On Jan 27, 2010, at 5:58 AM, Vincent Le Guilloux wrote:
> Quoting Rajarshi Guha <rajarshi.g...@gmail.com>:
>
> Yes indeed :). I had a quick look at the source code, and saw that
> the problem arises in this loop:
>
> // look for symmetric & asymmetric atoms for the gamma descriptor
> for (int i = 0; i < 3; i++) {
> double ns = 0.0;
> double na = 0.0;
> for (int j = 0; j < ac.getAtomCount(); j++) {
> boolean foundmatch = false;
> for (int k = 0; k < ac.getAtomCount(); k++) {
> if (k == j) continue;
> if (scores[j][i] == -1 * scores[k][i]) {
> ns++;
> foundmatch = true;
> break;
> }
> }
> if (!foundmatch) na++;
> }
> double n = (double) ac.getAtomCount();
> gamma[i] = -1.0 * ((ns / n) * Math.log(ns / n) / Math.log(2.0) +
> (na / n) * Math.log(1.0 / n) / Math.log(2.0));
> gamma[i] = 1.0 / (1.0 + gamma[i]);
> }
>
> The problem is that the number of symmetric atom ns is always 0. As
> a consequence, ns/n = 0 and Math.log(ns / n) = -Infinity, which
> leads to the NaN value.
>
> I'm guessing that a default value is obviously needed when ns is 0,
> which would fix this issue.
> However I think the algorithm is broken as ns should not always be 0
> as it is currently the case. I don't really know if the algorithm
> used is theorically OK to detect symmetric atoms,
That is true - but for pyrrole, the number of symmetric atoms should
be > 0 and so ns should be > 0. So I think the bigger problem is that
the actual determination of symmetric and asymmetric atoms is faulty
> Also, just a last remark and I stop bothering you: why don't you
> just send a warning or something like that, instead of an exception,
> when 2D coordinates are detected?
I think the policy, in general for any descriptor error, was to throw
exceptions
----------------------------------------------------
Rajarshi Guha | NIH Chemical Genomics Center
http://www.rguha.net | http://ncgc.nih.gov
----------------------------------------------------
I live in my own little world...
but it's OK, they like me there
------------------------------------------------------------------------------
The Planet: dedicated and managed hosting, cloud storage, colocation
Stay online with enterprise data centers and the best network in the business
Choose flexible plans and management services without long-term contracts
Personal 24x7 support from experience hosting pros just a phone call away.
http://p.sf.net/sfu/theplanet-com
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
