Hi gilleain, my problem is not specific to any particular molecule or descriptor. The point is that for some molecules, the computation may hang. I cannot control which smiles could be uploaded so there might be possibly any garbage.
Arsenious acid with BCUT was the point where I found that this problem can arise. Also, pubchem (http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=518740&loc=ec_rcs) lists the molecule, so I expect it to be a valid input. Krab gilleain torrance wrote: > > Hi Krab, > > I'm not sure if descriptors are interruptible in the way you describe. > It might be good for there to be a general ITimeout interface for > classes, the same way that the ring finder uses. > > However, a small point : are you sure about that smiles of arsenious > acid. It seems to be a ring system: > > http://www.daylight.com/daycgi/depict?4f315b41735d324f5b41735d314f32 > > gilleain > > On 11/14/11, Krab <[email protected]> wrote: >> >> Hi, >> is there any way to interrupt computation of >> org.openscience.cdk.qsar.IMolecularDescriptor? >> >> For example, the computation of BCUT of arsenious acid (O1[As]2O[As]1O2) >> hangs for long time, I left it to run during weekend and it still did not >> finish. >> >> I need to run the calculations in batch on server where I can't predict >> which molecules a user would upload. So I need to stop each descriptor's >> calculation after some timeout even if it's not finished. >> >> >From what I've seen in the source, I think the descriptors don't check >> their >> interrupted state, so interrupting a thread would be pointless. Now I can >> imagine only to start new thread for each calculation and eventually use >> Thread.stop(). >> >> Is there a better way? Also will this be safe? I presume it should be OK, >> but I can't inspect every descriptor to tell whether an exception at >> arbitrary location could leave any global object at inconsistent state or >> any resource open. >> >> Thank you for your time. >> >> Krab >> -- >> View this message in context: >> http://old.nabble.com/Interrupting-descriptor-computation-tp32839007p32839007.html >> Sent from the cdk-user mailing list archive at Nabble.com. >> >> >> ------------------------------------------------------------------------------ >> RSA(R) Conference 2012 >> Save $700 by Nov 18 >> Register now >> http://p.sf.net/sfu/rsa-sfdev2dev1 >> _______________________________________________ >> Cdk-user mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > > -- View this message in context: http://old.nabble.com/Interrupting-descriptor-computation-tp32839007p32839548.html Sent from the cdk-user mailing list archive at Nabble.com. ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
