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({'widgetType':Pmw.ComboBox,
'name':'FileBaseName',
'tooltip':'FileBaseName = just the name part from map files (FileBaseName.C.map)',
'wcfg':{'label_text':"File Base Name: ",
'dropdown':1,
'scrolledlist_items':fileList,
'entryfield_value':entryfield_value,
'selectioncommand':self.selectGrid,
'labelpos':'w',}
})
ifd.append({'widgetType':Pmw.EntryField,
'name':'#_of_pts',
'tooltip':'#_of_pts = number of fill points you want to use (int)',
'wcfg':{'label_text':"Number of Points:",
'labelpos':'w',
'value':'100',
'validate':{'validator':'integer'}
}
})
ifd.append({'name':"StartLoc",
'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.changeCross,
'entrypackcfg':{'side':'left'},},
})
ifd.append({'widgetType':ExtendedSliderWidget,
'name':'gridPointsY',
'parent':'StartLoc',
'wcfg':{'label':'Y: ',
'width':190,
'immediate':1,
'command':self.changeCross,
'entrypackcfg':{'side':'left'},},
})
ifd.append({'widgetType':ExtendedSliderWidget,
'name':'gridPointsZ',
'parent':'StartLoc',
'wcfg':{'label':'Z: ',
'width':190,
'immediate':1,
'command':self.changeCross,
'entrypackcfg':{'side':'left'},},
})
ifd.append({'name':"output",
'widgetType':Pmw.Group,
'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'}
})
def initselect(arg):
self.selectGrid(entryfield_value)
self.ifd = ifd
self.save = self.vf.ICmdCaller.commands.value[None]
self.vf.setICOM(self, topCommand=0)
self.vf.setIcomLevel( Atom )
val = self.vf.getUserInput(ifd,modal=0, blocking=1,
initFunc=initselect)
if self.save:
self.vf.setICOM(self.save)
self.save = None
if val:
if not val['FileBaseName'][0]:
msg = "AutoGrid files are missing.\n"
msg += "Please generate grid maps and/or make sure \nthat they are in the current working directory."
tkMessageBox.showerror("Error!", msg)
return
cmdString = [sys.executable, AutoLigandPath]
cmdString.append(val['FileBaseName'][0])
self.fileBaseName = val['FileBaseName'][0]
cmdString.append(str(val['#_of_pts']))
cmdString.append(str(val['gridPointsX']))
cmdString.append(str(val['gridPointsY']))
cmdString.append(str(val['gridPointsZ']))
if sys.platform == "win32":
self.cmdTxt = subprocess.list2cmdline(cmdString)
else:
self.cmdTxt = ' '.join(cmdString)
if val['showProgress']:
self.cmdTxt += " -out-progress"
self.showPlayer = True
else:
self.showPlayer = False
self.cmd = SysCmdInThread(self.cmdTxt, shell=True)
self.cmd.start()
self.checkResults()
self.N_of_pts = val['#_of_pts']
else:
self.hideGeoms()
class AutoLigandCommand(MVCommand, MVAtomICOM):
"GUI for AutoLigand: extends MVCommand, overwrites guiCallback"
def __init__(self, func=None):
MVCommand.__init__(self, func)
MVAtomICOM.__init__(self)
self.save = None
self.showPlayer = False
self.floodFile = None
def onAddCmdToViewer(self):
from DejaVu.Points import CrossSet
self.cross = CrossSet('Cross', materials=((1.,1.,0),),
inheritMaterial=0, protected=True,
offset=1.0,lineWidth=5, visible=0, pickable=0)
from DejaVu.IndexedPolygons import IndexedPolygons
from DejaVu.Box import Box
from DejaVu.Spheres import Spheres
from DejaVu import viewerConst
from DejaVu.bitPatterns import patternList
from opengltk.OpenGL import GL
face=((0,3,2,1),(3,7,6,2),(7,4,5,6),(0,1,5,4),(1,2,6,5),(0,4,7,3))
coords=((1,1,-1),(-1,1,-1),(-1,-1,-1),(1,-1,-1),(1,1,1),(-1,1,1),(-1,-1,1),(1,-1,1))
#new style RGB->
materials=((0,0,1),(0,1,0),(0,0,1),(0,1,0),(1,0,0),(1,0,0),)
box=IndexedPolygons('Box', materials=materials, vertices=coords, faces=face,
inheritMaterial=0, visible=0, protected=True)
box.Set(frontPolyMode=GL.GL_LINE)
box.Set(backPolyMode=GL.GL_LINE)
box.Set(culling=GL.GL_NONE)
box.inheritShading=0
box.shading=GL.GL_FLAT
box.Set(matBind=viewerConst.PER_PART)
