Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-20

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All times shown according to UTC.

Time Nick Message
04:33 jbrefort joined #cdk
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09:54 rojasm joined #cdk
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12:12 edrin joined #cdk
12:23 egonw joined #cdk
12:23 rojasm hi egonw
12:24 egonw hi rojasm
12:24 egonw just back from lunch
12:24 egonw well, almost...
12:24 egonw still bits of cleaning up to do...
12:24 egonw you'll be around this afternoon?
12:24 egonw I realized later...
12:24 egonw that...
12:24 rojasm yes I will be
12:24 egonw the BondBreakingReaction was indeed a problem with the atom type matcher
12:24 rojasm I answered your mail
12:24 egonw that it allowed a incorrect oxygen
12:24 egonw as it assumed an extra hydrogen
12:24 rojasm yes
12:25 egonw that bug you menion is implemented and closed
12:25 egonw and actually used in the branch...
12:25 egonw concluding: back on track :)
12:25 rojasm ok. !
12:25 egonw btw, I don't think either we did any other reaction yet
12:26 rojasm I think either
12:26 egonw will clean up the house now...
12:26 egonw will be back in some 30-45 minutes or so...
12:26 rojasm perfect
12:28 edrin my application gets an xml schema at runtime. it then wants to marshal/unmarshal/validate xml documents according to this schema at runtime. how can I do this without compiling the schema's classes? I want to do all this at runtime...
12:31 egonw edrin: use JDOM or so...
12:32 egonw that will get you an XML document Object
12:32 egonw for any schema...
12:32 egonw but will not in itself validate
12:32 egonw but those should be separate steps anyway I guess...
12:39 edrin yup
13:50 dleidert joined #cdk
16:12 egonw rojasm: OK, found the problem...
16:15 egonw it C.plus.sp2 which requires three neighbors...
16:16 egonw but the BreakingBond reaction of C-H -> C+ + H- gives two carbon neighbors...
16:16 egonw need to think wether that's an atom type bug, or a missing atom type...
16:17 egonw going to make dinner first now...
18:23 carsten joined #cdk
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19:22 CIA-18 cdk: egonw * r9931 /branches/miguelrojasch/reaction/src/org/ope​nscience/cdk/config/data/cdk_atomtypes.xml: Fixed properties of two atom types
19:22 CIA-18 cdk: egonw * r9932 /branches/miguelrojasch/reaction/src/org/open​science/cdk/atomtype/CDKAtomTypeMatcher.java: Easier to debug
20:33 CIA-18 cdk: egonw * r9933 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (2 files in 2 dirs): Fixed test: testing was inconsistent with comment, and with results which did match the comments
20:40 CIA-18 cdk: egonw * r9934 /branches/miguelrojasch/reaction/src​/org/openscience/cdk/test/reaction/t​ype/BreakingBondReactionTest.java: Fixed two tests: wrong charge on oxygen; twice adding bond to wrong molecule
20:57 CIA-18 cdk: egonw * r9935 /branches/miguelrojasch/reaction/src​/org/openscience/cdk/test/reaction/ (ReactionProcessTest.java type/BreakingBondReactionTest.java): Added testing of meta method for IReactionProcess classes
21:11 CIA-18 cdk: egonw * r9936 /branches/miguelrojasch/reaction/src/o​rg/openscience/cdk/test/reaction/type/ (21 files): All IReactionProcess tests now extend ReactionProcessTest
21:34 CIA-18 cdk: egonw * r9937 /trunk/cdk/src/org/openscience/cdk/​test/smiles/SmilesParserTest.java: Added test for bug report #1875949
21:38 CIA-18 cdk: egonw * r9938 /branches/miguelrojasch/reaction/sr​c/org/openscience/cdk/test/tools/St​ructureResonanceGeneratorTest.java: Use import, and fixed test by adding workaround for bug in the SmilesParser
21:41 egonw Enough for today...
21:42 egonw a number of bug fixes, test fixes... found two bugs...
21:46 edrin joined #cdk

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