From: Andreas T. <atr...@gm...> - 2009-12-09 09:51:00
|
Hello Egon, here is the UIT timeout fix. Regards Andreas -- Preisknaller: GMX DSL Flatrate für nur 16,99 Euro/mtl.! http://portal.gmx.net/de/go/dsl02 |
From: Andreas T. <atr...@gm...> - 2009-12-10 09:12:38
Attachments:
0002-Added-a-unit-test-for-the-UIT-timeout-fix.patch
|
Hello Egon, here is the UIT timeout fix unit test. Regards Andreas -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01 |
From: Egon W. <ego...@gm...> - 2009-12-09 10:20:22
|
On Wed, Dec 9, 2009 at 10:50 AM, Andreas Truszkowski <atr...@gm...> wrote: > here is the UIT timeout fix. Please send me the unit test you mentioned... Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Syed A. R. <s9...@go...> - 2009-12-09 10:23:06
|
(CDK)" <cdk...@li...>, "cdk...@li..." <cdk...@li...> I have also fixed the UIT time out which is available via SMSD code. -- ----------------------------------------- Dr. S. Asad Rahman Research Scientist EMBL-EBI Cambridge CB10 1SD UK ----------------------------------------- On 9 Dec 2009, at 10:19, Egon Willighagen <ego...@gm...> wrote: > On Wed, Dec 9, 2009 at 10:50 AM, Andreas Truszkowski > <atr...@gm...> wrote: >> here is the UIT timeout fix. > > Please send me the unit test you mentioned... > > Egon > > -- > Post-doc @ Uppsala University > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > --- > --- > --- > --------------------------------------------------------------------- > Return on Information: > Google Enterprise Search pays you back > Get the facts. > http://p.sf.net/sfu/google-dev2dev > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Egon W. <ego...@gm...> - 2009-12-28 14:07:37
|
On Wed, Dec 9, 2009 at 11:22 AM, Syed Asad Rahman <s9...@go...> wrote: > I have also fixed the UIT time out which is available via SMSD code. How do the two solutions compare? And can you attach your solution as patch? Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Egon W. <ego...@gm...> - 2010-02-01 13:46:03
|
Syed, Andreas: On Mon, Feb 1, 2010 at 2:41 PM, Syed Asad Rahman <s9...@go...> wrote: > Combining both the solutions will defiantly produce an elegant solution as this can cater to the needs of various users. Can I expect a joint solution? (I'd love that! :) Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Andreas T. <atr...@gm...> - 2010-01-27 13:03:53
|
Egon Willighagen schrieb: > On Wed, Dec 9, 2009 at 11:22 AM, Syed Asad Rahman <s9...@go...> wrote: > >> I have also fixed the UIT time out which is available via SMSD code. >> > > How do the two solutions compare? And can you attach your solution as patch? > > Egon > Is there meanwhile a solution which adresses this problem? Andreas |
From: Egon W. <ego...@gm...> - 2010-01-27 13:13:47
|
On Wed, Jan 27, 2010 at 1:36 PM, Andreas Truszkowski <atr...@gm...> wrote: > Egon Willighagen schrieb: >> On Wed, Dec 9, 2009 at 11:22 AM, Syed Asad Rahman <s9...@go...> wrote: >>> I have also fixed the UIT time out which is available via SMSD code. >> >> How do the two solutions compare? And can you attach your solution as patch? > > Is there meanwhile a solution which adresses this problem? Dunno. Have you spoken with Asad and compared solutions? Which one is better? If not, please do. Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Syed A. R. <s9...@go...> - 2010-01-27 13:15:41
|
You can have a look at the CDK UIT code in the SMSD http://github.com/asad/cdk-smsd/tree/smsd/src/main/org/openscience/cdk/smsd/algorithm/cdk/ ************************************************ Syed Asad Rahman (PhD, PG, B.Engg) Research Scientist EMBL-EBI WTGC, Hinxton CB10 1SD Cambridge, UK Phone: +44- (0)1223 492550 Fax: +44- (0)1223 494486 as...@eb... www.ebi.ac.uk /~asad ************************************************* On 27 Jan 2010, at 12:36, Andreas Truszkowski wrote: > Egon Willighagen schrieb: >> On Wed, Dec 9, 2009 at 11:22 AM, Syed Asad Rahman <s9...@go...> wrote: >> >>> I have also fixed the UIT time out which is available via SMSD code. >>> >> >> How do the two solutions compare? And can you attach your solution as patch? >> >> Egon >> > > Is there meanwhile a solution which adresses this problem? > > Andreas > > ------------------------------------------------------------------------------ > 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-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Andreas T. <atr...@gm...> - 2010-01-27 13:55:14
|