box.polygonstipple.Set(pattern=patternList[0])
box.Set(stipplePolygons=1)
box.transparent=0
self.box = box
self.spheres = Spheres('Spheres', visible=0, inheritMaterial=0, radii=(0.3,), protected=True)
self.halo = Spheres('Halo', visible=0, inheritMaterial=0, radii=(0.5,), protected=True)
from DejaVu.Geom import Geom
AutoLigand_geoms = Geom("AutoLigand_geoms", shape=(0,0))
self.vf.GUI.VIEWER.AddObject(AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.cross, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.box, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.spheres, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.halo, parent=AutoLigand_geoms)
self.grids = {}
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({'widgetType':Pmw.ComboBox,
'name':'FileBaseName',
'tooltip':'FileBaseName = just the name part from map files (FileBaseName.C.map)',
'wcfg':{'label_text':"File Base Name: ",
'dropdown':1,
'scrolledlist_items':fileList,
'entryfield_value':entryfield_value,
'selectioncommand':self.selectGrid,
'labelpos':'w',}
})
ifd.append({'widgetType':Pmw.EntryField,
'name':'#_of_pts',
'tooltip':'#_of_pts = number of fill points you want to use (int)',
'wcfg':{'label_text':"Number of Points:",
'labelpos':'w',
'value':'100',
'validate':{'validator':'integer'}
}
})
ifd.append({'name':"StartLoc",
'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.changeCross,
'entrypackcfg':{'side':'left'},},
})
ifd.append({'widgetType':ExtendedSliderWidget,
'name':'gridPointsY',
'parent':'StartLoc',
'wcfg':{'label':'Y: ',
'width':190,
'immediate':1,
'command':self.changeCross,
'entrypackcfg':{'side':'left'},},
})
ifd.append({'widgetType':ExtendedSliderWidget,
'name':'gridPointsZ',
'parent':'StartLoc',
'wcfg':{'label':'Z: ',
'width':190,
'immediate':1,
'command':self.changeCross,
'entrypackcfg':{'side':'left'},},
})
ifd.append({'name':"output",
'widgetType':Pmw.Group,
'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'}
})
def initselect(arg):
self.selectGrid(entryfield_value)
self.ifd = ifd
self.save = self.vf.ICmdCaller.commands.value[None]
self.vf.setICOM(self, topCommand=0)
self.vf.setIcomLevel( Atom )
val = self.vf.getUserInput(ifd,modal=0, blocking=1,
initFunc=initselect)
if self.save:
self.vf.setICOM(self.save)
self.save = None
if val:
if not val['FileBaseName'][0]:
msg = "AutoGrid files are missing.\n"
msg += "Please generate grid maps and/or make sure \nthat they are in the current working directory."
tkMessageBox.showerror("Error!", msg)
return
cmdString = [sys.executable, AutoLigandPath]
cmdString.append(val['FileBaseName'][0])
self.fileBaseName = val['FileBaseName'][0]
cmdString.append(str(val['#_of_pts']))
cmdString.append(str(val['gridPointsX']))
cmdString.append(str(val['gridPointsY']))
cmdString.append(str(val['gridPointsZ']))
if sys.platform == "win32":
self.cmdTxt = subprocess.list2cmdline(cmdString)
else:
self.cmdTxt = ' '.join(cmdString)
if val['showProgress']:
self.cmdTxt += " -out-progress"
self.showPlayer = True
else:
self.showPlayer = False
self.cmd = SysCmdInThread(self.cmdTxt, shell=True)
self.cmd.start()
self.checkResults()
self.N_of_pts = val['#_of_pts']
else:
self.hideGeoms()
def selectGrid(self, value):
if not value:
return
lines = open(value+".maps.fld").readlines()
if not lines: return
for line in lines:
if line.startswith("#SPACING"):
spacing = float(line.split()[-1])
if line.startswith("#NELEMENTS"):
tmp = line.split()
dimX = int(tmp[1])
dimY = int(tmp[2])
dimZ = int(tmp[3])
if line.startswith("#CENTER"):
tmp = line.split()
centerX = float(tmp[1])
centerY = float(tmp[2])
centerZ = float(tmp[3])
#this variables are the same used in AutoLigand.py
