def test_3d_rot():
import geometry
p = [10,1,1]
t = geometry.create_transformation_to_coincide_point_with_z_axis( [-9,1,4], p)
print t.transform_xyz( *p)
print t.transform_xyz( -9,1,4)
inv = t.get_inverse()
print inv.transform_xyz( *t.transform_xyz( *p))
def test_3d_rot():
import geometry
p = [10, 1, 1]
t = geometry.create_transformation_to_coincide_point_with_z_axis(
[-9, 1, 4], p)
print t.transform_xyz(*p)
print t.transform_xyz(-9, 1, 4)
inv = t.get_inverse()
print inv.transform_xyz(*t.transform_xyz(*p))
def _get_3dtransform_for_drawing( self, b):
"""this is a helper method that returns a transform3d which rotates
a bond and its neighbors to coincide with the x-axis and rotates neighbors to be in (x,y)
plane."""
atom1, atom2 = b.vertices
x1,y1,z1 = atom1.coords
x2,y2,z2 = atom2.coords
t = geometry.create_transformation_to_coincide_point_with_z_axis( [x1,y1,z1],[x2,y2,z2])
x,y,z = t.transform_xyz( x2,y2,z2)
# now rotate to make the plane of neighbor atoms coincide with x,y plane
angs = []
for n in atom1.neighbors + atom2.neighbors:
if n is not atom1 and n is not atom2:
nx,ny,nz = t.transform_xyz( *n.coords)
ang = math.atan2( ny, nx)
if ang < -0.00001:
ang += math.pi
angs.append( ang)
ang = sum( angs) / len( angs)
t.set_rotation_z( ang + math.pi/2.0)
t.set_rotation_y( math.pi/2.0)
return t
def _get_3dtransform_for_drawing(self, b):
"""this is a helper method that returns a transform3d which rotates
a bond and its neighbors to coincide with the x-axis and rotates neighbors to be in (x,y)
plane."""
atom1, atom2 = b.vertices
x1, y1, z1 = atom1.coords
x2, y2, z2 = atom2.coords
t = geometry.create_transformation_to_coincide_point_with_z_axis(
[x1, y1, z1], [x2, y2, z2])
x, y, z = t.transform_xyz(x2, y2, z2)
# now rotate to make the plane of neighbor atoms coincide with x,y plane
angs = []
for n in atom1.neighbors + atom2.neighbors:
if n is not atom1 and n is not atom2:
nx, ny, nz = t.transform_xyz(*n.coords)
ang = math.atan2(ny, nx)
if ang < -0.00001:
ang += math.pi
angs.append(ang)
ang = sum(angs) / len(angs)
t.set_rotation_z(ang + math.pi / 2.0)
t.set_rotation_y(math.pi / 2.0)
return t
