def __init__(self, parent, W, H):
wx.Panel.__init__(self, parent, id=-1, pos=(0, 0), size=(350, H-265), name="ProtocolsPanel")
self.W = W
self.H = H
self.parent = parent
self.SetBackgroundColour("#333333")
self.Show()
if (platform.system() == "Windows"):
self.label = wx.StaticText(self, -1, "Protocols", (5, 5), (340, 25), wx.ALIGN_CENTRE)
self.label.SetFont(wx.Font(12, wx.DEFAULT, wx.ITALIC, wx.BOLD))
elif (platform.system() == "Darwin"):
self.label = wx.StaticBitmap(self, -1, wx.Image(self.parent.scriptdir + "/images/osx/protocols/lblProtocols.png", wx.BITMAP_TYPE_PNG).ConvertToBitmap(), pos=(5, 5), size=(340, 25))
else:
self.label = wx.StaticText(self, -1, "Protocols", style=wx.ALIGN_CENTRE)
self.label.SetFont(wx.Font(12, wx.DEFAULT, wx.ITALIC, wx.BOLD))
resizeTextControlForUNIX(self.label, 0, self.GetSize()[0])
self.label.SetForegroundColour("#FFFFFF")
if (platform.system() == "Darwin"):
self.protMenu = wx.ComboBox(self, pos=(5, 30), size=(230, 25), choices=[], style=wx.CB_READONLY)
else:
self.protMenu = wx.ComboBox(self, pos=(5, 30), size=(230, 25), choices=[], style=wx.CB_READONLY | wx.CB_SORT)
self.protMenu.SetToolTipString("List of currently available protocols")
self.default_protocols = ["Antibody Modeling",
"Biological Tools",
"Docking",
"Energy Minimization",
"Ensemble Browser",
"Ensemble Generation",
"Flexible Peptide Docking",
"Loop Modeling (KIC)",
"Module Manager",
"Molecular Surfaces",
"Point Mutant Scan",
"Point Mutations",
"Protein Design (Fixbb)",
"Protein Design (MSD)",
"Residue/Ligand Creator",
"Structure Prediction (Comparative Modeling)",
"Superimposition"]
self.readModules()
self.protMenu.SetSelection(self.protocols.index("Superimposition"))
if (platform.system() == "Darwin"):
self.GoBtn = wx.BitmapButton(self, id=-1, bitmap=wx.Image(self.parent.scriptdir + "/images/osx/protocols/GoBtn.png", wx.BITMAP_TYPE_PNG).ConvertToBitmap(), pos=(240, 30), size=(100, 25))
else:
self.GoBtn = wx.Button(self, id=-1, label="Go!", pos=(240, 30), size=(100, 25))
self.GoBtn.SetForegroundColour("#000000")
self.GoBtn.SetFont(wx.Font(10, wx.DEFAULT, wx.NORMAL, wx.BOLD))
self.GoBtn.Bind(wx.EVT_BUTTON, self.changeProtocol)
self.GoBtn.SetToolTipString("Change to the selected protocol")
self.currentProtocol = "Superimposition"
self.protPanel = SuperimpositionPanel(self, W, H)
class ProtocolsPanel(wx.Panel):
def __init__(self, parent, W, H):
wx.Panel.__init__(self, parent, id=-1, pos=(0, 0), size=(350, H-265), name="ProtocolsPanel")
self.W = W
self.H = H
self.parent = parent
self.SetBackgroundColour("#333333")
self.Show()
if (platform.system() == "Windows"):
self.label = wx.StaticText(self, -1, "Protocols", (5, 5), (340, 25), wx.ALIGN_CENTRE)
self.label.SetFont(wx.Font(12, wx.DEFAULT, wx.ITALIC, wx.BOLD))
elif (platform.system() == "Darwin"):
self.label = wx.StaticBitmap(self, -1, wx.Image(self.parent.scriptdir + "/images/osx/lblProtocols.png", wx.BITMAP_TYPE_PNG).ConvertToBitmap(), pos=(5, 5), size=(340, 25))
else:
self.label = wx.StaticText(self, -1, "Protocols", style=wx.ALIGN_CENTRE)
self.label.SetFont(wx.Font(12, wx.DEFAULT, wx.ITALIC, wx.BOLD))
resizeTextControlForUNIX(self.label, 0, self.GetSize()[0])
self.label.SetForegroundColour("#FFFFFF")
if (platform.system() == "Darwin"):
self.protMenu = wx.ComboBox(self, pos=(5, 30), size=(230, 25), choices=[], style=wx.CB_READONLY)
else:
self.protMenu = wx.ComboBox(self, pos=(5, 30), size=(230, 25), choices=[], style=wx.CB_READONLY | wx.CB_SORT)
self.protMenu.SetToolTipString("List of currently available protocols")
self.default_protocols = ["Antibody Modeling",
"Docking",
"Energy Minimization",
"Ensemble Browser",
"Ensemble Generation",