self.xcent = int(dimX/2)
self.ycent = int(dimY/2)
self.zcent = int(dimZ/2)
self.centerx = centerX
self.centery = centerY
self.centerz = centerZ
self.spacing = spacing
c = [centerX,centerY,centerZ]
xlen = round(spacing*dimX, 4)
ylen = round(spacing*dimY, 4)
zlen = round(spacing*dimZ, 4)
self.minX = c[0]-xlen*0.5
self.maxX = c[0]+xlen*0.5
if self.grids.has_key(value):
centerX = self.grids[value][0]
centerY = self.grids[value][1]
centerZ = self.grids[value][2]
self.ifd.entryByName['gridPointsX']['widget'].configure(minval=self.minX,
maxval=self.maxX,
)
self.minY = c[1]-ylen*0.5
self.maxY = c[1]+ylen*0.5
self.ifd.entryByName['gridPointsY']['widget'].configure(minval=self.minY,
maxval=self.maxY,
)
self.minZ = c[2]-zlen*0.5
self.maxZ = c[2]+zlen*0.5
self.ifd.entryByName['gridPointsZ']['widget'].configure(minval=self.minZ,
maxval=self.maxZ,
)
self.cross.Set(vertices=((centerX,centerY,centerZ),))
self.ifd.entryByName['gridPointsX']['widget'].set(centerX)
self.ifd.entryByName['gridPointsY']['widget'].set(centerY)
self.ifd.entryByName['gridPointsZ']['widget'].set(centerZ)
pts = [ (self.maxX, self.maxY, self.minZ),
(self.minX, self.maxY, self.minZ),
(self.minX, self.minY, self.minZ),
(self.maxX, self.minY, self.minZ),
(self.maxX, self.maxY, self.maxZ),
(self.minX, self.maxY, self.maxZ),
(self.minX, self.minY, self.maxZ),
(self.maxX, self.minY, self.maxZ)
]
self.box.Set(visible=1)
self.cross.Set(visible=1)
self.box.vertexSet.vertices.array[:] = pts
self.box.RedoDisplayList()
self.vf.GUI.VIEWER.Normalize_cb()
self.vf.GUI.VIEWER.Redraw()
def changeCross(self, val):
centerX = self.ifd.entryByName['gridPointsX']['widget'].get()
centerY = self.ifd.entryByName['gridPointsY']['widget'].get()
centerZ = self.ifd.entryByName['gridPointsZ']['widget'].get()
grid = self.ifd.entryByName['FileBaseName']['widget'].get()
if grid:
self.grids[grid] = [centerX,centerY,centerZ]
self.cross.Set(visible=1)
self.cross.Set(vertices=((centerX,centerY,centerZ),))
self.vf.GUI.VIEWER.Redraw()
def checkResults(self):
"""Checks the queue for results until we get one"""
if self.cmd.ok.configure()['state'][-1] == 'normal':
if self.showPlayer:
self.openPklData()
else:
molName = "FILL_"+str(self.N_of_pts)+"out1"
if os.path.exists(molName+".pdb"):
self.vf.readMolecule(molName+".pdb")
self.vf.displaySticksAndBalls(molName, cradius=0.0, sticksBallsLicorice="Sticks and Balls")
self.vf.displayLines(molName, negate=True, displayBO=False)
self.vf.colorByAtomType(molName, ['sticks', 'balls'])
self.vf.GUI.ROOT.after(2050, self.hideGeoms)
return
self.vf.GUI.ROOT.after(100, self.checkResults)
def hideGeoms(self):
self.box.Set(visible=0)
self.cross.Set(visible=0)
self.spheres.Set(visible=0)
self.halo.Set(visible=0)
def __call__(self, atom, **kw):
if not atom:
return 'ERROR'
atoms = self.vf.expandNodes(atom)
if not atoms:
return 'ERROR'
atoms = atoms.findType(Atom)
if not atoms:
return 'ERROR'
apply( self.doitWrapper, (atoms,), kw)
def doit(self, atoms=None):
if len(atoms)==0: return
atom = atoms[0]
if self.minX < atom.coords[0] > self.maxX:
return
if self.minY < atom.coords[1] > self.maxY:
return
if self.minZ < atom.coords[2] > self.maxZ:
return
self.ifd.entryByName['gridPointsX']['widget'].set(atom.coords[0])
self.ifd.entryByName['gridPointsY']['widget'].set(atom.coords[1])
self.ifd.entryByName['gridPointsZ']['widget'].set(atom.coords[2])
self.cross.Set(visible=1)
self.cross.Set(vertices=((atom.coords[0], atom.coords[1], atom.coords[2]),))
self.vf.GUI.VIEWER.Redraw()
def openPklData(self):
self.vf.AutoLigandMovieCommand(self.fileBaseName+'_flood.pkl')
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()
class AutoLigandCommand(MVCommand, MVAtomICOM):
