Camelia, the Perl 6 bug

IRC log for #cdk, 2008-10-15

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All times shown according to UTC.

Time Nick Message
00:23 CIA-14 cdk: rajarshi * r12639 /cdk/branches/cdk-1.2.x/src/main/org/openscience/​cdk/smiles/smarts/parser/ASTNonCHHeavyAtom.java: Added Javadocs and proper module tags
00:48 CIA-14 cdk: rajarshi * r12640 /cdk/branches/cdk-1.2.x/src/main/org/openscien​ce/cdk/smiles/smarts/parser/SMARTSParser.jjt: Updated BNF spec to take into account the updates
02:21 CIA-14 cdk: rajarshi * r12641 /cdk/branches/cdk-1.2.x/src/ (9 files in 5 dirs): Added support for the ^ SMARTS symbol (an OE extension) which allows one to specify an atom of a given hybridization. Add unit test and updated docs
02:27 CIA-14 cdk: rajarshi * r12642 /cdk/branches/cdk-1.2.x/src/test/org/openscience​/cdk/smiles/smarts/parser/SMARTSSearchTest.java: Added another test case for the ^ SMARTS symbol
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08:31 egonw hi shk3, gilleain
08:31 CIA-62 cdk: egonw * r12643 /cdk/branches/cdk-1.2.x/.gitignore: Ignore any .class file; none should ever reach SVN
08:32 gilleain hi egon
08:34 shk3 hi egone
08:34 * shk3 going for lunch
08:34 egonw gilleain: I'm about to upload some JCP patches to the egonw-jchempaint brnach
08:34 shk3 coffee, this is
08:34 egonw ah...
08:34 egonw was already wondering...
08:34 egonw :)
08:49 CIA-62 cdk: egonw * r12644 /cdk/branches/egonw-jchempaint/src/main/org​/openscience/cdk/io/cml/CMLCoreModule.java: Topy in comments
08:49 CIA-62 cdk: egonw * r12645 /cdk/branches/egonw-jchempaint/src/main/org​/openscience/cdk/io/cml/CMLCoreModule.java: Fixed implicit hydrogen count (patch by Rajarshi)
08:50 egonw ok, forgot about that...
08:50 CIA-62 cdk: egonw * r12646 /cdk/branches/egonw-jchempaint/src​/test/org/openscience/cdk/io/cml/ (CML23FragmentsTest.java cml23TestFramework.xml): Added test for bug #2142400
08:51 CIA-62 cdk: egonw * r12647 /cdk/branches/egonw-jchempaint/src/main/org​/openscience/cdk/io/cml/CMLCoreModule.java: Convert CML into CDK hydrogenCounts (closes #2142400)
08:51 CIA-62 cdk: egonw * r12648 /cdk/branches/egonw-jchempa​int/doc/refs/cheminf.bibx: Added missing reference: kind2007
08:52 CIA-62 cdk: egonw * r12649 /cdk/branches/egonw-jchempaint/ (2 files in 2 dirs): Added missing KAB78 reference
08:52 CIA-62 cdk: egonw * r12650 /cdk/branches/egonw-jchempaint/src/m​ain/org/openscience/cdk/graph/invari​ant/EquivalentClassPartitioner.java: Fixed ID to match references in doc/refs/cheminf.xml
08:53 CIA-62 cdk: egonw * r12651 /cdk/branches/egonw-jchempaint/build.props: 1.1 is the development series for 1.2
08:53 CIA-62 cdk: egonw * r12652 /cdk/branches/egonw-jchempaint/build.xml: Fixed bad variable syntax
08:53 CIA-62 cdk: egonw * r12653 /cdk/branches/egonw-jchempa​int/src/cdk-apps.manifest: Removed obsolete file
08:54 CIA-62 cdk: egonw * r12654 /cdk/branches/egonw-jchempaint/ (3 files in 2 dirs): Fixing sourcedist building: fixes paths, smarts/*.jtt to include; release with Jonathan's Jumbo build
08:54 CIA-62 cdk: egonw * r12655 /cdk/branches/egonw-jchempaint/build.xml: Include test source files too
08:54 CIA-62 cdk: egonw * r12656 /cdk/branches/egonw-jchempaint/.gitignore: Ignore sourcedist creations
08:54 CIA-62 cdk: egonw * r12657 /cdk/branches/egonw-jchempaint/README: Added notice about testing not being available from sourcedists
08:54 CIA-62 cdk: egonw * r12658 /cdk/branches/egonw-jchempaint/build.xml: More updates to get the sourcedist working
08:55 CIA-62 cdk: egonw * r12659 /cdk/branches/egonw-jchempaint/src/META-INF/ (9 files): Ship with Jonathan's Jumbo version
08:57 jpansane1 moin
08:57 zarah hi jpansane1
08:58 CIA-62 cdk: egonw * r12660 /cdk/branches/egonw-jchempaint​/src/main/org/openscience/cdk/ (51 files in 15 dirs): First batch of JavaDoc fixes
09:00 gilleain Ah, sorry egon. We were at coffee.
