Class AverageKernel

dscribe/kernels/averagekernel.py:21–48

Used to compute a global similarity of structures based on the average similarity of local atomic environments in the structure. More precisely, returns the similarity kernel K as: .. math:: K(A, B) = \\frac{1}{N M}\sum_{ij} C_{ij}(A, B) where :math:`N` is the number of ato

class AverageKernel(LocalSimilarityKernel):
    """Used to compute a global similarity of structures based on the average
    similarity of local atomic environments in the structure. More precisely,
    returns the similarity kernel K as:

    .. math::
        K(A, B) = \\frac{1}{N M}\sum_{ij} C_{ij}(A, B)

    where :math:`N` is the number of atoms in structure :math:`A`, :math:`M` is
    the number of atoms in structure :math:`B` and the similarity between local
    atomic environments :math:`C_{ij}` has been calculated with the pairwise
    metric (e.g. linear, gaussian) defined by the parameters given in the
    constructor.
    """

    def get_global_similarity(self, localkernel):
        """
        Computes the average global similarity between two structures A and B.

        Args:
            localkernel(np.ndarray): NxM matrix of local similarities between
                structures A and B, with N and M atoms respectively.
        Returns:
            float: Average similarity between the structures A and B.
        """
        K_ij = np.mean(localkernel)

        return K_ij