"GUI for AutoLigand: extends MVCommand, overwrites guiCallback"
def __init__(self, func=None):
MVCommand.__init__(self, func)
MVAtomICOM.__init__(self)
self.save = None
self.showPlayer = False
self.floodFile = None
def onAddCmdToViewer(self):
from DejaVu.Points import CrossSet
self.startCross = CrossSet('StartCross',
materials=((1., 1., 0), ),
inheritMaterial=0,
protected=True,
offset=1.0,
lineWidth=5,
visible=0,
pickable=0,
listed=0)
self.endCross = CrossSet('EndCross',
materials=((0, 1, 1), ),
inheritMaterial=0,
protected=True,
offset=1.0,
lineWidth=5,
visible=0,
pickable=0,
listed=0)
from DejaVu.IndexedPolygons import IndexedPolygons
from DejaVu.Box import Box
from DejaVu.Spheres import Spheres
from DejaVu import viewerConst
from DejaVu.bitPatterns import patternList
from opengltk.OpenGL import GL
face = ((0, 3, 2, 1), (3, 7, 6, 2), (7, 4, 5, 6), (0, 1, 5, 4),
(1, 2, 6, 5), (0, 4, 7, 3))
coords = ((1, 1, -1), (-1, 1, -1), (-1, -1, -1), (1, -1, -1),
(1, 1, 1), (-1, 1, 1), (-1, -1, 1), (1, -1, 1))
#new style RGB->
materials = (
(0, 0, 1),
(0, 1, 0),
(0, 0, 1),
(0, 1, 0),
(1, 0, 0),
(1, 0, 0),
)
box = IndexedPolygons('Box',
materials=materials,
vertices=coords,
faces=face,
inheritMaterial=0,
visible=0,
protected=True,
listed=0)
box.Set(frontPolyMode=GL.GL_LINE)
box.Set(backPolyMode=GL.GL_LINE)
box.Set(culling=GL.GL_NONE)
box.inheritShading = 0
box.shading = GL.GL_FLAT
box.Set(matBind=viewerConst.PER_PART)
box.polygonstipple.Set(pattern=patternList[0])
box.Set(stipplePolygons=1)
box.transparent = 0
self.box = box
self.spheres = Spheres('Spheres',
visible=0,
inheritMaterial=0,
radii=(0.3, ),
protected=True,
listed=0)
self.halo = Spheres('Halo',
visible=0,
inheritMaterial=0,
radii=(0.5, ),
protected=True,
listed=0)
from DejaVu.Geom import Geom
AutoLigand_geoms = Geom("AutoLigand_geoms", shape=(0, 0), listed=0)
self.vf.GUI.VIEWER.AddObject(AutoLigand_geoms,
parent=self.vf.GUI.miscGeom)
self.vf.GUI.VIEWER.AddObject(self.startCross, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.endCross, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.box, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.spheres, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.halo, parent=AutoLigand_geoms)
self.grids = {}
self.vf.showCitation.citations["AutoLigand"] = """
Please acknowledge the use of the AutoLigand that results
in any published work, including scientific papers, films
and videotapes, by citing the following reference:
Harris R, Olson AJ, Goodsell DS. Proteins. (2008) 70 1506..
"""
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()
def pageChanged(self, name):
if name == 'Single Fill':
self.startCross.Set(visible=1)
elif name == 'Connected Fill':
self.endCross.Set(visible=1)
else:
self.startCross.Set(visible=0)
self.endCross.Set(visible=0)
def selectGrid(self, value):
if not value:
return
lines = open(value + ".maps.fld").readlines()
if not lines: return
for line in lines:
if line.startswith("#SPACING"):
spacing = float(line.split()[-1])
if line.startswith("#NELEMENTS"):
tmp = line.split()
dimX = int(tmp[1])
dimY = int(tmp[2])
dimZ = int(tmp[3])
if line.startswith("#CENTER"):
tmp = line.split()
centerX = float(tmp[1])
centerY = float(tmp[2])
centerZ = float(tmp[3])
#this variables are the same used in AutoLigand.py
self.xcent = int(dimX / 2)
self.ycent = int(dimY / 2)
self.zcent = int(dimZ / 2)
self.centerx = centerX
self.centery = centerY
self.centerz = centerZ
self.spacing = spacing
c = [centerX, centerY, centerZ]
xlen = round(spacing * dimX, 4)
ylen = round(spacing * dimY, 4)
zlen = round(spacing * dimZ, 4)
self.minX = c[0] - xlen * 0.5
self.maxX = c[0] + xlen * 0.5
if self.grids.has_key(value):
centerX = self.grids[value][0]
