Scripts: changeaxes.py

# Change atom coordinates so that model so that a z vector specified with 3 numbers becomes the z-axis,
# and a y-vector goes to the yz-plane and a specified point goes to the origin.
#
#       runscript orient.py #3 .7,.2,.12  -0.1,.2,.8  22.3,44.5,-19.0
#
# Arguments are z, y and origin in coordinates of the specified model.  Axes vectors need not be normalized.

def move_atoms(mnum, zarg, yarg, oarg):
    mid = int(mnum.lstrip('#'))
    from chimera import openModels, Molecule
    mlist = openModels.list(id = mid, modelTypes = [Molecule])

    z = [float(v) for v in zarg.split(',')]
    y = [float(v) for v in yarg.split(',')]
    o = [float(v) for v in oarg.split(',')]

    import Matrix as M
    xa, ya, za = M.orthonormal_frame(z, y)
    f = ((xa[0],ya[0],za[0],o[0]),
         (xa[1],ya[1],za[1],o[1]),
         (xa[2],ya[2],za[2],o[2]))      # Map standard axes to specified ones.
    finv = M.invert_matrix(f)
    xfinv = M.chimera_xform(finv)

    for m in mlist:
        for a in m.atoms:
            a.setCoord(xfinv.apply(a.coord()))

if len(arguments) != 4:
    from chimera import replyobj
    replyobj.status('Requires 4 arguments <model-id> <z-axis> <y-axis> <origin>')
else:
    mnum, zarg, yarg, oarg = arguments
    move_atoms(mnum, zarg, yarg, oarg)