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from ViewerFramework.VFCommand import Command, CommandGUI
from DejaVu.Spheres import Spheres
from DejaVu.Arrows import Arrows
from MolKit.molecule import Atom
import numpy
import math
#from Pmv.moleculeViewer import EditAtomsEvent
#from DejaVu.Transformable import translateEvent
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(numpy.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 = numpy.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 = numpy.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 = numpy.array(self.forces_list)
self.target.setConformation(1)
point = numpy.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 = numpy.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 = numpy.array(self.forces_list)
self.target.setConformation(1)
point = numpy.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 = numpy.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 = numpy.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 = numpy.zeros((self.N_forces,3),'f')
return numpy.array(self.getTargetCenter())
else :
return None
def getPush(self,target=True):
pos = self.getHandlerPos()
if target : targetpos = numpy.array(self.getTargetCenter())
else :
targetpos = self.findNeighbor(pos[0].tolist())
if targetpos == None : return numpy.array([0.,0.,0.])
force = - numpy.array(pos[0]) + targetpos
d=math.sqrt(numpy.sum(force*force))
return force*1/(d*d)
#else : return numpy.array([0.,0.,0.])
def getSteered(self):
pos = self.getHandlerPos()
force = numpy.array(pos) - numpy.array(self.getTargetCenter())
#d=math.sqrt(numpy.sum(force[0]*force[0]))
#if d > 30. : return numpy.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 = numpy.array(coords) + (numpy.array(pos) - numpy.array(self.getTargetCenter()))#numpy.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
commandList = [
{'name':'handler', 'cmd':Handler(),
'gui': None},
]
def initModule(viewer):
for dict in commandList:
# print 'dict',dict
viewer.addCommand(dict['cmd'], dict['name'], dict['gui'])
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