09:01 CIA-62 cdk: egonw * r12661 /cdk/branches/egonw-jchempaint​/src/main/org/openscience/cdk/ (29 files in 13 dirs): Second batch of JavaDoc fixes
09:01 gilleain I've been blue-sky developing on my brnach.
09:01 CIA-62 cdk: egonw * r12662 /cdk/branches/egonw-jchempaint/src/main/o​rg/openscience/cdk/isomorphism/matchers/ (IQueryAtom.java IQueryAtomContainer.java): Rmoved unescessary import reducing a dependnecy
09:02 CIA-62 cdk: egonw * r12663 /cdk/branches/egonw-jchempaint/src/main/or​g/openscience/cdk/geometry/BondTools.java: added better commeentary
09:03 CIA-62 cdk: egonw * r12664 /cdk/branches/egonw-jchempaint/src/main/org/op​enscience/cdk/similarity/DistanceMoment.java: Cleaned up Javadocs and moved some code to 1.5 idiom
09:03 gilleain Commit flood! Man the barriers!
09:03 CIA-62 cdk: egonw * r12665 /cdk/branches/egonw-jchempaint/.gitignore: Ignore more autogenerated stuff
09:03 CIA-62 cdk: egonw * r12666 /cdk/branches/egonw-jchempaint/src/main/o​rg/openscience/cdk/io/ReaderFactory.java: If something is already a GzipInputStream, don't test for gzip-ness again; reuse guessFormat
09:04 CIA-62 cdk: egonw * r12667 /cdk/branches/egonw-jchempaint/src/test/org​/openscience/cdk/io/ReaderFactoryTest.java: Workaround for bug #2153298
09:04 CIA-62 cdk: egonw * r12668 /cdk/branches/egonw-jchempaint/src/test/org​/openscience/cdk/io/ChemObjectIOTest.java: Make a general assertion to all readers about the IChemObject's they accept, which should include IChemFile, IMolecule, IChemModel or IReaction
09:05 CIA-62 cdk: egonw * r12669 /cdk/branches/egonw-jchempaint/s​rc/test/org/openscience/cdk/io/ (ChemObjectReaderTest.java SimpleChemObjectReaderTest.java): Added test classes for two more interfaces
09:05 CIA-62 cdk: egonw * r12670 /cdk/branches/egonw-jchempaint/src/test/org​/openscience/cdk/io/ChemObjectIOTest.java: Test that for each IChemObject implementation, at least on object is accepted.
