def _getligprop(self, filename):
""" calculate basic properties from PDBQT ligand
mw, hba, hbd, heavy atoms
"""
try:
lines = hf.getLines(filename)
atoms = hf.getAtoms(lines)
except:
return False, sys.exc_info()[1]
if len(lines) == 0:
return False, "empty file"
if len(atoms) == 0:
return False, "no atoms (INVALID FILE)"
try:
tors = int(lines[-1].split()[1])
except:
return False, "no torsions (INVALID FILE)"
# hb
hba, hbd = [ len(x) for x in hf.findHbAccepDon(atoms) ]
# atypes ( report all types with duplicates, to be used for updating lib types)
atypes = [ x.split()[-1] for x in atoms ]
# heavy
heavy = len([ x for x in atypes if not x == 'HD' ])
# mw
mw = 0
for a in atypes:
mw += hf.adtypes.get( a, [None,0])[1]
atypes = list(set(atypes)) #[ x.split()[-1] for x in atoms ]))
return True, {'tors' : tors, 'heavy' : heavy, 'mw' : mw, 'hba' : hba, 'hbd': hbd, 'atypes': atypes }
def _getligprop(self, filename):
""" calculate basic properties from PDBQT ligand
mw, hba, hbd, heavy atoms
"""
try:
lines = hf.getLines(filename)
atoms = hf.getAtoms(lines)
except:
return False, sys.exc_info()[1]
if len(lines) == 0:
return False, "empty file"
if len(atoms) == 0:
return False, "no atoms (INVALID FILE)"
try:
tors = int(lines[-1].split()[1])
except:
return False, "no torsions (INVALID FILE)"
# hb
hba, hbd = [len(x) for x in hf.findHbAccepDon(atoms)]
# atypes ( report all types with duplicates, to be used for updating lib types)
atypes = [x.split()[-1] for x in atoms]
# heavy
heavy = len([x for x in atypes if not x == "HD"])
# mw
mw = 0
for a in atypes:
mw += hf.adtypes.get(a, [None, 0])[1]
atypes = list(set(atypes)) # [ x.split()[-1] for x in atoms ]))
return True, {"tors": tors, "heavy": heavy, "mw": mw, "hba": hba, "hbd": hbd, "atypes": atypes}
def writeLogJson(self, logname, compression = False):
""" write log in json format
"""
if not len(self.results.keys()):
print "cowardly refusing to write an empty file"
return
#hf.writejson(logname, self.results, compression)
hf.writemarshal(logname, self.results, compression)
def makedirname(event=None):
""" ButtonRelease """
chars = hf._allowedfilenamechars()
text = self._lname.getvalue()
if not len(text):
self._dname.setvalue('')
valid = [ x for x in text if x in hf._allowedfilenamechars()]
valid = "".join(valid).lower()
self._dname.setvalue(valid)
def saveServerInfo(self, fname=None):
"""save the server db and handle password saving"""
if fname==None:
fname = self.getServerInfoFile()
srv_db = copy.deepcopy(self.settings['servers'])
for s in srv_db['ssh'].keys():
srv = srv_db['ssh'][s]
if '_save_passwd_' in srv.keys():
del srv['_save_passwd_']
else:
srv['password'] = None
hf.writejson(fname, srv_db, compression=True)
def _checkdirs(self, autocreate =True):
""" check and create necessary raccoon dirs"""
dirs = [ self.settings['racdir'], self.settings['datadir'] ,
self.settings['tempdir'], self.settings['dockingdir'],
self.settings['targetdir'] ]
for d in dirs:
if not os.path.isdir(d):
if autocreate:
print "dir [%s] does not exist. Creating it..." % d
hf.makeDir( fullpath = d)
else:
return False
return True
def export(self, event=None):
""" export list of problematic files"""
buff = []
for f, e in self.problematic:
f = ":".join(f) # handle multiple files per ligand
buff.append("%s,%s" % (f, e) )
t = 'Select problematic log filename'
ft = [("Any file type...", "*")]
idir = self.app._lastdir
suggest = 'problematic_results.csv'
fname = tfd.asksaveasfilename(parent=self.interior(),
title=t, filetypes=ft, initialdir=idir, initialfile=suggest)
if not fname:
return
hf.writeList(fname, buff, addNewLine=1)
def readConfig(self, fname=None):
""" read the confielf.saveServerInfo()
# g file """
#print "READING CONFIG FILE"
if fname == None:
fname = self.getConfigFile()
data = hf.readjson(fname)
if data:
self.settings = data
def loadTargetDb(self, fname=None):
""" read the database where known used targets
are stored
"""
if fname == None:
fname = self.getTargetDbFile()
data = hf.readjson(fname, compression = False)
if data:
self.knownTargets = data
self.dprint("Target dbase initialized: %d items" % len(self.knownTargets.keys()) )
def __init__(self, parent, app, ligands=None, receptor=None, logfile=None, job=None, auto=False, debug=False):
""" """
rb.RaccoonDefaultWidget.__init__(self, parent)
DebugTools.DebugObj.__init__(self, debug)
Pmw.Dialog.__init__(self, parent, buttons = ('Stop',),
defaultbutton='Stop', title = 'Processing results',
command=self.stop, master=self.parent)
bbox = self.component('buttonbox')
for i in range(bbox.numbuttons()):
bbox.button(i).configure(font=self.FONT, default='disabled', **self.BORDER)
self.job = job
self.app = app
self.auto = auto
self.problematic = []
self._current = ('none', 'none', 'none')
self.status = False
if self.job:
self.getData()
else:
self.ligands = ligands
if receptor:
self.receptor = receptor
else:
self.receptor = self.app.resultsProcessor.processor.recname
self.logfile = logfile
self.dirname = os.path.dirname(os.path.normpath(logfile))
self.logfile = os.path.basename(os.path.normpath(logfile))
# build GUI
d = self.interior()
f = tk.Frame(d)
tk.Label(f, text='Processing: ',
font=self.FONTbold).pack(side='left', anchor='w', padx=9)
self.label = tk.Label(f, text='', font=self.FONT, anchor='w')
self.label.pack(side='left', anchor='w')
f.pack(expand=0, fill='x',side='top', anchor='n',pady=5)
x = tk.Frame(d)
self.pc_var = tk.DoubleVar(value=0.)
self.progress = hf.ProgressBar(x, self.pc_var, w=300)
self.progress.pack(expand=1, fill='x',anchor='n', side='top',padx=9,pady=3)
x.pack(expand=1, fill='x', anchor='n', side='top', pady=5)
status = self.check()
if status == True:
self.STOP = False
# if successful: import the generated logfile
# the log file must be saved with the name of the directory?
# receptor Name?
self.interior().after(100, self.start)
self.activate()
else:
self.STOP = True
self.problematic = [['None', status ]]
self.label.configure(text='DONE')
self.updateButton()
def targetFingerprint(self, fname):
""" return target fingerprint and alias name """
try:
fobj = open(fname, 'r')
self.dprint("file opened [%s]" % fname)
except:
e = sys.exc_info()[1]
self.dprint("error opening file [%s]:%s" % (fname, e))
return (False, e)
fingerp = hf.hashfile(fobj)
alias = os.path.basename(fname)
return (fingerp, alias)
def _checkfiles(self, autocreate=True):
""" check and create necessary raccoon files"""
files = [ self.settings['config_file'], self.settings['history'],
self.settings['server_dbase'] , self.settings['target_db'] ]
for f in files:
if not os.path.isfile(f):
if autocreate:
t = hf.touch(f)
if not t:
#print "error in file [%s] : [%s]" % (f,t)
return False
return True
def upload(self, dirname=None, destpath=None, autoregister=False, overwrite=False, bg=False):
"""upload the library to the remote server $dest path"""
if dirname == None:
dirname = hf.validFilename(self.name())
if dirname == '':
dirname = 'libdir'
self.dprint("warning: lib dirname empty, providing substutute [%s]" % libdir)
if destpath == None:
destpath == self.server.getLibraryPath()
if (self.server == None) or (self.server == 'localhost'):
self._localcopy( dirname, destpath, autoregister, overwrite, bg)
else:
self._remotecopy( dirname, destpath, autoregister, overwrite, bg)
self.updatestatus()
def searchLigands(self, dirname, cb=None): #, pattern= '*_out.pdbqt'):
""" scan dir for vina results"""
pattern_list = { 'autodock' : '*.dlg',
'vina' : '*_out.pdbqt',
}
pattern = pattern_list[ self.app.getDockingEngine() ]
dockfiles = hf.pathToList(dirname, recursive = True, pattern = pattern)
#self.dprint("found %s dockfiles" % dockfiles)
result = {}
for d in dockfiles:
name = os.path.basename(d).split("_out.pdbqt")[0]
result[name] = d
return result
def readServerInfo(self, fname=None):
"""read the server db and handle password saving"""
if fname==None:
fname = self.getServerInfoFile()
data = hf.readjson(fname, compression=True)
if data:
srv_db = data
for _type in srv_db.keys():
if _type =='ssh':
for name in srv_db[_type].keys():
