def updateView(self):
# Change the PyMOL view to only show the current model and optionally the base model that is
# always shown, if one is indicated by the modelMenu
# This is accomplished by making everything outside of the view transparent
# Why did I use transparency? -> because "hiding" views causes PyMOL to lose the display
# information (i.e. it will forget if you had lines/sticks/spheres shown)
# You don't lose this information by fiddling with transparencies
if (len(self.selectedModels) == 0):
return
model = self.selectedModels[self.currentModel]
self.lblSelected.SetLabel(model)
if (platform.system() == "Linux"):
resizeTextControlForUNIX(self.lblSelected, 35, 250)
# The selection "seqsele" refers to what the user has indicated should be in the ensemble browsing
# If it's not in "seqsele", then it will never be shown by the browser
# First make everything transparent and turn off cartoons (the user will have to deal with the
# cartoon settings changing)
self.cmd.hide("cartoon", "all")
self.cmd.set_bond("stick_transparency", 1, "all")
self.cmd.set("sphere_transparency", 1, "all") # Use "set" for sphere_transparency
# Now define a selection for the intersection of the current model atoms and "sele"
self.cmd.select("ensemblesele", "seqsele and model " + model)
self.cmd.show("cartoon", "ensemblesele")
self.cmd.set_bond("stick_transparency", 0, "ensemblesele")
self.cmd.set("sphere_transparency", 0, "ensemblesele") # Use "set" for sphere_transparency
# Now show the "always show" model if one if selected and it's not the current model
alwaysshow = self.modelMenu.GetStringSelection()
logInfo("Browser view changed to show " + model + " with Always Show set to " + alwaysshow)
if (alwaysshow != "None" and alwaysshow != "" and alwaysshow != model):
self.cmd.select("ensemblesele", "seqsele and model " + alwaysshow)
self.cmd.show("cartoon", "ensemblesele")
self.cmd.set_bond("stick_transparency", 0.7, "ensemblesele") # So you know which one is the "always shown" one
self.cmd.set("sphere_transparency", 0, "ensemblesele") # Use "set" for sphere_transparency
self.cmd.delete("ensemblesele") # Clean up
self.cmd.enable("seqsele") # This is needed otherwise the sequence window removes the selection since it is not enabled
def rightClick(self, event):
self.currentModel = self.currentModel + 1
if (self.currentModel >= len(self.selectedModels)):
self.currentModel = len(self.selectedModels) - 1
self.updateView()
logInfo("Right button clicked")
def leftClick(self, event):
self.currentModel = self.currentModel - 1
if (self.currentModel < 0):
self.currentModel = 0
self.updateView()
logInfo("Left button clicked")
def changeProtocol(self, event):
logInfo("Go button clicked")
selectedProtocol = self.protMenu.GetStringSelection()
if (selectedProtocol != self.currentProtocol and selectedProtocol != ""):
# Destroy the old panel so we can free memory up and create the new protocol panel
if (self.currentProtocol == "Superimposition"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Energy Minimization"):
# Check to see if the user has accepted the minimization
# If not, ask if they really want to proceed
if (self.protPanel.buttonState == "Finalize!"):
dlg = wx.MessageDialog(self, "You have not accepted your minimization and the results will be lost if you proceed. Proceed anyway?", "Minimization Not Accepted", wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo("Go cancelled due to unaccepted minimization")
dlg.Destroy()
return
dlg.Destroy()
logInfo("Minimization job rejected")
# Try to delete the minimized model if the user doesn't want to accept it
try:
self.cmd.remove("minimized_view")
self.cmd.delete("minimized_view")
except:
pass
self.cmd.label("all", "")
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Ensemble Browser"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Ensemble Generation"):
# Check to see if the user has accepted the design
# If not, ask if they really want to proceed
if (self.protPanel.buttonState == "Cancel!"):
dlg = wx.MessageDialog(self, "Your ensemble is not finished and the results will be lost if you proceed. Proceed anyway?", "Design Not Accepted", wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo("Go cancelled due to unfinished ensemblegen job")
dlg.Destroy()
return
logInfo("Ensemblegen job rejected")
dlg.Destroy()
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Protein Design (Fixbb)"):
# Check to see if the user has accepted the design
# If not, ask if they really want to proceed
if (self.protPanel.buttonState == "Finalize!"):
dlg = wx.MessageDialog(self, "You have not accepted your design and the results will be lost if you proceed. Proceed anyway?", "Design Not Accepted", wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo("Go cancelled due to unaccepted fixbb job")
dlg.Destroy()
return
logInfo("Fixbb job rejected")
dlg.Destroy()
# Try to delete the design model if the user doesn't want to accept it
try:
self.cmd.remove("designed_view")
self.cmd.delete("designed_view")
except:
pass
self.cmd.label("all", "")
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Residue/Ligand Creator"):
try:
self.cmd.remove("params")
self.cmd.delete("params")
except:
pass
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Point Mutations"):
try:
self.cmd.remove("rotamer_view")
self.cmd.delete("rotamer_view")
except:
pass
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Point Mutant Scan"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Loop Modeling (KIC)"):
# Check to see if the user has accepted the loop model
# If not, ask if they really want to proceed
if (self.protPanel.buttonState == "Finalize!"):
dlg = wx.MessageDialog(self, "You have not accepted your loop model and the results will be lost if you proceed. Proceed anyway?", "KIC Not Accepted", wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo("Go cancelled due to unaccepted KIC job")
dlg.Destroy()
return
logInfo("KIC job rejected")
dlg.Destroy()
# Try to delete the design model if the user doesn't want to accept it
try:
self.cmd.remove("kic_view")
self.cmd.delete("kic_view")
except:
pass
self.cmd.label("all", "")
self.protPanel.Destroy()
elif (self.currentProtocol == "Docking"):
# Check to see if the user has accepted the docking model
# If not, ask if they really want to proceed
if (self.protPanel.buttonState != "Dock!"):
dlg = wx.MessageDialog(self, "You have not accepted your docking model and the results will be lost if you proceed. Proceed anyway?", "Docking Not Accepted", wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo("Go cancelled due to unaccepted docking job")
dlg.Destroy()
return
logInfo("Docking job rejected")
dlg.Destroy()
# Try to delete the design model if the user doesn't want to accept it
try:
self.cmd.remove("dock_view")
self.cmd.delete("dock_view")
except:
pass
self.cmd.label("all", "")
self.protPanel.Destroy()
elif (self.currentProtocol == "Structure Prediction (Comparative Modeling)"):
# Check to see if the user has accepted the docking model
# If not, ask if they really want to proceed
if (self.protPanel.buttonState == "Finalize!"):
dlg = wx.MessageDialog(self, "You have not accepted your comparative modeling structure and the results will be lost if you proceed. Proceed anyway?", "Docking Not Accepted", wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo("Go cancelled due to unaccepted comparative modeling job")
dlg.Destroy()
return
logInfo("Comparative modeling job rejected")
dlg.Destroy()
# Try to delete the design model if the user doesn't want to accept it
try:
self.cmd.remove("thread_view")
self.cmd.delete("thread_view")
except:
pass
self.cmd.label("all", "")
self.protPanel.Destroy()
elif (self.currentProtocol == "Protein Design (MSD)"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Antibody Modeling"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Molecular Surfaces"):
try:
self.cmd.delete("curr_surf_recp")
except:
pass
try:
self.cmd.delete("curr_surf_lig")
except:
pass
self.cmd.hide("surface", "all")
if (self.parent.Selection.showSurf):
self.currentProtocol = "n/a"
self.parent.Selection.displaySurfaces()
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Flexible Peptide Docking"):
self.protPanel.Destroy()
del self.protPanel
self.currentProtocol = selectedProtocol
self.seqWin.cannotDelete = False
# Restart the Rosetta daemon to clear its memory up
self.parent.restartDaemon()
logInfo("Changed protocol to " + selectedProtocol)
if (selectedProtocol == "Superimposition"):
self.protPanel = SuperimpositionPanel(self, self.W, self.H)
elif (selectedProtocol == "Energy Minimization"):
self.protPanel = MinimizationPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Ensemble Browser"):
self.protPanel = EnsembleBrowserPanel(self, self.W, self.H)
elif (selectedProtocol == "Ensemble Generation"):
self.protPanel = EnsembleGenPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Protein Design (Fixbb)"):
