VMD-L Mailing List

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri May 11 2012 - 04:35:07 CDT

Well well, it looks like I emailed faster than I thought. Please
ignore the previous message. Apparently I need to troubleshoot my
problem better.

Sorry for the noise,
Jerome

On 11 May 2012 11:32, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> Hi everyone,
>
> When measure cluster is used with fitrmsd as a distance function, and
> any single alignment fails (that happens often when looking at folding
> of small peptides), then my impression is that the whole clustering
> aborts. It would be pretty useful to make the behavior a little more
> fault-tolerant, e.g. a logical thing to do is, if the alignment fails,
> to decide that the distance is infinite for all practical purposes.
>
> It could look roughly like this:
> (MeasureCluster.C:370)
>
> static float cluster_get_rmsd(const float *Frame1Pos, const float *Frame2Pos,
>                               AtomSel *sel, float *weights) {
>    float distance = 0.0f;
>    if (measure_rmsd(sel, sel, sel->num_atoms, Frame1Pos, Frame2Pos,
> weights, &distance) == MEASURE_NOERR) {
>        return distance;
>    } else {
>        return 1e20;   // effectively infinite distance, could be any
> VERY_LARGE_FLOAT
>    }
> }
>
> Note: I haven't tested this, as I don't have an up-to-date build
> environment these days, and no time to get it running right now. This
> is why I am making this a mere suggestion and not a patch.
>
> Cheers,
> Jerome