app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL Class Reference

Public Member Functions
def	__init__
def	auto_change_observer
def	auto_change_keep_observer_history
def	auto_change_send_observer_energies
def	makeWindow
def	SendPose
	Grid ###. More...
def	SendEPose
def	SendNewPose
def	color_residue
	Coloring Functions ####. More...
def	color_region
def	color_regions

Static Public Attributes
tuple	varValue = self.auto_send.get()
list	func = self.pymol_functions[option]
tuple	optionSP = option.split(";")
list	term = optionSP[0]
tuple	Newname = os.path.basename(self.pose.pdb_info().name())

Detailed Description

Pymol Visualization Window
Version 2.0 ONLY

Constructor & Destructor Documentation

def app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.__init__	(		self,
			pose
	)

References app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.auto_change_keep_observer_history(), app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.auto_change_observer(), app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.auto_change_send_observer_energies(), app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring.pose, PDB_IOBenchmark.pose, SmallMoverBenchmark.pose, app.pyrosetta_toolkit.modules.protocols.ProtocolBaseClass.ProtocolBaseClass.pose, app.pyrosetta_toolkit.window_main.frames.InputFrame.InputFrame.pose, app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.pose, app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow.pose, app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput.pose, app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl.pose, app.pyrosetta_toolkit.pyrosetta_toolkit.main_window.pose, toolbox.generate_resfile.ResfileWriter.pose, ShearMoverBenchmark.pose, ScoreBenchmark.pose, src.PyMolLink.PyMOL_Mover, and src.PyMolLink.PyMOL_Observer.

Member Function Documentation

def app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.auto_change_keep_observer_history	(		self,
			name,
			index,
			mode
	)

Referenced by app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.__init__().

def app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.auto_change_observer	(		self,
			name,
			index,
			mode
	)

This class handles all PyMOL integration with the GUI.  

Referenced by app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.__init__().

def app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.auto_change_send_observer_energies	(		self,
			name,
			index,
			mode
	)

Referenced by app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.__init__().

def app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.color_region	(		self,
			resnum_start,
			resnum_end,
			color = "magenta",
			all_other = "blue"
	)

References app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring.pose, PDB_IOBenchmark.pose, SmallMoverBenchmark.pose, app.pyrosetta_toolkit.modules.protocols.ProtocolBaseClass.ProtocolBaseClass.pose, app.pyrosetta_toolkit.window_main.frames.InputFrame.InputFrame.pose, app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.pose, app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow.pose, app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput.pose, app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl.pose, app.pyrosetta_toolkit.pyrosetta_toolkit.main_window.pose, toolbox.generate_resfile.ResfileWriter.pose, ShearMoverBenchmark.pose, ScoreBenchmark.pose, and basic::options::OptionKeys::relax::range.range.

def app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.color_regions	(		self,
			regions,
			color = "magenta",
			all_other = "blue"
	)

References app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring.pose, PDB_IOBenchmark.pose, SmallMoverBenchmark.pose, app.pyrosetta_toolkit.modules.protocols.ProtocolBaseClass.ProtocolBaseClass.pose, app.pyrosetta_toolkit.window_main.frames.InputFrame.InputFrame.pose, app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.pose, app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput.pose, app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow.pose, app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl.pose, app.pyrosetta_toolkit.pyrosetta_toolkit.main_window.pose, toolbox.generate_resfile.ResfileWriter.pose, ShearMoverBenchmark.pose, and ScoreBenchmark.pose.

def app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.color_residue	(		self,
			rosetta_resnum,
			color = "magenta",
			all_other = "blue"
	)

Coloring Functions ####.

Colors residue using PyMol Mover send energies.  I don't know how to *not* color the other residues.

References app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring.pose, PDB_IOBenchmark.pose, SmallMoverBenchmark.pose, app.pyrosetta_toolkit.modules.protocols.ProtocolBaseClass.ProtocolBaseClass.pose, app.pyrosetta_toolkit.window_main.frames.InputFrame.InputFrame.pose, app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.pose, app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput.pose, app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow.pose, app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl.pose, app.pyrosetta_toolkit.pyrosetta_toolkit.main_window.pose, toolbox.generate_resfile.ResfileWriter.pose, ShearMoverBenchmark.pose, and ScoreBenchmark.pose.

def app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.makeWindow	(		self,
			row,
			column,
			main,
			ScoreObject
	)

References app.pyrosetta_toolkit.window_modules.vicinity_options.vicinity_window.vicinityrelaxwindow.main, app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow.main, app.pyrosetta_toolkit.window_main.frames.OutputFrame.OutputFrame.main, app.pyrosetta_toolkit.window_main.frames.QuickProtocolsFrame.QuickProtocolsFrame.main, app.pyrosetta_toolkit.window_main.frames.InputFrame.InputFrame.main, app.pyrosetta_toolkit.window_modules.insert_bfactor.InsertBFactor.InsertBFactor.main, app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol.main, app.pyrosetta_toolkit.modules.protocols.GraftingProtocols.GraftMoverWindow.main, app.pyrosetta_toolkit.window_modules.options_system.OptionSystemManager.OptionSystemManager.main, app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow.main, app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl.main, app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.main, app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignProtocols.main, app.pyrosetta_toolkit.window_modules.protocol_builder.ProtocolBuilder.MainProtocols.main, name, app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring.score, numeric::RocPoint.score(), app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl.score, FragmentAssemblyMover.score(), app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignWrapper.score, app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.SendEPose(), app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.SendNewPose(), and app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.SendPose().

def app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.SendEPose	(		self,
			option
	)

Referenced by app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.makeWindow().

def app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.SendNewPose

(

self

)

Referenced by app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.makeWindow().

def app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.SendPose	(		self,
			option
	)

Grid ###.

Pose Sending ####

References app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring.pose, PDB_IOBenchmark.pose, SmallMoverBenchmark.pose, app.pyrosetta_toolkit.modules.protocols.ProtocolBaseClass.ProtocolBaseClass.pose, app.pyrosetta_toolkit.window_main.frames.InputFrame.InputFrame.pose, app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.pose, app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow.pose, app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput.pose, app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl.pose, app.pyrosetta_toolkit.pyrosetta_toolkit.main_window.pose, toolbox.generate_resfile.ResfileWriter.pose, ShearMoverBenchmark.pose, ScoreBenchmark.pose, app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring.score, numeric::RocPoint.score(), app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl.score, FragmentAssemblyMover.score(), and app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignWrapper.score.

Referenced by app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.makeWindow().

Member Data Documentation

list app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.func = self.pymol_functions[option]

static

Sends pose according to option. Will Fix as callback.

tuple app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.Newname = os.path.basename(self.pose.pdb_info().name())

static

Changes the name of the pose so that the next thing sent is a new object...

tuple app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.optionSP = option.split(";")

static

list app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.term = optionSP[0]

static

tuple app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL.varValue = self.auto_send.get()

static

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The documentation for this class was generated from the following file:

• src/python/bindings/app/pyrosetta_toolkit/window_modules/pymol_integration/PyMOL.py