def make3Dboxviewer(self, target):
""" create the config camera and add the default box object"""
# grid cam name
name = 'gridcam'
if self.app.viewer == None:
# XXX reinitialize fonts?
self.app.viewer = RaccoonPmvCamera.EmbeddedMolViewer()
self.app.molviewer = self.app.viewer.mv
self.app.parent.bind_all('<F12>', self.app.viewer.togglepmv)
# adding config camera
if self.camera == None:
self.camera = self.app.viewer.addCamera(target, name)
self.camera_name = name
from DejaVu.Box import Box
from MolKit import Read
self.Box3D = Box('Grid_box')
self.Box3D.Set(xside=0.001, yside=0.001, zside=0.001)
self.app.molviewer.GUI.VIEWER.AddObject(self.Box3D)
self.app.viewer.cameras[name]['structures'].append(self.Box3D)
def doit(self, nodes, showPacking=False, **kw):
if nodes is None or not nodes:
return
# Check the validity of th
molecules = nodes.top.uniq()
molecule = molecules[0]
if not hasattr(mol, 'spaceGroup'):
return
matrices = instanceMatricesFromGroup(molecule)
geom = molecule.geomContainer.geoms['master']
geom.Set(instanceMatrices=matrices) #packing
if not molecule.geomContainer.geoms.has_key('Unit Cell'):
fractCoords = ((1, 1, 0), (0, 1, 0), (0, 0, 0), (1, 0, 0),
(1, 1, 1), (0, 1, 1), (0, 0, 1), (1, 0, 1))
coords = []
coords = molecule.crystal.toCartesian(fractCoords)
box = Box('Unit Cell', vertices=coords)
self.vf.GUI.VIEWER.AddObject(box, parent=geom)
molecule.geomContainer.geoms['Unit Cell'] = box
def guiCallback(self):
molNames = []
for mol in self.vf.Mols:
if hasattr(mol, 'spaceGroup'):
molNames.append(mol.name)
if not molNames:
tkMessageBox.showinfo(
"Crystal Info is Needed",
"No Molecule in the Viewer has Crystal Info.")
return
ifd = InputFormDescr(title='Crystal Info')
ifd.append({
'name': 'moleculeList',
'widgetType': Pmw.ScrolledListBox,
'tooltip': 'Select a molecule with Crystal Info.',
'wcfg': {
'label_text': 'Select Molecule: ',
'labelpos': 'nw',
'items': molNames,
'listbox_selectmode': 'single',
'listbox_exportselection': 0,
'usehullsize': 1,
'hull_width': 100,
'hull_height': 150,
'listbox_height': 5
},
'gridcfg': {
'sticky': 'nsew',
'row': 1,
'column': 0
}
})
val = self.vf.getUserInput(ifd, modal=1, blocking=1)
if val:
molecule = self.vf.getMolFromName(val['moleculeList'][0])
matrices = instanceMatricesFromGroup(molecule)
geom = molecule.geomContainer.geoms['master']
geom.Set(instanceMatrices=matrices)
if not molecule.geomContainer.geoms.has_key('Unit Cell'):
fractCoords = ((1, 1, 0), (0, 1, 0), (0, 0, 0), (1, 0, 0),
(1, 1, 1), (0, 1, 1), (0, 0, 1), (1, 0, 1))
coords = []
coords = molecule.crystal.toCartesian(fractCoords)
box = Box('Unit Cell', vertices=coords)
self.vf.GUI.VIEWER.AddObject(box, parent=geom)
molecule.geomContainer.geoms['Unit Cell'] = box
ifd = InputFormDescr(title='Crystal Options')
visible = molecule.geomContainer.geoms['Unit Cell'].visible
if visible:
showState = 'active'
else:
showState = 'normal'
ifd.append({
'name': 'Show Cell',
'widgetType': Tkinter.Checkbutton,
'text': 'Hide Unit Cell',
'state': showState,
'gridcfg': {
'sticky': Tkinter.W
},
'command': CallBackFunction(self.showUnitCell, molecule)
})
ifd.append({
'name': 'Show Packing',
'widgetType': Tkinter.Checkbutton,
'text': 'Hide Packing',
'state': 'active',
'gridcfg': {
'sticky': Tkinter.W
},
'command': CallBackFunction(self.showPacking, molecule)
})
val = self.vf.getUserInput(ifd, modal=0, blocking=1)
if not val:
geom.Set(instanceMatrices=[numpy.eye(4, 4)])
molecule.geomContainer.geoms['Unit Cell'].Set(visible=False)
class ConfigTab(rb.TabBase, rb.RaccoonDefaultWidget):
def __init__(self, app, parent, debug=False):
rb.TabBase.__init__(self, app, parent, debug = False)
rb.RaccoonDefaultWidget.__init__(self, parent)
self.resource = self.app.resource
self.dockengine = self.app.dockengine
self.app.eventManager.registerListener(RaccoonEvents.SetDockingEngine, self.handleEngine)
self.app.eventManager.registerListener(RaccoonEvents.ReceptorListChange, self.setReceptorList)
self.app.eventManager.registerListener(RaccoonEvents.ReceptorListChange, self.nuke)
self.camera = None # embedded camera object
self._loaded_struct = []
self._boxevent = RaccoonEvents.SearchConfigChange()
self._searchevent = None # XXX TODO?