Hello Syed, the peoblem in your solution is that if the timeout is reached an exception will be thrown. It is impossible to get the solutions which were found before the timeout is reached. But in my work it is possible to get this ones and I need this behaviour in my work. Andreas Syed Asad Rahman schrieb: > You can have a look at the CDK UIT code in the SMSD > > http://github.com/asad/cdk-smsd/tree/smsd/src/main/org/openscience/cdk/smsd/algorithm/cdk/ > > > > ************************************************ > Syed Asad Rahman (PhD, PG, B.Engg) > Research Scientist > > EMBL-EBI > WTGC, > Hinxton CB10 1SD > Cambridge, UK > > Phone: +44- (0)1223 492550 > Fax: +44- (0)1223 494486 > as...@eb... > www.ebi.ac.uk /~asad > > ************************************************* > > On 27 Jan 2010, at 12:36, Andreas Truszkowski wrote: > > >> Egon Willighagen schrieb: >> >>> On Wed, Dec 9, 2009 at 11:22 AM, Syed Asad Rahman <s9...@go...> wrote: >>> >>> >>>> I have also fixed the UIT time out which is available via SMSD code. >>>> >>>> >>> How do the two solutions compare? And can you attach your solution as patch? >>> >>> Egon >>> >>> >> Is there meanwhile a solution which adresses this problem? >> >> Andreas >> >> ------------------------------------------------------------------------------ >> 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-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> > > > ------------------------------------------------------------------------------ > 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-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > |
From: Syed A. R. <s9...@go...> - 2010-01-27 15:02:25
|
Hi Andreas, My implementation will throw an exception if and only if you have a time-out, which is logical. If a solution was found before time-out, it will be reported. So where is the debate as you can always set the upper bound for the time-out. For me this is logical but may be I am missing your point. Asad ************************************************ Syed Asad Rahman (PhD, PG, B.Engg) Research Scientist EMBL-EBI WTGC, Hinxton CB10 1SD Cambridge, UK Phone: +44- (0)1223 492550 Fax: +44- (0)1223 494486 as...@eb... www.ebi.ac.uk /~asad ************************************************* On 27 Jan 2010, at 13:54, Andreas Truszkowski wrote: > Hello Syed, > > the peoblem in your solution is that if the timeout is reached an > exception will be thrown. It is impossible to get the solutions which > were found before the timeout is reached. > But in my work it is possible to get this ones and I need this behaviour > in my work. > > Andreas > > Syed Asad Rahman schrieb: >> You can have a look at the CDK UIT code in the SMSD >> >> http://github.com/asad/cdk-smsd/tree/smsd/src/main/org/openscience/cdk/smsd/algorithm/cdk/ >> >> >> >> ************************************************ >> Syed Asad Rahman (PhD, PG, B.Engg) >> Research Scientist >> >> EMBL-EBI >> WTGC, >> Hinxton CB10 1SD >> Cambridge, UK >> >> Phone: +44- (0)1223 492550 >> Fax: +44- (0)1223 494486 >> as...@eb... >> www.ebi.ac.uk /~asad >> >> ************************************************* >> >> On 27 Jan 2010, at 12:36, Andreas Truszkowski wrote: >> >> >>> Egon Willighagen schrieb: >>> >>>> On Wed, Dec 9, 2009 at 11:22 AM, Syed Asad Rahman <s9...@go...> wrote: >>>> >>>> >>>>> I have also fixed the UIT time out which is available via SMSD code. >>>>> >>>>> >>>> How do the two solutions compare? And can you attach your solution as patch? >>>> >>>> Egon >>>> >>>> >>> Is there meanwhile a solution which adresses this problem? >>> >>> Andreas >>> >>> ------------------------------------------------------------------------------ >>> 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-devel mailing list >>> Cdk...@li... >>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>> >> >> >> ------------------------------------------------------------------------------ >> 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-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> > > > ------------------------------------------------------------------------------ > 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-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Andreas T. <atr...@gm...> - 2010-01-27 16:45:01
Attachments:
0001-TimeOutFix.patch
|