09:06 CIA-62 cdk: egonw * r12671 /cdk/branches/egonw-jchempaint/src/test/o​rg/openscience/cdk/io/XYZReaderTest.java: More testing
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09:06 CIA-62 cdk: egonw * r12672 /cdk/branches/egonw-jchempaint/src/main​/org/openscience/cdk/io/XYZReader.java: Added unit test annotation
09:07 CIA-62 cdk: egonw * r12673 /cdk/branches/egonw-jchempaint/src/test/org​/openscience/cdk/io/ChemObjectIOTest.java: Added more testing
09:07 CIA-62 cdk: egonw * r12674 /cdk/branches/egonw-jchempaint/src/test/org/open​science/cdk/io/SimpleChemObjectReaderTest.java: Test reading in all accepted IChemObject's
09:07 CIA-62 cdk: egonw * r12675 /cdk/branches/egonw-jchempaint/s​rc/META-INF/test-io.cdkdepends: The module test-io now tests accepting all common interface implementations, which adds these dependencies
09:08 CIA-62 cdk: egonw * r12676 /cdk/branches/egonw-jchempaint/src/main​/org/openscience/cdk/io/XYZReader.java: Added missing annotation
09:09 CIA-62 cdk: egonw * r12677 /cdk/branches/egonw-jchempaint/s​rc/main/org/openscience/cdk/io/ (22 files): Fixed a bug present in many readers: it would not accept a subclass if ChemFile (e.g. NNChemFile) even if ChemFile itself was accepted
09:10 CIA-62 cdk: egonw * r12678 /cdk/branches/egonw-jchempaint/s​rc/main/org/openscience/cdk/io/ (10 files): Added missing TestClass annotation
09:13 CIA-62 cdk: egonw * r12679 /cdk/branches/egonw-jchempaint/s​rc/main/org/openscience/cdk/io/ (48 files in 5 dirs): Added testClose annotation
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09:15 CIA-62 cdk: egonw * r12680 /cdk/branches/egonw-jchempaint/s​rc/main/org/openscience/cdk/io/ (48 files in 5 dirs): Added missing testAccepts, testSetReader_InputStream and testSetReader_Reader unit test annotation
09:16 CIA-62 cdk: egonw * r12681 /cdk/branches/egonw-jchempaint/s​rc/test/org/openscience/cdk/io/ (MDLV2000ReaderTest.java PCCompoundASNReaderTest.java): Extend SimpleChemObjectReaderTest for more extensive testing
09:28 thomasku moin
09:28 zarah hi thomasku
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11:13 CIA-62 cdk: gilleain * r12682 /cdk/branches/gilleain-jchempaint/src/ (12 files in 6 dirs):
11:13 CIA-62 cdk: -Added a FontManager class.
11:13 CIA-62 cdk: -Improved the scaling so that it center-scales.
11:28 rojasm after 3 days I have already cloned with git CDK project in my home
11:28 rojasm incredible fast
11:32 egonw :)
11:32 egonw but it worked now?
11:32 egonw I just read they upgraded SVN
11:32 egonw which might have caused your git-svn problem earlier
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11:34 egonw what the hell is git-svn doing???
11:34 CIA-62 cdk: egonw * r12683 /cdk/branches/egonw-jchempaint/src/main/o​rg/openscience/cdk/io/ReaderFactory.java: Java5 equivalent of the Java6 constructor (I think)
11:34 CIA-62 cdk: egonw * r12684 /cdk/branches/egonw-jchempaint/src/test/org/op​enscience/cdk/io/formats/ChemFormatTest.java: Added missing unit tests for getSupportedDataFeatures and getRequiredDataFeatures
11:34 egonw (better, what the hell did I do in the egonw-jchempaint branch???)
11:35 * egonw is heading back to a meeting
11:38 CIA-62 cdk: egonw * r12685 /cdk/branches/egonw-jchempaint/src/m​ain/org/openscience/cdk/io/formats/ (89 files): Added annotation for testGetSupportedDataFeatures
11:42 CIA-62 cdk: egonw * r12686 /cdk/branches/egonw-jchempaint/src/m​ain/org/openscience/cdk/io/formats/ (88 files): Added annotation for testGetRequiredDataFeatures
11:42 CIA-62 cdk: egonw * r12687 /cdk/branches/egonw-jchempaint/src/test/org/opens​cience/cdk/io/formats/ChemFormatMatcherTest.java: Added test class for the IChemFormatMatcher interface
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11:45 CIA-62 cdk: egonw * r12688 /cdk/branches/egonw-jchempaint/src/t​est/org/openscience/cdk/io/formats/ (46 files): Extend ChemFormatMatcherTest if the tested object instanceof IChemFormatMatcher
11:45 CIA-62 cdk: egonw * r12689 /cdk/branches/egonw-jchempaint/src/main/​org/openscience/cdk/modeling/forcefield/ (16 files): Ascribed copyright to Violeta who wrote this code between 2005 and 2007(?)