centerY = self.grids[value][1]
centerZ = self.grids[value][2]
self.ifd.entryByName['gridPointsX']['widget'].configure(
minval=self.minX,
maxval=self.maxX,
)
self.ifd.entryByName['gridPointsXEnd']['widget'].configure(
minval=self.minX,
maxval=self.maxX,
)
self.minY = c[1] - ylen * 0.5
self.maxY = c[1] + ylen * 0.5
self.ifd.entryByName['gridPointsY']['widget'].configure(
minval=self.minY,
maxval=self.maxY,
)
self.ifd.entryByName['gridPointsYEnd']['widget'].configure(
minval=self.minY,
maxval=self.maxY,
)
self.minZ = c[2] - zlen * 0.5
self.maxZ = c[2] + zlen * 0.5
self.ifd.entryByName['gridPointsZ']['widget'].configure(
minval=self.minZ,
maxval=self.maxZ,
)
self.ifd.entryByName['gridPointsZEnd']['widget'].configure(
minval=self.minY,
maxval=self.maxY,
)
self.startCross.Set(vertices=((centerX, centerY, centerZ), ))
self.ifd.entryByName['gridPointsX']['widget'].set(centerX)
self.ifd.entryByName['gridPointsY']['widget'].set(centerY)
self.ifd.entryByName['gridPointsZ']['widget'].set(centerZ)
self.ifd.entryByName['gridPointsXEnd']['widget'].set(centerX + 12)
self.ifd.entryByName['gridPointsYEnd']['widget'].set(centerY + 12)
self.ifd.entryByName['gridPointsZEnd']['widget'].set(centerZ + 12)
self.endCross.Set(vertices=((centerX + 12, centerY + 12,
centerZ + 12), ))
pts = [(self.maxX, self.maxY, self.minZ),
(self.minX, self.maxY, self.minZ),
(self.minX, self.minY, self.minZ),
(self.maxX, self.minY, self.minZ),
(self.maxX, self.maxY, self.maxZ),
(self.minX, self.maxY, self.maxZ),
(self.minX, self.minY, self.maxZ),
(self.maxX, self.minY, self.maxZ)]
self.box.Set(visible=1)
#self.startCross.Set(visible=1)
self.box.vertexSet.vertices.array[:] = pts
self.box.RedoDisplayList()
self.vf.GUI.VIEWER.Normalize_cb()
self.vf.GUI.VIEWER.Redraw()
def changeStartCross(self, val):
centerX = self.ifd.entryByName['gridPointsX']['widget'].get()
centerY = self.ifd.entryByName['gridPointsY']['widget'].get()
centerZ = self.ifd.entryByName['gridPointsZ']['widget'].get()
grid = self.ifd.entryByName['FileBaseName']['widget'].get()
if grid:
self.grids[grid] = [centerX, centerY, centerZ]
self.startCross.Set(visible=1)
self.startCross.Set(vertices=((centerX, centerY, centerZ), ))
self.vf.GUI.VIEWER.Redraw()
def changeEndCross(self, val):
centerX = self.ifd.entryByName['gridPointsXEnd']['widget'].get()
centerY = self.ifd.entryByName['gridPointsYEnd']['widget'].get()
centerZ = self.ifd.entryByName['gridPointsZEnd']['widget'].get()
grid = self.ifd.entryByName['FileBaseName']['widget'].get()
#self.endCross.Set(visible=1)
self.endCross.Set(vertices=((centerX, centerY, centerZ), ))
self.vf.GUI.VIEWER.Redraw()
def checkResults(self):
"""Checks the queue for results until we get one"""
if self.cmd.ok.configure()['state'][-1] == 'normal':
if self.showPlayer:
self.openPklData()
else:
molName = "FILL_" + str(self.N_of_pts) + "out1"
if os.path.exists(molName + ".pdb"):
self.vf.readMolecule(molName + ".pdb")
self.vf.displaySticksAndBalls(
molName,
cradius=0.0,
sticksBallsLicorice="Sticks and Balls")
self.vf.displayLines(molName, negate=True, displayBO=False)
self.vf.colorByAtomType(molName, ['sticks', 'balls'])
self.vf.GUI.ROOT.after(2050, self.hideGeoms)
return
self.vf.GUI.ROOT.after(100, self.checkResults)
def hideGeoms(self):
self.box.Set(visible=0)
self.startCross.Set(visible=0)
self.endCross.Set(visible=0)
self.spheres.Set(visible=0)
self.halo.Set(visible=0)
def __call__(self, atom, **kw):
if not atom:
return 'ERROR'
atoms = self.vf.expandNodes(atom)
if not atoms:
return 'ERROR'
atoms = atoms.findType(Atom)
if not atoms:
return 'ERROR'
apply(self.doitWrapper, (atoms, ), kw)
def doit(self, atoms=None):
if len(atoms) == 0: return
