Package AutoDockTools

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Package AutoDockTools

Submodules

AutoDockTools.AppService_services
AutoDockTools.AppService_services_types
AutoDockTools.AutoDockBondClassifier
AutoDockTools.ConfPlayer: Graphical User Interface to Play AutoDock Conformations which are results of docking experiment
AutoDockTools.Conformation
AutoDockTools.DlgParser: This Object parses the result of an AutoDock job and returns a dictionary.
AutoDockTools.Docking: This Object is the result of an AutoDock job.
AutoDockTools.DockingParameters
AutoDockTools.EntropiaParser
AutoDockTools.EpdbParser: This Object parses the result of an AutoDock command mode epdb operation.
AutoDockTools.GridParameters
AutoDockTools.GridParameters_AD4
AutoDockTools.MoleculePreparation
AutoDockTools.Objects
AutoDockTools.ResultParser
AutoDockTools.TrajParser: This Object parses the result of a trajectory AutoDock run and returns a dictionary.
AutoDockTools.Utilities24

AutoDockTools.VisionInterface

AutoDockTools.XMLParser: This Object parses the xml result of an AutoDock operation.
AutoDockTools.adthosts
AutoDockTools.atomTypeTools: This module implements classes to support AutoDock atomtypes including: NonpolarHydrogenMerger: a class which detects and then merges nonpolarHydrogens with the heavy atoms to which each is bound.
AutoDockTools.autoanalyzeCommands: This Module facilitates analyzing results of autodock jobs.
AutoDockTools.autodockHosts
AutoDockTools.autodpfCommands: This Module facilitates producing a docking parameter file for AutoDock.
AutoDockTools.autoflexCommands: This Module facilitates producing a files for AutoDock.
AutoDockTools.autogpfCommands: This Module facilitates producing a grid parameter file for AutoGrid.
AutoDockTools.autopilotCommands: This Module facilitates the launching of large numbers of AutoDock jobs
AutoDockTools.autostartCommands: This Module facilitates starting autogrid and autodock jobs and managing them
AutoDockTools.autotorsCommands: This Module facilitates selecting and formatting a ligand for a subsequent AutoDock run.
AutoDockTools.cluster: Some definitions: cluster: a list of conformations all within tolerance RMSD.
AutoDockTools.cluster_ad
AutoDockTools.cmdlib
AutoDockTools.energyCalculator: This class calculates the AutoDock internal energy for a set of atoms.
AutoDockTools.energyConstants
AutoDockTools.histogram
AutoDockTools.interactiveHistogramGraph
AutoDockTools.lib_parameter_file_writer
AutoDockTools.modlib
AutoDockTools.pixelMap2D
AutoDockTools.pyAutoDockCommands: This Module contains commands which allow the user to compute various component pair-wise energies of the autodock305 forcefield and assign the results to individual atoms.
AutoDockTools.sol_par

Functions

setdmode(mode, mv)
load display commands for mode and set them as default command for new molecule

setcmode(mode, mv)
load color commands for mode and set them as default command for new molecule

startADT(argv, AdtScriptPath)
The main function for running AutoDockTools

Variables

hostDict = {'enos': {'autodock': 'autodock3', 'autogrid': 'auto...

h = 'enos'

FlagCheck = 1

CRITICAL_DEPENDENCIES = ['MolKit', 'mglutil', 'Pmw', 'Numeric', 'ViewerFrame...

NONCRITICAL_DEPENDENCIES = ['PyBabel', 'PyAutoDock', 'PIL', 'NetworkEditor', 'V...

Function Details

setdmode(mode, mv)

load display commands for mode and set them as default command for new molecule

setcmode(mode, mv)

load color commands for mode and set them as default command for new molecule

startADT(argv, AdtScriptPath)

The main function for running AutoDockTools

Variables Details

hostDict

None

Value:

{'enos': {'autodock': 'autodock3', 'autogrid': 'autogrid3', 'host': 'e
nos', 'queuetype': 'int', 'userSpecific': 0}}

h

None

Value:

'enos'

FlagCheck

None

Value:

CRITICAL_DEPENDENCIES

None

Value:

['MolKit',
 'mglutil',
 'Pmw',
 'Numeric',
 'ViewerFramework',
 'Pmv',
 'DejaVu',
 'opengltk']

NONCRITICAL_DEPENDENCIES

None

Value:

['PyBabel', 'PyAutoDock', 'PIL', 'NetworkEditor', 'Vision', 'ZSI', 'Su
pport']