# switch for loading multiple receptors in the viewer
self.recLoaderMultiMode = tk.BooleanVar(value=False)
self._currRec = []# [ { 'name':xxxx, 'obj':[ rigid, flex ], 'fname':xxxx }, ... ]
self.initIcons()
self.makeInterface()
def initIcons(self):
""" initialize the icons for the interface"""
icon_path = CADD.Raccoon2.ICONPATH
f = icon_path + os.sep + 'system.png'
self._ICON_sys = ImageTk.PhotoImage(Image.open(f))
f = icon_path + os.sep + 'center_mol.png'
self._ICON_center_mol = ImageTk.PhotoImage(Image.open(f))
f = icon_path + os.sep + 'center_all.png'
self._ICON_center_all = ImageTk.PhotoImage(Image.open(f))
f = icon_path + os.sep + 'center_box.png'
self._ICON_center_box = ImageTk.PhotoImage(Image.open(f))
f = icon_path + os.sep + 'water.png'
self._ICON_water = ImageTk.PhotoImage(Image.open(f))
f = icon_path + os.sep + 'floppy.png'
self._ICON_floppy = ImageTk.PhotoImage(Image.open(f))
f = icon_path + os.sep + 'open.png'
self._ICON_open = ImageTk.PhotoImage(Image.open(f))
f = icon_path + os.sep + 'default.gif'
self._ICON_default = ImageTk.PhotoImage(Image.open(f))
f = icon_path + os.sep + 'singleMol.png'
self._ICON_single = ImageTk.PhotoImage(Image.open(f))
f = icon_path + os.sep + 'multiMol.png'
self._ICON_multi = ImageTk.PhotoImage(Image.open(f))
def handleEngine(self, event=None):
""" handle widget display for different engines """
#print "DD_CONFIG> EVENT notified that docking engine is now [%s]" % event.dockingengine
self.dockengine = event.dockingengine
def openConfig(self, fname = None):
""" import data from a vina config """
ad_ext = ("*.dpf", "*.DPF")
ag_ext = ("*.gpf", "*.GPF")
vina_ext = ("*.conf", "*.CONF")
anyfile = ("Any file...", ("*"))
if fname == None:
if self.dockengine == 'vina':
t = 'Select Vina config file to import'
ftypes = [("Vina config file", vina_ext), anyfile ]
elif self.dockingengine == 'ad':
t = 'Select AutoDock/AutoGrid parameter files to import'
ftypes = [ ("AutoDock parameter file", ad_ext),
("AutoGrid parameter file", ag_ext),
anyfile ]
fname = tfd.askopenfilename(parent=self.frame, title=t, filetypes = ftypes)
if not fname: return
#print "GOT FNAME[%s]" % fname
if not fname: return
# parse vina config
if self.dockengine == 'vina':
accepted = self._loadvinaconf(fname)
# parse ad configs
elif self.dockingengine =='ad':
name, ext = os.path.splitext(fname)
if ext.lower() == 'dpf':
accepted = self._loaddpf(fname)
elif ext.lower() == 'gpf':
accepted = self._loadgpf(fname)
t = 'Docking parameters'
if len(accepted):
m = ('The following docking parameters '
'have been accepted:\n\n%s' ) % ("\n".join(accepted))
i = 'info'
else:
m = ('No docking parametes have been imported!\n'
'Inspect the config file and try again')
i = 'error'
tmb.showinfo(parent=self.frame, title=t, message=m, icon=i)
self.app.eventManager.dispatchEvent(self._boxevent)
# XXX TODO
# self.app.eventManager.dispatchEvent(self._searchevent)
def _loadvinaconf(self, fname, quiet=False):
""" actual parser of vina CONF file """
accepted = []
# load data
config = self.app.engine.gridBoxFromConf(fname)
if not config:
if not quiet:
t = 'Config file error'
m = ('There was an error loading the config file.\n'
'Inspect it and try again...')
