Camelia, the Perl 6 bug

IRC log for #cdk, 2011-06-17

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All times shown according to UTC.

Time Nick Message
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11:24 maclean hi
11:24 zarah ni hao maclean
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12:30 maclean hi egonw
12:31 egonw hej maclean!
12:32 maclean how's it going?
12:32 egonw oh well...
12:32 egonw having fun in general :)
12:32 maclean :)
12:32 maclean Asad, and I have been working with an intern (Nimish) on KEGG atomtypes.
12:33 maclean He's done a great job, but we're wondering now about a few things...
12:33 egonw I'm all ears
12:34 maclean Ok. So there are a few issues: 1) Ionic crystals (eg ZnO)
12:34 maclean 2) Charge in dative covalent/coordinate bonds (eg chlorophyll, fe-haem, etc)
12:35 maclean Uhhh. 3) Totally weird stuff.
12:35 maclean Like ruthenium red : http://www.genome.jp/dbget-bin/www_bget?cpd:C13932
12:37 maclean Obviously, there are tons of things. One important CDK issue is that the Molecule class now throws an UnsupportedOperationExeption for getLonePairCount.
12:49 egonw huh?
12:49 egonw that latter sounds not so ood
12:49 egonw ggg
12:50 egonw that latter sounds not so good
12:52 maclean In CDK version 1.3.8
12:52 maclean It means that atom typing may fail for Molecule, but not AtomContainer.
12:52 maclean (when lone pairs are checked)
12:57 egonw ouch
12:57 egonw can you please file a bug report?
12:57 egonw you may have found the cause of a weird, rare, but persistent problem!
12:59 egonw there was some inconsistency nagging me as I could not find the problem, not even with stepping through the code
12:59 egonw (though I never had that exception)
13:00 maclean Ok, will do.
13:06 egonw thanx
13:06 egonw received
13:08 egonw that reminds me...
13:08 egonw I need to hurry making a copy of KEGG
13:08 maclean Yes, indeed.
13:08 maclean Only a little while left...
13:08 egonw two weekd
13:09 egonw mmm... there is even KEGG software on the FTP site
13:11 maclean Is there?
13:11 maclean I was looking for that. No wait, I was looking for PubChem softwares.
13:11 maclean Anyway, got to grab some lunch. Be back in a while.
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13:59 maclean egonw : Lone Pair counting has changed between CDK 1.3.8 and 1.4.x ?
13:59 egonw no
13:59 egonw well... it seems it did...
13:59 egonw but not intentionally
13:59 egonw btw, 1.3.8 is also 1.4.x
13:59 egonw but I guess you mean between 1.3.8 and 1.3.11
14:00 maclean Well, you used to be able to do "myMol.getLonePairCount(atom)", now there is only "getLonePairCount()"
14:00 maclean I guess I do, yes.
14:00 egonw I'm honestly not sure what is going on...
14:01 maclean Lol : http://ambit.sourceforge.net/ambit2-core/apido​cs/ambit2/core/groups/SuppleAtomContainer.html
14:01 zarah maclean's link is also http://tinyurl.com/6aarao7
14:02 egonw mmm.... IMolecules has not changed
14:02 egonw verified that now
14:08 maclean So lone pairs reference atoms, and not v.v.?
14:09 egonw yes
14:09 egonw because they are part of the AtomContainer
14:09 egonw (which really is a a AtomAndElectronContainerContainer
14:09 egonw ... but that was so long :)
14:13 maclean oh
14:15 egonw maclean: there is getConnectedLonePairsCount(IAtom)
14:15 maclean Ah!
14:17 egonw btw, I love a stacktrace
14:17 egonw to get a clue where to start lookin
14:17 egonw g
14:30 maclean Well, just the molecule class, really....
14:39 egonw cannot reproduce
14:40 egonw I need a stacktrace
14:56 egonw I went through UnsupportedMethodExceptions, but nothing interesting shows up
14:56 egonw and Molecule.getLonePairCount() is directly inherited from AtomContainer
15:00 maclean And I've downloaded the same version, and can't find the method.
15:01 maclean It's not in the interfaces, either - I thought that NetBeans might have added the UnsMethEx by itself.
15:01 egonw what same version, whcih method?
15:02 maclean 1.3.8 : getLonePairCount(IAtom)
15:03 egonw but, but ...
15:03 egonw egonw@toxbank53:~/var/Projects/SourceForge/git/cdk$ git log cdk-1.3.8.. src/main/org/openscience/cd​k/interfaces/IMolecule.java
15:03 egonw egonw@toxbank53:~/var/Projects/SourceForge/git/cdk$ git log cdk-1.3.8.. src/main/org/openscience/cdk/Molecule.java
15:03 egonw there are no patches since 1.3.8...
15:04 maclean Okay, so in the version that we downloaded last week (I'm checking what it was) there was a method in the IAtomContainer interface.
15:04 maclean Called "getLonePairCount(IAtom)".
15:05 maclean I think that NetBeans was automatically filling in the implementation of this method in the Molecule class.
15:09 maclean Sorry, I know this looks like a wild goose chase.
15:12 egonw git log cdk-1.3.6.. src/main/org/openscience/cdk/i​nterfaces/IAtomContainer.java
15:12 egonw is empty too
15:13 maclean It's bizarre. Well, mark the bug as 'closed' I suppose. Sorry about that.
15:13 egonw no problem
15:18 egonw maclean: shall I move the report to a patch report, for the unit test I added?
15:18 maclean Hmmm. Well it doesn't seem worthwhile to test something that never occurs.
15:19 maclean However, tests (in general) for the cdk interfaces, to make sure that implementations support all thier operations.
15:19 maclean Which I guess already exist...
15:19 egonw well, the existing test casted to IAtomContainer...
15:20 egonw that should theoretically not matter, I guess
15:20 egonw but you never know
15:20 egonw moreover, if someone ever implements MOlecule to not extend AtomContainer, this method helps
15:20 egonw mmm... I need to catch my train now
15:20 egonw cu later
15:21 maclean cu
15:21 maclean and thanks
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18:55 egonw uploaded the volume descriptor to the patch tracker
19:36 CIA-71 cdk: Egon Willighagen cdk-1.4.x * rdcc63e3 / src/test/org/openscience/cdk/geo​metry/volume/VABCVolumeTest.java :
19:36 CIA-71 cdk: Three more example structures from the spreadsheet
19:36 CIA-71 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> (+9 more commits...) - http://bit.ly/khoks4
20:17 egonw I cool
20:30 egonw O cool
21:14 CIA-71 cdk: Egon Willighagen cdk-1.4.x * rdc0203e / src/main/org/openscience/cdk/g​eometry/volume/VABCVolume.java :
21:14 CIA-71 cdk: Removed hardcoded use of a specific IChemObjectBuilder implementation
21:14 CIA-71 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/kbWxGI
21:15 CIA-71 cdk: Egon Willighagen cdk-1.4.x * rdaf5a5a / src/test/org/openscience/cdk/geo​metry/volume/VABCVolumeTest.java :
21:15 CIA-71 cdk: Fixed assignment to the proper module
21:15 CIA-71 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/iqXmhm
21:15 CIA-71 cdk: Egon Willighagen cdk-1.4.x * rbc2382b / src/test/org/openscience/cdk/mo​dulesuites/MstandardTests.java :
21:15 CIA-71 cdk: Run the tests as part of the full test suite
21:15 CIA-71 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/kOfKI9
21:15 CIA-71 cdk: Rajarshi Guha cdk-1.4.x * re24a572 / src/main/org/openscience/cdk/dic​t/data/descriptor-algorithms.owl : annotated VABCVolume descriptor as a topological descriptor - http://bit.ly/llXp9w
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