def Start(self):
# self.queue.put(lambda: self.top.top.root.withdraw())
cmd.window('hide')
cmd.refresh_wizard()
cmd.orient()
cmd.window('show')
# self.queue.put(lambda: cmd.window('show'))
self.ErrorCode = 1
try:
self.State = cmd.get_state()
self.config_mouse = General_cmd.get_config_mouse()
cmd.config_mouse('three_button_editing')
self.exc = [ self.SphereDisplay ]
General_cmd.mask_Objects(self.exc)
# success
self.ErrorCode = 0
except:
self.queue.put(lambda: self.App.DisplayMessage(" ERROR: Could not start the Sphere wizard", 1))
self.queue.put(lambda: self.App.DisplayMessage(" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
if self.DisplaySphere():
self.queue.put(lambda: self.App.DisplayMessage(" ERROR: Could not display the Sphere", 1))
self.queue.put(lambda: self.App.DisplayMessage(" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
def Start(self):
self.queue.put(lambda: self.FlexAID.root.withdraw())
cmd.window('hide')
cmd.window('show')
# self.queue.put(lambda: cmd.window('show'))
cmd.refresh_wizard()
self.ErrorCode = 1
try:
self.selection_mode = cmd.get("mouse_selection_mode")
cmd.set("mouse_selection_mode", 0) # set selection mode to atomic
# Mask objects
self.exc = [self.LigDisplay]
General_cmd.mask_Objects(self.exc)
self.ErrorCode = 0
except:
self.queue.put(lambda: self.FlexAID.DisplayMessage(" ERROR: Could not start the Anchor Atom wizard", 1))
self.queue.put(lambda: self.FlexAID.DisplayMessage(" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
# Display the ligand from the PDB file
if self.DisplayLigand() or self.RefreshDisplay():
self.queue.put(lambda: self.FlexAID.DisplayMessage(" ERROR: Could not display the ligand", 1))
self.queue.put(lambda: self.FlexAID.DisplayMessage(" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
# remove any possible selection before selecting atoms
cmd.deselect()
def Start(self):
self.queue.put(lambda: self.FlexAID.root.withdraw())
cmd.window('hide')
self.queue.put(lambda: cmd.window('show'))
cmd.refresh_wizard()
# Display the ligand from the PDB file
if self.DisplayLigand():
self.FlexAID.DisplayMessage("Error while trying to display the ligand from PDB file", 1)
self.Quit_Wizard(self.ErrorCode)
return
# Color the Atoms based on their type
if self.ColorByType():
self.FlexAID.DisplayMessage("Error while coloring the ligand atoms by type", 1)
self.Quit_Wizard(self.ErrorCode)
return
# Mask everythign except modifyable object (ligand)
self.exc = [self.LigDisplay]
General.mask_Objects(self.exc)
self.selection_mode = cmd.get("mouse_selection_mode")
cmd.set("mouse_selection_mode", 0) # set selection mode to atomic
# remove any possible selection before selecting atoms
cmd.deselect()
self.ErrorCode += 1
def automate(self):
# Hide the PyMOL viewer window
# This not only increases the search speed, sometimes significantly,
# but also may prevent the user from accidentally interfering with
# automatic selections
cmd.window('hide')