i = 'error'
tmb.showinfo(parent=self.frame, title=t, message=m, icon=i)
return False
# center
center = [ config[k] for k in 'center_x', 'center_y', 'center_z' ]
if self.app.engine.setBoxCenter(center):
for i in range(3):
self._thumbw_array[i].set( center[i])
accepted.append('center')
# size
size = [ config[k] for k in 'size_x', 'size_y', 'size_z' ]
if self.app.engine.setBoxSize(size):
for i in range(3):
self._thumbw_array[i+3].set( size[i])
accepted.append('size')
# search parms
for k in ['exhaustiveness', 'num_modes', 'energy_range']:
if not config[k] == None:
v = config[k]
self.app.engine.vina_settings[k] = v
self.vinaWidgets[k].setvalue(v)
accepted.append(k)
# dispatch config EVENT
#event = RaccoonEvents.SearchConfigChange()
self.app.eventManager.dispatchEvent(self._boxevent)
return accepted
def _loaddpf(self, fname):
""" """
# load data
# set widgets
pass
def _loadgpf(self, fname):
""" """
# load data
# set widgets
pass
def saveConfig(self):
""" """
pass
def setWheelBox(self, wheelname, value):
""" wheel callback that sets center/size values in
the docking engine
"""
cx, cy, cz = self.app.engine.box_center
sx, sy, sz = self.app.engine.box_size
if wheelname=='center_x':
cx = value
elif wheelname=='center_y':
cy = value
elif wheelname=='center_z':
cz = value
elif wheelname=='size_x':
sx = value
elif wheelname=='size_y':
sy = value
elif wheelname=='size_z':
sz = value
self.app.engine.box_center = [ cx, cy, cz ]
self.app.engine.box_size = [ sx, sy, sz ]
for i in self.app.engine.box_center :
if i == None:
return
self.Box3D.Set(center = (cx, cy, cz))
self.Box3D.Set(xside=sx, yside=sy , zside=sz)
self.app.eventManager.dispatchEvent(self._boxevent)
# if a full triplet is defined, sync the data with the engine config internals
if not None in self.app.engine.box_center:
self.app.engine.setBoxCenter( self.app.engine.box_center )
if not None in self.app.engine.box_size:
self.app.engine.setBoxSize( self.app.engine.box_size )
def makeInterfaceLocal(self):
"""filler for now"""
pass
def makeInterfaceOpal(self):
""" """
pass
def makeInterface(self):
""" create interface for ssh """
self.resetFrame()
colors = { 'center_x' : '#ff3333',
'center_y' : 'green',
'center_z' : '#00aaff',
'size_x' : '#ff3333',
'size_y' : 'green',
'size_z' : '#0099ff',
}
frame_set = { 'ring_bd' : 1, 'ring_highlightbackground' :'black', 'ring_borderwidth' : 2,
'ring_highlightcolor' : 'black', 'ring_highlightthickness' : 1, 'ring_relief' : 'flat',
'groupchildsite_bg':'white', 'groupchildsite_relief':'sunken','ring_bg':'white',
'tag_bd' : '1', 'tag_highlightbackground' :'black', 'tag_borderwidth':2,
'tag_highlightcolor' : 'black', 'tag_highlightthickness': 1}
frame_set = { 'ring_bd' : 1, 'ring_highlightbackground' :'black', 'ring_borderwidth' : 2,
'ring_highlightcolor' : 'black', 'ring_highlightthickness' : 1, 'ring_relief' : 'flat'}
frame_set = {}
bset = { 'bg' : '#95bed5', 'width' : 22, 'height': 22, 'relief' : 'raised'}
