Package AutoDockTools :: Module autoflexCommands

Module autoflexCommands


This Module facilitates producing a  files for AutoDock. The steps in this process are:

    * Set the macromolecule: 

        o Read a PDBQT Macromolecule 

        o Choose Macromol...

    * Select which residues are to be flexible in macromolecule using Pmv selection tools:

        o ICOM Select 

        o SelectFromString

        o Select Spherical Region

    * The results of the previous steps are written to a file. The user selects a filename via a filebrowser.

Classes

[hide private]

AF_MacroReader
allows user to select a filename for the macromolecule

AF_MacroChooser
allows user to choose a molecule already present for the macromolecule

AF_SelectResidues
allows user to set up a set of residues in macromolecule whose sidechains are to be flexed in an autodock run

AF_ProcessResidues
allows user to process interactively a set of residues in macromolecule whose sidechains are to be flexed in an autodock run

AF_ProcessHingeResidues
allows user to process interactively a set of hinge residues in macromolecule whose sidechains are to be flexed in an autodock run

AF_EditHinge
allows user to remove atoms to be moved from a hinge interactively

AF_SetHinge
allows user to setup a hinge interactively to be flexed in an autodock run

AF_SetBondRotatableFlag
set the flag that tells whether a bond is rotatable in aan AutoDock ligand

AF_StepBack

AF_FlexFileWriter
allows user to choose an output filename and write autoflex stuff

AF_RigidFileWriter
allows user to choose an output filename and write reduced macromolecule

AF_LigandDirectoryWriter
allows user to choose a directory of formatted ligands and write flexible output for each ligand

Functions

[hide private]

'name':'ADflex_writeFlexDir','cmd':AF_LigandDirectoryWriter(),'gui':AF_LigandDirectoryWriterGUI}

initModule(vf)

Variables

[hide private]

menuText = {'Edit Hinge': 'Edit Hinge...', 'writeRigid': 'Save ...

AF_MacroReaderGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AF_MacroChooserGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AF_SelectResiduesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AF_ProcessResiduesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AF_ProcessHingeResiduesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AF_EditHingeGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AF_SetHingeGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AF_StepBackGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AF_FlexFileWriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AF_RigidFileWriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AF_LigandDirectoryWriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

'name':'ADflex_writeFlexDir','cmd':AF_LigandDirectoryWriter(),'gui':AF_LigandDirectoryWriterGUI}

commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...

Function Details

[hide private]

initModule(vf)

source code

None

Variables Details

[hide private]

menuText

None

Value:

{'AutoFlexMB': 'Flexible Residues',
 'Choose Macro': 'Choose Macromolecule...',
 'Edit Hinge': 'Edit Hinge...',
 'InputMB': 'Input',
 'Read Macro': 'Open Macromolecule...',
 'Set Hinge': 'Set up Hinge...',
 'Set Residues': 'Choose Torsions in Currently Selected Residues...',
 'Step Back': 'Redisplay Macromolecule',
...

AF_MacroReaderGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb719a18c>

AF_MacroChooserGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb719a20c>

AF_SelectResiduesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb719a26c>

AF_ProcessResiduesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb719a32c>

AF_ProcessHingeResiduesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb719a3ac>

AF_EditHingeGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb719a46c>

AF_SetHingeGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb719a72c>

AF_StepBackGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb719a7cc>

AF_FlexFileWriterGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb719a82c>

AF_RigidFileWriterGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb719a88c>

AF_LigandDirectoryWriterGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb719a8ec>

commandList

None

Value:

[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb719a18c>
,
  'name': 'ADflex_readMacro'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb719a20c>
,
  'name': 'ADflex_chooseMacro'},
...