def blenderstructure(self, ):
nat = len(self.xyz.atomtypes)
# create atoms
for i in range(0, nat):
loc = Mathutils.Vector(self.xyz.coord[i])
me = Mesh.Primitives.Icosphere(spheresubdivisions,
atomicradii[self.xyz.atomtypes[i]])
me.materials = [materials[self.xyz.atomtypes[i]]]
for face in me.faces:
face.smooth = True
obj = self.scene.objects.new(me, 'Atom')
obj.setLocation(loc)
# form bonds between atoms
for i in range(0, nat):
for j in range(i + 1, nat):
vec1 = Mathutils.Vector(self.xyz.coord[i])
vec2 = Mathutils.Vector(self.xyz.coord[j])
vec = vec2 - vec1
distcovalent = covalentradii[self.xyz.atomtypes[
i]] + covalentradii[self.xyz.atomtypes[j]]
print "vec.length = %s distcovalent = %s" % (vec.length,
distcovalent)
if (vec.length - distcovalent) <= 0.10 * distcovalent:
me = Mesh.Primitives.Tube(32, stickradius, vec.length)
for face in me.faces:
face.smooth = True
obj = self.scene.objects.new(me, 'Bond')
axis = Mathutils.CrossVecs(Vector([0, 0, 1]), vec)
angle = Mathutils.AngleBetweenVecs(Vector([0, 0, 1]), vec)
rotmat = Mathutils.RotationMatrix(angle, 4, "R", axis)
obj.setMatrix(obj.matrix * rotmat)
obj.setLocation((vec1 + vec2) * 0.5)
# vectors
scale = 1.0 #1000.0 #1.0 #1000.0
for i in range(0, nat):
loc = Mathutils.Vector(self.xyz.coord[i])
vec = Mathutils.Vector(self.xyz.vectors[i]) * scale
# arrow tail
me = Mesh.Primitives.Tube(32, arrowradius, vec.length)
me.materials = [materials["arrow"]]
for face in me.faces:
face.smooth = True
obj = self.scene.objects.new(me, "Arrow-Tail")
axis = Mathutils.CrossVecs(Vector([0, 0, 1]), vec)
angle = Mathutils.AngleBetweenVecs(Vector([0, 0, 1]), vec)
rotmat = Mathutils.RotationMatrix(angle, 4, "R", axis)
obj.setMatrix(obj.matrix * rotmat)
obj.setLocation(loc + 0.5 * vec)
# arrow head
me = Mesh.Primitives.Cone(32, 2 * arrowradius, 0.5)
me.materials = [materials["arrow"]]
for face in me.faces:
face.smooth = True
obj = self.scene.objects.new(me, "Arrow-Head")
axis = Mathutils.CrossVecs(Vector([0, 0, 1]), vec)
angle = Mathutils.AngleBetweenVecs(Vector([0, 0, 1]), vec)
rotmat = Mathutils.RotationMatrix(angle + 180.0, 4, "R", axis)
obj.setMatrix(obj.matrix * rotmat)
obj.setLocation(loc + vec)
def blenderstructure(self, ):
for i in range(len(self.xyz.atomtypes)):
me = Mesh.Primitives.Icosphere(spheresubdivisions,
atomicradii[self.xyz.atomtypes[i]])
me.materials = [materials[self.xyz.atomtypes[i]]]
for face in me.faces:
face.smooth = True
obj = self.scene.objects.new(me, 'Mesh')
obj.setLocation(self.xyz.coord[i][0], self.xyz.coord[i][1],
self.xyz.coord[i][2])
for i in range(len(self.xyz.atomtypes)):
for j in range(i + 1, len(self.xyz.atomtypes)):
vec1 = Mathutils.Vector(self.xyz.coord[i])
vec2 = Mathutils.Vector(self.xyz.coord[j])
vec = vec2 - vec1
distcovalent = covalentradii[self.xyz.atomtypes[
i]] + covalentradii[self.xyz.atomtypes[j]]
if (vec.length - distcovalent) <= 0.10 * distcovalent:
me = Mesh.Primitives.Tube(32, stickradius, vec.length)
for face in me.faces:
face.smooth = True
obj = self.scene.objects.new(me, 'Cylinder')
axis = Mathutils.CrossVecs(Vector([0, 0, 1]), vec)
angle = Mathutils.AngleBetweenVecs(Vector([0, 0, 1]), vec)
rotmat = Mathutils.RotationMatrix(angle, 4, "R", axis)
obj.setMatrix(obj.matrix * rotmat)
obj.setLocation((vec1 + vec2) * 0.5)
def cross(v_id, edges):
def get_vec(edge):
if edge.v1 == v_id:
return edge.v2.co + edge.v1.co
return edge.v1.co + edge.v2.co
edges = list(edges)
vec1 = get_vec(edges[0])
vec2 = get_vec(edges[1])
return Mathutils.CrossVecs(vec1, vec2).normalize()