bset = { 'bg' : '#2e363b', 'width' : 22, 'height': 22, 'relief' : 'raised'}
bset = { 'bg' : '#a6abae', 'width' : 22, 'height': 22, 'relief' : 'raised'}
bset = { 'bg' : '#969b9d' } # 'width' : 22, 'height': 22, 'relief' : 'raised'}
bset = {}
bset.update(self.BORDER)
# left frame
lframe = tk.Frame(self.frame)
# button tollbar
tk.Frame(lframe, height=7).pack(expand=0, fill='x', padx=0, pady=0, side='top', anchor='n')
# minispacer
bframe = tk.Frame(lframe)
b = tk.Button(bframe, text='Load...', command = self.openConfig, image= self._ICON_open, compound='left',
height=14,**bset)
b.pack(expand=1,fill='x', anchor='w', side='left',padx=1)
b.pack(expand=1,fill='x', anchor='w', side='left',padx=1)
bframe.pack(expand=0, fill='x', padx=0, pady=0, side='top', anchor='n')
########################## center wheels
self._thumbw_array = []
c_group = Pmw.Group(lframe, tag_text='Center', tag_font=self.FONTbold, **frame_set)
for lab in ['center_x', 'center_y', 'center_z']:
cb = CallbackFunction(self.setWheelBox, lab)
tw = ThumbWheel(
c_group.interior(), labCfg={'text':lab, 'side':'left','fg':colors[lab],
'bg':'black', 'width':9 }, showLabel=1,
width=90, height=14, type=float, value=0.0,
callback=cb, continuous=True,
oneTurn=5, wheelPad=0)
tw.pack(side='top', pady=2,anchor='n')
self._thumbw_array.append(tw)
c_group.pack(side='top', anchor='n', expand=0,fill='x',ipadx=2,ipady=3, padx=1)
########################## size wheels
s_group = Pmw.Group(lframe, tag_text='Size', tag_font=self.FONTbold, **frame_set)
for lab in ['size_x', 'size_y', 'size_z']:
cb = CallbackFunction(self.setWheelBox, lab)
tw = ThumbWheel(
s_group.interior(), labCfg={'text':lab, 'side':'left','fg':colors[lab],
'bg':'black', 'width':9 }, showLabel=1,
width=90, height=14, type=float, value=0.0, min=0.0001,
callback=cb, continuous=True,
oneTurn=5, wheelPad=0)
tw.pack(side='top', pady=2,anchor='n')
self._thumbw_array.append(tw)
s_group.pack(side='top', anchor='n', expand=0,fill='x',ipadx=2,ipady=3, padx=1,pady=2)
########################## search settings
self.searchparmgroup = Pmw.Group(lframe, tag_text='Search parameters', tag_font=self.FONTbold, **frame_set)
# autodock search parms
self.buildSearchADPanel(target = self.searchparmgroup )
# vina search parms
self.buildSearchVinaPanel(target = self.searchparmgroup )
self.searchparmgroup.pack(side='top', anchor='n', expand=0,fill='x',ipadx=2,ipady=3, padx=1,pady=5)
########################## Receptors
self._receptors_group = Pmw.Group(lframe, tag_text='Receptor list', tag_font=self.FONTbold,collapsedsize=3, **frame_set)
# important
self.receptorListbox = Pmw.ScrolledListBox(self._receptors_group.interior(), listbox_highlightbackground = 'black',
# selectioncommand=self.loadreceptor,
listbox_selectbackground='yellow')
self.receptorListbox.pack(expand=1, fill='both',padx=3, pady=0)
self.receptorListbox.component('listbox').bind('<ButtonRelease-1>', self.loadreceptor)
