54a02c7a3ca3cce7e62f92e0a27244d27f8d9e83,prody/ensemble/functions.py,,refineEnsemble,#Any#Any#Any#,622

Before Change

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

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

After Change

    // rmsd = ensemble.getRMSDs()
    // ref_i = np.argmin(rmsd)
    ref_i = kwargs.pop("ref", 0)
    if isinstance(ref_i, Integral):
        pass
    elif isinstance(ref_i, str):
        labels = ensemble.getLabels()
        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 //////

Instances