def run_pdb2pqr(self, currentPDB): """Run pdb2pqr, prepare input for apbs""" pdbfile = getPDBFile(currentPDB) pdblist, errlist = readPDB(pdbfile) # # Instantiate pdb2pqr # myDefinition = Definition() myProtein = Protein(pdblist, myDefinition) # # Setup everything # myRoutines = Routines(myProtein, verbose) myRoutines.updateResidueTypes() myRoutines.updateSSbridges() myRoutines.updateBonds() myRoutines.setTermini() myRoutines.updateInternalBonds() myforcefield = Forcefield(ff, myDefinition, None) myRoutines.applyNameScheme(myforcefield) myRoutines.findMissingHeavy() myRoutines.addHydrogens() myRoutines.debumpProtein() myProtein.reSerialize() # # Add and optimze hydrogens: # from src.hydrogens import hydrogenRoutines myRoutines.updateInternalBonds() myRoutines.calculateDihedralAngles() myhydRoutines = hydrogenRoutines(myRoutines) # # Now optimize hydrogens # myhydRoutines.setOptimizeableHydrogens() myhydRoutines.initializeFullOptimization() myhydRoutines.optimizeHydrogens() myhydRoutines.cleanup() myRoutines.setStates() 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() # # Assign charges # for chain in myProtein.getChains(): for residue in chain.get("residues"): for atom in residue.get("atoms"): atomname = atom.get("name") charge, radius = myforcefield.getParams1(residue, atomname) atom.set("radius", radius) atom.set("ffcharge", charge) # # method = "" async = 0 split = 0 import pdb2pka.inputgen_pKa as IP igen = IP.inputGen(currentPDB) igen.maps = None igen.set_type('background') igen.pdie = 8.0 igen.sdie = 80.0 all_center, extent = igen.getCenter() igen.setfineCenter(all_center) print 'Center: %5.1fA %5.1fA %5.1fA' % ( all_center[0], all_center[1], all_center[2]) print 'Extent: %5.1fA %5.1fA %5.1fA' % (extent[0], extent[1], extent[2]) apbs_inputfile = igen.printInput() return myProtein, apbs_inputfile
def run_pdb2pqr(self,currentPDB): """Run pdb2pqr, prepare input for apbs""" pdbfile = getPDBFile(currentPDB) pdblist, errlist = readPDB(pdbfile) # # Instantiate pdb2pqr # myDefinition = Definition() myProtein = Protein(pdblist, myDefinition) # # Setup everything # myRoutines = Routines(myProtein, verbose) myRoutines.updateResidueTypes() myRoutines.updateSSbridges() myRoutines.updateBonds() myRoutines.setTermini() myRoutines.updateInternalBonds() myforcefield=Forcefield(ff, myDefinition, None) myRoutines.applyNameScheme(myforcefield) myRoutines.findMissingHeavy() myRoutines.addHydrogens() myRoutines.debumpProtein() myProtein.reSerialize() # # Add and optimze hydrogens: # from src.hydrogens import hydrogenRoutines myRoutines.updateInternalBonds() myRoutines.calculateDihedralAngles() myhydRoutines = hydrogenRoutines(myRoutines) # # Now optimize hydrogens # myhydRoutines.setOptimizeableHydrogens() myhydRoutines.initializeFullOptimization() myhydRoutines.optimizeHydrogens() myhydRoutines.cleanup() myRoutines.setStates() 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() # # Assign charges # for chain in myProtein.getChains(): for residue in chain.get("residues"): for atom in residue.get("atoms"): atomname = atom.get("name") charge, radius = myforcefield.getParams1(residue, atomname) atom.set("radius", radius) atom.set("ffcharge", charge) # # method="" async=0 split=0 import pdb2pka.inputgen_pKa as IP igen = IP.inputGen(currentPDB) igen.maps=None igen.set_type('background') igen.pdie=8.0 igen.sdie=80.0 all_center,extent=igen.getCenter() igen.setfineCenter(all_center) print 'Center: %5.1fA %5.1fA %5.1fA' %(all_center[0],all_center[1],all_center[2]) print 'Extent: %5.1fA %5.1fA %5.1fA' %(extent[0],extent[1],extent[2]) apbs_inputfile=igen.printInput() return myProtein, apbs_inputfile
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
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