pele.angleaxis.aamindist

class pele.angleaxis.aamindist.TransformAngleAxisCluster

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class TransformAngleAxisCluster(TransformPolicy):

transformation rules for angle axis clusters

TransformAngleAxisCluster.translate()

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def translate(self, X, d):

apply a translation

TransformAngleAxisCluster.rotate()

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def rotate(self, X, mx):

rotate the com + angle-axis position X by the rotation matrix mx

TransformAngleAxisCluster.invert()

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def invert(self, X):

invert the structure

TransformAngleAxisCluster.permute()

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def permute(self, X, perm):

apply a permutation

Parameters:

Xnp array

The configuration

permlist of integers

a list of integers giving the new order of the molecules. The length of perm must be the number of rigid bodies.

class pele.angleaxis.aamindist.MeasureAngleAxisCluster

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class MeasureAngleAxisCluster(MeasurePolicy):

measure rules for angle axis clusters

MeasureAngleAxisCluster.get_com()

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def get_com(self, X):

return the center of mass

MeasureAngleAxisCluster.align()

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def align(self, coords1, coords2):

align the rotations so that the atomistic coordinates will be in best alignment

MeasureAngleAxisCluster.get_dist()

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def get_dist(self, x1, x2):

compute the distance between two configurations

MeasureAngleAxisCluster.find_permutation()

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def find_permutation(self, X1, X2):

find the rotation which minimizes the distance between the structures

MeasureAngleAxisCluster.find_rotation()

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def find_rotation(self, X1, X2):

find the rotation which minimizes the distance between the structures

class pele.angleaxis.aamindist.MeasureRigidBodyCluster

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class MeasureRigidBodyCluster(MeasureAngleAxisCluster):

perform measurements on clusters of rigid bodies

class pele.angleaxis.aamindist.ExactMatchAACluster

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class ExactMatchAACluster(ExactMatchCluster):

test whether two structure are exactly the same

class pele.angleaxis.aamindist.MinPermDistAACluster

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class MinPermDistAACluster(MinPermDistCluster):

minimize the distance between two structures