7cd15d13d91e2de78d53a5cdac661e63f64d59e8,prody/dynamics/adaptive.py,,checkConvergence,#Any#Any#,187

Before Change

    target_rmsd = kwargs.get("target_rmsd", 1.0)
    cutoff = kwargs.get("cutoff", 15)

    if min_rmsd_diff is not None:
        if rmsds[-2] - rmsds[-1] < min_rmsd_diff:
            LOGGER.warn(
                "The RMSD decrease fell below {0}".format(min_rmsd_diff))
            return True

    if rmsds[-1] < target_rmsd:
        LOGGER.warn("The RMSD fell below target RMSD {0}".format(target_rmsd))
        return True

After Change

    cutoff = kwargs.get("cutoff", 15)

    if len(rmsds) > 4:
        drmsd = np.abs(np.diff(rmsds))

        if np.all(drmsd[-4:] < min_rmsd_diff):
            LOGGER.warn(
                "The RMSD decrease fell below {0}".format(min_rmsd_diff))
            return True

Instances