Within the UIT class, it is possible to get more then one solution if you search for subgraph isomorphs (e.g. UIT.getSubgraphMaps(..)). Some molecule combinations can produce more than thousand subgraph maps but it takes ages (several minutes). So if I set the timeout to a shorter period I can retrieve all founded maps (and ignore all remaining ones). The solution with the Exception is not the problem but you have no chance to get the data produced up to this point. My solution (attached to this mail) has got the problem that the user will be not informed about timeouts --> It would be nice to combine both solutions. Andreas Syed Asad Rahman schrieb: > Hi Andreas, > > My implementation will throw an exception if and only if you have a time-out, which is logical. If a solution was found before time-out, it will be reported. > So where is the debate as you can always set the upper bound for the time-out. > > For me this is logical but may be I am missing your point. > > Asad > > ************************************************ > Syed Asad Rahman (PhD, PG, B.Engg) > Research Scientist > > EMBL-EBI > WTGC, > Hinxton CB10 1SD > Cambridge, UK > > Phone: +44- (0)1223 492550 > Fax: +44- (0)1223 494486 > as...@eb... > www.ebi.ac.uk /~asad > > ************************************************* > > On 27 Jan 2010, at 13:54, Andreas Truszkowski wrote: > > >> Hello Syed, >> >> the peoblem in your solution is that if the timeout is reached an >> exception will be thrown. It is impossible to get the solutions which >> were found before the timeout is reached. >> But in my work it is possible to get this ones and I need this behaviour >> in my work. >> >> Andreas >> >> Syed Asad Rahman schrieb: >> >>> You can have a look at the CDK UIT code in the SMSD >>> >>> http://github.com/asad/cdk-smsd/tree/smsd/src/main/org/openscience/cdk/smsd/algorithm/cdk/ >>> >>> >>> >>> ************************************************ >>> Syed Asad Rahman (PhD, PG, B.Engg) >>> Research Scientist >>> >>> EMBL-EBI >>> WTGC, >>> Hinxton CB10 1SD >>> Cambridge, UK >>> >>> Phone: +44- (0)1223 492550 >>> Fax: +44- (0)1223 494486 >>> as...@eb... >>> www.ebi.ac.uk /~asad >>> >>> ************************************************* >>> >>> On 27 Jan 2010, at 12:36, Andreas Truszkowski wrote: >>> >>> >>> >>>> Egon Willighagen schrieb: >>>> >>>> >>>>> On Wed, Dec 9, 2009 at 11:22 AM, Syed Asad Rahman <s9...@go...> wrote: >>>>> >>>>> >>>>> >>>>>> I have also fixed the UIT time out which is available via SMSD code. >>>>>> >>>>>> >>>>>> >>>>> How do the two solutions compare? And can you attach your solution as patch? >>>>> >>>>> Egon >>>>> >>>>> >>>>> >>>> Is there meanwhile a solution which adresses this problem? >>>> >>>> Andreas >>>> >>>> ------------------------------------------------------------------------------ >>>> 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-devel mailing list >>>> Cdk...@li... >>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>>> >>>> >>> ------------------------------------------------------------------------------ >>> 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-devel mailing list >>> Cdk...@li... >>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>> >>> >>> >> ------------------------------------------------------------------------------ >> 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-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> > > |
From: Andreas T. <atr...@gm...> - 2010-01-28 20:05:32
|
Hello Syed, I have cogitated about our problem. I you then code in the RGraph class like that // Add flag whether timeout is reached boolean timeoutReached = false; private void checkTimeOut() throws CDKException { if (timeout > -1 && timeManager.getElapsedTimeInMinutes() > timeout) { stop = true; // throw new CDKException("Timeout exceeded in getOverlaps"); timeoutReached = true; } } The search prozess will break immediately and it is possible to get the retrieved results and to see that the timeout was reached. Additionally I think it is only nescessary to interrupt the RGraph class from its work because that is the timeconsuming step (correct me if I am wrong). Regards, Andreas Andreas Truszkowski schrieb: > Within the UIT class, it is possible to get more then one solution if > you search for subgraph isomorphs (e.g. UIT.getSubgraphMaps(..)). Some > molecule combinations can produce more than thousand subgraph maps but > it takes ages (several minutes). So if I set the timeout to a shorter > period I can retrieve all founded maps (and ignore all remaining ones). > The solution with the Exception is not the problem but you have no > chance to get the data produced up to this point. > My solution (attached to this mail) has got the problem that the user > will be not informed about timeouts > --> It would be nice to combine both solutions. > > Andreas > > Syed Asad Rahman schrieb: >> Hi Andreas, >> >> My implementation will throw an exception if and only if you have a >> time-out, which is logical. If a solution was found before time-out, >> it will be reported. >> So where is the debate as you can always set the upper bound for the >> time-out. >> >> For me this is logical but may be I am missing your point. >> >> Asad >> >> ************************************************ >> Syed Asad Rahman (PhD, PG, B.Engg) >> Research Scientist >> >> EMBL-EBI WTGC, Hinxton CB10 >> 1SD Cambridge, UK >> Phone: +44- (0)1223 492550 Fax: +44- (0)1223 494486 >> as...