def startKarrigell(self,port,karrigell_start,karrigell_init):
""" start the webserver Karrigell on the port specify in input
return False for failure , True for sucess
"""
if hasattr(self,'cmd'):
del(self.cmd)
print "Trying to start Karrigell on port %d"%port
self.cmd = SysCmdInThread("python -u %s -P %d %s "%(karrigell_start,
port,karrigell_init),
hasGui=False)
self.cmd.start()
status = self.checkKarrigellStatus()
if not status:
# print try to start on another port
port = port + 1
if port > 8180:
self.warningMsg("Could not start Karrigell server, no port available")
return False,0
else:
status,port =self.startKarrigell(port,karrigell_start,karrigell_init)
return status,port
def guiCallback(self, event=None):
fileList = []
fld_list = glob.glob('*.maps.fld')
if not fld_list:
tkMessageBox.showinfo(
"AutoLigand Info",
"AutoLigand requires input AutoGrid maps. \nPlease click OK to select directory containing grid maps."
)
folder = tkFileDialog.askdirectory(title="Select A Folder")
if folder:
os.chdir(folder)
fld_list = glob.glob('*.maps.fld')
else:
return
for fld in fld_list:
fileList.append(fld.split('.')[0])
entryfield_value = ""
if fileList:
fileList.sort()
entryfield_value = fileList[0]
ifd = InputFormDescr(title="Run AutoLigand")
ifd.append({
'name': "fileName",
'widgetType': Pmw.Group,
'container': {
'fileName': 'w.interior()'
},
'wcfg': {
'tag_text': "Base Name for Receptor Map Files"
},
})
ifd.append({
'widgetType': Pmw.ComboBox,
'name': 'FileBaseName',
'parent': 'fileName',
'tooltip':
'FileBaseName = Just the name part from map files (i.e., FileBaseName.C.map)',
'wcfg': {
'dropdown': 1,
'scrolledlist_items': fileList,
'entryfield_value': entryfield_value,
'selectioncommand': self.selectGrid,
'labelpos': 'w',
}
})
ifd.append({
'name': "nGroup",
'widgetType': Pmw.Group,
'container': {
'nGroup': 'w.interior()'
},
'tooltip':
'Number of heavy atom for ligand or number of fill points to use.',
'wcfg': {
'tag_text': "Number of "
},
})
ifd.append({
'widgetType': Pmw.RadioSelect,
'parent': 'nGroup',
'name': 'type',
'defaultValue': 'Points',
'listtext': ["Heavy Atoms", "Points"],
})
ifd.append({
'widgetType': Pmw.EntryField,
'parent': 'nGroup',
'name': 'number',
'wcfg': {
'labelpos': 'w',
'value': '100',
'validate': {
'validator': 'integer'
}
}
})
ifd.append({
'widgetType':
Pmw.NoteBook,
'name':
'autoligandNotebook',
'container': {
'Single Fill': "w.page('Single Fill')",
'Connected Fill': "w.page('Connected Fill')",
'Scan': "w.page('Scan')"
},
'componentcfg': [
{
'name': 'Single Fill',
'cfg': {}
},
{
'name': 'Connected Fill',
'cfg': {}
},
{
'name': 'Scan',
'cfg': {}
},
# {'raisecommand':self.pageChanged}
],
'wcfg': {
'raisecommand': self.pageChanged
},
'gridcfg': {
'sticky': 'we'
},
})
#Single Fill
ifd.append({
'name': "StartLoc",
'parent': 'Single Fill',
'widgetType': Pmw.Group,
'container': {
'StartLoc': 'w.interior()'
},
'wcfg': {
'tag_text': "Start Location"
},
})
ifd.append({
'widgetType': ExtendedSliderWidget,
'name': 'gridPointsX',
'parent': 'StartLoc',
'wcfg': {
'label': 'X: ',
'width': 190,
'immediate': 1,
'command': self.changeStartCross,
'entrypackcfg': {
'side': 'left'
},
},
})
ifd.append({
'widgetType': ExtendedSliderWidget,
'name': 'gridPointsY',
'parent': 'StartLoc',
'wcfg': {
'label': 'Y: ',
'width': 190,
'immediate': 1,
'command': self.changeStartCross,
'entrypackcfg': {
'side': 'left'
},
},
})
ifd.append({
'widgetType': ExtendedSliderWidget,
'name': 'gridPointsZ',
'parent': 'StartLoc',
'wcfg': {
'label': 'Z: ',
'width': 190,
'immediate': 1,
'command': self.changeStartCross,
'entrypackcfg': {
'side': 'left'
},
},
})
ifd.append({
'name': "output",
'widgetType': Pmw.Group,
'parent': 'Single Fill',
'container': {
'output': 'w.interior()'
},
'wcfg': {
'tag_text': "Output Options"
},
})
ifd.append({
'name': 'pdbFile',
'tooltip':
"""Creates PDB_fill_#Nout1.pdb file where #N is the number of fill points.""",
'parent': 'output',
'widgetType': Tkinter.Checkbutton,
'defaultValue': 1,
'wcfg': {
'text': 'Create PDB of the Final Fill',
'state': 'disabled',
},
'gridcfg': {
'sticky': 'w'
}
})
ifd.append({
'name': 'showProgress',
'parent': 'output',
'tooltip':
"""Save intermediate results in a file and open flood player when AutoLigand finishes.""",
'widgetType': Tkinter.Checkbutton,
'defaultValue': 0,
'wcfg': {
'text': 'Save Intermediate Results for Movie',
'variable': Tkinter.IntVar(),
},
'gridcfg': {
'sticky': 'w'
}
})
#Connected Fill
ifd.append({
'widgetType': Tkinter.Label,
'name': 'label',
'parent': 'Connected Fill',
'wcfg': {
'text': 'Select End Location for Connected Fill'
}
})
ifd.append({
'name': "EndLoc",
'parent': 'Connected Fill',
'widgetType': Pmw.Group,
'container': {
'EndLoc': 'w.interior()'
},
'wcfg': {
'tag_text': "End Location"
},
})
ifd.append({
'widgetType': ExtendedSliderWidget,
'name': 'gridPointsXEnd',
'parent': 'EndLoc',
'wcfg': {
'label': 'X: ',
'width': 190,
'immediate': 1,
'command': self.changeEndCross,
'entrypackcfg': {
'side': 'left'
},
},
})
ifd.append({
'widgetType': ExtendedSliderWidget,
'name': 'gridPointsYEnd',
'parent': 'EndLoc',
'wcfg': {
'label': 'Y: ',
'width': 190,
'immediate': 1,
'command': self.changeEndCross,
'entrypackcfg': {
'side': 'left'
},
},
})
ifd.append({
'widgetType': ExtendedSliderWidget,
'name': 'gridPointsZEnd',
'parent': 'EndLoc',
'wcfg': {
'label': 'Z: ',
'width': 190,
'immediate': 1,
'command': self.changeEndCross,
'entrypackcfg': {
'side': 'left'
},
},
})
#Connected Fill
# ifd.append({'widgetType':Tkinter.Label,
# 'name':'label',
# 'parent':'Scan',
# 'wcfg':{'text':"""Results from the Scan mode will
#be available under\n"""+os.getcwd()}
# })
ifd.append({
'widgetType': Pmw.EntryField,
'parent': 'Scan',
'name': 'nFills',
'wcfg': {
'label_text': "Number of Fills:",
'labelpos': 'w',
'value': '10',
'validate': {
'validator': 'integer'
}
}
})
def initselect(arg):
self.selectGrid(entryfield_value)
self.ifd = ifd
self.save = self.vf.ICmdCaller.commands.value["Shift_L"]
self.vf.setICOM(self, modifier="Shift_L", topCommand=0)
self.vf.setIcomLevel(Atom)
self.endCross.Set(visible=0)
val = self.vf.getUserInput(ifd,
modal=0,
blocking=1,
initFunc=initselect)
if self.save:
self.vf.setICOM(self.save, modifier="Shift_L", topCommand=0)
self.save = None
# import pdb;pdb.set_trace()
if val:
if not val['FileBaseName'][0]:
msg = "AutoGrid files are missing.\n"
msg += "Please generate grid maps. AutoLigand requires input AutoGrid maps."
tkMessageBox.showerror("Error!", msg)
return
selection = self.ifd.entryByName['autoligandNotebook'][
'widget'].getcurselection()
cmdString = [sys.executable, AutoLigandPath]
cmdString.append('-r')
cmdString.append(val['FileBaseName'][0])
self.fileBaseName = val['FileBaseName'][0]
if val['type'] == 'Points':
cmdString.append('-p')
cmdString.append(str(val['number']))
else:
cmdString.append('-a')
cmdString.append(str(val['number']))
val['number'] = 6 * int(val['number'])
if selection in ['Single Fill', 'Connected Fill']:
cmdString.append('-x')
cmdString.append(str(val['gridPointsX']))
cmdString.append('-y')
cmdString.append(str(val['gridPointsY']))
cmdString.append('-z')
cmdString.append(str(val['gridPointsZ']))
if selection == 'Connected Fill':
cmdString.append('-i')
cmdString.append(str(val['gridPointsXEnd']))
cmdString.append('-j')
cmdString.append(str(val['gridPointsYEnd']))
cmdString.append('-k')
cmdString.append(str(val['gridPointsZEnd']))
if os.name == 'nt': #sys.platform == "win32":
self.cmdTxt = subprocess.list2cmdline(cmdString)
else:
self.cmdTxt = ' '.join(cmdString)
if val['showProgress']:
self.cmdTxt += " -m"
self.showPlayer = True
else:
self.showPlayer = False
self.cmd = SysCmdInThread(self.cmdTxt, shell=True)
self.cmd.start()
self.checkResults()
self.N_of_pts = val['number']
elif selection == "Scan":
cmdString.append('-f')
cmdString.append(str(val['nFills']))
if os.name == 'nt': #sys.platform == "win32":
self.cmdTxt = subprocess.list2cmdline(cmdString)
else:
self.cmdTxt = ' '.join(cmdString)
self.cmdTxt += ' &' #run in a background
subprocess.Popen(self.cmdTxt, shell=True)
tkMessageBox.showinfo("Success!",
"""AutoLigand launched successfully.""")
else:
self.hideGeoms()
