def addfiles(self, accepted):
""" """
for rec in accepted:
r = rec[0]
rec_data = self.app.engine.RecBook[r]
types = ""
unk = ''
flex_res = '[no]'
chains = ''
for a in sorted(rec_data['atypes']):
types += " %s" % a
types = types.strip()
for a in sorted(rec_data['atypes_unknown']):
unk += ' %s' % a
unk = unk.strip()
if rec_data['is_flexible']: # in rec_data.keys():
#print "ISFLEXI"
flex_res = " ".join(rec_data['flex_res'])
chains = " ".join(rec_data['chains'])
self.recFileManager.listbox.insert('end', rec_data['name'], chains,
len(rec_data['residues']),
flex_res, types, unk,
rec_data['filename'])
# EVENT
# XXX TEMPORARY
self.app.configTab.setReceptorList()
#elif action=='del':
#print "FIND A WAY TO DELETE SOMETHING FROM self.tab2.recContainer"
# find the index!
#self.tab1.ligContainer.listbox.delete(0,END)
# XXX Obsolete
# pass
e = RaccoonEvents.UserInputRequirementUpdate('rec')
self.app.eventManager.dispatchEvent(e)
self.updatereccount()
def libselect_cb_ssh(self, libname = None, filters = {}): #, event=None):
""" manage the selection of a library for cluster submission
TODO filters now are empty, so the entire library
is selected by default
"""
if libname == None:
try:
s = self.ligLibPanel.listbox.curselection()[0]
sel = self.ligLibPanel.listbox.get(s)[0]
except:
return
libname = sel[0]
#print "SELECTED LIB=[%s]" % libname
self.dprint("SELECTED LIB=[%s]" % libname)
# need ask the server for the lib
lib = self.app.server.getLibrary(libname)
if lib == None:
t = 'Library selection'
i = 'error'
m = ('There was an error selecting the library.\n\n'
'The library "%s" does not exist on the server' % libname)
tmb.showinfo(parent=self.ligLibPanel, title=t,message=m, icon=i)
return False
self.app.ligand_source = [ {'lib': lib, 'filters' : filters } ]
self._selectedLib.config(text='%s' % libname)
e = RaccoonEvents.UserInputRequirementUpdate('lig')
self.app.eventManager.dispatchEvent(e)
return True
def destroy(self, obj, event=None):
""" remove a filter from the filters db
and destroy the widget
"""
obj.pack_forget()
self.filters.remove(obj)
e = RaccoonEvents.FilterInteractionEvent()
self.eventManager.dispatchEvent(e)
def updatereccount(self):
"""update labels and list in the config panel in the """
# update the count of accepted receptors
msg = 'Accepted structures [ %s ]' % len(self.app.engine.RecBook)
self.recGroup.configure(tag_text=msg)
## XXX THIS IS THE CONFIG PANEL ENTRY
## self.GUI_rec_list_container.insert('end', rec_data['name'])
e = RaccoonEvents.ReceptorListChange()
self.app.eventManager.dispatchEvent(e)
def setAllInactive(self, event=None):
""" set all filters inactive"""
change = False
for o in self.filters:
if o.isActive():
o.disable()
change = True
if change:
e = RaccoonEvents.FilterInteractionEvent()
self.eventManager.dispatchEvent(e)
def setAllActive(self, event=None):
""" set all filters active"""
change = False
for o in self.filters:
if not o.isActive():
o.enable(quiet=True)
if o.isActive():
change = False
if change:
e = RaccoonEvents.FilterInteractionEvent()
self.eventManager.dispatchEvent(e)
def _call_lib_manager_del(self,event=None):
# test if there's a server
if self.app.server == None:
title ='No server selected'
msg = ('Connect to a server in the Setup tab '
'to remove libraries...')
tmb.showinfo(parent = self.frame, title = title, message = msg)
return
# test if it is racconized
if not self.app.server.properties['ready']:
title ='Server is not ready'
msg = ('The server has not been prepared ("racconized") yet.\n\n'
'Prepare it in the Setup tab and try again.')
tmb.showinfo(parent = self.frame, title = title, message = msg)
return
if len(self.app.server.getLibraries()) == 0:
title ='No libraries'
msg = ('The server does not have libraries installed.')
tmb.showinfo(parent = self.frame, title = title, message = msg)
return
try:
s = self.ligLibPanel.listbox.curselection()[0]
sel = self.ligLibPanel.listbox.get(s)[0]
except:
#print "Nothing selected, leaving..."
return
libname = sel[0]
t = 'Delete library'
m = ('The library "%s" is going to be deleted.\n\n'
'All files on the remote server are going to be erased.\n\n'
'Are you sure?') % libname
w = 'warning'
i = 'info'
e = 'error'
if not tmb.askyesno(parent=self.parent, title=t, message=m, icon =w):
return
# deselect library to be deleted if it is selected
if len(self.app.ligand_source):
if libname == self.app.ligand_source[0]['lib'].name:
self.libdeselect_cb()
reply = self.app.server.delLibrary(libname, delfiles=True)
if reply:
m = 'Operation completed'
tmb.showinfo(parent = self.parent, title=t, message = m, icon = i)
else:
m = 'Operation was *NOT successful'
tmb.showinfo(parent = self.parent, title=t, message = m, icon = e)
self.app.setBusy()
e = RaccoonEvents.ServerConnection()
self.app.eventManager.dispatchEvent(e)
self.app.setReady()
def invertStatus(self, event=None):
""" invert filter status"""
change = False
for o in self.filters:
if o.isActive():
o.disable()
change = True
else:
o.enable(quiet=True)
if o.isActive():
change = True
if change:
e = RaccoonEvents.FilterInteractionEvent()
self.eventManager.dispatchEvent(e)
def prepare_ligands_for_guse(self):
""" Prepare ligands for gUSE. This includes looping through all ligands and compressing them in a zip file (ligands.zip)
"""
# if there are no ligands attached
if len(self._ligand_list) == 0:
return
# this class is needed in order access the ligands themselves and put them in an iterable libraryOfLigands
# because of the way the original Raccoon2 has been written (preparing libraries for a cluster)
class Library():
def __init__(self, ligands, name = 'noname'):
self.info = { 'name' : name,
'count' : 0,
'date' : None,
'format' : None,
'index_file': None,
'comments': "",
'properties' : {},
'type' : None,
}
self.ligands = ligands
def name(self):
""" used for sorting libraries """
return self.info['name']
def get_ligands(self):
return self.ligands
libraryOfLigands = Library(list(self._ligand_list))
self.app.ligand_source = [ {'lib': libraryOfLigands, 'filters' : None } ]
# show the appropriate message in line with the way it was written in the original Raccoon2
try:
title ='Ligands prepared successfully'
msg = ('The ligands have been prepared succesfully.')
tmb.showinfo(parent = self.win.interior(), title = title, message = msg)
del self._ligand_list[:]
e = RaccoonEvents.UserInputRequirementUpdate('lig')
self.app.eventManager.dispatchEvent(e)
except:
title ='Error while preparing ligands for gUSE'
msg = ('There was an error while uploading the ligands, make sure they are named correctly.')
tmb.showinfo(parent = self.win.interior(), title = title, message = msg)
self.destroy()
def deletefiles(self, nuke=False, event=None):
if nuke == True:
# EVENT UPDATES
self.app.engine.removeReceptors()
self.recFileManager.listbox.delete(0, 'end')
self.updatereccount()
else:
try:
s = self.recFileManager.listbox.curselection()[0]
sel = self.recFileManager.listbox.get(s)[0]
except:
#print "BB_REC> Nothing selected, leaving..."
return
name = sel[0]
self.app.engine.removeReceptors([name])
self.recFileManager.listbox.delete(s)
e = RaccoonEvents.UserInputRequirementUpdate('rec')
self.app.eventManager.dispatchEvent(e)
self.updatereccount()
def _go(event=None):
#server.debug = True
#libobj.debug= True
self.app.setBusy()
if comment:
libobj.info['comment'] = comment
libobj.upload( dirname, remotepath, autoregister=0, bg = True)
self.RUNNING = True
self._stopclosebutton.configure(text= 'Stop', command=stop)
status = server.transfer.progress(percent=1)
while status < 100.:
if server.transfer._STOP: break
status = server.transfer.progress(percent=1)
pc_var.set(status)
self.bar.update()
time.sleep(0.2)
self.RUNNING = False
libobj.debug = True # DEBUG
if server.transfer._status['completed']:
# EVENT trigger the event refresh of server list
#idxfile = remotepath + '/'+ dirname +'/'+'library.db'
#idxfile = 'library.db'
self._statuslab1.configure(text='Generating index file')
self._statuslab2.configure(text='...saving...')
libobj.saveIndex()
self._statuslab1.configure(text='Registering library to Library Index')
self._statuslab2.configure(text='...ongoing...')
libobj.register()
self._statuslab1.configure(text='\nLibrary upload completed!')
self._statuslab2.configure(text=' ')
del self._ligand_list[:]
self.delete(nuke=True)
e = RaccoonEvents.ServerConnection()
self.app.eventManager.dispatchEvent(e)
else:
error = server.transfer_status['error']
self._statuslab1.configure(text='Error trasnferring files!')
self._statuslab2.configure(text=error)
self._stopclosebutton.configure(text= 'Close', command=forceclose)
self.app.setReady()
def __init__(self, app, parent, debug=False):
rb.TabBase.__init__(self, app, parent, debug = False)
rb.RaccoonDefaultWidget.__init__(self, parent)
self.resource = self.app.resource
self.dockengine = self.app.dockengine
self.app.eventManager.registerListener(RaccoonEvents.SetDockingEngine, self.handleEngine)
self.app.eventManager.registerListener(RaccoonEvents.ReceptorListChange, self.setReceptorList)
self.app.eventManager.registerListener(RaccoonEvents.ReceptorListChange, self.nuke)
self.camera = None # embedded camera object
self._loaded_struct = []
self._boxevent = RaccoonEvents.SearchConfigChange()
self._searchevent = None # XXX TODO?
# switch for loading multiple receptors in the viewer
self.recLoaderMultiMode = tk.BooleanVar(value=False)
self._currRec = []# [ { 'name':xxxx, 'obj':[ rigid, flex ], 'fname':xxxx }, ... ]
self.initIcons()
self.makeInterface()
def nuke(self, event=None, quiet=False):
""" remove all the filters at once"""
if len(self.filters) == 0: return
if not quiet:
for o in self.filters:
if o.isActive():
t = 'Remove all filters'
i = 'info'
m = (
'All interaction filters are going to be removed.\n\nAre you sure?'
)
if not tmb.askyesno(
parent=self.interior(), title=t, message=m,
icon=i):
return
break
for o in self.filters:
o.pack_forget()
self.filters = []
e = RaccoonEvents.FilterInteractionEvent()
self.eventManager.dispatchEvent(e)
def libdeselect_cb(self):
""" deselect the library"""
self.app.ligand_source = []
self._selectedLib.config(text='%s' % '(none)')
e = RaccoonEvents.UserInputRequirementUpdate('lig')
self.app.eventManager.dispatchEvent(e)
def __init__(self, parent, update_cb=None, debug=False): #, destroy_cb):
rb.RaccoonDefaultWidget.__init__(self, parent)
DebugTools.DebugObj.__init__(self, debug)
Pmw.Group.__init__(self,
parent=parent,
tag_text='Target interactions',
tag_font=self.FONTbold,
ring_border=1,
ring_highlightcolor='black',
ring_highlightbackground='black',
ring_highlightthickness=1,
ring_relief='flat')
self.eventManager = RaccoonEvents.RaccoonEventManager()
self.eventManager.registerListener(
RaccoonEvents.FilterInteractionEvent, self.update)
self.initIcons()
self.filters = []
self.update_cb = update_cb
self.container = tk.Frame(
self.interior()) # this contains the widgets on the left
# build toolbar
self.toolbar = tk.Frame(self.container)
# add button
b = tk.Button(self.toolbar,
text='+',
image=self._ICON_add,
command=self.add,
**self.BORDER)
b.pack(anchor='w', side='left')
# remove button
b = tk.Button(self.toolbar,
text='-',
image=self._ICON_del,
**self.BORDER)
b.pack(anchor='w', side='left', padx=1)
selmenu = [
None,
['Remove inactive', 'normal', self.removeInactive],
['Remove all', 'normal', self.nuke],
]
menu = rb.RacMenu(b, selmenu, placement='under')
# selection button menu
b = tk.Button(self.toolbar,
text='s',
image=self._ICON_selmenu,
**self.BORDER)
b.pack(anchor='w', side='left', padx=0)
selmenu = [
None,
['Activate all', 'normal', self.setAllActive],
['Deactivate all', 'normal', self.setAllInactive],
['Invert active/inactive', 'normal', self.invertStatus],
]
menu = rb.RacMenu(b, selmenu, placement='under')
# mode pulldown
self._mode_choices = {'match all': 'all', 'match any': 'any'}
self.modeChoice = OptionMenuFix(
self.toolbar,
menubutton_font=self.FONT,
menu_font=self.FONT,
menubutton_width=10,
menubutton_bd=1,
menubutton_highlightbackground='black',
menubutton_borderwidth=1,
menubutton_highlightcolor='black',
menubutton_highlightthickness=1,
menubutton_height=1,
#command = self.trigger,
items=sorted(self._mode_choices.keys(), reverse=True),
)
f = tk.Frame(self.toolbar)
self.labelActiveFilt = tk.IntVar(value='0')
tk.Label(f, text='active filters:', font=self.FONT).pack(anchor='w',
side='left')
tk.Label(f, textvar=self.labelActiveFilt,
font=self.FONTbold).pack(anchor='w', side='left')
f.pack(anchor='w', side='left', padx=15)
self.modeChoice.pack(anchor='w', side='right', padx=1)
self.toolbar.pack(anchor='w',
side='top',
expand=1,
fill='x',
padx=4,
pady=2)
# build filter filtFrame
self.filtFrame = Pmw.ScrolledFrame(
self.container,
horizflex='expand', # vertflex='expand',
vscrollmode='static',
hscrollmode='dynamic')
#self.filtFrame.component('hull').configure(**self.BORDER)
self.filtFrame.component('clipper').configure(bg='white')
self.filtFrame.component('frame').configure(relief='flat', bg='white')
#self.filtFrame.component('vertscrollbar').bind("<Button-4>", self.mousescroll)
for c in [
'borderframe', 'clipper', 'frame', 'horizscrollbar', 'hull',
'vertscrollbar'
]:
self.filtFrame.component(c).bind("<Button-4>", self.mousescroll)
self.filtFrame.component(c).bind("<Button-5>", self.mousescroll)
self.interior().bind("<Button-4>", self.mousescroll)
self.interior().bind("<Button-5>", self.mousescroll)
self.filtFrame.pack(anchor='w',
side='top',
expand=1,
fill='both',
padx=4,
pady=2)
self.container.pack(anchor='w', side='left', expand=1, fill='both')
self.percentageFrame = tk.Frame(
self.interior()) # this contains the widgets on the right
# pie
self.pie = hf.PercentPie(self.percentageFrame, radius=50)
self.pie.pack(anchor='n', side='top', padx=5, pady=5)
#self.pie.set_percent(20)
# passed label
f = tk.Frame(self.percentageFrame)
tk.Label(f, text='passed :', font=self.FONTbold).pack(side='left',
anchor='w')
self.statusLabel = tk.Label(f,
text='0',
width=8,
anchor='w',
font=self.FONT)
self.statusLabel.pack(side='left', anchor='w')
f.pack(anchor='n', side='top')
#self.percentageFrame.pack(anchor='e',side='left', expand=1, fill='y')
self.percentageFrame.pack(expand=0, fill=None, anchor='e', side='left')
def sendEvent(self):
""" trigger the event"""
e = RaccoonEvents.FilterInteractionEvent()
self.eventManager.dispatchEvent(e)