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#############################################################################
#
# Author: Ruth HUEY, Michel F. SANNER
#
# Copyright: M. Sanner TSRI 2008
#
#############################################################################
# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/autoflex41Commands.py,v 1.4 2013/05/09 17:01:27 rhuey Exp $
#
# $Id: autoflex41Commands.py,v 1.4 2013/05/09 17:01:27 rhuey Exp $
#
#
#
#
#
"""
This Module facilitates producing a formatted flexible residue file 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
* Set which torsions in the sidechains of those residues are to be flexible interactively
* The results of the previous steps are written to two files:
o one containing the sidechains of the flexible residues with special keywords
o a second containing the rigid portion of the macromolecule
"""
from ViewerFramework.VFCommand import CommandGUI
from AutoDockTools.autoflexCommands import AF_MacroReader,\
AF_MacroChooser, AF_SelectResidues, AF_ProcessResidues,\
AF_ProcessHingeResidues, AF_EditHinge, AF_SetHinge,\
AF_SetBondRotatableFlag, AF_StepBack, AF_FlexFileWriter,\
AF_RigidFileWriter, AF_LigandDirectoryWriter, AF_SetupCovalentFlexibleResidue,\
menuText
AF_MacroReaderGUI=CommandGUI()
AF_MacroReaderGUI.addMenuCommand('AutoTools41Bar', menuText['AutoFlexMB'], \
menuText['Read Macro'], cascadeName = menuText['InputMB'])
AF_MacroChooserGUI=CommandGUI()
AF_MacroChooserGUI.addMenuCommand('AutoTools41Bar', menuText['AutoFlexMB'],
menuText['Choose Macro'], cascadeName = menuText['InputMB'])
AF_SelectResiduesGUI = CommandGUI()
AF_SelectResiduesGUI.addMenuCommand('AutoTools41Bar', menuText['AutoFlexMB'],menuText['Set Residues'])
AF_ProcessResiduesGUI = CommandGUI()
AF_ProcessHingeResiduesGUI = CommandGUI()
AF_EditHingeGUI = CommandGUI()
AF_EditHingeGUI.addMenuCommand('AutoTools41Bar', menuText['AutoFlexMB'],\
menuText['Edit Hinge'])
AF_SetHingeGUI = CommandGUI()
AF_SetHingeGUI.addMenuCommand('AutoTools41Bar', menuText['AutoFlexMB'],\
menuText['Set Hinge'])
AF_SetupCovalentFlexibleResidueGUI = CommandGUI()
AF_SetupCovalentFlexibleResidueGUI.addMenuCommand('AutoTools41Bar', menuText['AutoFlexMB'],\
menuText['Setup Covalent Residue'])
AF_StepBackGUI = CommandGUI()
AF_StepBackGUI.addMenuCommand('AutoTools41Bar', menuText['AutoFlexMB'], menuText['Step Back'])
AF_FlexFileWriterGUI = CommandGUI()
AF_FlexFileWriterGUI.addMenuCommand('AutoTools41Bar', menuText['AutoFlexMB'], \
menuText['writeFlexible'], cascadeName = menuText['WriteMB'])
AF_RigidFileWriterGUI = CommandGUI()
AF_RigidFileWriterGUI.addMenuCommand('AutoTools41Bar', menuText['AutoFlexMB'], \
menuText['writeRigid'], cascadeName = menuText['WriteMB'])
AF_LigandDirectoryWriterGUI = CommandGUI()
AF_LigandDirectoryWriterGUI.addMenuCommand('AutoTools41Bar', menuText['AutoFlexMB'], \
menuText['writeDir'], cascadeName = menuText['WriteMB'])
commandList = [
{'name':'AD41flex_readMacro','cmd':AF_MacroReader(),'gui':AF_MacroReaderGUI},
{'name':'AD41flex_chooseMacro','cmd':AF_MacroChooser(),'gui':AF_MacroChooserGUI},
{'name':'AD41flex_setResidues','cmd':AF_SelectResidues(),'gui':AF_SelectResiduesGUI},
#{'name':'AD41flex_processResidues','cmd':AF_ProcessResidues(),'gui':None},
#{'name':'AD41flex_processHingeResidues','cmd':AF_ProcessHingeResidues(),'gui':None},
{'name':'AD41flex_setupCovalentResidue', 'cmd':AF_SetupCovalentFlexibleResidue(), 'gui':AF_SetupCovalentFlexibleResidueGUI},
#{'name':'AD41flex_setBondRotatableFlag','cmd':AF_SetBondRotatableFlag(),'gui':None},
#{'name':'AD41flex_setHinge','cmd':AF_SetHinge(),'gui':AF_SetHingeGUI},
#{'name':'AD41flex_editHinge','cmd':AF_EditHinge(),'gui':None},
{'name':'AD41flex_stepBack','cmd':AF_StepBack(),'gui':AF_StepBackGUI},
{'name':'AD41flex_writeFlexFile','cmd':AF_FlexFileWriter(),'gui':AF_FlexFileWriterGUI},
{'name':'AD41flex_writeRigidFile','cmd':AF_RigidFileWriter(),'gui':AF_RigidFileWriterGUI},
#{'name':'AD41flex_writeFlexDir','cmd':AF_LigandDirectoryWriter(),'gui':AF_LigandDirectoryWriterGUI}
]
def initModule(vf):
for dict in commandList:
vf.addCommand(dict['cmd'], dict['name'], dict['gui'])
if not hasattr(vf, 'ADflex_processResidues'):
vf.addCommand(AF_ProcessResidues(), 'ADflex_processResidues', None)
if not hasattr(vf, 'ADflex_setBondRotatableFlag'):
vf.addCommand(AF_SetBondRotatableFlag(), 'ADflex_setBondRotatableFlag', None)
vf.ADflex_setResidues = vf.AD41flex_setResidues
if vf.hasGui and 'AutoTools41Bar' in vf.GUI.menuBars.keys():
vf.GUI.menuBars['AutoTools41Bar'].menubuttons[menuText['AutoFlexMB']].config(bg='tan',underline='-1')
if not hasattr(vf.GUI, 'adtBar'):
vf.GUI.adtBar = vf.GUI.menuBars['AutoTools41Bar']
vf.GUI.adtFrame = vf.GUI.adtBar.menubuttons.values()[0].master
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