@eb... www.ebi.ac.uk /~asad >> ************************************************* >> >> On 27 Jan 2010, at 13:54, Andreas Truszkowski wrote: >> >> >>> Hello Syed, >>> >>> the peoblem in your solution is that if the timeout is reached an >>> exception will be thrown. It is impossible to get the solutions >>> which were found before the timeout is reached. >>> But in my work it is possible to get this ones and I need this >>> behaviour in my work. >>> >>> Andreas >>> >>> Syed Asad Rahman schrieb: >>> >>>> You can have a look at the CDK UIT code in the SMSD >>>> >>>> http://github.com/asad/cdk-smsd/tree/smsd/src/main/org/openscience/cdk/smsd/algorithm/cdk/ >>>> >>>> >>>> >>>> >>>> ************************************************ >>>> Syed Asad Rahman (PhD, PG, B.Engg) >>>> Research Scientist >>>> >>>> EMBL-EBI WTGC, Hinxton CB10 >>>> 1SD Cambridge, UK >>>> Phone: +44- (0)1223 492550 Fax: +44- (0)1223 494486 >>>> as...@eb... www.ebi.ac.uk /~asad >>>> ************************************************* >>>> >>>> On 27 Jan 2010, at 12:36, Andreas Truszkowski wrote: >>>> >>>> >>>> >>>>> Egon Willighagen schrieb: >>>>> >>>>> >>>>>> On Wed, Dec 9, 2009 at 11:22 AM, Syed Asad Rahman >>>>>> <s9...@go...> wrote: >>>>>> >>>>>> >>>>>> >>>>>>> I have also fixed the UIT time out which is available via SMSD >>>>>>> code. >>>>>>> >>>>>>> >>>>>>> >>>>>> How do the two solutions compare? And can you attach your >>>>>> solution as patch? >>>>>> >>>>>> Egon >>>>>> >>>>>> >>>>>> >>>>> Is there meanwhile a solution which adresses this problem? >>>>> >>>>> Andreas >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> >>>>> 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-devel mailing list >>>>> Cdk...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>>>> >>>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> 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-devel mailing list >>>> Cdk...@li... >>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>>> >>>> >>>> >>> ------------------------------------------------------------------------------ >>> >>> 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-devel mailing list >>> Cdk...@li... >>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>> >> >> > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > 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-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Syed A. R. <s9...@go...> - 2010-02-01 13:50:21
|
Yes please, but I would also like to retain the R-Graph time out checks. ************************************************ Syed Asad Rahman (PhD, PG, B.Engg) Research Scientist EMBL-EBI WTGC, Hinxton CB10 1SD Cambridge, UK Phone: +44- (0)1223 492537 Fax: +44- (0)1223 494486 as...@eb... www.ebi.ac.uk /~asad ************************************************* On 1 Feb 2010, at 13:45, Egon Willighagen wrote: > Syed, Andreas: > > On Mon, Feb 1, 2010 at 2:41 PM, Syed Asad Rahman <s9...@go...> wrote: >> Combining both the solutions will defiantly produce an elegant solution as this can cater to the needs of various users. > > Can I expect a joint solution? (I'd love that! :) > > Egon > > > -- > Post-doc @ Uppsala University > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Egon W. <ego...@gm...> - 2010-02-01 13:51:55
|
On Mon, Feb 1, 2010 at 2:50 PM, Syed Asad Rahman <s9...@go...> wrote: > Yes please, but I would also like to retain the R-Graph time out checks. Well, that's the idea of you and Andreas making a joint patch, not ? :) Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Andreas T. <atr...@gm...> - 2010-02-01 20:10:10
|
