Camelia, the Perl 6 bug

IRC log for #cdk, 2008-08-14

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All times shown according to UTC.

Time Nick Message
03:42 CIA-34 cdk: mesprague * r12060 /cdk/branches/mesprague-jgrapht/ (4 files in 3 dirs): First upload of JGraphMol class.
03:48 CIA-34 cdk: mesprague * r12061 /cdk/branches/mesprague-symmetry/src/main/org​/openscience/cdk/geometry/GeometryTools.java: Added draft PermAnalyzer class which converts Permutations SymmetryElements, Draft of PointGroupFinder, and skeletal outline of SymTools class.
05:03 bag joined #cdk
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08:43 thomas_ku moin
08:43 zarah hi thomas_ku
09:54 jonalv can someone help me with IChemObjectListeners?
09:54 jonalv they seem to fire strange events
09:54 jonalv and never for the atomcontainer...
09:55 jonalv I have an atomcontainer and I need to listen to when it changes
10:00 jonalv @seen egonw
10:00 zarah egonw was last seen 2008-08-13T12:01:53 in #bioclipse saying 'brilliant name :)'
10:05 jonalv ping
10:57 maclean joined #cdk
11:14 maclean I don't seem to have a MockIFile in net.bioclipse.core. Can anyone hint as to why?
11:22 maclean Aha. It turned out to be because I didn't have core.tests.
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13:37 maclean Random question, but you can have ring closure numbers higher than 9 in SMILES, can't you?
13:55 maclean Answer: no, of course not, because of multiple closures.
13:55 maclean Maybe I'll stop asking stupid questions today...
14:07 shk3 I think there is a syntax
14:07 shk3 with [] or so, but not sure
14:07 shk3 but I remember something vaguely
14:09 CIA-34 cdk: egonw * r12062 /cdk/trunk/pmd/ (custom.xml customNaming.xml): Loosend PMD warnings: we do not care about large classes at this moment; fixed description custom task (30 length was tested, not 20); getFlag() is fine
14:14 CIA-34 cdk: egonw * r12063 /cdk/trunk/src/main/org/op​enscience/cdk/fingerprint/ (6 files): A bit more clear on what type of exception is to be expected
14:17 maclean No, percent signs, it seems.
14:24 maclean Oops, you can't round-trip the SmilesParser and the SmilesGenerator with these large rings.
14:24 maclean Or, if you can, there's some trick I don't know.
14:29 shk3 don't think
14:29 shk3 there is
14:29 shk3 a clear bug, I would say
14:45 CIA-34 cdk: egonw * r12064 /cdk/trunk/pmd/wz-pmd-report.xslt: Fixed reporting of line numbers with PMD 4.2.2
14:48 CIA-34 cdk: gilleain * r12065 /cdk/trunk/src/test/org/openscience/​cdk/smiles/SmilesGeneratorTest.java: Test for bug 2051597 : SmilesGenerator not producing double-digit ring closures properly.
14:49 CIA-34 cdk: egonw * r12066 /cdk/trunk/src/main/org/openscience/c​dk/atomtype/CDKAtomTypeMatcher.java: Moved checking of symbol to higher level method, which reduces unnedded method calls (though those may be removed by compiler optimization?)
15:29 maclean Ack! Mispelled class name! Gah.
15:34 CIA-34 cdk: egonw * r12067 /cdk/trunk/src/main/org/openscience/c​dk/atomtype/CDKAtomTypeMatcher.java: Code cleanup: reducing code complexity
16:11 maclean @seen goglepox
16:11 zarah I have not seen goglepox
16:45 CIA-34 cdk: egonw * r12068 /cdk/trunk/src/main/org/openscience/​cdk/fingerprint/IFingerprinter.java: Moved IFingerprinter to core, as it depends on CDKException (as PMD wanted it not to use 'throws Exception' which is a good point)
16:45 maclean I've seen a few "throws Exception"...
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18:45 CIA-34 cdk: egonw * r12069 /cdk/trunk/src/main/org/openscience/c​dk/atomtype/CDKAtomTypeMatcher.java: Optimized performance by reducing the number of isRingAtom() and getRing() calls; perceiving nitrogen types is still the most time consuming step.
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21:59 CIA-34 cdk: rajarshi * r12070 /cdk/trunk/build.xml: Added some code to obtain the current svn revision. Should be used to name the daily builds

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