def gui(): glClearColor(0,0,0,1) glClear(GL_COLOR_BUFFER_BIT|GL_DEPTH_BUFFER_BIT) glEnable(GL_DEPTH_TEST) glViewport(0,0,500,500) glMatrixMode(GL_PROJECTION) glLoadIdentity() #glFrustum(-100,100,-100,100,30,500) glOrtho(-10,10,-10,10,-500,500) vect3=vect norm=sqrt(vect3[0]**2+vect3[1]**2+vect3[2]**2) vect3=vect3/norm vect2=Vector(0,1,0)-vect3[1]*vect3 norm=sqrt(vect2[0]**2+vect2[1]**2+vect2[2]**2) vect2=vect2/norm vecCros=Mathutils.CrossVecs(vect3,vect2) norm=sqrt(vecCros[0]**2+vecCros[1]**2+vecCros[2]**2) vect1=vecCros/norm buf2=Buffer(GL_FLOAT,16,[vect1[0],vect1[1],vect1[2],0, vect2[0],vect2[1],vect2[2],0, vect3[0],vect3[1],vect3[2],0, 0,0,0,1]) #buf2=Buffer(GL_FLOAT,16,[1,0,0,v1, # 0,1,0,v2, # 0,0,1,v3, # 0,0,0,1]) # glMultMatrixf(buf) glTranslatef(0,0,-50) glMatrixMode(GL_MODELVIEW) glLoadIdentity() # glRotatef(a,1,1,1) glMultMatrixf(buf2) myCube() changeA()
def animatedensity(self, filenamelist, renderingpath, isovalue):
context = self.scene.getRenderingContext()
context.extensions = True
context.renderPath = renderingpath
#context.imageType=Render.JPEG
context.sFrame = 1
context.eFrame = 1
context.sizeX = width
context.sizeY = height
cubeobject = cube(filenamelist[0])
cubeobject.readCube()
atoms = []
ipokeytypeloc = Object.IpoKeyTypes.LOC
ipokeytyperot = Object.IpoKeyTypes.ROT
for i in range(len(cubeobject.atomtypes)):
me = Mesh.Primitives.Icosphere(
spheresubdivisions,
atomicradii.get(cubeobject.atomtypes[i], 2.0))
me.materials = [
materials.get(cubeobject.atomtypes[i], materials["default"])
]
for face in me.faces:
face.smooth = True
obj = self.scene.objects.new(me, 'Atom')
obj.setLocation(cubeobject.coord[i][0], cubeobject.coord[i][1],
cubeobject.coord[i][2])
atoms.append(obj)
bonds = []
for i in range(len(cubeobject.atomtypes)):
for j in range(i + 1, len(cubeobject.atomtypes)):
vec1 = Mathutils.Vector(cubeobject.coord[i])
vec2 = Mathutils.Vector(cubeobject.coord[j])
vec = vec2 - vec1
distcovalent = covalentradii.get(
cubeobject.atomtypes[i], 2.0) + covalentradii.get(
cubeobject.atomtypes[j], 2.0)
if (vec.length - distcovalent) <= 0.10 * distcovalent:
me = Mesh.Primitives.Tube(32, stickradius, vec.length)
for face in me.faces:
face.smooth = True
obj = self.scene.objects.new(me, 'Cylinder')
axis = Mathutils.CrossVecs(Vector([0, 0, 1]), vec)
angle = Mathutils.AngleBetweenVecs(Vector([0, 0, 1]), vec)
rotmat = Mathutils.RotationMatrix(angle, 4, "R", axis)
obj.setMatrix(obj.matrix * rotmat)
obj.setLocation((vec1 + vec2) * 0.5)
bonds.append([i, j, vec, obj, vec.length])
self.isosurface(cubeobject, isovalue)
context.render()
filename = "RENDER/image_0000.jpg"
context.saveRenderedImage(filename)
for j in range(1, len(filenamelist)):
print(("Rendering:", j))
filename = "RENDER/image_%04d.jpg" % (j)
for ob in self.scene.objects:
if "Lobe" in ob.name:
self.scene.unlink(ob)
cubeobject = cube(filenamelist[j])
cubeobject.readCube()
for i in range(len(atoms)):
atoms[i].setLocation(cubeobject.coord[i][0],
cubeobject.coord[i][1],
cubeobject.coord[i][2])
atoms[i].insertIpoKey(ipokeytypeloc)
for i in range(len(bonds)):
vec1 = Mathutils.Vector(cubeobject.coord[bonds[i][0]])
vec2 = Mathutils.Vector(cubeobject.coord[bonds[i][1]])
vec = vec2 - vec1
dist = vec.length
axis = Mathutils.CrossVecs(bonds[i][2], vec)
angle = Mathutils.AngleBetweenVecs(bonds[i][2], vec)
rotmat = Mathutils.RotationMatrix(angle, 4, "R", axis)
bonds[i][3].setMatrix(bonds[i][3].matrix * rotmat)
bonds[i][3].setLocation((vec1 + vec2) * 0.5)
bonds[i][3].setSize(1.0, 1.0, dist / bonds[i][4])
bonds[i][3].insertIpoKey(ipokeytypeloc)
bonds[i][3].insertIpoKey(ipokeytyperot)
bonds[i][2] = vec
bonds[i][4] = dist
self.isosurface(cubeobject, isovalue)
context.render()
context.saveRenderedImage(filename)