self.receptorListbox.component('listbox').bind('<Button-3>', self._delreceptor)
tb = tk.Frame(self._receptors_group.interior())
# single-multi load buttons
self.recLoaderMode_single = tk.Radiobutton(tb, text='Single', image = self._ICON_single, indicatoron=False,
variable=self.recLoaderMultiMode, value = False, compound='left', height=16, **bset)
self.recLoaderMode_single.pack(anchor='n', side='left',pady=1,expand=1,fill='x',padx=1)
self.recLoaderMode_multi = tk.Radiobutton(tb, text='Multi', image = self._ICON_multi, indicatoron=False,
variable=self.recLoaderMultiMode, value = True, compound='left', height=16, **bset)
self.recLoaderMode_multi.pack(anchor='n', side='left',pady=1,expand=1,fill='x',padx=1)
tb.pack(expand=0, fill='x',anchor='s',side='bottom',padx=3)
self._receptors_group.pack(side='bottom', anchor='n', expand=1, fill='both',ipadx=4,ipady=4, padx=1,pady=0)
lframe.pack(side = 'left', anchor='n', expand='n', fill='y', padx=0, pady=0)
###### 3D Viewer
rframe = tk.Frame(self.frame)
spacer = tk.Frame(rframe, width=5) #, bg='red')
spacer.pack(expand=0,fill='y',side='left',anchor='w')
spacer.pack_propagate(0)
vgroup = Pmw.Group(rframe, tag_text = '3D viewer', tag_font=self.FONTbold,groupchildsite_bg='black', **frame_set)
# TOOLBAR
vtoolbar = tk.Frame(vgroup.interior())
vtoolbar.pack(side='left', anchor='w', expand=0, fill='y')
cb = CallbackFunction(self.centerView, None)
tk.Button(vtoolbar, text='Center\nall', image = self._ICON_center_all, width=22, height=22,
command=cb, **bset).pack(anchor='n', side='top')
cb = CallbackFunction(self.centerView, 'mol')
tk.Button(vtoolbar, text='Center\nmol', image = self._ICON_center_mol, width=22, height=22,
command=cb, **bset ).pack(anchor='n', side='top')
cb = CallbackFunction(self.centerView, 'box')
tk.Button(vtoolbar, text='Center\nbox', image = self._ICON_center_box, width=22, height=22,
command=cb, **bset ).pack(anchor='n', side='top',pady=1)
# 3d Viewer settings XXX TODO
#tk.Button(vtoolbar, text='Settings', image = self._ICON_sys, width=22, height=22, **bset).pack(anchor='n', side='top')
vgroup.pack(side='right', anchor='e', expand=1, fill='both', padx=0, pady=0)
# 3D viewer
self.make3Dboxviewer(vgroup.interior())
rframe.pack(side = 'right', anchor='n', expand=1, fill='both',padx=0, pady=0)
if self.app.dockengine == 'vina':
self.setSearchParmsVina()
elif self.app.dockengine == 'autodock':
self.setSearchParmsAD()
self.frame.pack(expand=1, fill='both',anchor='n', side='top')
def _delreceptor(self, event=None):
""" """
return
# XXX TODO TO REMOVE RECEPTORS FROM HERE
parent = self.receptorListbox
try:
sel = parent.getvalue()
#print "SEL", sel
menu = tk.Menu(parent=parent, tearoff=False, takefocus=1)
txt = 'Delete "%s"' % sel
menu.add_command(txxt, state='normal', command = self.receptor)
except:
#print "nothing"
pass
def make3Dboxviewer(self, target):
""" create the config camera and add the default box object"""
# grid cam name
name = 'gridcam'
if self.app.viewer == None:
# XXX reinitialize fonts?
self.app.viewer = RaccoonPmvCamera.EmbeddedMolViewer()
self.app.molviewer = self.app.viewer.mv
self.app.parent.bind_all('<F12>', self.app.viewer.togglepmv)
# adding config camera
if self.camera == None:
self.camera = self.app.viewer.addCamera(target, name)
self.camera_name = name
from DejaVu.Box import Box
from MolKit import Read
self.Box3D = Box('Grid_box')
self.Box3D.Set(xside=0.001, yside=0.001, zside=0.001)
self.app.molviewer.GUI.VIEWER.AddObject(self.Box3D)
self.app.viewer.cameras[name]['structures'].append(self.Box3D)
def centerView(self, target=None, event=None):
""" center view in the 3D config viewer"""
#root = self.app.viewer.rootObject
showBox = False
if target == 'box':
print "Center box"
item = self.Box3D
elif target == 'mol':
print "center mol"
self.Box3D.visible = False
item = None
showBox = True
else:
print "CENTER ALL"
item = None
self.app.viewer.centerView(item)
if showBox:
self.Box3D.visible = True
def getRecLoaderMode(self):
""" check the value of variable self.recLoaderMultiMode
True : keep adding receptors to the current
False : delete previous receptors upon loading of the selected one
"""
return self.recLoaderMultiMode.get()
def loadreceptor(self, event=None):
""" load the receptor in the viewer deleting previous mols
if necessary
"""
# TOP
# TOP ######################
self.receptorListbox.component('listbox').unbind('<ButtonRelease-1>')
try:
recname = self.receptorListbox.getvalue()[0]
except:
self.receptorListbox.component('listbox').bind('<ButtonRelease-1>', self.loadreceptor)
return
mode = 'single'
if self.recLoaderMultiMode.get() == 1:
mode = 'multi'
cam = self.camera_name
viewer = self.app.viewer
#print "Loading rec", recname,
#print "MODE", mode
self.app.setBusy()
if mode == 'single' and len(self._currRec)>1:
# delete non-main
for i in range(len(self._currRec)-1):
obj = self._currRec[i+1]['obj']
for o in obj: viewer.deleteInCamera(o,cam)
self._currRec.pop(i+1)
recfiles = self.app.engine.getRecFiles(recname)
recfname = recfiles[0]
for i in range(len(self._currRec)):
rec = self._currRec[i]
if (rec['name'] == recname) and (rec['fname'] == recfname):
if i == 0:
# already loaded and main
self.receptorListbox.component('listbox').bind('<ButtonRelease-1>', self.loadreceptor)
self.app.setReady()
return
else:
# already loaded but not main
# put selected mol as first
self._currRec = [ self._currRec[i] ] + self._currRec[:i] + self._currRec[i+1:]
# FIXME apply STYLES (main, secondary)
self.app.setReady()
return
# the current main is not the selected one
if mode == 'single' and len(self._currRec) > 0:
obj = self._currRec[0]['obj']
for o in obj: viewer.deleteInCamera(o, cam)
self._currRec = []
newrec = { 'name' : recname, 'fname' : recfname }
newrec['obj'] = [ viewer.loadInCamera(f, cam) for f in recfiles ]
self._currRec = [newrec] + self._currRec
self.receptorListbox.component('listbox').bind('<ButtonRelease-1>', self.loadreceptor)
self.app.setReady()
def nuke(self, event=None):
""" remove all currently loaded receptors"""
# we need to protect the box!
#print "NUKE CALLED"
for rec in self._currRec:
#print "DELETING REC", rec
for o in rec['obj']:
self.app.viewer.deleteInCamera(o, self.camera_name)
self._currRec = []
def buildSearchVinaPanel(self, target):
""" create the panel with vina search settings"""
try:
# avoid double packaging
self.searchParmVinaPanel
return
except:
f = self.searchParmVinaPanel = tk.Frame(target.interior())
target.configure(tag_text = 'Search parameters [ VINA ]')
self.vinaWidgets = {}
# exhaustiveness
tk.Label(f, text='exhaustiveness', width =15,anchor='e').grid(row=1,column=1,sticky='we',padx=5)
self.searchParmVina_exhaustiveness = Pmw.EntryField( f, validate = hf.validatePosNonNullInt,
entry_justify='right', entry_width=8)
self.searchParmVina_exhaustiveness.grid(row=1, column=2,sticky='we',columnspan=1)
def d(event=None): self.setDefSearchParmVina('exhaustiveness')
tk.Button(f, text='D', image=self._ICON_default, command=d).grid(row=1,column=3, sticky='e')
