bb958949caaba2341ae5662c484d5106d68e4aed,prody/ensemble/functions.py,,refineEnsemble,#Any#Any#Any#,622

Before Change

    from numpy import argsort

    ////// obtain reference index
    rmsd = ensemble.getRMSDs()
    ref_i = np.argmin(rmsd)

    ////// calculate pairwise RMSDs //////
    RMSDs = ensemble.getRMSDs(pairwise=True)

After Change

        ref_i = labels.index(ref_i)
    else:
        LOGGER.warn("cannot found any conformation with the label %s in the ensemble"%str(ref_i))
    if not ref_i in P:
        P = [ref_i] + P

    ////// calculate pairwise RMSDs //////
    RMSDs = ensemble.getRMSDs(pairwise=True)

    def getRefinedIndices(A):
        deg = A.sum(axis=0)

Instances