atom = atoms[0]
if self.minX < atom.coords[0] > self.maxX:
return
if self.minY < atom.coords[1] > self.maxY:
return
if self.minZ < atom.coords[2] > self.maxZ:
return
selection = self.ifd.entryByName['autoligandNotebook'][
'widget'].getcurselection()
if selection == "Single Fill":
self.ifd.entryByName['gridPointsX']['widget'].set(atom.coords[0])
self.ifd.entryByName['gridPointsY']['widget'].set(atom.coords[1])
self.ifd.entryByName['gridPointsZ']['widget'].set(atom.coords[2])
# self.startCross.Set(visible=1)
self.startCross.Set(vertices=((atom.coords[0], atom.coords[1],
atom.coords[2]), ))
elif selection == "Connected Fill":
self.ifd.entryByName['gridPointsXEnd']['widget'].set(
atom.coords[0])
self.ifd.entryByName['gridPointsYEnd']['widget'].set(
atom.coords[1])
self.ifd.entryByName['gridPointsZEnd']['widget'].set(
atom.coords[2])
self.endCross.Set(vertices=((atom.coords[0], atom.coords[1],
atom.coords[2]), ))
self.vf.GUI.VIEWER.Redraw()
def openPklData(self):
self.vf.AutoLigandMovieCommand(self.fileBaseName + '_flood.pkl')
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()
class AutoLigandCommand(MVCommand, MVAtomICOM):
"GUI for AutoLigand: extends MVCommand, overwrites guiCallback"
def __init__(self, func=None):
MVCommand.__init__(self, func)
MVAtomICOM.__init__(self)
self.save = None
self.showPlayer = False
self.floodFile = None
def onAddCmdToViewer(self):
from DejaVu.Points import CrossSet
self.startCross = CrossSet(
"StartCross",
materials=((1.0, 1.0, 0),),
inheritMaterial=0,
protected=True,
offset=1.0,
lineWidth=5,
visible=0,
pickable=0,
listed=0,
)
self.endCross = CrossSet(
"EndCross",
materials=((0, 1, 1),),
inheritMaterial=0,
protected=True,
offset=1.0,
lineWidth=5,
visible=0,
pickable=0,
listed=0,
)
from DejaVu.IndexedPolygons import IndexedPolygons
from DejaVu.Box import Box
from DejaVu.Spheres import Spheres
from DejaVu import viewerConst
from DejaVu.bitPatterns import patternList
from opengltk.OpenGL import GL
face = ((0, 3, 2, 1), (3, 7, 6, 2), (7, 4, 5, 6), (0, 1, 5, 4), (1, 2, 6, 5), (0, 4, 7, 3))
coords = ((1, 1, -1), (-1, 1, -1), (-1, -1, -1), (1, -1, -1), (1, 1, 1), (-1, 1, 1), (-1, -1, 1), (1, -1, 1))
# new style RGB->
materials = ((0, 0, 1), (0, 1, 0), (0, 0, 1), (0, 1, 0), (1, 0, 0), (1, 0, 0))
box = IndexedPolygons(
"Box",
materials=materials,
vertices=coords,
faces=face,
inheritMaterial=0,
visible=0,
protected=True,
listed=0,
)
box.Set(frontPolyMode=GL.GL_LINE)
box.Set(backPolyMode=GL.GL_LINE)
box.Set(culling=GL.GL_NONE)
box.inheritShading = 0
box.shading = GL.GL_FLAT
box.Set(matBind=viewerConst.PER_PART)
box.polygonstipple.Set(pattern=patternList[0])
box.Set(stipplePolygons=1)
box.transparent = 0
self.box = box
self.spheres = Spheres("Spheres", visible=0, inheritMaterial=0, radii=(0.3,), protected=True, listed=0)
self.halo = Spheres("Halo", visible=0, inheritMaterial=0, radii=(0.5,), protected=True, listed=0)
from DejaVu.Geom import Geom
AutoLigand_geoms = Geom("AutoLigand_geoms", shape=(0, 0), listed=0)
self.vf.GUI.VIEWER.AddObject(AutoLigand_geoms, parent=self.vf.GUI.miscGeom)
self.vf.GUI.VIEWER.AddObject(self.startCross, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.endCross, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.box, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.spheres, parent=AutoLigand_geoms)
self.vf.GUI.VIEWER.AddObject(self.halo, parent=AutoLigand_geoms)
self.grids = {}
self.vf.showCitation.citations[
"AutoLigand"
] = """
Please acknowledge the use of the AutoLigand that results
in any published work, including scientific papers, films
and videotapes, by citing the following reference:
Harris R, Olson AJ, Goodsell DS. Proteins. (2008) 70 1506..
"""
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()
def pageChanged(self, name):
if name == "Single Fill":
self.startCross.Set(visible=1)
elif name == "Connected Fill":
self.endCross.Set(visible=1)
else:
self.startCross.Set(visible=0)
self.endCross.Set(visible=0)
def selectGrid(self, value):
if not value:
return
lines = open(value + ".maps.fld").readlines()
if not lines:
return
for line in lines:
if line.startswith("#SPACING"):
spacing = float(line.split()[-1])
if line.startswith("#NELEMENTS"):
tmp = line.split()
dimX = int(tmp[1])
dimY = int(tmp[2])
dimZ = int(tmp[3])
if line.startswith("#CENTER"):
tmp = line.split()
centerX = float(tmp[1])
centerY = float(tmp[2])
centerZ = float(tmp[3])
# this variables are the same used in AutoLigand.py
self.xcent = int(dimX / 2)
self.ycent = int(dimY / 2)
self.zcent = int(dimZ / 2)
self.centerx = centerX
self.centery = centerY
self.centerz = centerZ
self.spacing = spacing
c = [centerX, centerY, centerZ]
xlen = round(spacing * dimX, 4)
ylen = round(spacing * dimY, 4)
zlen = round(spacing * dimZ, 4)
self.minX = c[0] - xlen * 0.5
self.maxX = c[0] + xlen * 0.5
if self.grids.has_key(value):
centerX = self.grids[value][0]
centerY = self.grids[value][1]
centerZ = self.grids[value][2]
self.ifd.entryByName["gridPointsX"]["widget"].configure(minval=self.minX, maxval=self.maxX)
self.ifd.entryByName["gridPointsXEnd"]["widget"].configure(minval=self.minX, maxval=self.maxX)
self.minY = c[1] - ylen * 0.5
self.maxY = c[1] + ylen * 0.5
self.ifd.entryByName["gridPointsY"]["widget"].configure(minval=self.minY, maxval=self.maxY)
self.ifd.entryByName["gridPointsYEnd"]["widget"].configure(minval=self.minY, maxval=self.maxY)
self.minZ = c[2] - zlen * 0.5
self.maxZ = c[2] + zlen * 0.5
self.ifd.entryByName["gridPointsZ"]["widget"].configure(minval=self.minZ, maxval=self.maxZ)
self.ifd.entryByName["gridPointsZEnd"]["widget"].configure(minval=self.minY, maxval=self.maxY)
self.startCross.Set(vertices=((centerX, centerY, centerZ),))
self.ifd.entryByName["gridPointsX"]["widget"].set(centerX)
self.ifd.entryByName["gridPointsY"]["widget"].set(centerY)
self.ifd.entryByName["gridPointsZ"]["widget"].set(centerZ)
self.ifd.entryByName["gridPointsXEnd"]["widget"].set(centerX + 12)
self.ifd.entryByName["gridPointsYEnd"]["widget"].set(centerY + 12)
self.ifd.entryByName["gridPointsZEnd"]["widget"].set(centerZ + 12)
self.endCross.Set(vertices=((centerX + 12, centerY + 12, centerZ + 12),))
pts = [
(self.maxX, self.maxY, self.minZ),
(self.minX, self.maxY, self.minZ),
(self.minX, self.minY, self.minZ),
(self.maxX, self.minY, self.minZ),
(self.maxX, self.maxY, self.maxZ),
(self.minX, self.maxY, self.maxZ),
(self.minX, self.minY, self.maxZ),
(self.maxX, self.minY, self.maxZ),
]
self.box.Set(visible=1)
# self.startCross.Set(visible=1)
self.box.vertexSet.vertices.array[:] = pts
self.box.RedoDisplayList()
self.vf.GUI.VIEWER.Normalize_cb()
self.vf.GUI.VIEWER.Redraw()
def changeStartCross(self, val):
centerX = self.ifd.entryByName["gridPointsX"]["widget"].get()
centerY = self.ifd.entryByName["gridPointsY"]["widget"].get()
centerZ = self.ifd.entryByName["gridPointsZ"]["widget"].get()
grid = self.ifd.entryByName["FileBaseName"]["widget"].get()
if grid:
self.grids[grid] = [centerX, centerY, centerZ]
self.startCross.Set(visible=1)
self.startCross.Set(vertices=((centerX, centerY, centerZ),))
self.vf.GUI.VIEWER.Redraw()
def changeEndCross(self, val):
centerX = self.ifd.entryByName["gridPointsXEnd"]["widget"].get()
centerY = self.ifd.entryByName["gridPointsYEnd"]["widget"].get()
centerZ = self.ifd.entryByName["gridPointsZEnd"]["widget"].get()
grid = self.ifd.entryByName["FileBaseName"]["widget"].get()
# self.endCross.Set(visible=1)
self.endCross.Set(vertices=((centerX, centerY, centerZ),))
self.vf.GUI.VIEWER.Redraw()
def checkResults(self):
"""Checks the queue for results until we get one"""
if self.cmd.ok.configure()["state"][-1] == "normal":
if self.showPlayer:
self.openPklData()
else:
molName = "FILL_" + str(self.N_of_pts) + "out1"
if os.path.exists(molName + ".pdb"):
self.vf.readMolecule(molName + ".pdb")
self.vf.displaySticksAndBalls(molName, cradius=0.0, sticksBallsLicorice="Sticks and Balls")
self.vf.displayLines(molName, negate=True, displayBO=False)
self.vf.colorByAtomType(molName, ["sticks", "balls"])
self.vf.GUI.ROOT.after(2050, self.hideGeoms)
return
self.vf.GUI.ROOT.after(100, self.checkResults)
def hideGeoms(self):
self.box.Set(visible=0)
self.startCross.Set(visible=0)
self.endCross.Set(visible=0)
self.spheres.Set(visible=0)
self.halo.Set(visible=0)
def __call__(self, atom, **kw):
if not atom:
return "ERROR"
