def onAddCmdToViewer(self):
# Check first is any of the command that superimpose depends on are
# already loaded.
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands', 'setICOM', 'Pmv',
topCommand = 0)
if not self.vf.commands.has_key('superimposeAtoms'):
self.vf.loadCommand('superImposeCommands', 'superimposeAtoms',
'Pmv', topCommand = 0)
if not self.vf.commands.has_key('startContinuousPicking'):
self.vf.loadCommand('dejaVuCommands','startContinuousPicking',
'ViewerFramework', topCommand = 0)
if not self.vf.commands.has_key('stopContinuousPicking'):
self.vf.loadCommand('dejaVuCommands','stopContinuousPicking',
'ViewerFramework', topCommand = 0)
if not self.vf.commands.has_key('labelByExpression'):
self.vf.loadCommand('labelCommands', 'labelByExpression', 'Pmv',
topCommand = 0)
self.sphere1 = Spheres(name='elt1', radii=0.5,
materials = ( (0.,1.,0.),), protected=True)
self.sphere2 = Spheres(name = 'elt2', radii=0.5,
materials = ( (1.,1.,0.),), protected=True)
def createGeometries(self, obj):
from DejaVu.Geom import Geom
geomC = obj.geomContainer
c = Geom('path', shape=(0,0), protected=True)
c.replace = 'force'
geomC.addGeom(c, parent=geomC.masterGeom)
for a in obj.allAtoms:
a.colors['path']=(1.,1.,1.)
a.opacities['path']=1.0
for chain in obj.chains:
if not hasattr(chain, 'sheet2D') or chain.sheet2D is None:
continue
# HACK TO DEBUG SECONDARYSTRUCTURE
if not chain.sheet2D.has_key('ssSheet2D') or \
chain.sheet2D['ssSheet2D'] is None:
continue
# Create a geometry per sheet2D
name = 'path'+ chain.id
g = Spheres( name, quality = 10, radii = 0.15, protected=True)
g.replace = 'force'
geomC.addGeom( g, parent=c)
self.managedGeometries.append(g)
# FIXME to update this geom we would have to implement
# self.updateGeom specifically for this command
geomC.atoms[name] = ResidueSet()
g.chain = chain
geomC.atomPropToVertices[name] = self.atomPropToVertices
geomC.geomPickToAtoms[name] = self.pickedVerticesToAtoms
geomC.geomPickToBonds[name] = None
def createGeometries(self, obj):
from DejaVu.Geom import Geom
geomC = obj.geomContainer
c = Geom('path', shape=(0, 0), protected=True)
c.replace = 'force'
geomC.addGeom(c, parent=geomC.masterGeom)
for a in obj.allAtoms:
a.colors['path'] = (1., 1., 1.)
a.opacities['path'] = 1.0
for chain in obj.chains:
if not hasattr(chain, 'sheet2D') or chain.sheet2D is None:
continue
# HACK TO DEBUG SECONDARYSTRUCTURE
if not chain.sheet2D.has_key('ssSheet2D') or \
chain.sheet2D['ssSheet2D'] is None:
continue
# Create a geometry per sheet2D
name = 'path' + chain.id
g = Spheres(name, quality=10, radii=0.15, protected=True)
g.replace = 'force'
geomC.addGeom(g, parent=c)
self.managedGeometries.append(g)
# FIXME to update this geom we would have to implement
# self.updateGeom specifically for this command
geomC.atoms[name] = ResidueSet()
g.chain = chain
geomC.atomPropToVertices[name] = self.atomPropToVertices
geomC.geomPickToAtoms[name] = self.pickedVerticesToAtoms
geomC.geomPickToBonds[name] = None
def initGeom(self):
from DejaVu.IndexedPolylines import IndexedPolylines
#from DejaVu.Labels import Labels
self.quality = 4
self.spheres = self.geom = Spheres('strutsSpheres',
materials=((0, 1, 0), ),
shape=(0, 3),
radii=0.1,
quality=4,
pickable=0,
inheritMaterial=0,
protected=True)
geoms = [self.spheres]
self.masterGeom = Geom('strutsAsSpheresGeoms',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
if self.vf.hasGui:
miscGeom = self.vf.GUI.miscGeom
hbond_geoms = check_hbond_geoms(self.vf.GUI)
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=hbond_geoms)
for item in geoms:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
self.hasGeom = 0
self.spacing = .40
self.radii = 0.1
self.verts = []
def onAddCmdToViewer(self):
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('measureDistance'):
self.vf.loadCommand('measureCommands',
'measureDistance',
'Pmv',
topCommand=0)
self.masterGeom = Geom('measureDistGeom', shape=(0, 0), pickable=0)
self.masterGeom.isScalable = 0
if self.vf.hasGui:
measure_geoms = check_measure_geoms(self.vf.GUI)
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=measure_geoms)
self.lines = IndexedPolylines('distLine',
materials=((1, 1, 0), ),
inheritMaterial=0,
lineWidth=3.,
stippleLines=1,
pickable=0)
self.labels = GlfLabels(name='distLabel',
shape=(0, 3),
font='arial1.glf',
fontStyle='solid3d',
fontScales=(.5, .5, .3),
inheritMaterial=0,
materials=((1, 1, 0), ))
self.spheres = Spheres(name='distSpheres',
shape=(0, 3),
inheritMaterial=0,
radii=0.2,
quality=15,
materials=((1., 1., 0.), ))
if self.vf.hasGui:
for item in [self.lines, self.labels, self.spheres]:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
def displaySphere(coords, rotate=False):
helper = self.autoPACK.apgui.helper
from DejaVu.Spheres import Spheres
spheres = Spheres(
"lipids",
centers=coords,
visible=1,
inheritMaterial=False,
)
self.GUI.VIEWER.AddObject(spheres)
if rotate: helper.rotateObj(spheres, [math.pi / 2.0, 0, 0])
return spheres
def onAddCmdToViewer(self):
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('addBonds'):
self.vf.loadCommand('bondsCommands',
'addBonds',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('removeBondsGC'):
self.vf.loadCommand('bondsCommands',
'removeBondsGC',
'Pmv',
topCommand=0)
self.masterGeom = Geom('addBondsGeom',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
self.spheres = Spheres(name='addBondsSpheres',
shape=(0, 3),
inheritMaterial=0,
radii=0.2,
quality=15,
materials=((1., 1., 0.), ),
protected=True)
if not self.vf.commands.has_key('labelByExpression'):
self.vf.loadCommand('labelCommands', [
'labelByExpression',
],
'Pmv',
topCommand=0)
if self.vf.hasGui:
miscGeom = self.vf.GUI.miscGeom
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=miscGeom)
self.vf.GUI.VIEWER.AddObject(self.spheres, parent=self.masterGeom)
def create(self, target, geom=None, imd=None, forceType="steered"):
self.target = target.findType(Atom) #should be an atom selection
self.imd = imd
if self.imd is not None:
self.slot = self.imd.slot
else:
self.slot = 0
self.initial_position = self.getTargetCenter()
self.previousForce = [0., 0., 0.]
self.scale_force = 0.5 #scale before display and send to MD
self.sphere_radius = 4.
if geom is None:
#by default the handler is a sphere
self.geom = Spheres('handler',
inheritMaterial=False,
centers=[
[0., 0., 0.],
],
radii=[2.],
visible=1)
if self.vf.hasGui: self.vf.GUI.VIEWER.AddObject(self.geom)
else:
self.geom = geom
#if self.vf.hasGui : self.geom.SetTranslation(Numeric.array(self.initial_position))
#else : self.geom.setLocation(self.initial_position[0],self.initial_position[1],self.initial_position[2])
if self.vf.hasGui: self.prepareQuickKeys()
self.N_forces = len(self.target)
self.atoms_list = self.target.number #need to check this
self.forces_list = Numeric.zeros((self.N_forces, 3), 'f')
self.arrow = None
self.isinited = True
self.handler_pattern = None
self.mol_pattern = None
#preaper the arrow that will represent the force
if self.vf.hasGui: self.prepareArrow()
self.forceType = forceType
def displaySphereCenter(center):
helper = self.autoPACK.apgui.helper
from DejaVu.Spheres import Spheres
spheres = Spheres(
"center",
centers=center,
radii=[
10.,
] * len(center),
visible=1,
inheritMaterial=False,
)
self.GUI.VIEWER.AddObject(spheres)
#helper.rotateObj(spheres,[math.pi/2.0,0,0])
return spheres
class SetTorsionGUICommand(MeasureTorsionGUICommand):
def guiCallback(self):
self.save = self.vf.ICmdCaller.commands.value["Shift_L"]
self.vf.setICOM(self, modifier="Shift_L", topCommand=0)
if not hasattr(self, 'form'):
self.buildForm()
else:
self.form.deiconify()
def onAddCmdToViewer(self):
if not hasattr(self.vf, 'GUI'):
return
self.undoNow = 0
self.save = None
from DejaVu.bitPatterns import pat3
from DejaVu.IndexedPolygons import IndexedPolygons
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('measureTorsion'):
self.vf.loadCommand('measureCommands',
'measureTorsion',
'Pmv',
topCommand=0)
self.masterGeom = Geom('setTorsionGeom',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
self.vf.GUI.VIEWER.AddObject(self.masterGeom,
parent=self.vf.GUI.miscGeom)
self.lines = IndexedPolygons(
'settorsionLine',
materials=((0, 1, 1), ),
inheritMaterial=0,
stipplePolygons=1,
protected=True,
)
if self.vf.userpref['Sharp Color Boundaries for MSMS'][
'value'] == 'blur':
self.lines.Set(
inheritSharpColorBoundaries=False,
sharpColorBoundaries=False,
)
self.lines.polygonstipple.Set(pattern=pat3) #, tagModified=False)
#self.lines.RenderMode(GL.GL_FILL, face=GL.GL_BACK)
self.lines.Set(backPolyMode=GL.GL_FILL)
self.labels = GlfLabels(name='settorsionLabel',
shape=(0, 3),
inheritMaterial=0,
materials=((0, 1, 1), ))
self.spheres = Spheres(name='settorsionSpheres',
shape=(0, 3),
radii=0.2,
quality=15,
inheritMaterial=0,
materials=((0., 1., 1.), ),
protected=True)
for item in [self.lines, self.labels, self.spheres]:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
self.snakeLength = 1
self.oldValue = None
self.torsionType = Tkinter.StringVar()
self.torsionType.set('1')
self.newAngList = Tkinter.StringVar()
self.TAHdata = None
self.molecule = None
#self.bondString = Tkinter.StringVar()
self.callbackDict = {}
self.callbackDict['measureDistanceGC'] = 'update'
self.callbackDict['measureAngleGC'] = 'update'
self.callbackDict['measureTorsionGC'] = 'update'
def onRemoveObjectFromViewer(self, mol):
lenAts = len(self.atomList)
#if cmd has no atoms on its list, nothing to do
if not lenAts:
return
#remove any atoms which are being deleted from viewer
self.atomList = AtomSet(self.atomList) - mol.allAtoms
#if some have been removed, do an update
if lenAts != len(self.atomList):
self.update()
self.extslider.set(0)
def __call__(self, atoms, angle=None, **kw):
"""torsion/None<-setTorsionGC(atoms, angle=None)
the torsion is returned when the number of atoms is a multiple of 4"""
ats = self.vf.expandNodes(atoms)
if not len(ats): return 'ERROR'
return apply(self.doitWrapper, (
ats,
angle,
), kw)
def doit(self, ats, angle):
for at in ats:
lenAts = len(self.atomList)
if lenAts and lenAts % 4 != 0 and at == self.atomList[-1]:
continue
if len(self.atomList) == 0:
self.molecule = at.top
if at.top == self.molecule:
self.atomList.append(at)
else:
#all atoms in torsion must be in same molecule ...(?)
s = at.full_name() + " not in " + self.molecule.full_name()
self.warningMsg(s)
return 'ERROR'
if len(self.atomList) > 4 * self.snakeLength:
self.atomList = self.atomList[4:]
self.update()
if len(self.atomList) == 4:
mol = self.atomList[0].top
at0, at1, at2, at3 = self.atomList
self.mov_atoms = mol.subTree(at1, at2, mol.allAtoms)
self.oldValue = self.vf.measureTorsion.doit(at0, at1, at2, at3)
self.origValue = self.oldValue
self.origCoords = self.mov_atoms.coords
if hasattr(self, 'extslider'):
self.extslider.set(self.oldValue, update=0)
if angle:
#angle is what you want to end up with
deltaAngle = angle - self.oldValue
#print 'deltaAngle=', deltaAngle, 'angle=', angle
self.transformCoords(deltaAngle)
if hasattr(self, 'extslider'):
self.extslider.set(angle, update=0)
#s = self.atomList[2].full_name()+'--'+self.atomList[3].full_name()
#self.bondString.set(s)
self.updateHistory()
##if self.undoNow: raise 'abc'
#return float(self.labelStrs[-1])
return
def update(self, forward=1, event=None):
if not len(self.atomList):
self.spheres.Set(vertices=[], tagModified=False)
self.labels.Set(vertices=[], tagModified=False)
self.lines.Set(vertices=[], tagModified=False)
self.vf.GUI.VIEWER.Redraw()
return
limit = self.snakeLength
#each time have to recalculate lineVertices
self.lineVertices = []
for at in self.atomList:
c1 = self.getTransformedCoords(at)
self.lineVertices.append(tuple(c1))
#display spheres:
self.spheres.Set(vertices=self.lineVertices, tagModified=False)
self.vf.GUI.VIEWER.Redraw()
#label with torsion
#lines between spheres are only drawn when angle completed
#that is, len(ats)%4=0
if len(self.lineVertices) < 4:
self.labels.Set(vertices=[], tagModified=False)
self.lines.Set(vertices=[], tagModified=False)
else:
#rebuild labels and polygons each time
self.labelCenters = []
self.labelStrs = []
#labelCenters, labelStrs,
#this gets done lenATs/4 times
numItems = len(self.atomList) / 4
for i in range(numItems):
at0, at1, at2, at3 = self.atomList[i * 4:i * 4 + 4]
torsion = self.vf.measureTorsion.doit(at0, at1, at2, at3)
torsionLabel = '%.3f' % torsion
self.labelStrs.append(torsionLabel)
c0 = self.getTransformedCoords(at0)
c1 = self.getTransformedCoords(at3)
newcenter = tuple((c0 + c1) / 2.0)
self.labelCenters.append(newcenter)
self.vf.GUI.VIEWER.Redraw()
items = self.callbackDict.keys()
#items = ['measureDistanceGC','measureAngleGC','measureTorsionGC']
#checkout whether measure update needs to be called
icomVals = self.vf.ICmdCaller.commands.value.values()
for item in items:
if not len(icomVals): break
if not hasattr(self.vf, item):
continue
exec('cmd = self.vf.' + item)
if cmd in icomVals:
#cmd.update()
s = self.callbackDict[item]
exec('self.vf.' + item + '.' + s + '()')
def transformCoords(self, deltaAngle):
""" deltaAngle is NOW not final angle wanted but relative"""
#mov_coords is the array of the coords of the atoms to be moved,
#x2 and x3 are atoms which define the axis of the transformation
#by deltaAngle. NB: effect is that mov_atoms.coords
#are transformed...
if not hasattr(self, 'mov_atoms'): return
if not len(self.mov_atoms): return
x1, x2, x3, x4 = self.atomList
nc = self.vf.setRelativeTorsion.doit(x2,
x3,
deltaAngle,
self.mov_atoms,
returnVal=1)
mol = x2.top
#mov_atoms = mol.subTree(x2, x3, mol.allAtoms)
for i in range(len(nc)):
at = self.mov_atoms[i]
at._coords[at.conformation] = nc[i].tolist()
event = EditAtomsEvent('coords', self.mov_atoms)
self.vf.dispatchEvent(event)
self.update()
#####Callback Functions for the Dial:
#####slideCallback
def slideCallback(self, eventval):
#print 'in slideCallback'
if len(self.atomList) != 4: return
if not hasattr(self, 'oldValue'): return
if self.oldValue == None:
return
#self.setupUndoBefore(self.atomList, self.oldValue)
try:
newAngle = self.extslider.get()
tT = self.torsionType.get()
at0, at1, at2, at3 = self.atomList
#torsion = self.vf.measureTorsion.doit(at0, at1, at2, at3)
torsion = self.oldValue
if tT == '1':
#NEWdeltaAngle = newAngle
deltaAngle = newAngle - torsion
else:
#NEWdeltaAngle = newAngle + torsion
deltaAngle = newAngle
self.transformCoords(deltaAngle)
#print 'deltaAngle=', deltaAngle
self.oldValue = newAngle
#self.oldValue = newAngle
except ValueError:
self.vf.GUI.message("error in slideCallback\n")
def rdSet(self, event=None):
#"""radiobutton selection of torsionType:
#Absolute: initial angle to be displayed in slider/entry
#Relative: 0 is displayed """
if self.torsionType.get() == '1':
aL = self.atomList
if len(aL) == 4:
torsion = self.vf.measureTorsion.doit(aL[0], aL[1], aL[2],
aL[3])
self.extslider.set(torsion)
else:
self.extslider.set(0)
def setupUndoBefore(self, ats, angle):
pass
#def setupUndoBefore(self, ats, angle):
##no atoms, <4 atoms,
#aSet = AtomSet(self.atomList)
#self.undoMenuString = self.name
#if len(self.atomList)==0:
#undoCmd = 'self.setTorsionGC.atomList=[]; self.setTorsionGC.update()'
#elif len(self.atomList)<4:
##need to step back here
#undoCmd = 'self.setTorsionGC.atomList=self.setTorsionGC.atomList[:-1]; self.setTorsionGC.update()'
#else:
##print 'self.oldValue=', self.oldValue
#undoCmd = 'self.setTorsionGC(\''+ aSet.full_name()+ '\',' + str(self.oldValue) + ', topCommand=0)'
##self.oldValue = str(self.extslider.get())
#self.vf.undo.addEntry((undoCmd), (self.name))
def setupUndoAfter(self, ats, angle, **kw):
#no atoms, <4 atoms,
aSet = AtomSet(self.atomList)
self.undoMenuString = self.name
if len(self.atomList) == 0:
undoCmd = 'self.setTorsionGC.atomList=[]; self.setTorsionGC.update()'
elif len(self.atomList) < 4:
#need to step back here
undoCmd = 'self.setTorsionGC.atomList=self.setTorsionGC.atomList[:-1]; self.setTorsionGC.update()'
elif self.origValue == self.oldValue:
return
else:
restoreAngle = self.origValue
self.undoNow = 1
undoCmd = 'self.setTorsionGC(\'' + aSet.full_name() + '\',' + str(
restoreAngle) + ', topCommand=0)'
self.vf.undo.addEntry((undoCmd), (self.name))
def Accept_cb(self):
apply(self.setupUndoAfter, (self.atomList, self.oldValue), {})
self.origValue = self.oldValue
def Done_cb(self):
self.vf.setICOM(self.save,
modifier="Shift_L",
mode='pick',
topCommand=0)
self.stopICOM()
def startICOM(self):
self.vf.setIcomLevel(Atom)
if not hasattr(self, 'form'):
self.buildForm()
else:
self.form.deiconify()
def stopICOM(self):
if hasattr(self, 'form'):
self.form.withdraw()
self.atomList = []
self.atomCenters = []
self.labelStrs = []
self.labelCenters = []
self.lineVertices = []
self.spheres.Set(vertices=[], tagModified=False)
self.lines.Set(vertices=[], faces=[], tagModified=False)
self.labels.Set(vertices=[], tagModified=False)
self.vf.GUI.VIEWER.Redraw()
#when cmd stops being icom, remove callback
## ehm = self.vf.GUI.ehm
## for event in ['<B2-Motion>', '<B3-Motion>']:
## if ehm.eventHandlers.has_key(event) and self.update_cb in \
## ehm.eventHandlers[event]:
## ehm.RemoveCallback(event, self.update_cb)
for event in ['<B2-Motion>', '<B3-Motion>']:
self.vf.GUI.removeCameraCallback(event, self.update_cb)
def repeat_transTors(self, event=None):
deltaAngle = self.extslider.get()
if self.torsionType.get() != '1':
self.transformCoords(deltaAngle)
#this is here in order to create a log message
nc = self.vf.setRelativeTorsion(self.atomList[1],
self.atomList[2],
deltaAngle,
self.mov_atoms,
returnVal=1)
event = EditAtomsEvent('coords', self.mov_atoms)
self.vf.dispatchEvent(event)
def new_Tors(self, event=0):
self.atomList = []
self.update()
#when called, most recent 4 atoms are in self.atomList
def updateHistory(self):
"""1: call TorsionHistory.getTorsion:
make a new TorsionAngle or add current angle to angleList
2: put TA.name_string into ListBox
3: best if insert a tuple (string to be displayed, item itself)
4: adjust size with self.historyList.configure(height=self.[].size)
5: limit overall size to 4"""
#print 'in updateHistory'
molecule = self.atomList[-1].top
if self.TAHdata is None:
self.TAHdata = TorsionHistory(molecule)
a1, a2, a3, a4 = self.atomList
newone = self.TAHdata.getTorsion(a1, a2, a3, a4)
#first check to see if it is in there already???
#need to get info back from getTorsion....(???)
if hasattr(self, 'historyList'):
if newone.new:
self.historyList.insert('end', newone.name_string)
if int(self.historyList.cget('height')) < 4:
self.historyList.configure(height=self.historyList.size())
if self.historyList.curselection():
self.historyList.select_clear(self.historyList.curselection())
newindex = self.TAHdata.getIndex(newone)
self.historyList.select_set(newindex)
self.historyList.see(newindex)
#set entry to a string ==current TA's angleList
newstring = ""
for item in newone.angleList:
newstring = newstring + " " + "%5.3f" % item
self.newAngList.set(newstring)
def HLCommand(self, event=None):
"""double-clicking selection in listbox causes curselection to be picked...
1:self.atomList set to atoms of curselection
2:self.mov_atoms set to atoms of curselection
3:self.selAtom[1-4].Set(vertices=atoms.coords)
4:reset entry +slider and init_bondAngle etc
5.add current angle to selection's.angleList"""
#get TA:
if self.historyList.get(0) == '': return
items = self.historyList.curselection()
if type(items) == types.TupleType:
items = items[0]
try:
items = map(int, items)
except ValueError:
pass
thisTA = self.TAHdata.torslist[items[0]]
#get currentAngle
current = thisTA.getCurrentAngle()
if not thisTA.inList(current):
thisTA.angleList.append(current)
newAts = AtomSet([thisTA.atom1,thisTA.atom2, thisTA.atom3,\
thisTA.atom4])
#reset self.molecule
self.atomList = []
self.molecule = newAts[0].top
self.doit(newAts, current)
#self.setTorsionAngle(thisTA.atom1, thisTA.atom2, thisTA.atom3, thisTA.atom4, current, 'A')
#self.drawTransformedAngle()
#self.updatespheres(items[0])
#self.update()
self.extslider.set(current, 0)
newstring = ""
for item in thisTA.angleList:
newstring = newstring + " " + "%5.3f" % item
self.newAngList.set(newstring)
def getAngList(self, event=None):
items = self.historyList.curselection()
try:
items = map(int, items)
except ValueError:
pass
thisTA = self.TAHdata.torslist[items[0]]
thisTA.angleList = map(float, split(self.newAngList.get()))
last = thisTA.angleList[-1]
newAts = AtomSet([thisTA.atom1,thisTA.atom2, thisTA.atom3,\
thisTA.atom4])
#reset self.molecule
self.atomList = []
self.molecule = newAts[0].top
self.doit(newAts, last)
#self.doit(thisTA.atom1, thisTA.atom2, thisTA.atom3, thisTA.atom4,last,'A')
#self.setTorsionAngle(thisTA.atom1, thisTA.atom2, thisTA.atom3, thisTA.atom4,last,'A')
#self.drawTransformedAngle()
#self.updatespheres(items[0])
self.extslider.set(last, 0)
def stepBack(self, event=None):
items = self.historyList.curselection()
if len(items) == 0: return
try:
items = map(int, items)
except ValueError:
pass
thisTA = self.TAHdata.torslist[items[0]]
####last angle is thisTA.angleList[-1]
if len(thisTA.angleList) > 1:
last = thisTA.angleList[-1]
lastIndex = thisTA.angleList.index(last)
thisTA.angleList = thisTA.angleList[:lastIndex]
last = thisTA.angleList[-1]
else:
last = thisTA.angleList[0]
newAts = AtomSet([thisTA.atom1,thisTA.atom2, thisTA.atom3,\
thisTA.atom4])
#reset self.molecule
self.atomList = []
self.molecule = newAts[0].top
self.doit(newAts, last)
#self.doit(thisTA.atom1, thisTA.atom2, thisTA.atom3, thisTA.atom4,last,'A')
#self.setTorsionAngle(thisTA.atom1, thisTA.atom2, thisTA.atom3, thisTA.atom4,last,'A')
#self.drawTransformedAngle()
#self.updatespheres(items[0])
newstring = ""
for item in thisTA.angleList:
newstring = newstring + " " + "%5.3f" % item
self.newAngList.set(newstring)
self.extslider.set(last, 0)
#IS THIS ENOUGH in order to create correct log?
self.mouseUp()
def startOver(self, event=None):
items = self.historyList.curselection()
if len(items) == 0: return
try:
items = map(int, items)
except ValueError:
pass
thisTA = self.TAHdata.torslist[items[0]]
self.resetAngle(thisTA)
def resetAngle(self, thisTA, event=None):
#first angle is thisTA.angleList[0]
ang = thisTA.angleList[0]
newAts = AtomSet([thisTA.atom1,thisTA.atom2, thisTA.atom3,\
thisTA.atom4])
#reset self.molecule
self.atomList = []
self.molecule = newAts[0].top
self.doit(newAts, ang)
#self.doit(thisTA.atom1, thisTA.atom2, thisTA.atom3, thisTA.atom4,ang,'A')
#self.setTorsionAngle(thisTA.atom1, thisTA.atom2, thisTA.atom3, thisTA.atom4,ang,'A')
if len(thisTA.angleList) > 1:
thisTA.angleList = thisTA.angleList[:1]
#self.drawTransformedAngle()
self.extslider.set(ang, 0)
self.mouseUp()
self.newAngList.set("%5.3f" % ang)
def resetAll(self, event=None):
if self.TAHdata == None: return
for item in self.TAHdata.torslist:
self.resetAngle(item)
self.spheres.Set(vertices=[], tagModified=False)
self.vf.GUI.VIEWER.Redraw()
def buildForm(self):
if hasattr(self, 'ifd'):
return
self.torsionType = Tkinter.StringVar()
self.torsionType.set('1')
self.ifd = ifd = InputFormDescr(title='Set Torsion Angle')
ifd.append({
'name': 'extLabel',
'widgetType': Tkinter.Label,
'wcfg': {
'text': 'Set Angle:\n(180=trans)'
},
'gridcfg': {
'sticky': Tkinter.W + Tkinter.E,
'columnspan': 2
}
})
ifd.append({
'name': 'extslider',
'widgetType': ExtendedSliderWidget,
'wcfg': {
'label': 'torsion',
'minval': -360.,
'maxval': 360.,
'width': 150,
'immediate': 1,
'command': self.slideCallback,
'sliderType': 'float',
'entrypackcfg': {
'side': 'bottom'
}
},
'gridcfg': {
'sticky': 'we',
'columnspan': 2
}
})
ifd.append({
'name': 'typeLabel',
'widgetType': Tkinter.Label,
'wcfg': {
'text': 'Torsion Type'
},
'gridcfg': {
'sticky': 'we',
'columnspan': 2
}
})
ifd.append({
'name': 'rdbut1',
'widgetType': Tkinter.Radiobutton,
'wcfg': {
'text': 'Absolute',
'variable': self.torsionType,
'value': 1,
'command': self.rdSet
},
'gridcfg': {
'sticky': 'we'
}
})
ifd.append({
'name': 'rdbut2',
'widgetType': Tkinter.Radiobutton,
'wcfg': {
'text': 'Relative ',
'variable': self.torsionType,
'value': 0,
'command': self.rdSet
},
'gridcfg': {
'sticky': 'we',
'row': -1,
'column': 1
}
})
ifd.append({
'name': 'historyList',
'widgetType': ListChooser,
'wcfg': {
'title': 'TorsionAngle\nTranformation History',
'mode': 'single',
'command': self.HLCommand,
'lbwcfg': {
'height': 5,
'selectforeground': 'yellow',
'exportselection': 0,
'width': 30
},
},
'gridcfg': {
'sticky': 'we',
'columnspan': 2
}
})
ifd.append({
'name': 'hbut1',
'widgetType': Tkinter.Button,
'wcfg': {
'text': 'Step Back ',
'command': self.stepBack
},
'gridcfg': {
'sticky': 'we',
'columnspan': 2
}
})
ifd.append({
'name': 'hbut2',
'widgetType': Tkinter.Button,
'wcfg': {
'text': 'Start Over ',
'command': self.startOver
},
'gridcfg': {
'sticky': 'we',
'columnspan': 2
}
})
ifd.append({
'name': 'hbut3',
'widgetType': Tkinter.Button,
'wcfg': {
'text': 'Reset All ',
'command': self.resetAll
},
'gridcfg': {
'sticky': 'we',
'columnspan': 2
}
})
ifd.append({
'name': 'angListEnt',
'widgetType': Tkinter.Entry,
'wcfg': {
'width': 5,
'command': self.getAngList,
'textvariable': self.newAngList
},
'gridcfg': {
'sticky': 'we',
'columnspan': 2
}
})
ifd.append({
'name': 'hbut4',
'widgetType': Tkinter.Button,
'wcfg': {
'text': 'Move',
'command': self.repeat_transTors
},
'gridcfg': {
'sticky': 'we',
'columnspan': 2
}
})
ifd.append({
'name': 'hbut5',
'widgetType': Tkinter.Button,
'wcfg': {
'text': 'New Torsion',
'command': self.new_Tors
},
'gridcfg': {
'sticky': 'we',
'columnspan': 2
}
})
#ifd.append({'name':'accept',
#'widgetType': Tkinter.Button,
#'wcfg':{'text' : 'Accept',
#'command': self.Accept_cb},
#'gridcfg':{'sticky':'we'}})
ifd.append({
'name': 'done',
'widgetType': Tkinter.Button,
'wcfg': {
'text': 'Done',
'command': self.Done_cb
},
'gridcfg': {
'sticky': 'we',
'columnspan': 2
}
})
#'gridcfg':{'sticky':'we','column':1, 'row':-1}})
self.form = self.vf.getUserInput(ifd, modal=0, blocking=0)
self.form.root.protocol('WM_DELETE_WINDOW', self.Done_cb)
self.extslider = self.ifd.entryByName['extslider']['widget']
self.extslider.draw.bind('<ButtonRelease-1>', self.mouseUp, add='+')
self.extslider.entry.bind('<Return>', self.mouseUp, add='+')
self.historyList = self.ifd.entryByName['historyList']['widget'].lb
#self.historyList.bind("<Double-Button-1>",self.HLCommand)
self.hbut1 = self.ifd.entryByName['hbut1']['widget']
self.hbut2 = self.ifd.entryByName['hbut2']['widget']
self.hbut3 = self.ifd.entryByName['hbut3']['widget']
self.angListEnt = self.ifd.entryByName['angListEnt']['widget']
def mouseUp(self, event=None):
#print "in mouseUp"
#fix this: atomList length dependent
if len(self.atomList) == 4:
at0, at1, at2, at3 = self.atomList
angle = self.extslider.get()
if self.torsionType.get() == '1':
self.vf.setTorsion(at0, at1, at2, at3, angle)
else:
self.vf.setRelativeTorsion(at1, at2, angle)
class SuperImposeAtomsGUICommand(MVCommand, MVAtomICOM):
"""
The SuperImposeAtomsGUICommand provides a GUI interface to the SuperImposeAtomsCommand.
