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src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/prepare_dpf42.py   Pymol-script-repo(Download)
                simulated_annealing_list4_2, epdb_list4_2
 
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
 
 
    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)
                simulated_annealing_list4_1
 
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
 
 
    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)
                simulated_annealing_list4
 
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
 
 
    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/GridParameters.py   Pymol-script-repo(Download)
import string, os.path, sys, types, glob
from MolKit import Read
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
import string
import numpy.oldnumeric as Numeric
            ligand = Read(ligand_filename)[0]
            ligand.buildBondsByDistance()
            ad4_typer = AutoDock4_AtomTyper()
            ad4_typer.setAutoDockElements(ligand)
            dict = {}
            receptor = Read(receptor_filename)[0]
            receptor.buildBondsByDistance()
            ad4_typer = AutoDock4_AtomTyper()
            ad4_typer.setAutoDockElements(receptor)
            dict = {}
        if self.verbose: 
            print "len(filelist)=", len(filelist)
        ad4_typer = AutoDock4_AtomTyper()
        type_dict = {}
        for f in filelist:
    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)
import types
from MolKit import Read
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
 
class DockingParameters(UserDict.UserDict):
    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/pdbqs_to_pdbqt.py   Pymol-script-repo(Download)
from MolKit.pdbWriter import PdbqtWriter
from MolKit.chargeCalculator import GasteigerChargeCalculator
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
 
 
    #possible clean-up???
    #need to type atoms + assign babel_types
    AD4_typer = AutoDock4_AtomTyper(set_aromatic_carbons=False)
    AD4_typer.setAutoDockElements(mol)
    if verbose:

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/MoleculePreparation.py   Pymol-script-repo(Download)
from AutoDockTools.atomTypeTools import SolvationParameterizer
from AutoDockTools.atomTypeTools import AromaticCarbonManager
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
 
from AutoDockTools.AutoDockBondClassifier import AutoDockBondClassifier
        except:
            pass
        atomTyper = AutoDock4_AtomTyper()
        atomTyper.setAutoDockElements(molecule, reassign=True) #4/15/05 catch here?
        if len(preserved):
            #NEED TO TYPE ATOMS!!
            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
                except:
                    pass
            atomTyper = AutoDock4_AtomTyper()
            atomTyper.setAutoDockElements(molecule, reassign=reassign) #
        else:
                except:
                    pass
            atomTyper = AutoDock4_AtomTyper()
            atomTyper.setAutoDockElements(receptor, reassign=reassign) #
        else:

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/VisionInterface/AdtNodes.py   Pymol-script-repo(Download)
from MolKit.molecule import Atom, AtomSet, Molecule, MoleculeSet
from MolKit.protein import Residue, ResidueSet, Chain, ChainSet
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
from AutoDockTools.atomTypeTools import NonpolarHydrogenMerger, LonepairMerger
from AutoDockTools.atomTypeTools import AromaticCarbonManager, SolvationParameterizer

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/pdbq_to_pdbqt.py   Pymol-script-repo(Download)
from MolKit.molecule import AtomSet
from MolKit.pdbWriter import PdbqtWriter
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
 
 
    #possible clean-up???
    #need to type atoms + assign babel_types
    AD4_typer = AutoDock4_AtomTyper()
    AD4_typer.setAutoDockElements(mol)
    if verbose:

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/prepare_gpf4.py   Pymol-script-repo(Download)
from AutoDockTools.GridParameters import GridParameters, grid_parameter_list4
from AutoDockTools.GridParameters import GridParameter4FileMaker
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
 
 

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