = Routines(myProtein, verbose)  #myDefinition)
    myRoutines.updateResidueTypes()
    myRoutines.updateSSbridges()
    myRoutines.updateBonds()
    myRoutines.setTermini()
    myRoutines.updateInternalBonds()

    myRoutines.applyNameScheme(Forcefield(ff, myDefinition, None))
    myRoutines.findMissingHeavy()
    myRoutines.addHydrogens()
    myRoutines.debumpProtein()

    #myRoutines.randomizeWaters()
    myProtein.reSerialize()
    #
    # Inject the information on hydrogen conformations in the HYDROGENS.DAT arrays
    # We get this information from ligand_titratable_groups
    #
    from src.hydrogens import hydrogenRoutines
    myRoutines.updateInternalBonds()
    myRoutines.calculateDihedralAngles()
    myhydRoutines = hydrogenRoutines(myRoutines)
    #
    # Here we should inject the info!!
    #
    myhydRoutines.setOptimizeableHydrogens()
    myhydRoutines.initializeFullOptimization()
    myhydRoutines.optimizeHydrogens()
    myhydRoutines.cleanup()
    myRoutines.setStates()

    #
    # Choose the correct forcefield
    #
    myForcefield = Forcefield(ff, myDefinition, None)
    if Lig:
        hitlist, misslist = myRoutines.applyForcefield(myForcefield)
        #
        # Can we get charges for the ligand?
        #
        templist = []
        ligsuccess = False
        for residue in myProtein.getResidues():
            if isinstance(residue, LIG):
                templist = []
                Lig.make_up2date(residue)
                net_charge = 0.0
                print 'Ligand', residue
                print 'Atom\tCharge\tRadius'
                for atom in residue.getAtoms():
                    if atom.mol2charge:
                        atom.ffcharge = atom.mol2charge
                    else:
                        atom.ffcharge = Lig.ligand_props[atom.name]["charge"]
                    #
                    # Find the net charge
                    #
                    net_charge = net_charge + atom.ffcharge
                    #
                    # Assign radius
                    #
                    atom.radius = Lig.ligand_props[atom.name]["radius"]
                    print '%s\t%6.4f\t%6.4f' % (atom.name, atom.ffcharge,
                                                atom.radius)
                    if atom in misslist:
                        misslist.pop(misslist.index(atom))
                        templist.append(atom)
                    #
                    # Store the charge and radius in the atom instance for later use
                    # This really should be done in a nicer way, but this will do for now
                    #
                    atom.secret_radius = atom.radius
                    atom.secret_charge = atom.ffcharge
                    #
                    #

                charge = residue.getCharge()
                if abs(charge - round(charge)) > 0.01:
                    # Ligand parameterization failed
                    myProtein.residues.remove(residue)
                    raise Exception('Non-integer charge on ligand: %8.5f' %
                                    charge)
                else:
                    ligsuccess = 1
                    # Mark these atoms as hits
                    hitlist = hitlist + templist
                #
                # Print the net charge
                #
                print 'Net charge for ligand %s is: %5.3f' % (residue.name,
                                                              net_charge)
        #
        # Temporary fix; if ligand was successful, pull all ligands from misslist
        # Not sure if this is needed at all here ...? (Jens wrote this)
        #
        if ligsuccess:
            templist = misslist[:]
            for atom in templist:
                if isinstance(atom.residue, Amino) or isinstance(
                        atom.residue, Nucleic):
                    continue
                misslist.remove(atom)

    if verbose:
        print "Created protein object (after processing myRoutines) -"
        print "\tNumber of residues in protein: %s" % myProtein.numResidues()
        print "\tNumber of atoms in protein   : %s" % myProtein.numAtoms()
    #
    # Create the APBS input file
    #
    import src.psize
    size = src.psize.Psize()

    method = ""
    split = 0

    igen = inputgen_pKa.inputGen(working_pdb_filename)
    #
    # For convenience
    #
    igen.pdie = pdie
    print 'Setting protein dielectric constant to ', igen.pdie
    igen.sdie = sdie
    igen.maps = maps
    if maps == 1:
        print "Using dielectric and mobile ion-accessibility function maps in PBE"
        if xdiel:
            igen.xdiel = xdiel
        else:
            raise PDB2PKAError('X dielectric map is missing')
        if ydiel:
            igen.ydiel = ydiel
        else:
            raise PDB2PKAError("Y dielectric map is missing\n")
        if zdiel:
            igen.zdiel = zdiel
        else:
            raise PDB2PKAError("Z dielectric map is missing\n")

        print 'Setting dielectric function maps: %s, %s, %s' % (
            igen.xdiel, igen.ydiel, igen.zdiel)

        if kappa:
            igen.kappa = kappa
        else:
            raise PDB2PKAError("Mobile ion-accessibility map is missing\n")

        print 'Setting mobile ion-accessibility function map to: ', igen.kappa

        if sd:
            xdiel_smooth, ydiel_smooth, zdiel_smooth = smooth(
                xdiel, ydiel, zdiel)
            igen.xdiel = xdiel_smooth
            igen.ydiel = ydiel_smooth
            igen.zdiel = zdiel_smooth
    #
    # Return all we need
    #
    return output_dir, myProtein, myRoutines, myForcefield, igen, ligand_titratable_groups, maps, sd