self.vinaWidgets['exhaustiveness'] = self.searchParmVina_exhaustiveness
# num modes
tk.Label(f, text='num.modes', width =15,anchor='e').grid(row=2,column=1,sticky='we',padx=5)
self.searchParmVina_nummodes = Pmw.EntryField( f, validate = hf.validatePosNonNullInt,
entry_justify='right', entry_width=8)
self.searchParmVina_nummodes.grid(row=2, column=2,sticky='we',columnspan=1)
def d(event=None): self.setDefSearchParmVina('num.modes')
tk.Button(f, text='D',image=self._ICON_default, command=d).grid(row=2,column=3, sticky='e')
self.vinaWidgets['num_modes'] = self.searchParmVina_nummodes
# energy range
tk.Label(f, text='energy range', width =15,anchor='e').grid(row=3,column=1,sticky='we',padx=5)
self.searchParmVina_energyrange = Pmw.EntryField( f, validate = hf.validateFloatPos,
entry_justify='right', entry_width=8)
self.searchParmVina_energyrange.grid(row=3, column=2,sticky='we',columnspan=1)
def d(event=None): self.setDefSearchParmVina('energy range')
tk.Button(f, text='D', image=self._ICON_default,command=d).grid(row=3,column=3, sticky='e')
self.vinaWidgets['energy_range'] = self.searchParmVina_energyrange
# executed only the first time
self.setDefSearchParmVina()
def buildSearchADPanel(self, target):
""" create the panel with autodock search settings"""
try:
# avoid double packaging
self.searchParmADPanel
return
except:
f = self.searchParmADPanel = tk.Frame(target.interior())
target.configure(tag_text = 'Search parameters [ AD ]')
tk.Label(f, text='GA SETTINGS SHOULD BE HERE', width =15,anchor='w').grid(row=2,column=1,sticky='we')
self.setDefSearchParmAD()
def setDefSearchParmVina(self, request = None):
""" """
#widgets = [ self.searchParmVina_exhaustiveness,
# self.searchParmVina_nummodes,
# self.searchParmVina_energyrange ]
values = []
wid = []
if request in ['exhaustiveness', None]:
values.append(8)
wid.append(self.vinaWidgets['exhaustiveness'])
if request in ['num_modes', None]:
values.append(9)
wid.append(self.vinaWidgets['num_modes'])
if request in ['energy_range', None]:
values.append(3)
wid.append(self.vinaWidgets['energy_range'])
for i in range(len(values)):
wid[i].setentry(values[i])
def setDefSearchParmAD(self, value = None):
#print "NO DEFAUILT SETTINGS FOR AD YET"
return
def setSearchParmsVina(self):
""" pack and activate the search parms panel for vina """
self.searchParmADPanel.pack_forget()
self.searchParmVinaPanel.pack(expand=0,fill='x',anchor='n',padx=0, pady=0)
def setSeachParmsAD(self):
""" pack and activate the search parms panel for autodock """
self.searchParmVinaPanel.pack_forget()
self.searchParmADPanel.pack(expand=0,fill='x',anchor='n',padx=0, pady=0)
def getSearchParmVina(self):
""" """
widgets = [ self.searchParmVina_exhaustiveness, self.searchParmVina_nummodes,
self.searchParmVina_energyrange ]
for w in widgets:
if not w.valid():
return False
return { 'exhaustiveness': self.searchParmVina_exhaustiveness.getvalue(),
'num.modes' : self.searchParmVina_nummodes.getvalue(),
'energyrange': self.searchParmVina_energyrange.getvalue(),
}
def getSearchParmAD(self):
""" """
# walk through ad parms and return settings
pass
def setReceptorList(self, event=None):
"""update the list of receptors shown in the picker for the config
settings
"""
self.receptorListbox.clear()
self.receptorListbox.setlist(sorted(self.app.engine.RecBook.keys()) )
vi.AddObject(gi, parent=gc)
orgaToMasterGeom[ingr] = gi
tet = IndexedPolygons('surfaceMesh',
vertices=orga.vertices,
faces=orga.faces,
normals=orga.vnormals,
inheritFrontPolyMode=False,
frontPolyMode='line',
inheritCulling=0,
culling='none',
inheritShading=0,
shading='flat')
vi.AddObject(tet, parent=g)
# display histo BB
hbb = Box('histoVolBB', cornerPoints=h1.boundingBox)
vi.AddObject(hbb)
if ViewerType == 'dejavu':
cp = vi.clipP[0]
vi.GUI.clipvar[0][0].set(1)
tet.AddClipPlane(cp, 1, False)
fpg = Points('notFreePoints')
vi.AddObject(fpg)
else:
fpg = Geom('notFreePoints')
vi.AddObject(fpg)
if ViewerType == 'dejavu':
vi.Reset_cb()
vi.Normalize_cb()