atoms = self.vf.expandNodes(atom)
if not atoms:
return "ERROR"
atoms = atoms.findType(Atom)
if not atoms:
return "ERROR"
apply(self.doitWrapper, (atoms,), kw)
def doit(self, atoms=None):
if len(atoms) == 0:
return
atom = atoms[0]
if self.minX < atom.coords[0] > self.maxX:
return
if self.minY < atom.coords[1] > self.maxY:
return
if self.minZ < atom.coords[2] > self.maxZ:
return
selection = self.ifd.entryByName["autoligandNotebook"]["widget"].getcurselection()
if selection == "Single Fill":
self.ifd.entryByName["gridPointsX"]["widget"].set(atom.coords[0])
self.ifd.entryByName["gridPointsY"]["widget"].set(atom.coords[1])
self.ifd.entryByName["gridPointsZ"]["widget"].set(atom.coords[2])
# self.startCross.Set(visible=1)
self.startCross.Set(vertices=((atom.coords[0], atom.coords[1], atom.coords[2]),))
elif selection == "Connected Fill":
self.ifd.entryByName["gridPointsXEnd"]["widget"].set(atom.coords[0])
self.ifd.entryByName["gridPointsYEnd"]["widget"].set(atom.coords[1])
self.ifd.entryByName["gridPointsZEnd"]["widget"].set(atom.coords[2])
self.endCross.Set(vertices=((atom.coords[0], atom.coords[1], atom.coords[2]),))
self.vf.GUI.VIEWER.Redraw()
def openPklData(self):
self.vf.AutoLigandMovieCommand(self.fileBaseName + "_flood.pkl")
class WebDrivenTutorial(Command):
"""start a web browser that can send commands over a socket to Viewerframework
We use Karrigell-2.0.3 as a light webserver. The source of Karrigell
need to be install in the python path.
When a server is started a webbrowser is started and display a url which
should point to a file in the web server root dir.
The commands take 2 keywords argument which specify the path to Karrigell
package, and the file to open in the webbrowser.
If not specify, we search the python path to find karrigell package, and give
the top level of the karigell folder as the file to open as a url.
"""
def onExitFromViewer(self):
""" method which will be call when the Viewer is closed"""
# we need to stop the Karigell webserver
if hasattr(self,'cmd'):
if not mswin:
import os,signal
print 'killing process Karrigell'
pid = self.cmd.com.pid
os.kill(pid,signal.SIGKILL)
#self.cmd.com.kill(signal.SIGKILL)
else:
pass
def doit(self,**kw):
import webbrowser
karrigell_path = kw['karrigell_path']
file = kw['file']
if karrigell_path is None:
server_root = self.findKarrigell()
if server_root is None:
self.warningMsg("Karrigell package not install, Webserver not started.")
else:
karrigell_path = server_root
# Karrigell folder should be in python path, we expect version-2.0.3
import os
# we create a absolute path as windows need it to under path
karrigell_start = os.path.realpath(os.path.join(karrigell_path,'Karrigell.py'))
karrigell_init = os.path.realpath(os.path.join(karrigell_path,'Karrigell.ini'))
status = False
port = 8080
status,port = self.startKarrigell(port,karrigell_start,karrigell_init)
if status:
print 'Karrigell started, listenning on port %d'%port
else:
print 'Karrigell could not be started'
return
# web page have to be in the server_root directory which
# is by default karrigell_path
if file is None:
file = ''
url2open = 'http://localhost:%d/'%port+file
webbrowser.open_new(url2open)
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 checkKarrigellStatus(self):
# check the status of Karrigell
# did the webserver started, if so we get the port back
#while not self.cmd.output.empty():
while(1):
if not self.cmd.output.empty():
data = self.cmd.output.get(False)
# server fail to start
if 'Address already in use' in data:
return False
# server start success
if 'running on port' in data:
return True
return False
def findKarrigell(self):
""" method which search the path to the Karrigel directory in the
python path"""
import sys,os
karrigell_path =None
for d in sys.path:
dirname = os.path.join(d,'Karrigell-2.0.3')
if os.path.exists(dirname):
karrigell_path = dirname
return karrigell_path
def guiCallback(self):
kw ={}
server_root = self.findKarrigell()
if server_root is None: return
file = self.vf.askFileOpen(types=[('all', '*')],
idir=server_root,
title='Select a web page or folder')
if file is not None:
import string
webpage = string.split(file,'Karrigell-2.0.3')[1]
kw['karrigell_path']=server_root
kw['file'] = webpage
apply(self.doitWrapper,(),kw)
def __call__(self,karrigell_path=None,file=None,**kw):
""" None<-web_tutorial( karrigell_path=None,file=None,**kw)
karrigell_path = path to server_root of Karrigell webserver
file = file or folder to show as url, should be in the webserver_root
"""
kw['karrigell_path'] = karrigell_path
kw['file'] = file
apply(self.doitWrapper,(),kw)