Camelia, the Perl 6 bug

IRC log for #cdk, 2010-04-07

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All times shown according to UTC.

Time Nick Message
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04:51 CIA-45 cdk: Egon Willighagen cdk-1.2.x * r068fb3b / (2 files in 2 dirs):
04:51 CIA-45 cdk: Moved test from the specific class to the abstract tests, as the behavior should be the same for NNMoleculeSet and DebugMoleculeSet too
04:51 CIA-45 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/a3bpXw
04:51 CIA-45 cdk: Egon Willighagen cdk-1.2.x * r4e5d6a1 / src/main/org/openscience/cdk/AtomContainerSet.java :
04:51 CIA-45 cdk: Apparently the super.clone() does not clone the pointer to the IAtomContainer[], causing a clone() followed by changing containers in the clone to overwrite the original IAtomContainer[]. Fixed by creating a new array.
04:51 CIA-45 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/cNl5Gr
04:51 CIA-45 cdk: Egon Willighagen cdk-1.2.x * r216c160 / src/main/org/openscience/cdk/MoleculeSet.java :
04:51 CIA-45 cdk: Removed duplication of cloning.
04:51 CIA-45 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/aguRrH
04:51 CIA-45 cdk: Egon Willighagen cdk-1.2.x * r3c1b07e / src/test/org/openscience/cdk/interf​aces/AbstractAtomContainerTest.java :
04:51 CIA-45 cdk: Unit test that the IAtom[] array is properly cloned, and overwriting entries in the clone does not overwrite entries on the original
04:51 CIA-45 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/cSoEUM
04:52 CIA-45 cdk: Egon Willighagen cdk-1.2.x * r38d5f8d / src/test/org/openscience/cdk/interf​aces/AbstractAtomContainerTest.java :
04:52 CIA-45 cdk: Added unit test to see of arrays are properly cloned, and that array entries of the original are not overwritten
04:52 CIA-45 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/aELbRO
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06:29 egonw moin
06:29 zarah oh hai egonw
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07:17 egonw s9asad:
07:17 egonw Testsuite: org.openscience.cdk.modulesuites.MsmsdTests
07:17 egonw Tests run: 214, Failures: 2, Errors: 0, Time elapsed: 18.671 sec
07:21 egonw ok, let me make a patch
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08:05 s9asad HI Egon Sorry got DC
08:05 s9asad A patch would be great
08:05 s9asad If i have access to CDK development branch, then I could further add or improvise upon the code
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10:29 CIA-45 cdk: shk3 * r15501 /detgen/trunk/ (5 files in 2 dirs): a good boost in performance
10:39 carsten joined #cdk
10:46 egonw hi carsten
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11:43 sneumann has anyone here every actually *seen* a JCAMP-CS file in the wild ?
11:43 sneumann http://www.jcamp-dx.org/protocols/dxcs01.pdf
11:43 zarah sneumann's link is also http://tinyurl.com/yktq6ne
11:44 sneumann JCAMP-CS: A Standard Exchange Format for Chemical Structure Information in Computer-Readable Form
11:51 egonw not here
11:55 sneumann :-)
11:55 sneumann looks as if you needed fortran to parse it ...
11:56 carsten moin egonw and rest
11:56 egonw sneumann: :)
11:56 egonw hi carsten
11:56 egonw carsten: anything interesting in the KDE GSoC?
11:57 carsten I didn't follow it to closely, no kalzium students though
11:57 carsten avogadro didn't apply :(
11:59 CIA-45 cdk: shk3 * r15502 /detgen/trunk/src/org/openscience/cdk/structg​en/deterministic/DeterministicGenerator.java: avoids string concatenations
12:11 egonw anyone here who likes a Google Wave account but does not have one yet?
12:12 * carsten has an account but doesn't like it ;-)
12:13 sneumann carsten: your alternative for collaborative realtime editing ?
12:14 carsten I dont even know what that is.  I am using google docs from time to time for that, yes
12:14 carsten for other things I am using the telefone
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14:52 CIA-45 cdk: mark_rynbeek * r15503 /jchempaint/trunk/src/ (5 files in 4 dirs): Fixed some tests. Updated getMol/setMol and copy paste to work with RG file format
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15:03 CIA-45 cdk: shk3 * r15504 /jchempaint/trunk/src/test/org/openscience/j​chempaint/JCPEditorAppletUndoRedoTest.java: comment was wrong
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