srv = srv_db[_type][name]
if not srv['password'] == None:
srv['_save_passwd_'] = None
self.settings['servers'] = srv_db
def upload(self, dirname=None, destpath=None, autoregister=False, overwrite=False, bg=False):
"""upload the library to the remote server $dest path"""
if dirname == None:
dirname = hf.validFilename(self.name())
if dirname == "":
dirname = "libdir"
self.dprint("warning: lib dirname empty, providing substutute [%s]" % libdir)
if destpath == None:
destpath == self.server.getLibraryPath()
if (self.server == None) or (self.server == "localhost"):
self._localcopy(dirname, destpath, autoregister, overwrite, bg)
else:
self._remotecopy(dirname, destpath, autoregister, overwrite, bg)
self.updatestatus()
def updateDownloadBigFile(self):
""" update download status of big files transfers"""
if self.checkPending() == False:
return 100.00
#self._counter
try:
self.dprint("checking local size of [%s]" % self._localfile)
curr_size = os.stat(self._localfile).st_size
self.dprint(' found %s' % curr_size)
except:
self.dprint('file checking error [%s]' % sys.exc_info()[1] )
curr_size = 0
pc = hf.percent(curr_size, self._total)
self.dprint("current size [%d/%d] : %2.3f%%" % (curr_size, self._total, pc) )
return pc
def _additems(self, items, propfunc=None, dup="rename", stopcheck=None, showpercent=None, GUI=None):
"""
add [items] to the current item list
propfunc functio to be used to calculate properties
dup = 'overwrite' duplicates not allowed (last kept)
dup = 'rename' duplicates renamed
dup = 'skip' duplicates not allowed (first kept)
"""
self.dprint("adding [%d] items" % len(items), new=1)
problematic = []
c = 1
# XXX FIXME profile here!
for i in items:
# source = i
checkreport = self._checkitem(i, dup=dup)
if checkreport:
name, destname = checkreport
# if self._checkitem(i):
# manage ligand properties
if propfunc:
report, prop = propfunc(i)
else:
report, prop = True, {}
if report:
self.items[name] = {
"source": i,
"fullpath": destname,
# destname can be updated with the suffix dir for splitting
"properties": prop,
}
else:
self.dprint("problematic item [%s] : [%s]" % (i, prop))
problematic.append([i, prop])
c += 1
if not stopcheck == None:
if stopcheck():
self.dprint("stopcheck() requested stopping...")
break
if not GUI == None:
GUI.update()
if not showpercent == None:
pc = hf.percent(c, len(items))
showpercent(pc)
self.updatestatus()
return problematic
def _additems(self, items, propfunc=None, dup = 'rename', stopcheck=None, showpercent=None, GUI=None):
"""
add [items] to the current item list
propfunc functio to be used to calculate properties
dup = 'overwrite' duplicates not allowed (last kept)
dup = 'rename' duplicates renamed
dup = 'skip' duplicates not allowed (first kept)
"""
self.dprint("adding [%d] items"% len(items), new=1)
problematic = []
c = 1
# XXX FIXME profile here!
for i in items:
#source = i
checkreport = self._checkitem(i, dup = dup)
if checkreport:
name, destname = checkreport
#if self._checkitem(i):
# manage ligand properties
if propfunc:
report, prop = propfunc(i)
else:
report, prop = True, {}
if report:
self.items[name] = { 'source' : i,
'fullpath' : destname,
# destname can be updated with the suffix dir for splitting
'properties': prop,
}
else:
self.dprint("problematic item [%s] : [%s]" % (i, prop))
problematic.append([ i, prop ])
c+=1
if not stopcheck==None:
if stopcheck():
self.dprint("stopcheck() requested stopping...")
break
if not GUI == None:
GUI.update()
if not showpercent == None:
pc = hf.percent(c, len(items) )
showpercent(pc)
self.updatestatus()
return problematic
def opendir(self, event=None, recursive=False):
""" scan dir(s) optionally recursively"""
title = "Select a directory to scan"
if recursive:
title += " recursively"
# add a GUI feedback:
# - GUIvar
# - progress bar
# progress = tk.StringVar('Processing
#
dirname = tfd.askdirectory(parent=self.frame, title=title, mustexist=True)
if dirname:
files = hf.pathToList(dirname, pattern="*.pdbqt", recursive=recursive) # XXX progress var here...