"Flexible Peptide Docking",
"Loop Modeling (KIC)",
"Module Manager",
"Molecular Surfaces",
"Point Mutant Scan",
"Point Mutations",
"Protein Design (Fixbb)",
"Protein Design (MSD)",
"Residue/Ligand Creator",
"Structure Prediction (Comparative Modeling)",
"Superimposition"]
self.readModules()
self.protMenu.SetSelection(self.protocols.index("Superimposition"))
if (platform.system() == "Darwin"):
self.GoBtn = wx.BitmapButton(self, id=-1, bitmap=wx.Image(self.parent.scriptdir + "/images/osx/GoBtn.png", wx.BITMAP_TYPE_PNG).ConvertToBitmap(), pos=(240, 30), size=(100, 25))
else:
self.GoBtn = wx.Button(self, id=-1, label="Go!", pos=(240, 30), size=(100, 25))
self.GoBtn.SetForegroundColour("#000000")
self.GoBtn.SetFont(wx.Font(10, wx.DEFAULT, wx.NORMAL, wx.BOLD))
self.GoBtn.Bind(wx.EVT_BUTTON, self.changeProtocol)
self.GoBtn.SetToolTipString("Change to the selected protocol")
self.currentProtocol = "Superimposition"
self.protPanel = SuperimpositionPanel(self, W, H)
def readModules(self):
self.protocols = self.default_protocols[:]
# Let's see if there are any custom modules to import
# Everything needs to be in a try/except block to prevent corrupted modules from
# crashing the whole program
# Ignore anything that does not import properly and write a message out to the terminal
olddir = os.getcwd()
goToSandbox("modules")
sys.path.append(os.getcwd())
moduledirs = glob.glob("*")
self.modules = {}
for moduledir in moduledirs:
# Ignore the template
if (moduledir == "template"):
continue
try:
module = __import__(moduledir)
except:
print "Failed to import " + moduledir + ", does " + moduledir + "/__init__.py exist?"
continue
try:
# Does the panel exist?
module.ModulePanel
except:
print "Failed to import " + moduledir + ", could not find the class \"ModulePanel\""
continue
# Look for the name of the protocol in the comments of the module's script
# If the name does not exist, just use the directory name
modulename = moduledir
fin = open(moduledir + "/__init__.py", "r")
for aline in fin:
if (aline.startswith("### PROTOCOL NAME:")):
modulename = aline.split("### PROTOCOL NAME:")[1].strip()
break
fin.close()
# Does this name exist already
nameTaken = False
for name in self.protocols:
if (name.strip() == modulename.strip()):
nameTaken = True
break
if (nameTaken):
i = 2
while (True):
nameTaken = False
for name in self.protocols:
if (name.strip() == modulename.strip() + " (" + str(i) + ")"):
nameTaken = True
break
if (not(nameTaken)):
modulename = modulename.strip() + " (" + str(i) + ")"
break
i += 1
# Add it into the list of protocols
addedIn = False
for i in range(0, len(self.protocols)):
if (modulename < self.protocols[i]):
addedIn = True
self.protocols.insert(i, modulename)
break
if (not(addedIn)):
self.protocols.append(modulename)
self.modules[modulename] = module
os.chdir(olddir)
self.protMenu.Clear()
self.protMenu.AppendItems(self.protocols)
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 == "Module Manager"):
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
else:
# Must be a custom module
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 == "Module Manager"):
self.protPanel = ModuleManagerPanel(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)
else:
# Custom module
# Custom modules are aware of PyMOL, the Sequence Window, and the SelectionPanel
# They also know about the Protocols Window through the parent variable
# They also will receive activation events
self.protPanel = self.modules[selectedProtocol].ModulePanel(self, self.modules[selectedProtocol].__file__, 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 setSeqWin(self, seqWin):
self.seqWin = seqWin