Hello, Syed Asad Rahman <s9...@go...> wrote: > Your solution holds good if one would like to get a solution within a time frame but not necessary Maximum Common Subgraph (MCS) but a subgraph. thats right. Syed Asad Rahman <s9...@go...> wrote: > My solution was designed to obtain the MCS at all occasions and if an exception occurred, the SMSD triggers a fallback MCS search engine; usually VFLib which handles larger graphs more efficiently. the only overlap between your work and mine is the RGraph class. So the RGraph class from you must only be changed like this: // Add flag whether timeout is reached boolean timeoutReached = false; private void checkTimeOut() throws CDKException { if (timeout > -1 && timeManager.getElapsedTimeInMinutes() > timeout) { stop = true; // throw new CDKException("Timeout exceeded in getOverlaps"); timeoutReached = true; } } So you must only check at the entrypoint to the RGraph class whether the timeout was reached or not via the timeoutReached flag. (then throw the exception) Syed Asad Rahman <s9...@go...> wrote: > Yes please, but I would also like to retain the R-Graph time out checks. No problem. Solution explained above. Egon Willighagen <ego...@gm... <mailto:ego...@gm...>> wrote: > Well, that's the idea of you and Andreas making a joint patch, not ? :) > It would be nice if Asad could change the files as shown above because I have no idea how his MCS class works. Then I would adapt the UniversalIsomorphismTester to his work when it is applied to the CDK. When will be the Small Molecule Subgraph Detector (SMSD) applied to the CDK? Regards, Andreas |
From: Syed A. R. <s9...@go...> - 2010-04-02 17:51:25
|
Hi Andreas, I have added your recommendation in the UIT module of the SMSD http://github.com/asad/cdk-smsd/blob/smsdNew/src/main/org/openscience/cdk/smsd/algorithm/cdk/CDKRGraph.java http://github.com/asad/cdk-smsd/blob/smsdNew/src/main/org/openscience/cdk/smsd/algorithm/cdk/CDKMCS.java Best wishes Asad Syed Asad Rahman (PhD, PG, B.Engg) Research Scientist s9...@go... On 1 Feb 2010, at 20:09, Andreas Truszkowski wrote: > Hello, > > Syed Asad Rahman <s9...@go...> wrote: > >> Your solution holds good if one would like to get a solution within a time frame but not necessary Maximum Common Subgraph (MCS) but a subgraph. > thats right. > > Syed Asad Rahman <s9...@go...> wrote: > >> My solution was designed to obtain the MCS at all occasions and if an exception occurred, the SMSD triggers a fallback MCS search engine; usually VFLib which handles larger graphs more efficiently. > the only overlap between your work and mine is the RGraph class. > So the RGraph class from you must only be changed like this: > > // Add flag whether timeout is reached > boolean timeoutReached = false; > > private void checkTimeOut() throws CDKException { > if (timeout > -1 && timeManager.getElapsedTimeInMinutes() > timeout) { > stop = true; // throw new CDKException("Timeout exceeded in getOverlaps"); > timeoutReached = true; > } > } > > So you must only check at the entrypoint to the RGraph class whether the > timeout was reached or not via the timeoutReached flag. (then throw the > exception) > > Syed Asad Rahman <s9...@go...> wrote: > >> Yes please, but I would also like to retain the R-Graph time out checks. > No problem. Solution explained above. > > Egon Willighagen <ego...@gm... > <mailto:ego...@gm...>> wrote: >> Well, that's the idea of you and Andreas making a joint patch, not ? :) >> > > It would be nice if Asad could change the files as shown above because I > have no idea how his MCS class works. > Then I would adapt the UniversalIsomorphismTester to his work when it is > applied to the CDK. > When will be the Small Molecule Subgraph Detector (SMSD) applied to the CDK? > > Regards, > Andreas > > > ------------------------------------------------------------------------------ > 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-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Syed A. R. <s9...@go...> - 2010-02-01 13:42:06
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Your solution holds good if one would like to get a solution within a time frame but not necessary Maximum Common Subgraph (MCS) but a subgraph. Correct me if I am wrong! Combining both the solutions will defiantly produce an elegant solution as this can cater to the needs of various users. My solution was designed to obtain the MCS at all occasions and if an exception occurred, the SMSD triggers a fallback MCS search engine; usually VFLib which handles larger graphs more efficiently. Thanks for the discussion and hope this helps. ************************************************ Syed Asad Rahman (PhD, PG, B.Engg) Research Scientist EMBL-EBI WTGC, Hinxton CB10 1SD Cambridge, UK Phone: +44- (0)1223 492537 Fax: +44- (0)1223 494486 as...