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src/p/e/pele-HEAD/pele/angleaxis/aatopology.py   pele(Download)
from pele.transition_states import _zeroev as zeroev
from pele.angleaxis.aamindist import TransformAngleAxisCluster
import _aadist
 
__all__ = ["AASiteType", "AATopology", "interpolate_angleaxis", "TakestepAA"]
    x2 = np.dot(R2, x.transpose()).transpose() + X2
 
    import _aadist
    print "site representation:", np.sum((x1-x2)**2)
    print "distance function:  ", site.distance_squared(X1, p1, X2, p2)