self.protPanel.setSeqWin(seqWin)
self.seqWin.setProtocolPanel(self.protPanel)
def setPyMOL(self, pymol):
self.pymol = pymol
self.cmd = pymol.cmd
self.stored = pymol.stored
self.protPanel.setPyMOL(pymol)
def setSelectWin(self, selectWin):
self.selectWin = selectWin
def activate(self):
self.cmd.enable("seqsele")
try:
self.protPanel.activate()
except:
# Probably a custom module that does not have the activate function implemented
print "WARNING: Could not activate the ProtocolPanel for " + self.currentProtocol
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 == "Module Manager"):
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
else:
# Must be a custom module
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 == "Module Manager"):
self.protPanel = ModuleManagerPanel(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)
else:
# Custom module
# Custom modules are aware of PyMOL, the Sequence Window, and the SelectionPanel
# They also know about the Protocols Window through the parent variable
# They also will receive activation events
self.protPanel = self.modules[selectedProtocol].ModulePanel(self, self.modules[selectedProtocol].__file__, 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.protPanel is not None):
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 == "Biological Tools"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Module Manager"):
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
else:
# Must be a custom module
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)
try:
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 == "Biological Tools"):
self.protPanel = BioToolsPanel(self, self.W, self.H)
elif (selectedProtocol == "Module Manager"):
self.protPanel = ModuleManagerPanel(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)
elif selectedProtocol == "Pathway Visualization (GeoFold)":
self.protPanel = DagViewPanel(self,self.W,self.H)
else:
# Custom module
# Custom modules are aware of PyMOL, the Sequence Window, and the SelectionPanel
# They also know about the Protocols Window through the parent variable
# They also will receive activation events
self.protPanel = self.modules[selectedProtocol].ModulePanel(self, self.modules[selectedProtocol].__file__, 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)
except:
self.protPanel = None
class ProtocolsPanel(wx.Panel):
def __init__(self, parent, W, H):
wx.Panel.__init__(self, parent, id=-1, pos=(0, 0), size=(350, H-265), name="ProtocolsPanel")
self.W = W
self.H = H
self.parent = parent
self.SetBackgroundColour("#333333")
self.Show()
if (platform.system() == "Windows"):
self.label = wx.StaticText(self, -1, "Protocols", (5, 5), (340, 25), wx.ALIGN_CENTRE)
self.label.SetFont(wx.Font(12, wx.DEFAULT, wx.ITALIC, wx.BOLD))
elif (platform.system() == "Darwin"):
self.label = wx.StaticBitmap(self, -1, wx.Image(self.parent.scriptdir + "/images/osx/protocols/lblProtocols.png", wx.BITMAP_TYPE_PNG).ConvertToBitmap(), pos=(5, 5), size=(340, 25))
else:
self.label = wx.StaticText(self, -1, "Protocols", style=wx.ALIGN_CENTRE)
self.label.SetFont(wx.Font(12, wx.DEFAULT, wx.ITALIC, wx.BOLD))
resizeTextControlForUNIX(self.label, 0, self.GetSize()[0])
self.label.SetForegroundColour("#FFFFFF")
if (platform.system() == "Darwin"):
self.protMenu = wx.ComboBox(self, pos=(5, 30), size=(230, 25), choices=[], style=wx.CB_READONLY)
else:
self.protMenu = wx.ComboBox(self, pos=(5, 30), size=(230, 25), choices=[], style=wx.CB_READONLY | wx.CB_SORT)
self.protMenu.SetToolTipString("List of currently available protocols")
self.default_protocols = ["Antibody Modeling",
"Biological Tools",
"Docking",
"Energy Minimization",