- For now Only two 2 sets of Atoms belonging to a ref molecule and a mobile molecule
can be superimposed simultaneously.
- The command provides two way of defining those two sets of atoms:
* By picking nodes at the different levels (Molecule, Chain, Residue, Atom) the first pick
will define the reference set and the second the mobile set. The picking process will have
be done later on the same way and defines a list of pairs of atoms.
If the user drags a box only the first node will be considered. Nodes are then converted into
an set of Atoms. The 'Edit Atoms Pairs' allows the user to see the pairs but also to alter those
sets. For example only the backbone atoms can be considered or all atoms etc. The user can also
create his own filter by typing a lambda function in the entry of the combobox.
If the 2 sets are not of the same length the extra atoms can be removed either from the beginning,
the end or half and half of the longest set allowing a bit more flexibility.
If the resulting 2 sets are None then the superimposition cannot be computed. You can reset the
process and start over or alter your set using the tools described above.
* By string: If the user knows the set of nodes of respectively the reference molecule and mobile
molecule to be use for the computation two string selector widgets allows him to proceed more
efficiently.
- Known bug:
* If the reference molecule is transformed independently of the mobile molecule the mobile
molecule will be superimposed onto the original location of the reference molecule. (Working on it)
* Cannot superimpose simultaneously multiple sets of molecule.
* And probably many more ....
"""
def __init__(self, func=None):
MVCommand.__init__(self, func)
MVAtomICOM.__init__(self)
self.refAtomList = []
self.inAtomList = []
#self.superImposedPairs = {}
self.newPairs = {}
self.pair = []
self.mobMolName = None
self.refMolName = None
self.filters = {'CA Atoms':lambda x: x.name == 'CA',
'Backbone Atoms': lambda x: x.name in ['CA', 'C',
'N', 'O',
'CA@A','C@A',
'N@A','O@A'],
'Heavy Atoms': lambda x: not x.element == 'H',
'All Atoms': None}
self.defaultFilter = 'Backbone Atoms'
def onAddCmdToViewer(self):
# Check first is any of the command that superimpose depends on are
# already loaded.
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands', 'setICOM', 'Pmv',
topCommand = 0)
if not self.vf.commands.has_key('superimposeAtoms'):
self.vf.loadCommand('superImposeCommands', 'superimposeAtoms',
'Pmv', topCommand = 0)
if not self.vf.commands.has_key('startContinuousPicking'):
self.vf.loadCommand('dejaVuCommands','startContinuousPicking',
'ViewerFramework', topCommand = 0)
if not self.vf.commands.has_key('stopContinuousPicking'):
self.vf.loadCommand('dejaVuCommands','stopContinuousPicking',
'ViewerFramework', topCommand = 0)
if not self.vf.commands.has_key('labelByExpression'):
self.vf.loadCommand('labelCommands', 'labelByExpression', 'Pmv',
topCommand = 0)
self.sphere1 = Spheres(name='elt1', radii=0.5,
materials = ( (0.,1.,0.),), protected=True)
self.sphere2 = Spheres(name = 'elt2', radii=0.5,
materials = ( (1.,1.,0.),), protected=True)
#self.form = None
def onRemoveObjectFromViewer(self,obj):
if hasattr(self.vf,'alignment'):
self.vf.alnEditor.deleteSequence(obj.name)
self.vf.alnEditor.redraw()
if obj.name == self.refMolName:
self.refMolName=None
if obj.name == self.mobMolName:
self.mobMolName=None
def guiCallback(self):
self.vf.setICOM(self, modifier="Shift_L", topCommand=0)
def buildFormDescr(self, formName):
if formName == 'superimpose':
idf = InputFormDescr(title="Set Superimposition Parameters")
idf.append( {'widgetType':Tkinter.Label,
'wcfg': {'text':'Get Nodes:'},
'gridcfg':{'sticky':'w'}})
self.typeVar = Tkinter.StringVar()
self.typeVar.set('By Picking')
idf.append( {'widgetType':Tkinter.Radiobutton,
'name': 'string',
'wcfg':{'variable':self.typeVar,
'text': 'From String',
'value':'From String',
'command':self.string_cb,
},
'gridcfg':{'sticky':'w', 'columnspan':3}})
idf.append( {'widgetType':Tkinter.Radiobutton,
'name': 'string',
'wcfg':{'variable':self.typeVar,
'text': 'From Alignment',
'value':'From Alignment',
'command':self.alignment_cb,
},
'gridcfg':{'sticky':'w', 'columnspan':3}})
idf.append( {'widgetType':Tkinter.Radiobutton,
'name': 'refPicking',
'wcfg':{'variable':self.typeVar,
'text': 'By Picking',
'value':'By Picking',
},
'gridcfg':{'sticky':'w'} })
idf.append( {'widgetType':Tkinter.Label,
'wcfg': {'text':'Reference nodes:'},
'gridcfg':{'sticky':'w'}})
idf.append( {'widgetType':Tkinter.Label,
'wcfg': {'text':'Mobile nodes:'},
'gridcfg':{'sticky':'e', 'row':-1}})
idf.append({'widgetType':Tkinter.Label,
'name':'firstNode',
'wcfg':{ 'text':''},
'gridcfg':{'sticky':'we'}})
idf.append({'widgetType': Tkinter.Label,
'name':'secondNode',
'wcfg':{ 'text':''},
'gridcfg':{'sticky':'we', 'row':-1}})
idf.append({'widgetType':Tkinter.Button,
'name':'editPairs',
'wcfg':{'text':'Edit Ref Atom -- Mob Atom Pairs',
'command':self.editPairs_cb,},
'gridcfg':{'sticky':'we','columnspan':3}
})
# Continuous Superimposition
idf.append({'widgetType':Tkinter.Checkbutton,
'name':'continuous',
'wcfg':{'variable':Tkinter.IntVar(),
'text':'Continuous Superimposition',
'command':self.continuous_cb,
'padx':10,'pady':10},
'gridcfg':{'sticky':'w'}})
# Reset & SuperImpose button.
idf.append({'widgetType':Tkinter.Button,
'name':'final',
'wcfg':{'width':15,'text':'Superimpose',
'command':self.superimpose_cb},
'gridcfg':{'sticky':'we', 'row':-1}})
idf.append({'widgetType':Tkinter.Button,
'name':'reset',
'wcfg':{'text':'Reset', 'command':self.reset_cb},
'gridcfg':{'sticky':'we', 'row':-1}})
elif formName == 'editPair':
idf = InputFormDescr(title='Edit Reference Atom - Mobile Atom Pairs')
idf.append({'widgetType':Pmw.ComboBox,
'name':'choice',
'defaultValue':self.defaultFilter,
'wcfg':
{'label_text':'Atoms to be consider for superimposition:',
'labelpos':'n','label_padx':10,'label_pady':10,
'scrolledlist_items': self.filters.keys(),
'selectioncommand':self.setDefault},
'gridcfg':{'sticky':'w'}})
# If sets not of the same length:
idf.append({'widgetType':Pmw.ComboBox,
'name':'slice',
'defaultValue':'Beginning',
'wcfg':
{'label_text':'Sets not of the same length',
'labelpos':'n','label_padx':10,'label_pady':10,
'scrolledlist_items':['Beginning',
'End',
'Half/Half']
},
'gridcfg':{'sticky':'w', 'row':-1}})
entries = map(lambda x: (x, None), self.newPairs.keys())
idf.append({'widgetType':ListChooser,
'name':'newpairs',
'wcfg':{'mode':'extended',
'entries':entries,
'lbwcfg':{'exportselection':1},
'title':'Reference Atoms -- Mobile Atoms'},
'gridcfg':{'sticky':'wens', 'columnspan':2}})
idf.append({'widgetType':Tkinter.Button,
'name': 'delete',
'wcfg':{'width':15,'text': 'Delete Pairs',
'command':self.delete_cb},
'gridcfg':{'sticky':'we', 'columnspan':2}})
idf.append({'widgetType':Tkinter.Button,
'name': 'dismiss',
'wcfg':{'text': 'DISMISS',
'command':self.dismiss_cb},
'gridcfg':{'sticky':'we', 'columnspan':2}})
elif formName == 'editString':
idf = InputFormDescr(title = 'Get Nodes From String')
idf.append({'widgetType':Tkinter.Label,
'wcfg':{'text':'Reference Nodes: '},
'gridcfg':{'sticky':'w'}})
idf.append({'widgetType':Tkinter.Label,
'wcfg':{'text':'Mobile Nodes: '},
'gridcfg':{'sticky':'w', 'row':-1}})
idf.append({'widgetType':Tkinter.Label,
'wcfg':{'text':' '},
'gridcfg':{'columnspan':2, 'sticky':'w'}})
idf.append({ 'widgetType':StringSelectorGUI,
'name':'refNodes','required':1,
'wcfg':{ 'molSet': self.vf.Mols,
'vf': self.vf,
'all':1,
'crColor':(1.,0.,0.),
},
'gridcfg':{'sticky':'we' }})
idf.append({ 'widgetType':StringSelectorGUI,
'name':'mobNodes','required':1,
'wcfg':{ 'molSet': self.vf.Mols,
'vf': self.vf,
'all':1,
'crColor':(0.,0.,1.),
},
'gridcfg':{'row':-1, 'sticky':'we' }})
return idf
def initICOM(self, modifier):
# Create the form if not existing yet
form = self.showForm(formName = 'superimpose', modal=0, blocking=0)
self.firstLabel = form.descr.entryByName['firstNode']['widget']
self.secondLabel = form.descr.entryByName['secondNode']['widget']
self.contVar = form.descr.entryByName['continuous']['wcfg']['variable']
self.pairForm = None
# set the callback of continuousPicking to label the picked node
# 1- get a handle on the cbManager
cbManager = self.vf.startContinuousPicking.cbManager
# 2- Save the existing callbacks
self.oldCallBacks = cbManager.callbacks
# 3- Set to the new callback
cbManager.SetCallback(CallBackFunction(self.labelByName))
self.vf.startContinuousPicking()
self.supcb = 0
def setDefault(self, text):
self.defaultFilter = text
if hasattr(self, 'pair') and len(self.pair) == 2:
filter = self.filters[text]
set1 = self.pair[0]
set2 = self.pair[1]
if filter:
set1 = set1.get(filter)
set2 = set2.get(filter)
if (set1 and set2) and (len(set1) == len(set2)):
self.updateChooser(set1, set2)
def editPairs_cb(self, event=None):
pairForm = self.showForm('editPair', force = 1, modal=0, blocking=0,
onDestroy= self.dismiss_cb)
# show panel with the listchooser of the panel and
# Choose the atoms to do the superimposition
self.chooser = pairForm.descr.entryByName['newpairs']['widget']
def dismiss_cb(self, event=None):
if self.cmdForms.has_key('editPair'):
self.cmdForms['editPair'].destroy()
del self.cmdForms['editPair']
def string_cb(self, event=None):
#get rid of the alignment GUI
if hasattr(self.vf,'alnEditor'):
self.vf.alnEditor.exit()
val = self.showForm('editString')
print val
if not val == {} or (val.has_key('refNodes') and val.has_key('mobNodes')):
apply(self.doitWrapper, (val['refNodes'],), {'log':0})
apply(self.doitWrapper, (val['mobNodes'],), {'log':0})
self.typeVar.set('By Picking')
def continuous_cb(self, event=None):
#get rid of the alignment GUI
if hasattr(self.vf,'alnEditor'):
self.vf.alnEditor.exit()
form = self.cmdForms['superimpose']
supButton = form.descr.entryByName['final']['widget']
if self.contVar.get() == 1:
supButton.configure(state=Tkinter.DISABLED)
if len(self.newPairs)>=4:
self.superimpose_cb()
else:
supButton.configure(state=Tkinter.NORMAL)
def labelByName(self, pick):
# Continuous labeling.
if pick is None: return
atom = self.vf.findPickedAtoms(pick)
if atom:
level = self.vf.ICmdCaller.level.value
self.vf.ICmdCaller.level.AddCallback(self.unlabelLevel)
if level == Molecule : level = Protein
self.node = atom.findType(level)
funcItems = map(lambda x: x.full_name(), self.node)
self.vf.labelByExpression(self.node,
font = 'arial1.glf',
location = 'First',
textcolor = 'red', only = 1,
lambdaFunc = 1,negate=0,
function = 'lambda x: str(x.full_name())\n\n',
topCommand=0,
)
def unlabelLevel(self, newLevel, oldLevel):
if not hasattr(self, 'node'): return
if oldLevel == Molecule: oldLevel = Protein
# need to be at the former level for all the former picked stuff
# so take it all.
node = self.vf.getSelection()
nodes = node.findType(oldLevel)
# Careful in labelByProperty fix a bug if no label should not break!
self.vf.labelByExpression(nodes, negate=1, log=0)
def stopICOM(self):
# Destroy the inputForm
self.cmdForms['superimpose'].root.destroy()
# Set the form to None.
del self.cmdForms['superimpose']
# Set back the continuousPicking to unsolicitedPick
cbManager = self.vf.startContinuousPicking.cbManager
if not len(self.oldCallBacks) == 0:
cbManager.SetCallback(self.oldCallBacks[0])
if len(self.oldCallBacks)>1:
for cb in self.oldCallBacks[1:]:
cbManager.AddCallBack(cb)
# Remove the unlabel callback bound to the self.vf.ICmdCaller.level
if self.unlabelLevel in self.vf.ICmdCaller.level.callbacks:
self.vf.ICmdCaller.level.RemoveCallback(self.unlabelLevel)
# Unlabel whatever is labeled
level = self.vf.ICmdCaller.level.value
nodes = self.vf.getSelection().findType(level)
if not nodes is None or len(nodes)!=0:
self.vf.labelByExpression(nodes, negate=1, log=0)
# Stop the continuous picking.
self.vf.stopContinuousPicking()
self.sphere1.Set(vertices=[], tagModified=False)
self.sphere2.Set(vertices=[], tagModified=False)
## self.visualFeedBack(vertices =[])
def updateChooser(self, set1, set2):
for elt1, elt2 in map(None, set1, set2):
key = elt1.full_name() + '--' + elt2.full_name()
self.newPairs[key] = (elt1, elt2)
if not self.pairForm is None:
entry = (key, None)
self.chooser.add(entry)
def reset_cb(self, event=None):
"""Button to reset the superimposition and the list of pairs."""
# Reset the chooser and the lists of pairs
if self.newPairs == {}: return
if not self.pairForm is None:
self.chooser.clear()
self.newPairs = {}
# Reset the geometry.
vi = self.vf.GUI.VIEWER
geom = self.mobileMol.geomContainer.masterGeom
oldCurrent = vi.currentObject
vi.SetCurrentObject(geom)
# transform only the given geometry.
if vi.redirectTransformToRoot == 1:
old = vi.redirectTransformToRoot
vi.TransformRootOnly(0)
else:
old = 0
# Right now reset all the transformations applied to the mobile object.
# Maybe should separate from the superimposition and only reset these.
vi.ResetCurrentObject()
# Put everything back like it was before.
if old == 1:
vi.TransformRootOnly(1)
vi.SetCurrentObject(oldCurrent)
self.sphere1.Set(vertices=[], tagModified=False)
self.sphere2.Set(vertices=[], tagModified=False)
self.firstLabel.configure(text='')
self.secondLabel.configure(text='')
## self.visualFeedBack.Set(vertices=[], tagModified=False)
def delete_cb(self, event = None):
# Delete the selected pair from the listchooser and from the pairlist
selectedNewPairs = self.chooser.get()
# Undisplay the label (Maybe only if the last pair is being deleted )
self.firstLabel.configure(text='')
self.secondLabel.configure(text='')
for pair in selectedNewPairs:
if len(self.chooser.entries) >=4:
self.chooser.remove(pair)
del self.newPairs[pair]
if self.contVar.get()==1 or self.supcb==1:
self.superimpose_cb()
def superimpose_cb(self, event=None):
if len(self.newPairs) >= 4 :
# Need at least 4 pairs of atoms to do the superimposition
setAtm1 = AtomSet(map(lambda x: x[0],
self.newPairs.values()))
setAtm2 = AtomSet(map(lambda x: x[1],
self.newPairs.values()))
if len(setAtm1) != len(setAtm2):
message = ' ERROR: the 2 sets of atoms are not of the length\nthe superimposition cannot be performed. '
self.warningMsg(msg)
return
self.vf.superimposeAtoms(setAtm1, setAtm2)
self.supcb = 1
## self.visualFeedBack.Set(vertices=self.visualVertices,
## tagModified=False)
def __call__(self, atoms, **kw):
ats = self.vf.expandNodes(atoms)
if not len(ats): return 'ERROR'
kw['redraw']=1
kw['log']=0
return apply(self.doitWrapper, (ats,), kw)
def doit(self, nodes):
"""
Create the 2 sets of atom that will be used to do the superimposition.
Then call the superImposeCommand with these 2 sets.
If continuous is on then the superimposition will be updated each time
a pair of atoms is added otherwise the superimposition will be updated
every 4 pairs of atoms.
"""
# Get the ICOM level
icomLevel = self.vf.ICmdCaller.level.value
# Not doing anything if no nodes picked:
if not nodes: return
if self.typeVar.get() == 'By Picking':
# only take the first node picked.
node = nodes[0]
nodeMol = node.top
elif self.typeVar.get() == 'From String':
node = nodes
molecules = nodes.top.uniq()
if len(molecules)>1:
# nodes need to belong to only one molecule
return
else: nodeMol = molecules[0]
elif self.typeVar.get() == 'From Alignment':
node = nodes
molecules = nodes.top.uniq()
if len(molecules)>1:
# nodes need to belong to only one molecule
return
else: nodeMol = molecules[0]
# 2- Get the atoms from the chosen nodes
atms = node.findType(Atom)
# First set of nodes == defines the first set of 1st elt in the pairs
if len(self.pair) == 0 :
self.secondLabel.configure(text ='')
# Defines reference molecule:
if self.newPairs == {}:
self.refMol = nodeMol
# Draw the feedBack sphere.
mGeom = self.refMol.geomContainer.masterGeom
self.vf.GUI.VIEWER.AddObject(self.sphere1, parent = mGeom)
if nodeMol != self.refMol:
self.firstLabel.configure(text ='')
# if the node belongs to the another molecule return.
# The pairs are defined allways in the same order.
return
self.pair.append(atms)
#self.pair.append(node)
if self.typeVar.get() == 'By Picking':
self.firstLabel.configure(text=node.full_name())
elif len(self.pair) == 1 :
# Creates Second set of elt in the pair.
if self.newPairs=={}:
if nodeMol != self.refMol:
# set the mobile molecule and finish the first pair
self.mobileMol = nodeMol
mGeom = self.mobileMol.geomContainer.masterGeom
self.vf.GUI.VIEWER.AddObject(self.sphere2,
parent = mGeom)
if nodeMol != self.mobileMol:
return
self.pair.append(atms)
#self.pair.append(node)
if self.typeVar.get() == 'By Picking':
self.secondLabel.configure(text=node.full_name())
# Now we have the two set of elts to create pairs:
# 1- Check if the 2 sets have the same length:
set1 = self.pair[0]
set1.sort()
set2 = self.pair[1]
set2.sort()
if not set1 or not set2:
print "ERROR: One of the sets is None"
return
elif len(set1) != len(set2):
if node.__class__ == Atom:
print 'ERROR: the 2 sets of atoms are not of the same size'
return
set1,set2
if node.__class__ in [Protein,ProteinSet, Residue, ResidueSet, Chain, ChainSet]:
filter = self.defaultFilter
if self.filters.has_key(filter):
set1 = self.pair[0].get(self.filters[filter])
set2 = self.pair[1].get(self.filters[filter])
if not set1 or not set2:
print 'ERROR: cannot compute the superimposition'
print 'not set1 or not set2'
return
elif len(set1) != len(set2):
print 'ERROR: cannot compute the superimposition'
print 'len(set1) != len(set2)'
return
#print 'set1', set1
#print 'set2', set2
self.updateChooser(set1, set2)
self.pair = []
if len(self.newPairs)>=4 and self.contVar.get() == 1:
# Continuous picking is on and superimposition can be done if
# there are more than 4 pairs.
self.superimpose_cb()
def alignment_cb(self, event=None):
if not hasattr(self.vf,'alignment'):
self.vf.alignment = Alignment()
if not hasattr(self.vf,'alnEditor'):
self.vf.alnEditor = PmvAlignmentEditor(vf=self.vf)
self.vf.alnEditor.alignment = self.vf.alignment
else:
self.vf.alnEditor.redraw()
self.vf.alnEditor.master.deiconify()
for mol in self.vf.Mols:
if mol.name not in self.vf.alignment.seqNames:
self.vf.alnEditor.getSequence(mol)
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 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"] = """
class MeasureDistanceGUICommand(MeasureGUICommand):
"""
This command measures distance between atoms.
Lines are drawn between pairs of consecutively picked atoms and labels
are display showing the distance.
\nPackage : Pmv
\nModule : measureCommands
\nClass : MeasureDistanceGUICommand
\nCommand : measureDistanceGC
\nSynopsis:\n
distance/None<---measureDistanceGC(atoms)
\nRequired Argument:\n
atoms --- atom(s)
"""
def __init__(self, func=None):
MeasureGUICommand.__init__(self, func=func)
self.flag = self.flag | self.objArgOnly
def guiCallback(self, event=None):
MeasureGUICommand.guiCallback(self, event)
self.vf.setICOM(self.vf.measureDistGUI,
modifier='Control_L',
topCommand=0)
def onAddCmdToViewer(self):
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('measureDistance'):
self.vf.loadCommand('measureCommands',
'measureDistance',
'Pmv',
topCommand=0)
self.masterGeom = Geom('measureDistGeom', shape=(0, 0), pickable=0)
self.masterGeom.isScalable = 0
if self.vf.hasGui:
measure_geoms = check_measure_geoms(self.vf.GUI)
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=measure_geoms)
self.lines = IndexedPolylines('distLine',
materials=((1, 1, 0), ),
inheritMaterial=0,
lineWidth=3.,
stippleLines=1,
pickable=0)
self.labels = GlfLabels(name='distLabel',
shape=(0, 3),
font='arial1.glf',
fontStyle='solid3d',
fontScales=(.5, .5, .3),
inheritMaterial=0,
materials=((1, 1, 0), ))
self.spheres = Spheres(name='distSpheres',
shape=(0, 3),
inheritMaterial=0,
radii=0.2,
quality=15,
materials=((1., 1., 0.), ))
if self.vf.hasGui:
for item in [self.lines, self.labels, self.spheres]:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
def __call__(self, atoms, **kw):
"""distance/None<---measureDistanceGC(atoms)
\natoms --- atom(s)"""
if type(atoms) is types.StringType:
self.nodeLogString = "'" + atoms + "'"
ats = self.vf.expandNodes(atoms)
if not len(ats): return 'ERROR'
return self.doitWrapper(*(ats, ), **kw)
def doit(self, ats):
for at in ats:
lenAts = len(self.atomList)
if lenAts and at == self.atomList[-1]:
continue
self.atomList.append(at)
self.update()
if len(self.labelStrs):
return float(self.labelStrs[-1])
def update(self, forward=1, event=None):
if not len(self.atomList):
self.spheres.Set(vertices=[])
#self.spheres.Set(vertices=[], tagModified=False)
self.labels.Set(vertices=[])
#self.labels.Set(vertices=[], tagModified=False)
self.lines.Set(vertices=[])
#self.lines.Set(vertices=[], tagModified=False)
return
self.lineVertices = []
#each time have to recalculate lineVertices
for at in self.atomList:
c1 = self.getTransformedCoords(at)
self.lineVertices.append(tuple(c1))
if len(self.lineVertices) % 2:
self.spheres.Set(vertices=[self.lineVertices[-1]])
else:
self.spheres.Set(vertices=[])
#self.spheres.Set(vertices=self.lineVertices, tagModified=False)
#setting spheres doesn't trigger redraw so do it explicitly
self.vf.GUI.VIEWER.Redraw()
#each time have to recalculate labelCenters and labelStrs
if len(self.lineVertices) > 1:
self.labelCenters = []
self.labelStrs = []
self.faces = []
numLabels = len(self.lineVertices) - 1
for i in range(0, numLabels, 2):
c0 = Numeric.array(self.lineVertices[i])
c1 = Numeric.array(self.lineVertices[i + 1])
newCenter = tuple((c1 + c0) / 2.0)
self.labelCenters.append(newCenter)
at1 = self.atomList[i]
at2 = self.atomList[i + 1]
d = self.vf.measureDistance(at1, at2, topCommand=0)
dLabel = '%.3f' % d
self.labelStrs.append(dLabel)
self.faces.append([i, i + 1])
#correct length of labels here
self.labels.Set(vertices=self.labelCenters, labels=self.labelStrs)
#tagModified=False)
self.lines.Set(vertices=self.lineVertices,
type=GL.GL_LINE_STRIP,
faces=self.faces,
freshape=1)
#tagModified=False)
elif len(self.lineVertices) == 1 and len(self.labelCenters) == 1:
#this fixes case of stepping back over 1st label
self.labels.Set(vertices=[])
#self.labels.Set(vertices=[], tagModified=False)
self.lines.Set(vertices=[])
def restore(self, event=None):
if __debug__:
if hasattr(DejaVu, 'functionName'): DejaVu.functionName()
self.cw.Set(self.savedColor, 'RGB')
if __name__ == '__main__':
import Tkinter
master = Tkinter.Toplevel()
from DejaVu import Viewer
vi = Viewer()
from DejaVu.colorMap import ColorMap
test = MaterialEditor(master, vi)
from DejaVu.Spheres import Spheres
s = Spheres('test',
centers=[[0., 0, 0], [5, 0, 0.], [0, 5, 0]],
quality=30,
matName='tropical',
matInd=0)
vi.AddObject(s)
from DejaVu.materialsDef.tropical import tropical
test.defineMaterial(tropical[0])
test.setObject(s)
## root1 = Tkinter.Tk()
## cc = ColorChooser(root1, title='Color chooser')
else:
r1 = r2 = radii[0] / 2.
self.entries.append('\t%s, %f, %s, %f\n' % (self.coord3(
v[f[i][j]]), r1, self.coord3(v[f[i][j + 1]]), r2))
if fp:
col = c[f[i][j]][:3]
else:
col = (1., 1., 1.)
self.entries.append(
"\tpigment { color rgb<%6.3f, %6.3f, %6.3f> }\n" %
tuple(col))
self.entries.append(
"\tfinish { specular 1 roughness 0.001 ambient 0.3 }\n")
self.endShape()
if __name__ == '__main__':
from DejaVu import Viewer
vi = Viewer()
from DejaVu.Spheres import Spheres
s = Spheres('test', centers=((0.0, 0., 0.), (3., 0., 0.)))
s.Set(quality=4)
vi.AddObject(s)
from DejaVu.povray3 import PovRay
p = PovRay()
p.addCamera(vi.cameras[0])
p.addLight(vi.lights[0])
p.addGeom(s)
p.write('test.pov')
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()
vi.Center_cb()
cam = vi.currentCamera
cam.master.master.geometry('%dx%d+%d+%d' % (400, 400, 92, 73))
vi.update()
cam.fog.Set(enabled=1)
sph = Spheres('debugSph', inheritMaterial=False)
vi.AddObject(sph)
from DejaVu import Viewer
vi = Viewer()
from DejaVu.IndexedPolygons import IndexedPolygons
f = []
n = smooth.shape[1]
f = map( lambda x: (x, x+1, x+n+1, x+n), range(smooth.shape[1]-1))
v = Numeric.array(Numeric.reshape(smooth, (-1,4))[:,:3])
p = IndexedPolygons('sheet2D', vertices = v, faces = f, protected=True,)
if self.vf.userpref['Sharp Color Boundaries for MSMS']['value'] == 'blur':
p.Set(inheritSharpColorBoundaries=False, sharpColorBoundaries=False,)
p.replace = False
vi.AddObject(p)
from DejaVu.Spheres import Spheres
ctrl.shape = (-1,4)
p = Spheres('ctrl', centers = ctrl[:, :3], radii = 0.6, protected=True)
p.replace = False
vi.AddObject(p)
from DejaVu.Spheres import Spheres
s = Spheres('sph', vertices = v, quality=5, protected=True)
s.radius = 0.2
vi.AddObject(s)
from MolKit import Read
mol = Read('../1crn.pdb')
allatoms = mol.chains.residues.atoms
caat = allatoms.get('CA')
coords = caat.coords
from DejaVu.Spheres import Spheres
p = Spheres('CA', centers = coords, radii = 0.6, protected=True)
class AddBondsGUICommand(MVCommand, MVAtomICOM):
"""
The AddBondGUICommand provides an interactive way of creating bonds between two given atoms by picking on them. To use this command you need first to load it into PMV. Then you can find the entry 'addBonds' under the Edit menu. To add bonds you just need to pick on the 2 atoms you want to bind. If you drag select a bunch of atoms, the command will buildBondsByDistance between them.This command is undoable.
\nPackage : Pmv
\nModule : bondsCommands
\nClass : AddBondsGUICommand
\nCommand : addBondsGC
\nSynopsis:\n
None<-addBondsGC(atoms)\n
\nRequired Arguments:\n
atoms : atom(s)\n
"""
def __init__(self, func=None):
MVCommand.__init__(self, func)
MVAtomICOM.__init__(self)
self.atomList = AtomSet([])
self.undoAtList = AtomSet([])
self.labelStrs = []
def onRemoveObjectFromViewer(self, obj):
removeAts = AtomSet([])
for at in self.atomList:
if at in obj.allAtoms:
removeAts.append(at)
self.atomList = self.atomList - removeAts
removeAts = AtomSet([])
for at in self.undoAtList:
if at in obj.allAtoms:
removeAts.append(at)
self.undoAtList = self.undoAtList - removeAts
self.update()
def onAddCmdToViewer(self):
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('addBonds'):
self.vf.loadCommand('bondsCommands',
'addBonds',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('removeBondsGC'):
self.vf.loadCommand('bondsCommands',
'removeBondsGC',
'Pmv',
topCommand=0)
self.masterGeom = Geom('addBondsGeom',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
self.spheres = Spheres(name='addBondsSpheres',
shape=(0, 3),
inheritMaterial=0,
radii=0.2,
quality=15,
materials=((1., 1., 0.), ),
protected=True)
if not self.vf.commands.has_key('labelByExpression'):
self.vf.loadCommand('labelCommands', [
'labelByExpression',
],
'Pmv',
topCommand=0)
if self.vf.hasGui:
miscGeom = self.vf.GUI.miscGeom
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=miscGeom)
self.vf.GUI.VIEWER.AddObject(self.spheres, parent=self.masterGeom)
def __call__(self, atoms, **kw):
"""None<-addBondsGC(atoms)
\natoms : atom(s)"""
if type(atoms) is StringType:
self.nodeLogString = "'" + atoms + "'"
ats = self.vf.expandNodes(atoms)
if not len(ats): return 'ERROR'
return apply(self.doitWrapper, (ats, ), kw)
def doit(self, ats):
if len(ats) > 2:
if len(self.atomList):
atSet = ats + self.atomList
else:
atSet = ats
parent = atSet[0].parent
parent.buildBondsByDistanceOnAtoms(atSet)
self.atomList = AtomSet([])
self.update(True)
else:
lenAts = len(self.atomList)
last = None
if lenAts:
last = self.atomList[-1]
top = self.atomList[0].top
for at in ats:
#check for repeats of same atom
if lenAts and at == last:
continue
#lenAts = len(self.atomList)
#if lenAts and at==self.atomList[-1]:
# continue
if lenAts and at.top != self.atomList[-1].top:
msg = "intermolecular bond to %s disallowed" % (
at.full_name())
self.warningMsg(msg)
self.atomList.append(at)
self.undoAtList.append(at)
lenAts = len(self.atomList)
self.update(True)
#if only have one atom, there is nothing else to do
if lenAts < 2: return
#now build bonds between pairs of atoms
atSet = self.atomList
if lenAts % 2 != 0:
atSet = atSet[:-1]
#all pairs of atoms will be bonded
#so keep only the last one
self.atomList = atSet[-1:]
lenAts = lenAts - 1
else:
self.vf.labelByExpression(self.atomList,
negate=1,
topCommand=0)
self.atomList = AtomSet([])
for i in range(0, lenAts, 2):
at1 = atSet[i]
at2 = atSet[i + 1]
self.vf.addBonds(at1, at2, origin='UserDefined', topCommand=0)
self.update(True)
def applyTransformation(self, pt, mat):
pth = [pt[0], pt[1], pt[2], 1.0]
return Numeric.dot(mat, pth)[:3]
def getTransformedCoords(self, atom):
if not atom.top.geomContainer:
return atom.coords
g = atom.top.geomContainer.geoms['master']
c = self.applyTransformation(atom.coords, g.GetMatrix(g))
return c.astype('f')
def update(self, event=None):
if not len(self.atomList):
self.spheres.Set(vertices=[], tagModified=False)
self.vf.labelByExpression(self.atomList, negate=1, topCommand=0)
if self.vf.hasGui:
self.vf.GUI.VIEWER.Redraw()
return
self.lineVertices = []
#each time have to recalculate lineVertices
for at in self.atomList:
c1 = self.getTransformedCoords(at)
self.lineVertices.append(tuple(c1))
if event:
self.spheres.Set(vertices=self.lineVertices, tagModified=False)
self.vf.labelByExpression(self.atomList,
function='lambda x: x.full_name()',
lambdaFunc=1,
textcolor='yellow',
format='',
negate=0,
location='Last',
log=0,
font='arial1.glf',
only=1,
topCommand=0)
#setting spheres doesn't trigger redraw so do it explicitly
if self.vf.hasGui:
self.vf.GUI.VIEWER.Redraw()
def guiCallback(self, event=None):
self.save = self.vf.ICmdCaller.commands.value["Shift_L"]
self.vf.setICOM(self, modifier="Shift_L", topCommand=0)
def setupUndoAfter(self, ats, **kw):
lenUndoAts = len(self.undoAtList)
lenAts = len(ats)
if lenAts == 1:
#after adding 1 self.atomList would be 1 or 0
if len(self.atomList) == 1:
s = '0'
ustr = '"c=self.addBondsGC; self.labelByExpression(c.atomList, negate=1, topCommand=0);c.atomList=c.atomList[:' + s + '];c.undoAtList=c.undoAtList[:-1];c.update()"'
else:
self.vf.undoCmdStack.remove(self.prev_undoCmds)
ind = str(lenUndoAts - 2)
ustr = '"c=self.addBondsGC;nodes=self.expandNodes(' + '\'' + self.undoAtList[
-2:].full_name(
) + '\'' + '); bonds=nodes.bonds[0];self.removeBondsGC(bonds, topCommand=0);c.atomList=nodes[:1];c.undoAtList=c.undoAtList[:' + ind + '];c.update()"'
elif lenUndoAts > lenAts:
ustr = '"c=self.addBondsGC;nodes=self.expandNodes(' + '\'' + ats.full_name(
) + '\'' + ');bonds = nodes.bonds[0];self.removeBondsGC(bonds, topCommand=0);c.undoAtList=c.undoAtList[:' + str(
lenAts) + ']"'
else:
ustr = '"c=self.addBondsGC;nodes=self.expandNodes(' + '\'' + ats.full_name(
) + '\'' + ');bonds = nodes.bonds[0];self.removeBondsGC(bonds, topCommand=0);c.undoAtList=c.undoAtList[:0]"'
if len(self.atomList) and lenAts > 1:
atStr = self.atomList.full_name()
estr = ';nodes=self.expandNodes(' + '\'' + self.atomList.full_name(
) + '\'' + ');c.atomList=nodes;c.update()"'
ustr = ustr + estr
self.undoCmds = "exec(" + ustr + ")"
self.prev_undoCmds = (self.undoCmds, "addBondsGC")
def startICOM(self):
self.vf.setIcomLevel(Atom, topCommand=0)
def stopICOM(self):
if len(self.atomList) != 0:
self.vf.labelByExpression(self.atomList, negate=1, topCommand=0)
del self.atomList[:]
self.labelStrs = []
self.spheres.Set(vertices=[], tagModified=False)
self.vf.GUI.VIEWER.Redraw()
self.save = None
class MeasureTorsionGUICommand(MeasureGUICommand):
"""Label torsion between four atoms (color coded cyan) Accumulates picked atoms.Draws polygons and labels showing the torsion angle between groups of 4 selected atoms (color-coded cyan).Userpref 'measureTorsionSL' sets the 'snakeLength' which is how many torsion measureDisplays can be seen at the same time.When more than that number are measured, the first torsion measured is no longer labeled.
\nPackage : Pmv
\nModule : measureCommands
\nClass : MeasureTorsionGUICommand
\nCommand : measureTorsionGC
\nSynopsis:\n
torsion/None<---measureTorsionGC(atoms)
\nRequired Argument:\n
atoms --- the atom(s)
\ntorsion --- returned when the number of atoms is a multiple of 4
"""
def __init__(self, func=None):
MeasureGUICommand.__init__(self, func=func)
self.flag = self.flag | self.objArgOnly
def onAddCmdToViewer(self):
from DejaVu.bitPatterns import pat3
from DejaVu.IndexedPolygons import IndexedPolygons
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('measureAngle'):
self.vf.loadCommand('measureCommands',
'measureAngle',
'Pmv',
topCommand=0)
self.masterGeom = Geom('measureTorsionGeom',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
if self.vf.hasGui:
measure_geoms = check_measure_geoms(self.vf.GUI)
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=measure_geoms)
self.lines = IndexedPolygons('torsionLine',
materials=((0, 1, 1), ),
culling=GL.GL_NONE,
inheritStipplePolygons=0,
inheritMaterial=0,
stipplePolygons=1,
backPolyMode=GL.GL_FILL,
frontPolyMode=GL.GL_FILL,
protected=True,
pickable=0)
if self.vf.userpref['Sharp Color Boundaries for MSMS'][
'value'] == 'blur':
self.lines.Set(
inheritSharpColorBoundaries=False,
sharpColorBoundaries=False,
)
self.lines.polygonstipple.Set(pattern=pat3)
#self.lines.polygonstipple.Set(pattern=pat3, tagModified=False)
#self.lines.RenderMode(GL.GL_FILL)
#self.lines.RenderMode(GL.GL_FILL, face=GL.GL_BACK)
self.labels = GlfLabels(name='torsionLabel',
shape=(0, 3),
font='arial1.glf',
fontStyle='solid3d',
fontScales=(.5, .5, .3),
inheritMaterial=0,
materials=((0, 1, 1), ))
self.spheres = Spheres(name='torsionSpheres',
shape=(0, 3),
inheritMaterial=0,
radii=0.2,
quality=15,
materials=((0., 1., 1.), ),
protected=True)
if self.vf.hasGui:
for item in [self.lines, self.labels, self.spheres]:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
doc = """Number of labeled torsions displayed.
Valid values are integers>0"""
self.vf.userpref.add('Measured Torsions',
4,
callbackFunc=[self.setLength_cb],
category="Molecules",
validateFunc=lambda x: x > 0,
doc=doc)
#used after startICOM is invoked
doc = """Continuous update of torsions if 'transformRoot only' is
turned off and viewer's current object is not Root."""
choices = ['yes', 'no']
self.vf.userpref.add('Continuous Update Torsion',
'yes',
choices,
callbackFunc=[self.continuousUpdate_cb],
category="Molecules",
doc=doc)
self.snakeLength = 4
def __call__(self, atoms, **kw):
"""torsion/None<-measureTorsionGC(atoms)
\natoms --- the atom(s)
\ntorsion --- returned when the number of atoms is a multiple of 4"""
if type(atoms) is types.StringType:
self.nodeLogString = "'" + atoms + "'"
ats = self.vf.expandNodes(atoms)
if not len(ats): return 'ERROR'
return apply(self.doitWrapper, (ats, ), kw)
def doit(self, ats):
for at in ats:
lenAts = len(self.atomList)
if lenAts and lenAts % 4 != 0 and at == self.atomList[-1]:
continue
self.atomList.append(at)
if len(self.atomList) > 4 * self.snakeLength:
self.atomList = self.atomList[4:]
self.update()
if len(self.labelStrs) and len(self.atomList) % 4 == 0:
return float(self.labelStrs[-1])
def update(self, forward=1, event=None):
if not len(self.atomList):
self.spheres.Set(vertices=[])
#self.spheres.Set(vertices=[], tagModified=False)
self.labels.Set(vertices=[])
#self.labels.Set(vertices=[], tagModified=False)
self.lines.Set(vertices=[])
#self.lines.Set(vertices=[], tagModified=False)
self.vf.GUI.VIEWER.Redraw()
return
limit = self.snakeLength
#each time have to recalculate lineVertices
self.lineVertices = []
for at in self.atomList:
c1 = self.getTransformedCoords(at)
self.lineVertices.append(tuple(c1))
#display spheres:
if len(self.lineVertices) % 4:
self.spheres.Set(
vertices=self.lineVertices[-(len(self.lineVertices) % 4):])
else:
self.spheres.Set(vertices=[])
#self.spheres.Set(vertices=self.lineVertices, tagModified=False)
self.vf.GUI.VIEWER.Redraw()
#label with torsion
#lines between spheres are only drawn when angle completed
#that is, len(ats)%4=0
if len(self.lineVertices) < 4:
self.labels.Set(vertices=[])
#self.labels.Set(vertices=[], tagModified=False)
self.lines.Set(vertices=[])
#self.lines.Set(vertices=[], tagModified=False)
else:
#rebuild labels and polygons each time
self.labelCenters = []
self.labelStrs = []
#labelCenters, labelStrs,
#this gets done lenATs/4 times
numItems = len(self.atomList) / 4
for i in range(numItems):
at0 = self.atomList[i * 4]
at1 = self.atomList[i * 4 + 1]
at2 = self.atomList[i * 4 + 2]
at3 = self.atomList[i * 4 + 3]
torsion = self.vf.measureTorsion(at0,
at1,
at2,
at3,
topCommand=0)
torsionLabel = '%.3f' % torsion
self.labelStrs.append(torsionLabel)
c0 = self.getTransformedCoords(at0)
c1 = self.getTransformedCoords(at3)
newcenter = tuple((c0 + c1) / 2.0)
self.labelCenters.append(newcenter)
#to reset labels, lines and fan, EACH TIME
self.labels.Set(vertices=self.labelCenters, labels=self.labelStrs)
#tagModified=False)
#if len(self.lineVertices)%4!=0:
#self.lineVertices = self.lineVertices[:numItems*4]
#only draw lines in groups of 4
#numItems*4
if len(self.atomList) % 4 == 0:
faces = range(numItems * 4)
faces = Numeric.reshape(faces, (-1, 4))
###FIX THIS
###on undo: if you have just wrapped, undoing the next pt
###breaks because trying to set the vertices uses the old
###faces
if not forward:
self.lines.Set(vertices=[], faces=[])
#self.lines.Set(vertices=[], faces=[], tagModified=False)
self.lines.Set(vertices=self.lineVertices,
faces=faces,
freshape=1)
#freshape=1, tagModified=False)
self.vf.GUI.VIEWER.Redraw()
else:
#this only works going forward: undo breaks here
if len(self.lines.faceSet.faces.array) > numItems:
faces = range((numItems + 1) * 4)
faces = Numeric.reshape(faces, (-1, 4))
if forward:
faces = faces[1:]
else:
faces = faces[:-1]
self.lines.Set(faces=faces)
self.vf.GUI.VIEWER.Redraw()
class MeasureAngleGUICommand(MeasureGUICommand):
"""Accumulates picked atoms.Draws fans, lines and labels labelling the angle between trios of selected atoms (color-coded orange).Userpref 'measureAngleSL' sets the 'snakeLength' which is how many angle measureDisplays can be seen at the same time.When more than that number are measured, the first angle measured is no longer labeled.
\nPackage : Pmv
\nModule : measureCommands
\nClass : MeasureAngleGUICommand
\nCommand : measureAngleGC
\nSynopsis:\n
angle/None<---measureAngleGC(atoms)
\nRequired Argument:\n
atoms --- atom(s)
\nangle --- returned when the number of atoms is a multiple of 3
"""
def __init__(self, func=None):
MeasureGUICommand.__init__(self, func=func)
self.flag = self.flag | self.objArgOnly
def onAddCmdToViewer(self):
from DejaVu.Arcs3D import Fan3D
from DejaVu.bitPatterns import pat3
self.arcNormals = []
self.arcVectors = []
self.arcCenters = []
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('measureAngle'):
self.vf.loadCommand('measureCommands',
'measureAngle',
'Pmv',
topCommand=0)
self.masterGeom = Geom('measureAngleGeom',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
if self.vf.hasGui:
measure_geoms = check_measure_geoms(self.vf.GUI)
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=measure_geoms)
self.lines = IndexedPolylines('angleLine',
materials=((1, .5, 0), ),
inheritMaterial=0,
lineWidth=3,
stippleLines=1,
protected=True,
pickable=0)
self.fan = Fan3D('angles',
materials=((1, .5, 0), ),
culling=GL.GL_NONE,
inheritMaterial=0,
stipplePolygons=1,
radii=(1., ),
inheritStipplePolygons=0,
backPolyMode=GL.GL_FILL,
pickable=0)
self.fan.polygonstipple.Set(pattern=pat3)
#self.fan.polygonstipple.Set(pattern=pat3, tagModified=False)
#self.fan.RenderMode(GL.GL_FILL)
#self.fan.RenderMode(GL.GL_FILL, face=GL.GL_BACK)
self.labels = GlfLabels(name='angleLabel',
shape=(0, 3),
font='arial1.glf',
fontStyle='solid3d',
fontScales=(.5, .5, .3),
inheritMaterial=0,
materials=((1., .5, 0.), ))
self.spheres = Spheres(name='angleSpheres',
shape=(0, 3),
inheritMaterial=0,
radii=0.2,
quality=15,
materials=((1., .5, 0.), ),
protected=True)
if self.vf.hasGui:
for item in [self.lines, self.labels, self.spheres, self.fan]:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
doc = """Number of labeled angles displayed.
Valid values are integers>0"""
self.vf.userpref.add('Number of Measure Angles',
4,
callbackFunc=[self.setLength_cb],
category="Molecules",
validateFunc=lambda x: x > 0,
doc=doc)
#used after startICOM is invoked
doc = """Continuous update of angles if 'transformRoot only' is
turned off and viewer's current object is not Root."""
choices = ['yes', 'no']
self.vf.userpref.add('Continuous Update Angle',
'yes',
choices,
callbackFunc=[self.continuousUpdate_cb],
category="Molecules",
doc=doc)
self.snakeLength = 4
def __call__(self, atoms, **kw):
"""angle/None<---measureAngleGC(atoms)
\natoms --- atom(s)
\nangle --- returned when the number of atoms is a multiple of 3"""
if type(atoms) is types.StringType:
self.nodeLogString = "'" + atoms + "'"
ats = self.vf.expandNodes(atoms)
if not len(ats): return 'ERROR'
return apply(self.doitWrapper, (ats, ), kw)
def doit(self, ats):
for at in ats:
lenAts = len(self.atomList)
if lenAts and lenAts % 3 != 0 and at == self.atomList[-1]:
continue
self.atomList.append(at)
l = len(self.atomList)
#for this command, reset after every 3
#wrap when len(atoms)=3*self.snakeLength+1
if l > 3 * self.snakeLength:
self.atomList = self.atomList[3:]
self.update()
if len(self.labelStrs) and len(self.atomList) % 3 == 0:
return float(self.labelStrs[-1])
def update(self, forward=1, event=None):
if not len(self.atomList):
self.spheres.Set(vertices=[])
#self.spheres.Set(vertices=[], tagModified=False)
self.labels.Set(vertices=[])
#self.labels.Set(vertices=[], tagModified=False)
self.lines.Set(vertices=[])
#self.lines.Set(vertices=[], tagModified=False)
self.vf.GUI.VIEWER.Redraw()
return
limit = self.snakeLength
#each time have to recalculate lineVertices
self.lineVertices = []
for at in self.atomList:
c1 = self.getTransformedCoords(at)
self.lineVertices.append(tuple(c1))
#display spheres:
if len(self.lineVertices) % 3:
self.spheres.Set(
vertices=self.lineVertices[-(len(self.lineVertices) % 3):])
else:
self.spheres.Set(vertices=[])
#self.spheres.Set(vertices=self.lineVertices, tagModified=False)
self.vf.GUI.VIEWER.Redraw()
#label with angle
#lines between spheres are only drawn when angle completed
#that is, len(ats)%3=0
if len(self.lineVertices) < 3:
self.labels.Set(vertices=[])
#self.labels.Set(vertices=[], tagModified=False)
self.fan.Set(vertices=[])
#self.fan.Set(vertices=[], tagModified=False)
self.lines.Set(vertices=[])
#self.lines.Set(vertices=[], tagModified=False)
else:
#should all of these be reset?
self.arcNormals = []
self.arcVectors = []
self.arcCenters = []
self.labelCenters = []
self.labelStrs = []
#rebuild arcNormals, arcVectors, arcCenters
#labelCenters, labelStrs,
#this gets done lenATs/3 times
numItems = len(self.atomList) / 3
for i in range(numItems):
at0 = self.atomList[i * 3]
at1 = self.atomList[i * 3 + 1]
at2 = self.atomList[i * 3 + 2]
ang = self.vf.measureAngle(at0, at1, at2, topCommand=0)
v, n = self.normal(at0, at1, at2)
self.arcNormals.append(n)
#self.arcNormals = self.arcNormals[-limit:]
self.arcVectors.append(v)
#self.arcVectors = self.arcVectors[-limit:]
self.arcCenters.append(self.getTransformedCoords(at1))
#self.arcCenters = self.arcCenters[-limit:]
angLabel = '%.3f' % ang
self.labelStrs.append(angLabel)
c0 = self.getTransformedCoords(at0)
c1 = self.getTransformedCoords(at2)
newcenter = tuple((c0 + c1) / 2.0)
self.labelCenters.append(newcenter)
#to reset labels, lines and fan, EACH TIME
self.labels.Set(vertices=self.labelCenters, labels=self.labelStrs)
#tagModified=False)
faces = range(numItems * 3)
faces = Numeric.reshape(faces, (-1, 3))
self.lines.Set(vertices=self.lineVertices,
type=GL.GL_LINE_STRIP,
faces=faces,
freshape=1)
#faces=faces, freshape=1, tagModified=False)
self.fan.angles = map(float, self.labelStrs)
self.fan.vectors = self.arcVectors
self.fan.Set(vertices=self.arcCenters, vnormals=self.arcNormals)
#tagModified=False)
def normal(self, at0, at1, at2):
c0 = self.getTransformedCoords(at0)
c1 = self.getTransformedCoords(at1)
c2 = self.getTransformedCoords(at2)
v1 = c1 - c0
v2 = c1 - c2
l1 = math.sqrt(Numeric.sum(v1 * v1))
l2 = math.sqrt(Numeric.sum(v2 * v2))
#FIXME
#protect against divide by 0
n = self.vvmult(v1 / l1, v2 / l2)
n = n / math.sqrt(Numeric.sum(n * n))
return -v2 / l2, n.astype('f')
class Handler(Command):
def create(self, target, geom=None, imd=None, forceType="steered"):
self.target = target.findType(Atom) #should be an atom selection
self.imd = imd
if self.imd is not None:
self.slot = self.imd.slot
else:
self.slot = 0
self.initial_position = self.getTargetCenter()
self.previousForce = [0., 0., 0.]
self.scale_force = 0.5 #scale before display and send to MD
self.sphere_radius = 4.
if geom is None:
#by default the handler is a sphere
self.geom = Spheres('handler',
inheritMaterial=False,
centers=[
[0., 0., 0.],
],
radii=[2.],
visible=1)
if self.vf.hasGui: self.vf.GUI.VIEWER.AddObject(self.geom)
else:
self.geom = geom
#if self.vf.hasGui : self.geom.SetTranslation(Numeric.array(self.initial_position))
#else : self.geom.setLocation(self.initial_position[0],self.initial_position[1],self.initial_position[2])
if self.vf.hasGui: self.prepareQuickKeys()
self.N_forces = len(self.target)
self.atoms_list = self.target.number #need to check this
self.forces_list = Numeric.zeros((self.N_forces, 3), 'f')
self.arrow = None
self.isinited = True
self.handler_pattern = None
self.mol_pattern = None
#preaper the arrow that will represent the force
if self.vf.hasGui: self.prepareArrow()
self.forceType = forceType
#self.vf.registerListener(translateEvent, self.getForces)
#self.vf.GUI.VIEWER.registerListener(translateEvent, self.getForces)
def getTargetCenter(self):
self.target.setConformation(self.slot)
coords = Numeric.array(self.target.coords) #self.allAtoms.coords
center = sum(coords) / (len(coords) * 1.0)
center = list(center)
for i in range(3):
center[i] = round(center[i], 4)
self.target.setConformation(0)
self.N_forces = len(coords)
return center
def prepareArrow(self):
force = Numeric.array(self.forces_list)
self.target.setConformation(1)
point = Numeric.array(self.target.coords)
self.target.setConformation(0)
vertices = []
faces = []
indice = 0
for i in range(self.N_forces):
vertices.append(point[i])
vertices.append(point[i] + force[i])
faces.append([indice, indice + 1])
indice = indice + 2
vertices = Numeric.array(vertices, 'f').tolist()
self.arrow = Arrows('pyarrow', vertices=vertices, faces=faces)
self.vf.GUI.VIEWER.AddObject(self.arrow)
def updateArrow(self):
if self.forceType != "move":
force = Numeric.array(self.forces_list)
self.target.setConformation(1)
point = Numeric.array(self.target.coords)
self.target.setConformation(0)
vertices = []
faces = []
indice = 0
for i in range(self.N_forces):
vertices.append(point[i])
vertices.append(point[i] + force[i])
faces.append([indice, indice + 1])
indice = indice + 2
vertices = Numeric.array(vertices, 'f').tolist()
self.arrow.Set(vertices=vertices, faces=faces)
def prepareQuickKeys(self):
import Tkinter
from mglutil.util.callback import CallBackFunction
#prepare the QuickKeys one for the root, one for the handler
self.vf.GUI.VIEWER.GUI.showHideQuickKeysVar.set(1)
xform = 'Object'
root = self.vf.GUI.VIEWER.rootObject
cbroot = CallBackFunction(self.vf.GUI.VIEWER.GUI.quickKey_cb, xform,
root, 1)
cbhandler = CallBackFunction(self.vf.GUI.VIEWER.GUI.quickKey_cb, xform,
self.geom, 0)
label = "Xform Scene"
labelHandler = "Xform Handler"
# create a button and add it to the Quick Keys panel
button = Tkinter.Button(self.vf.GUI.VIEWER.GUI.QuickKeysFrame,
text=label,
command=cbroot)
button.pack(side='top', expand=1, fill='y')
# create a button and add it to the Quick Keys panel
button = Tkinter.Button(self.vf.GUI.VIEWER.GUI.QuickKeysFrame,
text=labelHandler,
command=cbhandler)
button.pack(side='top', expand=1, fill='y')
def getHandlerPos(self):
if self.vf.hasGui:
if hasattr(self.vf, "art"):
from numpy import matrix
#the inverse matrix for molecule pattern
m1 = self.mol_pattern.mat_transfo
M1 = matrix(m1.reshape(4, 4))
#get the pattern transfor
m2 = self.handler_pattern.mat_transfo
M2 = matrix(m2.reshape(4, 4))
transfo = M2 * M1.I
pos = Numeric.array(transfo[3, :3])
else:
pos = self.geom.translation
else:
pos = self.geom.getLocation()
return pos
def findNeighbor(self, pos):
#loop or pmvcommands
self.vf.selectInSphere(pos,
self.sphere_radius, [self.imd.mol.name],
log=0)
node = self.vf.selection
if node != None:
self.target = node.findType(Atom)
self.N_forces = len(self.target)
self.atoms_list = self.target.number #need to check this
self.forces_list = Numeric.zeros((self.N_forces, 3), 'f')
return Numeric.array(self.getTargetCenter())
else:
return None
def getPush(self, target=True):
pos = self.getHandlerPos()
if target: targetpos = Numeric.array(self.getTargetCenter())
else:
targetpos = self.findNeighbor(pos[0].tolist())
if targetpos == None: return Numeric.array([0., 0., 0.])
force = -Numeric.array(pos[0]) + targetpos
d = math.sqrt(Numeric.sum(force * force))
return force * 1 / (d * d)
#else : return Numeric.array([0.,0.,0.])
def getSteered(self):
pos = self.getHandlerPos()
force = Numeric.array(pos) - Numeric.array(self.getTargetCenter())
#d=math.sqrt(Numeric.sum(force[0]*force[0]))
#if d > 30. : return Numeric.zeros(3)
#else :
return force
def getCoord(self):
pos = self.getHandlerPos()
mol = self.target.top
mol.allAtoms.setConformation(self.slot)
coords = mol.allAtoms.coords[:]
mol.allAtoms.setConformation(0)
force = Numeric.array(coords) + (Numeric.array(pos) - Numeric.array(
self.getTargetCenter())) #Numeric.array([1.0,0.,0.])
self.N_forces = len(coords)
return force
def getForces(self, event):
if event == None: obj = self.geom
else: obj = event.objects
if obj != self.geom: return 0
if self.forceType == "steered": force = self.getSteered()
elif self.forceType == "pushtarget": force = self.getPush(target=True)
elif self.forceType == "push": force = self.getPush(target=False)
elif self.forceType == "move": force = self.getCoord()
if self.forceType != "move":
for i in range(self.N_forces):
self.forces_list[i] = force * self.scale_force
else:
self.forces_list = force
self.previousForce = force
def onAddCmdToViewer(self):
if not hasattr(self.vf, 'GUI'):
return
self.undoNow = 0
self.save = None
from DejaVu.bitPatterns import pat3
from DejaVu.IndexedPolygons import IndexedPolygons
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('measureTorsion'):
self.vf.loadCommand('measureCommands',
'measureTorsion',
'Pmv',
topCommand=0)
self.masterGeom = Geom('setTorsionGeom',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
self.vf.GUI.VIEWER.AddObject(self.masterGeom,
parent=self.vf.GUI.miscGeom)
self.lines = IndexedPolygons(
'settorsionLine',
materials=((0, 1, 1), ),
inheritMaterial=0,
stipplePolygons=1,
protected=True,
)
if self.vf.userpref['Sharp Color Boundaries for MSMS'][
'value'] == 'blur':
self.lines.Set(
inheritSharpColorBoundaries=False,
sharpColorBoundaries=False,
)
self.lines.polygonstipple.Set(pattern=pat3) #, tagModified=False)
#self.lines.RenderMode(GL.GL_FILL, face=GL.GL_BACK)
self.lines.Set(backPolyMode=GL.GL_FILL)
self.labels = GlfLabels(name='settorsionLabel',
shape=(0, 3),
inheritMaterial=0,
materials=((0, 1, 1), ))
self.spheres = Spheres(name='settorsionSpheres',
shape=(0, 3),
radii=0.2,
quality=15,
inheritMaterial=0,
materials=((0., 1., 1.), ),
protected=True)
for item in [self.lines, self.labels, self.spheres]:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
self.snakeLength = 1
self.oldValue = None
self.torsionType = Tkinter.StringVar()
self.torsionType.set('1')
self.newAngList = Tkinter.StringVar()
self.TAHdata = None
self.molecule = None
#self.bondString = Tkinter.StringVar()
self.callbackDict = {}
self.callbackDict['measureDistanceGC'] = 'update'
self.callbackDict['measureAngleGC'] = 'update'
self.callbackDict['measureTorsionGC'] = 'update'
class SuperimposeAtomsGUICommand(SuperimposeCommand, MVAtomICOM):
"""
The SuperimposeAtomsGUICommand provides a GUI interface to the
SuperimposeAtomsCommand. This commands allows the user to create two sets
of atoms one reference and mobile of the same length by picking,
by string or using the alignment editor.
These two sets are then fed to the SuperimposeAtoms command.
- For now Only two 2 sets of Atoms belonging to a ref molecule and
a mobile molecule can be superimposed simultaneously.
- The command provides two way of defining those two sets of atoms:
* By picking nodes
* By string:
* Using the alignment editor
"""
# The superimposeAtomsGC provides an GU interface to allow the user to create two sets of atoms
# which will be used to do a pairwise superimposition.
def __init__(self, func=None):
MVCommand.__init__(self, func)
MVAtomICOM.__init__(self)
self.refAtomList = []
self.inAtomList = []
#self.superImposedPairs = {}
self.newPairs = {}
self.pair = []
self.mobMol = None
self.refMol = None
self.refNodes = {}
self.mobNodes = {}
self.filters = {
'CA Atoms':
lambda x: x.name == 'CA',
'Backbone Atoms':
lambda x: x.name in
['CA', 'C', 'N', 'O', 'CA@A', 'C@A', 'N@A', 'O@A'],
'Heavy Atoms':
lambda x: not x.element == 'H',
'All Atoms':
None
}
self.defaultFilter = 'Backbone Atoms'
## def doit(self, refAtoms, mobAtoms, updateGeom=True, showRMSD=True):
## """same as in SuperimposeCommand """
## SuperimposeCommand.doit(self, refAtoms, mobAtoms, updateGeom=True, showRMSD=True)
def onAddCmdToViewer(self):
# Check first is any of the command that superimpose depends on are
# already loaded.
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('superimposeAtoms'):
self.vf.loadCommand('superImposeCommands',
'superimposeAtoms',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('startContinuousPicking'):
self.vf.loadCommand('dejaVuCommands',
'startContinuousPicking',
'ViewerFramework',
topCommand=0)
if not self.vf.commands.has_key('stopContinuousPicking'):
self.vf.loadCommand('dejaVuCommands',
'stopContinuousPicking',
'ViewerFramework',
topCommand=0)
if not self.vf.commands.has_key('labelByExpression'):
self.vf.loadCommand('labelCommands',
'labelByExpression',
'Pmv',
topCommand=0)
self.sphere1 = Spheres(name='elt1',
radii=0.5,
materials=((0., 1., 0.), ),
protected=True)
self.sphere2 = Spheres(name='elt2',
radii=0.5,
materials=((1., 1., 0.), ),
protected=True)
def onRemoveObjectFromViewer(self, obj):
if hasattr(self.vf, 'alignment'):
self.vf.alnEditor.deleteSequence(obj.name)
self.vf.alnEditor.redraw()
if obj.name == self.refMol:
self.refMol = None
if obj.name == self.mobMol:
self.mobMol = None
##########################################################################
#### BY PICKING...
##########################################################################
def initICOM(self, modifier):
# set the callback of continuousPicking to label the picked node
# 1- get a handle on the cbManager
cbManager = self.vf.startContinuousPicking.cbManager
# 2- Save the existing callbacks
#self.oldCallBacks = cbManager.callbacks
# 3- Set to the new callback
cbManager.SetCallback(CallBackFunction(self.labelByName))
self.vf.startContinuousPicking()
self.supcb = 0
def labelByName(self, pick):
# Continuous labeling.
if pick is None: return
atom = self.vf.findPickedAtoms(pick)
if atom:
level = self.vf.ICmdCaller.level.value
self.vf.ICmdCaller.level.AddCallback(self.unlabelLevel)
if level == Molecule: level = Protein
self.node = atom.findType(level)
funcItems = map(lambda x: x.full_name(), self.node)
self.vf.labelByExpression(
self.node,
font='arial1.glf',
location='First',
textcolor='red',
only=0,
lambdaFunc=1,
negate=0,
function='lambda x: str(x.full_name())\n\n',
topCommand=0)
def unlabelLevel(self, newLevel, oldLevel):
if not hasattr(self, 'node'): return
if oldLevel == Molecule: oldLevel = Protein
# need to be at the former level for all the former picked stuff
# so take it all.
node = self.vf.getSelection()
nodes = node.findType(oldLevel)
# Careful in labelByProperty fix a bug if no label should not break!
self.vf.labelByExpression(nodes, negate=1, log=0)
def stopICOM(self):
# Destroy the inputForm
#self.cmdForms['superimpose'].root.destroy()
# Set the form to None.
#del self.cmdForms['superimpose']
# Set back the continuousPicking to unsolicitedPick
cbManager = self.vf.startContinuousPicking.cbManager
if not len(self.oldCallBacks) == 0:
cbManager.SetCallback(self.oldCallBacks[0])
if len(self.oldCallBacks) > 1:
for cb in self.oldCallBacks[1:]:
cbManager.AddCallBack(cb)
# Remove the unlabel callback bound to the self.vf.ICmdCaller.level
if self.unlabelLevel in self.vf.ICmdCaller.level.callbacks:
self.vf.ICmdCaller.level.RemoveCallback(self.unlabelLevel)
# Unlabel whatever is labeled
level = self.vf.ICmdCaller.level.value
nodes = self.vf.getSelection().findType(level)
if not nodes is None or len(nodes) != 0:
self.vf.labelByExpression(nodes, negate=1, log=0)
# Stop the continuous picking.
self.vf.stopContinuousPicking()
self.sphere1.Set(vertices=[])
self.sphere2.Set(vertices=[])
## self.visualFeedBack(vertices =[])
##########################################################################
####
##########################################################################
def createNodesSets(self, refnodes=None, mobnodes=None):
# Set the reference molecule and the mobile molecule....
# 1- set the reference molecule and the mobile
from MolKit.protein import ProteinSet
if refnodes:
refMols = refnodes.top.uniq()
if refMols == self.vf.Mols:
self.warningMsg(
"Reference and mobile molecules should be selected.")
return
if len(refMols) > 1:
self.warningMsg(
"Can have one and only one reference molecule.")
return
self.refMol = refMols[0]
if mobnodes:
mobMols = mobnodes.top.uniq()
if refMols == self.vf.Mols:
self.warningMsg(
"Reference and mobile molecules should be selected.")
return
if len(mobMols) > 1:
self.warningMsg("Can have one and only one mobile molecule.")
return
if mobMols[0] == self.refMol:
self.warningMsg(
"The mobile molecule must be different from the ref molecule"
)
return
self.mobMol = mobMols[0]
# 2- Create the entries for the refNodes listChooser
ebn = self.cmdForms['addPairs'].descr.entryByName
if refnodes:
reflc = ebn['refnodes']['widget']
for rn in refnodes:
if not rn.top == self.refMol: continue
self.refNodes[rn.full_name()] = rn
reflc.add((rn.full_name(), None))
# Create the entries for the mobNodes listChooser
if mobnodes:
moblc = ebn['mobnodes']['widget']
for mn in mobnodes:
if not mn.top == self.mobMol: continue
self.mobNodes[mn.full_name()] = mn
moblc.add((mn.full_name(), None))
def createPairs(self, refnames, mobnames, slice, choice):
# This is where the atom pairs are created
# Get the ref atom set
refAtms = AtomSet([])
mobAtms = AtomSet([])
for name in refnames:
refnod = self.refNodes[name]
atms = refnod.findType(Atom)
refAtms = refAtms + atms
for name in mobnames:
mobnod = self.mobNodes[name]
atms = mobnod.findType(Atom)
mobAtms = mobAtms + atms
# Now apply the filters to the sets
if choice:
refFiltAtms = refAtms.get(self.filters[choice])
mobFiltAtms = mobAtms.get(self.filters[choice])
if not len(refFiltAtms) == len(mobFiltAtms):
#print 'slicing', slice
self.warningMsg(
"the two sets of atoms needs to be of the same length")
return
ebn = self.cmdForms['pairs'].descr.entryByName
lc = ebn['newpairs']['widget']
for refatm, mobatm in map(None, refFiltAtms, mobFiltAtms):
#self.pairs.append((refatm, mobatm))
pairName = refatm.full_name() + '---' + mobatm.full_name()
self.newPairs[pairName] = (refatm, mobatm)
lc.add((pairName, None))
##########################################################################
#### GUI CALLBACKS
##########################################################################
def pick_cb(self):
ebn = self.cmdForms['addPairs'].descr.entryByName
cbVar = int(ebn['pick']['variable'].get())
if cbVar:
self.vf.setICOM(self, modifier="Shift_L", topCommand=0)
else:
self.stopICOM()
def string_cb(self):
ebn = self.cmdForms['addPairs'].descr.entryByName
cbVar = ebn['string']['variable']
#print cbVar.get()
if cbVar.get():
# if pushed show the form
val = self.showForm('editString', modal=1, blocking=0, force=1)
cbVar.set(0)
if val:
if not val['srefNodes'] and not val['smobNodes']: return
refnodes = val['srefNodes']
if refnodes:
refnodes.sort()
mobnodes = val['smobNodes']
if mobnodes: mobnodes.sort()
self.createNodesSets(refnodes, mobnodes)
def setDefault(self, text):
pass
## self.defaultFilter = text
## if hasattr(self, 'pair') and len(self.pair) == 2:
## filter = self.filters[text]
## set1 = self.pair[0]
## set2 = self.pair[1]
## if filter:
## set1 = set1.get(filter)
## set2 = set2.get(filter)
## if (set1 and set2) and (len(set1) == len(set2)):
## self.updateChooser(set1, set2)):
def delete_cb(self):
ebn = self.cmdForms['pairs'].descr.entryByName
lc = ebn['newpairs']['widget']
lc.clear()
self.newPairs = {}
return
def dismiss_cb(self):
if self.cmdForms.has_key('pairs'): self.cmdForms['pairs'].withdraw()
if self.cmdForms.has_key('addPairs'):
self.cmdForms['addPairs'].withdraw()
if self.cmdForms.has_key('editString'):
self.cmdForms['addPairs'].withdraw()
# Dismiss all the forms ???
## for v in self.cmdForms.values():
## v.withdraw()
def continuous_cb(self):
# Sets the continuous flag to the right value ????
pass
def reset_cb(self):
# Reset the superposition put back the mob molecule to the right place..
pass
def superimpose_cb(self):
refAtoms = AtomSet()
mobAtoms = AtomSet()
for pair in self.newPairs.values():
refAtoms.append(pair[0])
mobAtoms.append(pair[1])
apply(self.doitWrapper, (refAtoms, mobAtoms), {})
def add_cb(self):
val = self.showForm('addPairs',
modal=1,
blocking=0,
force=1,
okCfg={'text': 'Create Pairs'})
# need to get all the nodes... from each listchooser
if not val: return
# Need this for the order of the nodes in the pairs...
ebn = self.cmdForms['addPairs'].descr.entryByName
reflc = ebn['refnodes']['widget']
refnames = map(lambda x: x[0], reflc.entries)
moblc = ebn['mobnodes']['widget']
mobnames = map(lambda x: x[0], moblc.entries)
self.createPairs(refnames, mobnames, val['slice'][0], val['choice'][0])
def refremove_cb(self):
ebn = self.cmdForms['addPairs'].descr.entryByName
lc = ebn['refnodes']['widget']
sel = lc.get()
if sel:
lc.remove(sel[0])
if sel[0] in self.refNodes:
del self.refNodes[sel[0]]
def mobremove_cb(self):
ebn = self.cmdForms['addPairs'].descr.entryByName
lc = ebn['mobnodes']['widget']
sel = lc.get()
if sel:
lc.remove(sel[0])
if sel[0] in self.refNodes:
del self.mobNodes[sel[0]]
def refmoveup_cb(self):
ebn = self.cmdForms['addPairs'].descr.entryByName
lc = ebn['refnodes']['widget']
sel = lc.get()
if not sel: return
sel = sel[0]
selIndex = lc.entries.index((sel, None))
if selIndex == 0: return
lc.remove(sel)
lc.insert(selIndex - 1, sel)
lc.select(sel)
def mobmoveup_cb(self):
ebn = self.cmdForms['addPairs'].descr.entryByName
lc = ebn['mobnodes']['widget']
sel = lc.get()
if not sel: return
sel = sel[0]
selIndex = lc.entries.index((sel, None))
if selIndex == 0: return
lc.remove(sel)
lc.insert(selIndex - 1, sel)
lc.select(sel)
def refmovedown_cb(self):
ebn = self.cmdForms['addPairs'].descr.entryByName
lc = ebn['refnodes']['widget']
sel = lc.get()
if not sel: return
sel = sel[0]
selIndex = lc.entries.index((sel, None))
if selIndex == len(lc.entries) - 1: return
lc.remove(sel)
lc.insert(selIndex + 1, sel)
lc.select(sel)
def mobmovedown_cb(self):
ebn = self.cmdForms['addPairs'].descr.entryByName
lc = ebn['mobnodes']['widget']
sel = lc.get()
if not sel: return
sel = sel[0]
selIndex = lc.entries.index((sel, None))
if selIndex == len(lc.entries) - 1: return
lc.remove(sel)
lc.insert(selIndex + 1, sel)
lc.select(sel)
def guiCallback(self):
#form = self.showForm('pairs', modal=0, blocking=0)
val = self.showForm('pairs', modal=0, blocking=0)
def buildFormDescr(self, formName):
if formName == 'addPairs':
# CREATE PAIRS GROUP
idf = InputFormDescr(title="Superimpose")
idf.append({
'name': "mode",
'widgetType': Pmw.Group,
'container': {
'mode': 'w.interior()'
},
'wcfg': {
'tag_text': "Create Reference Nodes and Mobile Nodes Lists"
},
'gridcfg': {
'sticky': 'wnse'
}
})
idf.append({
'widgetType': Tkinter.Label,
'parent': 'mode',
'wcfg': {
'text': 'By String'
},
'gridcfg': {
'sticky': 'we'
}
})
idf.append({
'widgetType': Tkinter.Checkbutton,
'name': 'string',
'parent': 'mode',
#'tooltip':'Use the string selector to create refnode-mobnodes pairs',
'wcfg': {
'text': 'on/off',
'command': self.string_cb
},
'gridcfg': {
'sticky': 'we',
'row': -1
}
})
idf.append({
'widgetType': Tkinter.Label,
'parent': 'mode',
'wcfg': {
'text': 'By Picking'
},
'gridcfg': {
'sticky': 'we',
'row': -1
}
})
idf.append({
'widgetType': Tkinter.Checkbutton,
'name': 'pick',
'tooltip':
'Use the picking event to create refnode-mobnodes pairs',
'parent': 'mode',
'wcfg': {
'text': 'on/off',
'command': self.pick_cb
},
'gridcfg': {
'sticky': 'we',
'row': -1
}
})
###############################################################
## EDIT REF/MOB NODES
###############################################################
idf.append({
'name': "editnodes",
'widgetType': Pmw.Group,
'container': {
'editnodes': 'w.interior()'
},
'wcfg': {
'tag_text': "Edit Reference Nodes and Mobile Nodes Lists:"
},
'gridcfg': {
'sticky': 'wnse'
}
})
idf.append({
'name': 'refremove',
'parent': 'editnodes',
'widgetType': Tkinter.Button,
'tooltip': """ Remove the selected entry from the
commands to be applied to the object when loaded in the application""",
'wcfg': {
'text': 'REMOVE',
'width': 10,
'command': self.refremove_cb
},
'gridcfg': {
'sticky': 'we',
'row': 0,
'column': 0
}
})
idf.append({
'name': 'refoneup',
'parent': 'editnodes',
'widgetType': Tkinter.Button,
'tooltip': """Move the selected entry up one entry""",
'wcfg': {
'text': 'Move up',
'width': 10,
'command': self.refmoveup_cb
},
'gridcfg': {
'sticky': 'we',
'row': 1,
'column': 0
}
})
idf.append({
'name': 'refonedown',
'parent': 'editnodes',
'widgetType': Tkinter.Button,
'tooltip': """Move the selected entry down one entry""",
'wcfg': {
'text': 'Move down',
'width': 10,
'command': self.refmovedown_cb
},
'gridcfg': {
'sticky': 'we',
'row': 2,
'column': 0
}
})
# RefNodes listchooser
idf.append({
'widgetType': ListChooser,
'name': 'refnodes',
'parent': 'editnodes',
'tooltip': """list of the reference nodes""",
'wcfg': {
'entries': [],
'mode': 'single',
'lbwcfg': {
'exportselection': 0
},
'title': 'Reference Nodes'
},
'gridcfg': {
'sticky': 'we',
'row': 0,
'column': 1,
'rowspan': 3
}
})
# MobNodes listchooser
idf.append({
'widgetType': ListChooser,
'name': 'mobnodes',
'parent': 'editnodes',
'tooltip': """list of the mobile nodes""",
'wcfg': {
'entries': [],
'mode': 'single',
'lbwcfg': {
'exportselection': 0
},
'title': 'Mobile Nodes'
},
'gridcfg': {
'sticky': 'we',
'row': 0,
'column': 2,
'rowspan': 3
}
})
idf.append({
'name': 'mobremove',
'parent': 'editnodes',
'widgetType': Tkinter.Button,
'tooltip': """ Remove the selected mobile node""",
'wcfg': {
'text': 'REMOVE',
'width': 10,
'command': self.mobremove_cb
},
'gridcfg': {
'sticky': 'we',
'row': 0,
'column': 3
}
})
idf.append({
'name': 'moboneup',
'parent': 'editnodes',
'widgetType': Tkinter.Button,
'tooltip': """Move the selected entry up one entry""",
'wcfg': {
'text': 'Move up',
'width': 10,
'command': self.mobmoveup_cb
},
'gridcfg': {
'sticky': 'we',
'row': 1,
'column': 3
}
})
idf.append({
'name': 'mobonedown',
'parent': 'editnodes',
'widgetType': Tkinter.Button,
'tooltip': """Move the selected entry down one entry""",
'wcfg': {
'text': 'Move down',
'width': 10,
'command': self.mobmovedown_cb
},
'gridcfg': {
'sticky': 'we',
'row': 2,
'column': 3
}
})
###############################################################
## FILTERS
###############################################################
idf.append({
'name': "filter",
'widgetType': Pmw.Group,
'container': {
'filters': 'w.interior()'
},
'wcfg': {
'tag_text': "Apply Filters To The Ref/Mob nodes lists:"
},
'gridcfg': {
'sticky': 'wnse'
}
})
idf.append({
'widgetType': Pmw.ComboBox,
'name': 'choice',
'parent': 'filters',
'tooltip': """This filter allows the user to choose
which atom to consider from the ref node or mob nodes sets to create the atom pairs""",
'defaultValue': self.defaultFilter,
'wcfg': {
'scrolledlist_items': self.filters.keys(),
'selectioncommand': self.setDefault
},
'gridcfg': {
'sticky': 'w'
}
})
# If sets not of the same length:
idf.append({
'widgetType': Pmw.ComboBox,
'name': 'slice',
'parent': 'filters',
'defaultValue': 'Beginning',
'tooltip': """When the two sets of atoms are not of
the same length the user can chose what subset of the longest set to take,
beginning, the end or half and half""",
'wcfg': {
'scrolledlist_items': ['Beginning', 'End', 'Half/Half'],
},
'gridcfg': {
'sticky': 'w',
'row': -1
}
})
return idf
elif formName == 'pairs':
idf = InputFormDescr(title="Pairwise Superimposition")
# EDIT PAIRS GROUP
idf.append({
'name': "edit",
'widgetType': Pmw.Group,
'container': {
'edit': 'w.interior()'
},
'wcfg': {
'tag_text': "Edit Atom Pairs"
},
'gridcfg': {
'sticky': 'wnse'
}
})
entries = map(lambda x: (x, None), self.newPairs.keys())
idf.append({
'widgetType': ListChooser,
'name': 'newpairs',
'parent': 'edit',
'wcfg': {
'mode': 'extended',
'entries': entries,
'lbwcfg': {
'exportselection': 1
},
'title': 'Reference Atoms -- Mobile Atoms'
},
'gridcfg': {
'sticky': 'wens',
'columnspan': 2
}
})
idf.append({
'widgetType': Tkinter.Button,
'name': 'delete',
'parent': 'edit',
'wcfg': {
'width': 15,
'text': 'Add Pairs',
'command': self.add_cb
},
'gridcfg': {
'sticky': 'we'
}
})
idf.append({
'widgetType': Tkinter.Button,
'name': 'delete',
'parent': 'edit',
'wcfg': {
'width': 15,
'text': 'Delete Pairs',
'command': self.delete_cb
},
'gridcfg': {
'sticky': 'we',
'row': -1
}
})
idf.append({
'name': "superimpose",
'widgetType': Pmw.Group,
'container': {
'superimpose': 'w.interior()'
},
'wcfg': {
'tag_text': "Superimposation parameters"
},
'gridcfg': {
'sticky': 'wnse'
}
})
# Continuous Superimposition
idf.append({
'widgetType': Tkinter.Checkbutton,
'name': 'continuous',
'parent': 'superimpose',
'wcfg': {
'variable': Tkinter.IntVar(),
'text': 'Continuous',
'command': self.continuous_cb,
'padx': 10,
'pady': 10
},
'gridcfg': {
'sticky': 'w'
}
})
# Reset & SuperImpose button.
idf.append({
'widgetType': Tkinter.Button,
'name': 'final',
'parent': 'superimpose',
'wcfg': {
'width': 15,
'text': 'Superimpose',
'command': self.superimpose_cb
},
'gridcfg': {
'sticky': 'we',
'row': -1
}
})
idf.append({
'widgetType': Tkinter.Button,
'parent': 'superimpose',
'name': 'reset',
'wcfg': {
'text': 'Reset',
'command': self.reset_cb
},
'gridcfg': {
'sticky': 'we',
'row': -1
}
})
idf.append({
'widgetType': Tkinter.Button,
'name': 'dismiss',
'wcfg': {
'text': 'DISMISS',
'command': self.dismiss_cb
},
'gridcfg': {
'sticky': 'we',
'columnspan': 2
}
})
return idf
elif formName == 'editString':
idf = InputFormDescr(title='Get Nodes From String')
idf.append({
'name': "refgroup",
'widgetType': Pmw.Group,
'container': {
'refgroup': 'w.interior()'
},
'wcfg': {
'tag_text': "Reference Nodes:"
},
'gridcfg': {
'sticky': 'wnse'
}
})
idf.append({
'name': "mobgroup",
'widgetType': Pmw.Group,
'container': {
'mobgroup': 'w.interior()'
},
'wcfg': {
'tag_text': "Mobile Nodes:"
},
'gridcfg': {
'sticky': 'wnse',
'row': -1
}
})
idf.append({
'widgetType': StringSelectorGUI,
'parent': 'refgroup',
'name': 'srefNodes',
#'defaultValue':self.vf.Mols[0].name+", , , ",
'tooltip':
'Please select the reference nodes set. By default the ref nodes will be the first molecule loaded in the viewer',
'wcfg': {
'molSet': self.vf.Mols,
'vf': self.vf,
'all': 1,
'crColor': (1., 0., 0.),
'forceEmpty': 1,
},
'gridcfg': {
'sticky': 'we'
}
})
idf.append({
'widgetType': StringSelectorGUI,
'parent': 'mobgroup',
#'defaultValue':self.vf.Mols[1].name+", , , ",
'tooltip':
'Please select the mobile nodes set. By default the mobile nodes will be the second molecule loaded in the viewer',
'name': 'smobNodes',
'wcfg': {
'molSet': self.vf.Mols,
'vf': self.vf,
'all': 1,
'crColor': (0., 0., 1.),
'forceEmpty': 1,
},
'gridcfg': {
'row': -1,
'sticky': 'we'
}
})
return idf
def onAddCmdToViewer(self):
from DejaVu.bitPatterns import pat3
from DejaVu.IndexedPolygons import IndexedPolygons
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('measureAngle'):
self.vf.loadCommand('measureCommands',
'measureAngle',
'Pmv',
topCommand=0)
self.masterGeom = Geom('measureTorsionGeom',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
if self.vf.hasGui:
measure_geoms = check_measure_geoms(self.vf.GUI)
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=measure_geoms)
self.lines = IndexedPolygons('torsionLine',
materials=((0, 1, 1), ),
culling=GL.GL_NONE,
inheritStipplePolygons=0,
inheritMaterial=0,
stipplePolygons=1,
backPolyMode=GL.GL_FILL,
frontPolyMode=GL.GL_FILL,
protected=True,
pickable=0)
if self.vf.userpref['Sharp Color Boundaries for MSMS'][
'value'] == 'blur':
self.lines.Set(
inheritSharpColorBoundaries=False,
sharpColorBoundaries=False,
)
self.lines.polygonstipple.Set(pattern=pat3)
#self.lines.polygonstipple.Set(pattern=pat3, tagModified=False)
#self.lines.RenderMode(GL.GL_FILL)
#self.lines.RenderMode(GL.GL_FILL, face=GL.GL_BACK)
self.labels = GlfLabels(name='torsionLabel',
shape=(0, 3),
font='arial1.glf',
fontStyle='solid3d',
fontScales=(.5, .5, .3),
inheritMaterial=0,
materials=((0, 1, 1), ))
self.spheres = Spheres(name='torsionSpheres',
shape=(0, 3),
inheritMaterial=0,
radii=0.2,
quality=15,
materials=((0., 1., 1.), ),
protected=True)
if self.vf.hasGui:
for item in [self.lines, self.labels, self.spheres]:
self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom)
doc = """Number of labeled torsions displayed.
Valid values are integers>0"""
self.vf.userpref.add('Measured Torsions',
4,
callbackFunc=[self.setLength_cb],
category="Molecules",
validateFunc=lambda x: x > 0,
doc=doc)
#used after startICOM is invoked
doc = """Continuous update of torsions if 'transformRoot only' is
turned off and viewer's current object is not Root."""
choices = ['yes', 'no']
self.vf.userpref.add('Continuous Update Torsion',
'yes',
choices,
callbackFunc=[self.continuousUpdate_cb],
category="Molecules",
doc=doc)
self.snakeLength = 4
f = map( lambda x: (x, x+1, x+n+1, x+n), range(smooth.shape[1]-1))
v = Numeric.array(Numeric.reshape(smooth, (-1,4))[:,:3])
p = IndexedPolygons('sheet2D', vertices = v, faces = f, protected=True,)
if self.vf.userpref['sharpColorBoundariesForMsms']['value'] == 'blur':
p.Set(inheritSharpColorBoundaries=False, sharpColorBoundaries=False,)
p.replace = False
vi.AddObject(p)
from DejaVu.Spheres import Spheres
ctrl.shape = (-1,4)
p = Spheres('ctrl', centers = ctrl[:, :3], radii = 0.6, protected=True)
p.replace = False
vi.AddObject(p)
from DejaVu.Spheres import Spheres
s = Spheres('sph', vertices = v, quality=5, protected=True)
s.radius = 0.2
vi.AddObject(s)
from MolKit import Read
mol = Read('../1crn.pdb')
allatoms = mol.chains.residues.atoms
caat = allatoms.get('CA')
coords = caat.coords
from DejaVu.Spheres import Spheres
p = Spheres('CA', centers = coords, radii = 0.6, protected=True)
p.replace = False
vi.AddObject(p)
## from BioChem.protein import Protein
## from BioChem.pdbParser import PdbParser