self.protPanel = FixbbPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Residue/Ligand Creator"):
self.protPanel = ResidueCreatorPanel(self, self.W, self.H)
elif (selectedProtocol == "Point Mutations"):
self.protPanel = PointMutationsPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Point Mutant Scan"):
self.protPanel = PointMutantScanPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Loop Modeling (KIC)"):
self.protPanel = KICPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Docking"):
self.protPanel = DockingPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Structure Prediction (Comparative Modeling)"):
self.protPanel = CompModelPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Protein Design (MSD)"):
self.protPanel = MSDPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Antibody Modeling"):
self.protPanel = AntibodyPanel(self, self.W, self.H)
elif (selectedProtocol == "Molecular Surfaces"):
self.protPanel = SurfacesPanel(self, self.W, self.H)
self.cmd.hide("surface", "all")
elif (selectedProtocol == "Flexible Peptide Docking"):
self.protPanel = FlexPepDockPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
self.protPanel.setSeqWin(self.seqWin)
self.protPanel.setPyMOL(self.pymol)
self.protPanel.activate()
self.seqWin.setProtocolPanel(self.protPanel)
def changeProtocol(self, event):
logInfo("Go button clicked")
selectedProtocol = self.protMenu.GetStringSelection()
if (selectedProtocol != self.currentProtocol
and selectedProtocol != ""):
# Destroy the old panel so we can free memory up and create the new protocol panel
if (self.currentProtocol == "Superimposition"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Energy Minimization"):
# Check to see if the user has accepted the minimization
# If not, ask if they really want to proceed
if (self.protPanel.buttonState == "Finalize!"):
dlg = wx.MessageDialog(
self,
"You have not accepted your minimization and the results will be lost if you proceed. Proceed anyway?",
"Minimization Not Accepted",
wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo("Go cancelled due to unaccepted minimization")
dlg.Destroy()
return
dlg.Destroy()
logInfo("Minimization job rejected")
# Try to delete the minimized model if the user doesn't want to accept it
try:
self.cmd.remove("minimized_view")
self.cmd.delete("minimized_view")
except:
pass
self.cmd.label("all", "")
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Ensemble Browser"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Ensemble Generation"):
# Check to see if the user has accepted the design
# If not, ask if they really want to proceed
if (self.protPanel.buttonState == "Cancel!"):
dlg = wx.MessageDialog(
self,
"Your ensemble is not finished and the results will be lost if you proceed. Proceed anyway?",
"Design Not Accepted",
wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo(
"Go cancelled due to unfinished ensemblegen job")
dlg.Destroy()
return
logInfo("Ensemblegen job rejected")
dlg.Destroy()
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Protein Design (Fixbb)"):
# Check to see if the user has accepted the design
# If not, ask if they really want to proceed
if (self.protPanel.buttonState == "Finalize!"):
dlg = wx.MessageDialog(
self,
"You have not accepted your design and the results will be lost if you proceed. Proceed anyway?",
"Design Not Accepted",
wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo("Go cancelled due to unaccepted fixbb job")
dlg.Destroy()
return
logInfo("Fixbb job rejected")
dlg.Destroy()
# Try to delete the design model if the user doesn't want to accept it
try:
self.cmd.remove("designed_view")
self.cmd.delete("designed_view")
except:
pass
self.cmd.label("all", "")
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Residue/Ligand Creator"):
try:
self.cmd.remove("params")
self.cmd.delete("params")
except:
pass
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Point Mutations"):
try:
self.cmd.remove("rotamer_view")
self.cmd.delete("rotamer_view")
except:
pass
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Point Mutant Scan"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Loop Modeling (KIC)"):
# Check to see if the user has accepted the loop model
# If not, ask if they really want to proceed
if (self.protPanel.buttonState == "Finalize!"):
dlg = wx.MessageDialog(
self,
"You have not accepted your loop model and the results will be lost if you proceed. Proceed anyway?",
"KIC Not Accepted",
wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo("Go cancelled due to unaccepted KIC job")
dlg.Destroy()
return
logInfo("KIC job rejected")
dlg.Destroy()
# Try to delete the design model if the user doesn't want to accept it
try:
self.cmd.remove("kic_view")
self.cmd.delete("kic_view")
except:
pass
self.cmd.label("all", "")
self.protPanel.Destroy()
elif (self.currentProtocol == "Docking"):
# Check to see if the user has accepted the docking model
# If not, ask if they really want to proceed
if (self.protPanel.buttonState != "Dock!"):
dlg = wx.MessageDialog(
self,
"You have not accepted your docking model and the results will be lost if you proceed. Proceed anyway?",
"Docking Not Accepted",
wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo("Go cancelled due to unaccepted docking job")
dlg.Destroy()
return
logInfo("Docking job rejected")
dlg.Destroy()
# Try to delete the design model if the user doesn't want to accept it
try:
self.cmd.remove("dock_view")
self.cmd.delete("dock_view")
except:
pass
self.cmd.label("all", "")
self.protPanel.Destroy()
elif (self.currentProtocol ==
"Structure Prediction (Comparative Modeling)"):
# Check to see if the user has accepted the docking model
# If not, ask if they really want to proceed
if (self.protPanel.buttonState == "Finalize!"):
dlg = wx.MessageDialog(
self,
"You have not accepted your comparative modeling structure and the results will be lost if you proceed. Proceed anyway?",
"Docking Not Accepted",
wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_NO):
logInfo(
"Go cancelled due to unaccepted comparative modeling job"
)
dlg.Destroy()
return
logInfo("Comparative modeling job rejected")
dlg.Destroy()
# Try to delete the design model if the user doesn't want to accept it
try:
self.cmd.remove("thread_view")
self.cmd.delete("thread_view")
except:
pass
self.cmd.label("all", "")
self.protPanel.Destroy()
elif (self.currentProtocol == "Protein Design (MSD)"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Antibody Modeling"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Molecular Surfaces"):
try:
self.cmd.delete("curr_surf_recp")
except:
pass
try:
self.cmd.delete("curr_surf_lig")
except:
pass
self.cmd.hide("surface", "all")
if (self.parent.Selection.showSurf):
self.currentProtocol = "n/a"
self.parent.Selection.displaySurfaces()
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Flexible Peptide Docking"):
self.protPanel.Destroy()
del self.protPanel
self.currentProtocol = selectedProtocol
self.seqWin.cannotDelete = False
# Restart the Rosetta daemon to clear its memory up
self.parent.restartDaemon()
logInfo("Changed protocol to " + selectedProtocol)
if (selectedProtocol == "Superimposition"):
self.protPanel = SuperimpositionPanel(self, self.W, self.H)
elif (selectedProtocol == "Energy Minimization"):
self.protPanel = MinimizationPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Ensemble Browser"):
self.protPanel = EnsembleBrowserPanel(self, self.W, self.H)
elif (selectedProtocol == "Ensemble Generation"):
self.protPanel = EnsembleGenPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Protein Design (Fixbb)"):
self.protPanel = FixbbPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Residue/Ligand Creator"):
self.protPanel = ResidueCreatorPanel(self, self.W, self.H)
elif (selectedProtocol == "Point Mutations"):
self.protPanel = PointMutationsPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Point Mutant Scan"):
self.protPanel = PointMutantScanPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Loop Modeling (KIC)"):
self.protPanel = KICPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Docking"):
self.protPanel = DockingPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol ==
"Structure Prediction (Comparative Modeling)"):
self.protPanel = CompModelPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Protein Design (MSD)"):
self.protPanel = MSDPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
elif (selectedProtocol == "Antibody Modeling"):
self.protPanel = AntibodyPanel(self, self.W, self.H)
elif (selectedProtocol == "Molecular Surfaces"):
self.protPanel = SurfacesPanel(self, self.W, self.H)
self.cmd.hide("surface", "all")
elif (selectedProtocol == "Flexible Peptide Docking"):
self.protPanel = FlexPepDockPanel(self, self.W, self.H)
self.protPanel.setSelectWin(self.selectWin)
self.protPanel.setSeqWin(self.seqWin)
self.protPanel.setPyMOL(self.pymol)
self.protPanel.activate()
self.seqWin.setProtocolPanel(self.protPanel)
