From: Matt S. <mes...@gm...> - 2008-07-17 06:22:35
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I've offered to take on the JGraphT upgrade listed under junior jobs. Before I start writing code I wanted to poll this list and ask two questions. 1.) Are people using JGraphT with the CDK? If so what classes/functionality. 2.) Currently the following classes use JGraphT -Biconnectivity inspector -MinimalPathIterator -BFSShortestPath -BondsToAtomDescriptor -RDFProtonDescriptor_GHR_topol -XLogPDescriptor -MoleculeGraphs -SSSRFinder -SimpleCycleBasis -SimpleCycle -CycleBasis Do we want to continue this dependency or try to rewrite some/all of these classes to work without JGraphT. |
From: Rajarshi G. <rg...@in...> - 2008-07-18 15:20:01
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Jul 17, 2008, at 2:22 AM, Matt Sprague wrote: > I've offered to take on the JGraphT upgrade listed under junior jobs. > Before I start writing code I wanted to poll this list and ask two > questions. > > 1.) Are people using JGraphT with the CDK? If so what classes/ > functionality. > > 2.) Currently the following classes use JGraphT > -Biconnectivity inspector > -MinimalPathIterator > -BFSShortestPath > -BondsToAtomDescriptor > -RDFProtonDescriptor_GHR_topol > -XLogPDescriptor > -MoleculeGraphs > -SSSRFinder > -SimpleCycleBasis > -SimpleCycle > -CycleBasis > > Do we want to continue this dependency or try to rewrite some/all of > these classes to work without JGraphT. One reason I've not been too happy with JGraphT is that doesn't include a lot of graph theoretical operations (beyond d-f or b-f searches). However it does seem to be employed in a lot of places and I suspect that if we were to remove the dependency you would end up implementing a good fraction of JGraphT. Even updating to the latest version of JGraphT looks like a good bit of work, from a quick look at the new API However, ideally, I'd like to see a separate graph package within the CDK that handles representation and graph algorithms. So it might not be as extensive as JGraphT, but would still be a good bit of work. But this is probably not a cdk-junior job then :) - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- COBOL is for morons. -- E.W. Dijkstra -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkiAtJkACgkQZqGSLFHnnoRIBACgv5fEbyir8uYU8m+nhkZrlN4y zmgAoLnSpwyyNOLXxtGiYqBZVBEM0BTy =6b4g -----END PGP SIGNATURE----- |
From: Matt S. <mes...@gm...> - 2008-07-18 23:02:19
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On Fri, Jul 18, 2008 at 9:19 AM, Rajarshi Guha <rg...@in...> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > One reason I've not been too happy with JGraphT is that doesn't include a > lot of graph theoretical operations (beyond d-f or b-f searches). However it > does seem to be employed in a lot of places and I suspect that if we were to > remove the dependency you would end up implementing a good fraction of > JGraphT. > > Even updating to the latest version of JGraphT looks like a good bit of > work, from a quick look at the new API > > However, ideally, I'd like to see a separate graph package within the CDK > that handles representation and graph algorithms. So it might not be as > extensive as JGraphT, but would still be a good bit of work. But this is > probably not a cdk-junior job then :) > My tentative plan is to replace the MoleculeGraphs factory class with an IAtomContainer implementation that extends one of the JGraphT graph classes. Something like... public class JGraphMol extends SimpleGraph<IAtom, IBond> implements IAtomContainer The class would have methods that allow users to do simple DFS, BFS iterations, find the shortest path between two atoms, etc. The idea would be to provide the common simple functionality of JGraphT through the JGraphMol rather than using the JGraphT classes directly. Down the road this class could be phased out in favor of an AtomContainer backed by a CDK graph implementation. What do people think of this approach? -Matt |
From: Rajarshi G. <rg...@in...> - 2008-07-19 15:05:44
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Jul 18, 2008, at 7:02 PM, Matt Sprague wrote: > On Fri, Jul 18, 2008 at 9:19 AM, Rajarshi Guha <rg...@in...> > wrote: >> However, ideally, I'd like to see a separate graph package within >> the CDK >> that handles representation and graph algorithms. So it might not >> be as >> extensive as JGraphT, but would still be a good bit of work. But >> this is >> probably not a cdk-junior job then :) >> > > My tentative plan is to replace the MoleculeGraphs factory class with > an IAtomContainer implementation that extends one of the JGraphT graph > classes. Something like... > > public class JGraphMol extends SimpleGraph<IAtom, IBond> implements > IAtomContainer > > The class would have methods that allow users to do simple DFS, BFS > iterations, find the shortest path between two atoms, etc. The idea > would be to provide the common simple functionality of JGraphT through > the JGraphMol rather than using the JGraphT classes directly. Down the > road this class could be phased out in favor of an AtomContainer > backed by a CDK graph implementation. Sounds like a good idea - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- Brain fried -- Core dumped -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkiCAsQACgkQZqGSLFHnnoRjbwCdGnIvf0MgTsOkq2AsPbkOiT7j MZgAnj3TsXWZhu58/r2jBkUSvWm5sCaw =nWZ1 -----END PGP SIGNATURE----- |
From: Christoph S. <chr...@go...> - 2008-07-20 11:37:57
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Rajarshi Guha wrote: > On Jul 18, 2008, at 7:02 PM, Matt Sprague wrote: >> My tentative plan is to replace the MoleculeGraphs factory class with >> an IAtomContainer implementation that extends one of the JGraphT graph >> classes. Something like... > Sounds like a good idea I second this. C. -- Dr. Christoph Steinbeck Head of Chemoinformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |