def rotate(self, frame, axis, theta):
'''
Simple rotation about the x, y, or z axis.
right-handed rotation
Note that calcuations are in radians
Rotation is done in right-handed coordinate system
'''
cs = numpy.cos(theta)
si = numpy.sin(theta)
if(axis == 'x'):
mat = numpy.array([[1.0, 0.0, 0.0], [0.0, cs, -si], [0.0, si, cs]])
elif(axis == 'y'):
mat = numpy.array([[cs, 0.0, si], [0.0, 1.0, 0.0], [-si, 0.0, cs]])
elif(axis == 'z'):
mat = numpy.array([[cs, -si, 0.0], [si, cs, 0.0], [0.0, 0.0, 1.0]])
coordt = self._coor[frame, :].T
error, matrix_product = sasmath.matrix_multiply(mat, coordt)
ncoord = matrix_product.T
self._coor[frame, :] = ncoord
return
def rotate(self,frame,axis,theta): ''' Simple rotation about the x, y, or z axis. Note that calcuations are in radians ''' cs=numpy.cos(theta) ; si=numpy.sin(theta) if(axis=='x'): mat=numpy.array([[1.0,0.0,0.0],[0.0,cs,-si],[0.0,si,cs]]) elif(axis=='y'): mat=numpy.array([[cs,0.0,si],[0.0,1.0,0.0],[-si,0.0,cs]]) elif(axis=='z'): mat=numpy.array([[cs,-si,0.0],[si,cs,0.0],[0.0,0.0,1.0]]) coordt=self._coor[frame,:].T error,matrix_product = sasmath.matrix_multiply(mat,coordt) ncoord = matrix_product.T self._coor[frame,:]=ncoord return
def align(self, frame, coor_sub_2, com_sub_2, coor_sub_1, com_sub_1):
'''
Alignment of one object on top of another
"self" is aligned onto "other" using the basis
of molecule 2 to align onto the basis of molecule 1
and the transformation is then done to all the atoms of
molecule 2
'''
self.masscheck(frame)
self.calccom(frame)
u = sasmath.find_u(coor_sub_1, coor_sub_2)
tao = numpy.transpose(self.coor()[frame] - com_sub_2)
error, nat2 = sasmath.matrix_multiply(u, tao)
ncoor = numpy.transpose(nat2) + com_sub_1
self._coor[frame, :] = ncoor
return
def align(self,frame,coor_sub_2,com_sub_2,coor_sub_1,com_sub_1): ''' Alignment of one object on top of another "self" is aligned onto "other" using the basis of molecule 2 to align onto the basis of molecule 1 and the transformation is then done to all the atoms of molecule 2 ''' self.masscheck(frame) self.calccom(frame) u = sasmath.find_u(coor_sub_1, coor_sub_2) tao = numpy.transpose(self.coor()[frame] - com_sub_2) error,nat2 = sasmath.matrix_multiply(u,tao) ncoor = numpy.transpose(nat2) + com_sub_1 self._coor[frame,:] = ncoor return