# Text file to contain information about generated motifs, i.e., motif definition,
# backbone and tolerance parameters. The report indicates if the motif was not saved.
# An example of the report file entry (the ">" header lines: pdb [1jms], tolerance [1.2],
# number of chains on which the motif was found [1], ec code [2.7.7.31];
# subsequent lines: residue name, chain, residue number, and whether the bbn was on or off):
# > 1jms 1.2 1 2.7.7.31
# NA A 702 Off
# MG A 701 Off
# ASP A 434 On
reportfile = open(
glb.pathmaker(('report', '.txt'), root=glb.AUTOMOTIFSFOLDER), 'w')
# List of PDB IDs for which the program will attempt to generate auto motifs:
pdblist = lib.getPDBlist()
# Auto generate the motifs for for the pdb id list
self.autoGenerate(pdblist, reportfile)
reportfile.close()
cmd.window('show')
print ' ...done :)'
def Start(self):
self.queue.put(lambda: self.FlexAID.root.withdraw())
cmd.window('hide')
cmd.window('show')
# self.queue.put(lambda: cmd.window('show'))
cmd.refresh_wizard()
self.ErrorCode = 1
try:
#self.selection_mode = cmd.get_setting_legacy("mouse_selection_mode")
self.selection_mode = cmd.get("mouse_selection_mode")
cmd.set("mouse_selection_mode", 0) # set selection mode to atomic
# Mask objects
self.exc = [self.LigDisplay, self.PossFlexDisplay, self.SelFlexDisplay]
General_cmd.mask_Objects(self.exc)
self.ErrorCode = 0
except:
self.queue.put(lambda: self.top.DisplayMessage(" ERROR: Could not start the Flexible Bonds wizard", 1))
self.queue.put(lambda: self.top.DisplayMessage(" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
# Display the ligand from the PDB file
if self.DisplayLigand():
self.queue.put(lambda: self.top.DisplayMessage(" ERROR: Could not display the ligand", 1))
self.queue.put(lambda: self.top.DisplayMessage(" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
# Display all Possible Flexible Bonds
if self.show_FlexibleBonds():
self.queue.put(lambda: self.top.DisplayMessage(" ERROR: Could not display the flexible bonds", 1))
self.queue.put(lambda: self.top.DisplayMessage(" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
# Display all Selected Flexible Bonds
if self.show_SelectedBonds():
self.queue.put(lambda: self.top.DisplayMessage(" ERROR: Could not display the selected flexible bonds", 1))
self.queue.put(lambda: self.top.DisplayMessage(" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
# remove any possible selection before selecting atoms
cmd.deselect()
cmd.unpick()
def Start(self):
self.queue.put(lambda: self.FlexAID.root.withdraw())
cmd.window('hide')
cmd.window('show')
# self.queue.put(lambda: cmd.window('show'))
cmd.refresh_wizard()
self.ErrorCode = 1
try:
self.selection_mode = cmd.get("mouse_selection_mode")
cmd.set("mouse_selection_mode", 0) # set selection mode to atomic
# Mask objects
self.exc = [self.LigDisplay]
General_cmd.mask_Objects(self.exc)
self.ErrorCode = 0
except:
self.queue.put(lambda: self.FlexAID.DisplayMessage(
" ERROR: Could not start the Anchor Atom wizard", 1))
self.queue.put(lambda: self.FlexAID.DisplayMessage(
" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
# Display the ligand from the PDB file
if self.DisplayLigand() or self.RefreshDisplay():
self.queue.put(lambda: self.FlexAID.DisplayMessage(
" ERROR: Could not display the ligand", 1))
self.queue.put(lambda: self.FlexAID.DisplayMessage(
" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
# remove any possible selection before selecting atoms
cmd.deselect()
def Start(self):
# self.queue.put(lambda: self.top.top.root.withdraw())
cmd.window('hide')
cmd.refresh_wizard()
cmd.orient()
cmd.window('show')
# self.queue.put(lambda: cmd.window('show'))
self.ErrorCode = 1
try:
self.State = cmd.get_state()
self.config_mouse = General_cmd.get_config_mouse()
cmd.config_mouse('three_button_editing')
self.exc = [self.SphereDisplay]
General_cmd.mask_Objects(self.exc)
# success
self.ErrorCode = 0
except:
self.queue.put(lambda: self.App.DisplayMessage(
" ERROR: Could not start the Sphere wizard", 1))
self.queue.put(lambda: self.App.DisplayMessage(
" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
if self.DisplaySphere():
self.queue.put(lambda: self.App.DisplayMessage(
" ERROR: Could not display the Sphere", 1))
self.queue.put(lambda: self.App.DisplayMessage(
" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
def Start(self):
self.queue.put(lambda: self.FlexAID.root.withdraw())
cmd.window('hide')
cmd.window('show')
# self.queue.put(lambda: cmd.window('show'))
cmd.refresh_wizard()
# Display all Selected Flexible Bonds
if self.show_SelectedSC():
self.queue.put(lambda: self.FlexAID.DisplayMessage(" ERROR: Could not display selected flexible side-chains", 1))
self.Quit_Wizard()
return
#self.selection_mode = cmd.get_setting_legacy("mouse_selection_mode")
self.selection_mode = cmd.get("mouse_selection_mode")
cmd.set("mouse_selection_mode", 1) # set selection mode to residue
# Mask objects
self.exc = [ self.TargetName ]
General_cmd.mask_Objects(self.exc)
if General_cmd.object_Exists(self.FlexAID.Config1.BindingSiteDisplay):
cmd.zoom(self.FlexAID.Config1.BindingSiteDisplay)
else:
cmd.zoom(self.TargetName)
# remove any possible selection before selecting atoms
cmd.deselect()
self.ErrorCode += 1
#=======================================================================
''' update_SelectedSC : updates the view of selected flexible sc. '''