# files.append(hf.pathToList(dirname, pattern = '*.PDBQT', recursive = recursive)) # XXX ?
# hf.writeList('FOUND.log', files, addNewLine=1)
if len(files):
self._file_checker(files)
def opendir(self, event=None, recursive=False):
""" scan dir(s) optionally recursively"""
title = 'Select a directory to scan'
if recursive:
title += ' recursively'
# add a GUI feedback:
# - GUIvar
# - progress bar
# progress = tk.StringVar('Processing
#
dirname = tfd.askdirectory(parent=self.frame,
title=title,
mustexist=True)
if dirname:
files = hf.pathToList(
dirname, pattern='*.pdbqt',
recursive=recursive) # XXX progress var here...
#files.append(hf.pathToList(dirname, pattern = '*.PDBQT', recursive = recursive)) # XXX ?
#hf.writeList('FOUND.log', files, addNewLine=1)
if len(files):
self._file_checker(files)
def _remotecopy(self, dirname, destpath, autoregister=False, overwrite=False, bg=True):
""" perform the copy on remote path"""
# generating fullpath destination dir
self.path = destpath + '/' + dirname
if self.server.ssh.exists(self.path):
self.dprint('remote library dirname[%s] exist in the path[%s] => [%s]...' % (dirname, destpath, self.path))
if not overwrite:
self.dprint('overwrite not allowed, returning')
return
else:
self.server.ssh.remove([self.path])
# update the ligand destination with split_path
step = self.options['split']
items = sorted(self.items.keys())
total = len(items)
if (not step == None) and (step <= total):
count = 0
for i in items:
self.dprint("updating splitted name [%s] =>" % self.items[i]['fullpath']),
self.items[i]['fullpath'] = '/'.join([hf.splitdir(count, total, step),
self.items[i]['fullpath']])
self.dprint("[%s]" % self.items[i]['fullpath'])
count+=1
transfer_list = []
for i in items:
dest = '/'.join([dirname, self.items[i]['fullpath'] ])
transfer_list.append( [self.items[i]['source'], dest])
# transfer files
mule = self.server.transfer
self.dprint("starting the transfer with the mule[%s]" % mule)
mule.upload(files = transfer_list, remotedestpath=destpath, bg=bg)
self.dprint("mule started... ongoing...")
if autoregister:
if not bg:
libindex = self.path + '/' + 'library.db'
self.saveIndex(libindex)
self.registerLibrary(overwrite)
else:
print "AUTOREGISTER DISABLED! BACKGROUND UPLOAD (TO FIX)"
def _remotecopy(self, dirname, destpath, autoregister=False, overwrite=False, bg=True):
""" perform the copy on remote path"""
# generating fullpath destination dir
self.path = destpath + "/" + dirname
if self.server.ssh.exists(self.path):
self.dprint("remote library dirname[%s] exist in the path[%s] => [%s]..." % (dirname, destpath, self.path))
if not overwrite:
self.dprint("overwrite not allowed, returning")
return
else:
self.server.ssh.remove([self.path])
# update the ligand destination with split_path
step = self.options["split"]
items = sorted(self.items.keys())
total = len(items)
if (not step == None) and (step <= total):
count = 0
for i in items:
self.dprint("updating splitted name [%s] =>" % self.items[i]["fullpath"]),
self.items[i]["fullpath"] = "/".join([hf.splitdir(count, total, step), self.items[i]["fullpath"]])
self.dprint("[%s]" % self.items[i]["fullpath"])
count += 1
transfer_list = []
for i in items:
dest = "/".join([dirname, self.items[i]["fullpath"]])
transfer_list.append([self.items[i]["source"], dest])
# transfer files
mule = self.server.transfer
self.dprint("starting the transfer with the mule[%s]" % mule)
mule.upload(files=transfer_list, remotedestpath=destpath, bg=bg)
self.dprint("mule started... ongoing...")
if autoregister:
if not bg:
libindex = self.path + "/" + "library.db"
self.saveIndex(libindex)
self.registerLibrary(overwrite)
else:
print "AUTOREGISTER DISABLED! BACKGROUND UPLOAD (TO FIX)"
def buildGUI(self):
""" set the widgets shown"""
self.win = Pmw.Dialog(self.parent,
title=self.title,
buttons=('Stop', ),
command=self.stop)
button = self.win.component('buttonbox').button(0)
button.configure(font=self.FONT,
default='disabled',
cursor='arrow',
**self.BORDER)
# TITLE
# MESSAGE
# Status : [ Running, stopped, error
# Error: xxxxxxxxxxxxx
# Elapsed:
# Progress/process
i = tk.Frame(self.win.interior(),
relief='flat') #, bd=2) #, bg='white')
# message
f = tk.Frame(i) # , bg='white')
if self.image:
tk.Label(f, image=self.image).pack(anchor='w',
side='left',
expand=0,
padx=6,
pady=6)
tk.Label(f, text=self.message, font=self.FONT).pack(anchor='w',
side='left',
expand=0,
fill='x')
f.pack(side='top', anchor='w', expand=0, fill='x', pady=5, padx=3)
# status
i.pack(expand=0, fill='both')
i = tk.Frame(self.win.interior(), relief='sunken', bd=2, bg='white')
# SPACER
f = tk.Frame(i, bg='white')
tk.Label(f,
text='Status : ',
width=20,
anchor='e',
bg='white',
font=self.FONTbold).pack(anchor='w',
side='left',
expand=0,
fill='x')
self.status_label = tk.Label(f,
width=30,
text='ready',
anchor='w',
bg='white',
font=self.FONT)
self.status_label.pack(anchor='w', side='left', expand=0, fill='x')
f.pack(side='top', anchor='w', expand=0, fill='x', padx=3)
# elapsed time
if self.showtime:
f = tk.Frame(i, bg='white')
tk.Label(f,
text='Elapsed time : ',
width=20,
anchor='e',
bg='white',
font=self.FONTbold).pack(anchor='w',
side='left',
expand=0,
fill='x')
self.time_label = tk.Label(f,
width=30,
text='00 : 00 : 00',
anchor='w',
bg='white',
font=self.FONT)
self.time_label.pack(anchor='w', side='left', expand=0, fill='x')
f.pack(side='top', anchor='w', expand=0, fill='x', padx=3)
# error
f = tk.Frame(i)
self.error_title = tk.Label(f,
text=' ',
fg='red',
bg='white',
width=20,
anchor='e',
font=self.FONTbold)
self.error_title.pack(anchor='w', side='left', expand=0, fill='x')
self.error_label = tk.Label(f,
width=30,
text=' ',
font=self.FONT,
anchor='w',
bg='white')
self.error_label.pack(anchor='w', side='top', expand=0, fill='x')
f.pack(side='top', anchor='w', expand=0, fill='x', padx=3)
if self.progresstype == 'percent':
#create percent bar
f = tk.Frame(i, bg='white')
self.progressBar = hf.ProgressBarThreadsafe(i, w=300, h=20)
self.progressBar.pack(anchor='n',
side='top',
expand=0,
fill='none')
f.pack(side='top',
anchor='n',
expand=0,
fill='none',
padx=5,
pady=8)
elif self.progresstype == 'count':
# create counter label
# FIXME
pass
elif self.progresstype == None:
# create the default "is alive" feedback
self.dotsLabel = tk.Label(i, bg='white', text=self.rolling[0])
self.dotsLabel.pack()
pass
i.pack(expand=0, fill='both')
def writeConfig(self, fname=None):
""" write the config file """
# XXX FIXME NOT WORKING
if fname == None:
fname = self.getConfigFile()
self.settings = hf.writejson(fname, self.config)
def __init__(self, resource='local', dockengine='vina', eventmanager=None,
racdir = None, debug=False):
DebugTools.DebugObj.__init__(self, debug)
if eventmanager == None:
eventmanager = RaccoonEvents.RaccoonEventManager()
self.eventManager = eventmanager
self.dockengine = dockengine
self.engine = RaccoonEngine.RaccoonEngine()
self.engine.box_center = [ 0., 0., 0.]
# results business
self.results = {}
self.resPropertiesReset()
#self.eventManager.registerListener( RaccoonEvents.ResultsImportedDeleted, self.resPropertiesReset)
self.eventManager.registerListener( RaccoonEvents.ResultsImportedDeleted, self.updateResultsProperties)
self.eventManager.registerListener( RaccoonEvents.SyncJobHistory, self.syncServerHistory)
self.filterEngine = RaccoonFilterEngine.FilterEngine(self, debug)
# vs data source
self.ligand_source = [] # this will contain objects to be called
# to generate ligand filenames:
# { 'lib': RaccoonLibrary, 'filters' : {} }
self.knownTargets = {} # this is the database of all known and used targets stored with
# unique MD5sum id
# server object to wich we're connected
# this should be one of RaccoonRemoteServer ('ssh'), RaccoonOpalServer ('opal') or
# RaccoonLocalServer ('local') objects
#damjan begin
self.guse = None
#damjan end
self.server = None
self.history = {}
self.resource = resource # local, ssh, opal
self.dockingservice = None
self._system_info = hf.getOsInfo()
self.ready = False
self.settings = { 'engine' : dockengine,
'options': { 'save_username': True,
'save_password': False,
},
# from config files
'servers': { 'ssh' : {}, # 'garibaldi' : { ''address': 'garibaldi.scripps.edu',
# 'username': '******',
# 'password': None,
# 'pkey' : None, # file
# '_save_passwd_' : False,
# }
'opal': [],
},
'viewer': { }, # 3d viewer settings
}
self.resultsProcessor = vsg.RaccoonVsResultsGenerator(self, self.debug)
self.setDockEngine(dockengine)
#self.notebook.component('Config-tab').bind('<1>', cb)
# less important stuff
self._lastdir = None
# /less important stuff
if racdir == None:
racdir = os.getenv("RACDIR")
if racdir == None:
racdir = os.path.expanduser('~') + os.sep + 'raccoon'
print "[ RAC DIR SET TO [%s] ]" % racdir
self.initRac(racdir)
def callback(self, name, count):
""" callback to be passed to the processor"""
self.label.configure(text=name)
tot = len(self.ligands.keys())
self.pc_var.set( hf.percent(count, tot) )
self.progress.update()
def run_upload(self, name, dirname, remotepath, comment=None):
""" """
# self.run_upload(name = libname, dirname = dirname, remotepath = remotepath)
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 close(event=None):
if event == None:
#print "probably clicking on the corner..."
return
win.destroy()
def stop(event=None):
t = 'Stop transfer'
m = 'The transfer is incomplete: do you want to stop it?'
if not tmb.askyesno(parent = win.interior(), title=t, message=m):
return
server.transfer.stop()
self._stopclosebutton.configure(text= 'Close', command=close)
forceclose = CallbackFunction(close, True)
## print ">> adding ligands to lib object"
# threaded files scanning...
server = self.app.server
libobj = RaccoonLibraries.LigandLibrary( server, name = name )
libobj.options['split'] = 1000
func = libobj.addLigands
func_kwargs = {'ligands' : self._ligand_list }
m = ('Extracting ligand properties...' )
self.app.setBusy()
progressWin = rb.ProgressDialogWindowTk(parent = self.parent,
function = func, func_kwargs = func_kwargs,
title ='Ligand library', message = m,
operation = 'ligand properties extraction',
image = self._ICON_open, autoclose=True,
progresstype='percent')
progressWin.start()
problematic = progressWin.getResults()
if problematic == None: problematic = [] # normalize data structure
self.app.setReady()
#if response == None:
#libobj.addLigands(self._ligand_list) # XXX TODO FIXME
win = Pmw.MegaToplevel(master = self.win.interior(), title = 'Library manager')
win.userdeletefunc(close)
win.component('hull').configure(width=600, height=400)
fullpath = remotepath + '/' + dirname
self._statuslab1 = tk.Label(win.interior(), text = 'Transferring files...', font=self.FONTbold)
self._statuslab1.pack(expand=0, fill='x', anchor='w', side='top')
self._statuslab2 = tk.Label(win.interior(), text = 'Destination: %s' % fullpath, font=self.FONT)
self._statuslab2.pack(expand=0, fill='x', anchor='w', side='top')
pc_var = tk.DoubleVar(value=0.)
self.bar = hf.ProgressBar(win.interior(), pc_var)
self.bar.pack(expand=0, fill='none', anchor='n', side='top',padx=5, pady=3)
tk.Frame(win.interior(),height=2,width=1,bd=1,relief='sunken').pack(expand=0, fill='x', anchor='w', side='top')
self._stopclosebutton = tk.Button(win.interior(), text='STOP', font=self.FONT)
self._stopclosebutton.pack(expand=0, fill='none', anchor='s', side='bottom')
win.interior().after(50, _go)
win.activate() # geometry='centerscreenalways' )
def ask_upload(self):
"""upload to remote location"""
if len(self._ligand_list) == 0:
return
def close(event=None):
if event == 'Start':
server = self.app.server
# check if lib name is in use
libname = self._lname.getvalue()
lib = server.getLibrary(libname)
if lib: # and lib.info['type'] == self.info['type']:
t = 'Name already in use'
m = ('There is already a %s library with the same name.\n\n'
'Choose a different name and try again.') % self._type
i = 'warning'
tmb.showinfo(parent=win.interior(), title=t, message=m, icon=i)
return
# check directory name
dirname = self._dname.getvalue()
remotepath = self._remotepath.getvalue()
fullpath = remotepath + '/' + dirname
if server.ssh.exists(fullpath):
t = 'Directory exist'
m = ('There is already a directory with the same in the'
'remote path. Select a different dirname '
'and try again.')
i = 'warning'
tmb.showinfo(parent=win.interior(), title=t, message=m, icon=i)
self.app.setReady()
return
# comments, if any
comment = self._comment.get('1.0', 'end').strip()
win.destroy()
self.app.setBusy()
self.run_upload(name = libname,
dirname = dirname,
remotepath = remotepath,
comment = comment)
# once files habe been uploaded, clean up the engine from used files
self.app.engine.removeLigands()
self.app.setReady()
else:
win.destroy()
self.app.setReady()
def makedirname(event=None):
""" ButtonRelease """
chars = hf._allowedfilenamechars()
text = self._lname.getvalue()
if not len(text):
self._dname.setvalue('')
valid = [ x for x in text if x in hf._allowedfilenamechars()]
valid = "".join(valid).lower()
self._dname.setvalue(valid)
def setdefaultremote(event=None):
self._remotepath.setvalue( self.app.server.getLibraryPath() )
#settings = { 'split' : 1000,
# }
win = Pmw.Dialog(self.win.interior(), title = 'Upload library', buttons = ('Start','Cancel'),
command=close)
w = win.interior()
bbox = win.component('buttonbox')
for i in range(bbox.numbuttons()):
bbox.button(i).configure(font=self.FONT, default='disabled', **self.BORDER)
w.pack_configure(ipadx=10, ipady=10)
tk.Label(w, text=' ', image=self._ICON_upload, anchor='n', font=self.FONTbold).grid(row=0,
column=0, sticky='we', columnspan = 3)
tk.Label(w, text='Library name', anchor='e', font=self.FONT).grid(row=1, column=1, sticky='e')
self._lname = Pmw.EntryField( w, validate = {'min':1,'minstrict':0}, entry_width=30,
entry_font=self.FONT)
self._lname.component('entry').bind('<KeyRelease>', makedirname)
self._lname.grid(row=1, column=2,sticky='w',columnspan=1)
tk.Label(w, text='Remote path', anchor='e', font=self.FONT).grid(row=3, column=1, sticky='e')
self._remotepath = Pmw.EntryField( w, validate = {'min':1,'minstrict':0},
entry_width=30, entry_font=self.FONT)
self._remotepath.grid(row=3, column=2,sticky='w',columnspan=1)
tk.Button(w, text='D', command=setdefaultremote,image=self._ICON_default,
**self.BORDER).grid(row=3, column=3, sticky='w')
# FIXME probably useless, this should be hidden to the user!
#tk.Label(w, text='Directory name', anchor='e').grid(row=5, column=1, sticky='e',
# entry_font=self.FONT)
self._dname = Pmw.EntryField( w, validate = hf.validateFname, entry_width=30)
#self._dname.grid(row=5,column=2, sticky='w', columnspan=1)
tk.Label(w, text='Comments', anchor='e', font=self.FONT).grid(row=6, column=1, sticky='e')
self._comment = hf.TextCopyPaste( w, bg='white', height=10, width=30, font=self.FONT)
self._comment.grid(row=6,column=2, sticky='w')
setdefaultremote()
win.activate() # geometry='centerscreenalways' )
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')
