Did I find the right examples for you? yes no      Crawl my project      Python Jobs

All Samples(15)  |  Call(15)  |  Derive(0)  |  Import(0)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/MoleculePreparation.py   Pymol-script-repo(Download)
            pass
        atomTyper = AutoDock4_AtomTyper()
        atomTyper.setAutoDockElements(molecule, reassign=True) #4/15/05 catch here?
        if len(preserved):
            for atom, chargeList in preserved.items():
            delattr(molecule.allAtoms, 'autodock_element')
            atomTyper = AutoDock4_AtomTyper()
            atomTyper.setAutoDockElements(molecule, reassign=True) #4/15/05:catch here?
        #if self.debug: print "allAtoms.autodock_element=", molecule.allAtoms.autodock_element
        molecule.TORSDOF = molecule.possible_tors - len(molecule.guanidiniumbnds+molecule.amidebnds)
                    pass
            atomTyper = AutoDock4_AtomTyper()
            atomTyper.setAutoDockElements(molecule, reassign=reassign) #
        else:
            print file_type, " unknown type: must be .pdbqt, .pdbqs, .pdbq, .pdb or .mol2" 
                    pass
            atomTyper = AutoDock4_AtomTyper()
            atomTyper.setAutoDockElements(receptor, reassign=reassign) #
        else:
            print file_type, " unknown type: must be .pdbqt, .pdbqs, .pdbq, .pdb or .mol2" 

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/GridParameters.py   Pymol-script-repo(Download)
            ligand.buildBondsByDistance()
            ad4_typer = AutoDock4_AtomTyper()
            ad4_typer.setAutoDockElements(ligand)
            dict = {}
            for a in ligand.allAtoms:
            receptor.buildBondsByDistance()
            ad4_typer = AutoDock4_AtomTyper()
            ad4_typer.setAutoDockElements(receptor)
            dict = {}
            for a in receptor.allAtoms:
            m = Read(f)[0]
            m.buildBondsByDistance()
            ad4_typer.setAutoDockElements(m)
            for a in m.allAtoms:
                type_dict[a.autodock_element] = 1
    def getTypes(self, molecule):
        if not len(molecule.allAtoms.bonds[0]):
            molecule.buildBondsByDistance()
        ad4_typer = AutoDock4_AtomTyper(verbose=self.verbose)
        ad4_typer.setAutoDockElements(molecule)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/DockingParameters.py   Pymol-script-repo(Download)
    def getTypes(self, molecule):
        if not len(molecule.allAtoms.bonds[0]):
            molecule.buildBondsByDistance()
        ad4_typer = AutoDock4_AtomTyper(verbose=self.verbose)
        ad4_typer.setAutoDockElements(molecule)
    def getTypes(self, molecule):
        if not len(molecule.allAtoms.bonds[0]):
            molecule.buildBondsByDistance()
        ad4_typer = AutoDock4_AtomTyper(verbose=self.verbose)
        ad4_typer.setAutoDockElements(molecule)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/prepare_dpf42.py   Pymol-script-repo(Download)
    def getTypes(self, molecule):
        if not len(molecule.allAtoms.bonds[0]):
            molecule.buildBondsByDistance()
        ad4_typer = AutoDock4_AtomTyper(verbose=self.verbose)
        ad4_typer.setAutoDockElements(molecule)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/prepare_dpf41.py   Pymol-script-repo(Download)
    def getTypes(self, molecule):
        if not len(molecule.allAtoms.bonds[0]):
            molecule.buildBondsByDistance()
        ad4_typer = AutoDock4_AtomTyper(verbose=self.verbose)
        ad4_typer.setAutoDockElements(molecule)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/prepare_dpf4.py   Pymol-script-repo(Download)
    def getTypes(self, molecule):
        if not len(molecule.allAtoms.bonds[0]):
            molecule.buildBondsByDistance()
        ad4_typer = AutoDock4_AtomTyper(verbose=self.verbose)
        ad4_typer.setAutoDockElements(molecule)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/pdbq_to_pdbqt.py   Pymol-script-repo(Download)
    #need to type atoms + assign babel_types
    AD4_typer = AutoDock4_AtomTyper()
    AD4_typer.setAutoDockElements(mol)
    if verbose:
        print "set autodock4 autodock_element for ", mol.name

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/pdbqs_to_pdbqt.py   Pymol-script-repo(Download)
    #need to type atoms + assign babel_types
    AD4_typer = AutoDock4_AtomTyper(set_aromatic_carbons=False)
    AD4_typer.setAutoDockElements(mol)
    if verbose:
        print "set autodock4 autodock_element for ", mol.name