@eb... www.ebi.ac.uk /~asad ************************************************* On 28 Jan 2010, at 20:05, Andreas Truszkowski wrote: > Hello Syed, > > I have cogitated about our problem. > > I you then code in the RGraph class like that > > // Add flag whether timeout is reached > boolean timeoutReached = false; > > private void checkTimeOut() throws CDKException { > if (timeout > -1 && timeManager.getElapsedTimeInMinutes() > > timeout) { > stop = true; // throw new > CDKException("Timeout exceeded in getOverlaps"); > timeoutReached = true; > } > } > > The search prozess will break immediately and it is possible to get the > retrieved results and to see that the timeout was reached. > Additionally I think it is only nescessary to interrupt the RGraph class > from its work because that is the timeconsuming step (correct me if I am > wrong). > > Regards, > Andreas > > Andreas Truszkowski schrieb: >> Within the UIT class, it is possible to get more then one solution if >> you search for subgraph isomorphs (e.g. UIT.getSubgraphMaps(..)). Some >> molecule combinations can produce more than thousand subgraph maps but >> it takes ages (several minutes). So if I set the timeout to a shorter >> period I can retrieve all founded maps (and ignore all remaining ones). >> The solution with the Exception is not the problem but you have no >> chance to get the data produced up to this point. >> My solution (attached to this mail) has got the problem that the user >> will be not informed about timeouts >> --> It would be nice to combine both solutions. >> >> Andreas >> >> Syed Asad Rahman schrieb: >>> Hi Andreas, >>> >>> My implementation will throw an exception if and only if you have a >>> time-out, which is logical. If a solution was found before time-out, >>> it will be reported. >>> So where is the debate as you can always set the upper bound for the >>> time-out. >>> >>> For me this is logical but may be I am missing your point. >>> >>> Asad >>> >>> ************************************************ >>> Syed Asad Rahman (PhD, PG, B.Engg) >>> Research Scientist >>> >>> EMBL-EBI WTGC, Hinxton CB10 >>> 1SD Cambridge, UK >>> Phone: +44- (0)1223 492550 Fax: +44- (0)1223 494486 >>> as...@eb... www.ebi.ac.uk /~asad >>> ************************************************* >>> >>> On 27 Jan 2010, at 13:54, Andreas Truszkowski wrote: >>> >>> >>>> Hello Syed, >>>> >>>> the peoblem in your solution is that if the timeout is reached an >>>> exception will be thrown. It is impossible to get the solutions >>>> which were found before the timeout is reached. >>>> But in my work it is possible to get this ones and I need this >>>> behaviour in my work. >>>> >>>> Andreas >>>> >>>> Syed Asad Rahman schrieb: >>>> >>>>> You can have a look at the CDK UIT code in the SMSD >>>>> >>>>> http://github.com/asad/cdk-smsd/tree/smsd/src/main/org/openscience/cdk/smsd/algorithm/cdk/ >>>>> >>>>> >>>>> >>>>> >>>>> ************************************************ >>>>> Syed Asad Rahman (PhD, PG, B.Engg) >>>>> Research Scientist >>>>> >>>>> EMBL-EBI WTGC, Hinxton CB10 >>>>> 1SD Cambridge, UK >>>>> Phone: +44- (0)1223 492550 Fax: +44- (0)1223 494486 >>>>> as...@eb... www.ebi.ac.uk /~asad >>>>> ************************************************* >>>>> >>>>> On 27 Jan 2010, at 12:36, Andreas Truszkowski wrote: >>>>> >>>>> >>>>> >>>>>> Egon Willighagen schrieb: >>>>>> >>>>>> >>>>>>> On Wed, Dec 9, 2009 at 11:22 AM, Syed Asad Rahman >>>>>>> <s9...@go...> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>>> I have also fixed the UIT time out which is available via SMSD >>>>>>>> code. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> How do the two solutions compare? And can you attach your >>>>>>> solution as patch? >>>>>>> >>>>>>> Egon >>>>>>> >>>>>>> >>>>>>> >>>>>> Is there meanwhile a solution which adresses this problem? >>>>>> >>>>>> Andreas >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> >>>>>> 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-devel mailing list >>>>>> Cdk...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>>>>> >>>>>> >>>>> ------------------------------------------------------------------------------ >>>>> >>>>> 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-devel mailing list >>>>> Cdk...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>>>> >>>>> >>>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> 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-devel mailing list >>>> Cdk...@li... >>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>>> >>> >>> >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------------ >> 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-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel > > > ------------------------------------------------------------------------------ > 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-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |