Scripts: rotatoms.py

#
# Example code to rotate atoms about a specified line.
#
# Center is a point on the line (3-tuple) and direction is a vector parallel
# to the line (3-tuple), both being in global coordinates (not molecule
# coordinates). Angle is in degrees.
#
def rotate_atoms(atoms, center, direction, angle):

  cx, cy, cz = center
  dx, dy, dz = direction

  # Transform rxf shifts center to (0,0,0), rotates about (0,0,0),
  # then translates (0,0,0) back to center.
  from chimera import Xform
  rxf = Xform.translation(-cx,-cy,-cz)
  rxf.premultiply(Xform.rotation(dx,dy,dz,angle))
  rxf.premultiply(Xform.translation(cx,cy,cz))
  
  # Precompute transforms from global to molecule coordinates.
  mols = set(a.molecule for a in atoms)
  mxf = dict((m, m.openState.xform.inverse()) for m in mols)

  # Apply rotation to global atom coordinate then transform to molecule
  # coordinates and set new atom position.
  for a in atoms:
    a.setCoord(mxf[a.molecule].apply(rxf.apply(a.xformCoord())))

#
# Test
#
from chimera import selection
atoms = selection.currentAtoms()
rotate_atoms(atoms, (1,2,3), (1,1,0), 45)