"Ensemble Browser",
"Ensemble Generation",
"Flexible Peptide Docking",
"Loop Modeling (KIC)",
"Module Manager",
"Molecular Surfaces",
"Point Mutant Scan",
"Point Mutations",
"Protein Design (Fixbb)",
"Protein Design (MSD)",
"Residue/Ligand Creator",
"Structure Prediction (Comparative Modeling)",
"Superimposition"]
self.readModules()
self.protMenu.SetSelection(self.protocols.index("Superimposition"))
if (platform.system() == "Darwin"):
self.GoBtn = wx.BitmapButton(self, id=-1, bitmap=wx.Image(self.parent.scriptdir + "/images/osx/protocols/GoBtn.png", wx.BITMAP_TYPE_PNG).ConvertToBitmap(), pos=(240, 30), size=(100, 25))
else:
self.GoBtn = wx.Button(self, id=-1, label="Go!", pos=(240, 30), size=(100, 25))
self.GoBtn.SetForegroundColour("#000000")
self.GoBtn.SetFont(wx.Font(10, wx.DEFAULT, wx.NORMAL, wx.BOLD))
self.GoBtn.Bind(wx.EVT_BUTTON, self.changeProtocol)
self.GoBtn.SetToolTipString("Change to the selected protocol")
self.currentProtocol = "Superimposition"
self.protPanel = SuperimpositionPanel(self, W, H)
def readModules(self):
self.protocols = self.default_protocols[:]
# Let's see if there are any custom modules to import
# Everything needs to be in a try/except block to prevent corrupted modules from
# crashing the whole program
# Ignore anything that does not import properly and write a message out to the terminal
olddir = os.getcwd()
goToSandbox("modules")
sys.path.append(os.getcwd())
moduledirs = glob.glob("*")
self.modules = {}
for moduledir in moduledirs:
# Ignore the template
if (moduledir == "template"):
continue
try:
module = __import__(moduledir)
except:
print "Failed to import " + moduledir + ", does " + moduledir + "/__init__.py exist?"
continue
try:
# Does the panel exist?
module.ModulePanel
except:
print "Failed to import " + moduledir + ", could not find the class \"ModulePanel\""
continue
# Look for the name of the protocol in the comments of the module's script
# If the name does not exist, just use the directory name
modulename = moduledir
fin = open(moduledir + "/__init__.py", "r")
for aline in fin:
if (aline.startswith("### PROTOCOL NAME:")):
modulename = aline.split("### PROTOCOL NAME:")[1].strip()
break
fin.close()
# Does this name exist already
nameTaken = False
for name in self.protocols:
if (name.strip() == modulename.strip()):
nameTaken = True
break
if (nameTaken):
i = 2
while (True):
nameTaken = False
for name in self.protocols:
if (name.strip() == modulename.strip() + " (" + str(i) + ")"):
nameTaken = True
break
if (not(nameTaken)):
modulename = modulename.strip() + " (" + str(i) + ")"
break
i += 1
# Add it into the list of protocols
addedIn = False
for i in range(0, len(self.protocols)):
if (modulename < self.protocols[i]):
addedIn = True
self.protocols.insert(i, modulename)
break
if (not(addedIn)):
self.protocols.append(modulename)
self.modules[modulename] = module
os.chdir(olddir)
self.protMenu.Clear()
self.protMenu.AppendItems(self.protocols)
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.protPanel is not None):
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 == "Biological Tools"):
self.protPanel.Destroy()
del self.protPanel
elif (self.currentProtocol == "Module Manager"):
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
else:
# Must be a custom module
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)
try:
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 == "Biological Tools"):
self.protPanel = BioToolsPanel(self, self.W, self.H)
elif (selectedProtocol == "Module Manager"):
self.protPanel = ModuleManagerPanel(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)
else:
# Custom module
# Custom modules are aware of PyMOL, the Sequence Window, and the SelectionPanel
# They also know about the Protocols Window through the parent variable
# They also will receive activation events
self.protPanel = self.modules[selectedProtocol].ModulePanel(self, self.modules[selectedProtocol].__file__, 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)
except:
self.protPanel = None
def setSeqWin(self, seqWin):
self.seqWin = seqWin
self.protPanel.setSeqWin(seqWin)
self.seqWin.setProtocolPanel(self.protPanel)
def setPyMOL(self, pymol):
self.pymol = pymol
self.cmd = pymol.cmd
self.stored = pymol.stored
self.protPanel.setPyMOL(pymol)
def setSelectWin(self, selectWin):
self.selectWin = selectWin
def activate(self):
self.cmd.enable("seqsele")
try:
self.protPanel.activate()
except:
# Probably a custom module that does not have the activate function implemented
print "WARNING: Could not activate the ProtocolPanel for " + self.currentProtocol
class ProtocolsPanel(wx.Panel):
def __init__(self, parent, W, H):
wx.Panel.__init__(self, parent, id=-1, pos=(0, 0), size=(350, H-265), name="ProtocolsPanel")
self.W = W
self.H = H
self.parent = parent
self.SetBackgroundColour("#333333")
self.Show()
if (platform.system() == "Windows"):
self.label = wx.StaticText(self, -1, "Protocols", (5, 5), (340, 25), wx.ALIGN_CENTRE)
self.label.SetFont(wx.Font(12, wx.DEFAULT, wx.ITALIC, wx.BOLD))
elif (platform.system() == "Darwin"):
self.label = wx.StaticBitmap(self, -1, wx.Image(self.parent.scriptdir + "/images/osx/lblProtocols.png", wx.BITMAP_TYPE_PNG).ConvertToBitmap(), pos=(5, 5), size=(340, 25))
else:
self.label = wx.StaticText(self, -1, "Protocols", style=wx.ALIGN_CENTRE)
self.label.SetFont(wx.Font(12, wx.DEFAULT, wx.ITALIC, wx.BOLD))
resizeTextControlForUNIX(self.label, 0, self.GetSize()[0])
self.label.SetForegroundColour("#FFFFFF")
self.protocols = ["Antibody Modeling",
"Docking",
"Energy Minimization",
"Ensemble Browser",
"Ensemble Generation",
"Flexible Peptide Docking",
"Loop Modeling (KIC)",
"Molecular Surfaces",
"Point Mutant Scan",
"Point Mutations",
"Protein Design (Fixbb)",
"Protein Design (MSD)",
"Residue/Ligand Creator",
"Structure Prediction (Comparative Modeling)",
"Superimposition"]
if (platform.system() == "Darwin"):
self.protMenu = wx.ComboBox(self, pos=(5, 30), size=(230, 25), choices=self.protocols, style=wx.CB_READONLY)
else:
self.protMenu = wx.ComboBox(self, pos=(5, 30), size=(230, 25), choices=self.protocols, style=wx.CB_READONLY | wx.CB_SORT)
self.protMenu.SetSelection(self.protocols.index("Superimposition"))
self.protMenu.SetToolTipString("List of currently available protocols")
if (platform.system() == "Darwin"):
self.GoBtn = wx.BitmapButton(self, id=-1, bitmap=wx.Image(self.parent.scriptdir + "/images/osx/GoBtn.png", wx.BITMAP_TYPE_PNG).ConvertToBitmap(), pos=(240, 30), size=(100, 25))
else:
self.GoBtn = wx.Button(self, id=-1, label="Go!", pos=(240, 30), size=(100, 25))
self.GoBtn.SetForegroundColour("#000000")
self.GoBtn.SetFont(wx.Font(10, wx.DEFAULT, wx.NORMAL, wx.BOLD))
self.GoBtn.Bind(wx.EVT_BUTTON, self.changeProtocol)
self.GoBtn.SetToolTipString("Change to the selected protocol")
self.currentProtocol = "Superimposition"
self.protPanel = SuperimpositionPanel(self, W, H)
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 setSeqWin(self, seqWin):
self.seqWin = seqWin
self.protPanel.setSeqWin(seqWin)
self.seqWin.setProtocolPanel(self.protPanel)
def setPyMOL(self, pymol):
self.pymol = pymol
self.cmd = pymol.cmd
self.stored = pymol.stored
self.protPanel.setPyMOL(pymol)
def setSelectWin(self, selectWin):
self.selectWin = selectWin
def activate(self):
self.cmd.enable("seqsele")
self.protPanel.activate()