11:46 CIA-62 cdk: egonw * r12690 /cdk/branches/egonw-jchempaint/src/test/org/open​science/cdk/atomtype/StructGenMatcherTest.java: Overwriting default initialization methods from AbstractAtomTypeTest for the matcher; fixes NPEs all over the place, because AbstractAtomTypeTest.getFactory() was returning null
11:47 CIA-62 cdk: egonw * r12691 /cdk/branches/egonw-jchempaint/s​rc/test/org/openscience/cdk/io/ (22 files): Most readers now use SimpleChemObjectReaderTest
11:48 CIA-62 cdk: egonw * r12692 /cdk/branches/egonw-jchempaint/src/test/org/o​penscience/cdk/io/formats/JMEFormatTest.java: Oops, JME is not a IChemFormatMatcher. Fixes many NPEs
11:48 CIA-62 cdk: egonw * r12693 /cdk/branches/egonw-jchempaint/tools/ (nightly.config.sample nightly.py): Added new build script and example config
11:49 CIA-62 cdk: egonw * r12694 /cdk/branches/egonw-jchempaint/src/ (2 files in 2 dirs): Renamed test method to be more meaningful. Fixes bug #2151934
11:50 CIA-62 cdk: egonw * r12695 /cdk/branches/egonw-jchempaint/src/ (2 files in 2 dirs): Ensured that if formal charge is not set, we don't crash. Added unit test. Fixes bug #2149621
11:50 CIA-62 cdk: egonw * r12696 /cdk/branches/egonw-jchempaint/build.xml: Updated so that dist-large includes common-cli. Fixes bug #2151521
11:50 CIA-62 cdk: egonw * r12697 /cdk/branches/egonw-jchempaint/build.xml: Got rid of the step where we jar up commons-cli into the large jar file, since CLI apps are now in a separate package
11:50 CIA-62 cdk: egonw * r12698 /cdk/branches/egonw-jchempaint/ (build.xml src/META-INF/smarts.cdkdepends): Updated buil script since now smarts will depend on extra
11:52 CIA-62 cdk: egonw * r12699 /cdk/branches/egonw-jchempaint/src/ (7 files in 4 dirs): Updated SMARTS parser to support the G? symbol, where ? is a number indicating the periodic table group number. This is an extension that is supported by MOE
11:52 CIA-62 cdk: egonw * r12700 /cdk/branches/egonw-jchempaint/src/​test/org/openscience/cdk/smiles/sma​rts/parser/SMARTSSearchTest.java: Updated test for G symbol
11:53 CIA-62 cdk: egonw * r12701 /cdk/branches/egonw-jchempaint/src/ (2 files in 2 dirs): Added some validation for the G symbol, so that only valid periodic table group numbers (1 to 18) are allowed
11:54 CIA-62 cdk: egonw * r12702 /cdk/branches/egonw-jchempaint/src/​test/org/openscience/cdk/smiles/sma​rts/parser/SMARTSSearchTest.java: Added another test for the G symbol
11:54 CIA-62 cdk: egonw * r12703 /cdk/branches/egonw-jchempaint/src/main/org/opens​cience/cdk/smiles/smarts/parser/SMARTSParser.jjt: Cleaned up JJT spec
11:54 CIA-62 cdk: egonw * r12704 /cdk/branches/egonw-jchempaint/README: Fixed typo; LGPL is really v2, not v3
11:55 CIA-62 cdk: egonw * r12705 /cdk/branches/egonw-jchempaint/src​/META-INF/test-smarts.cdkdepends: Added missing dependency
11:55 CIA-62 cdk: egonw * r12706 /cdk/branches/egonw-jchempaint/.gitignore: Ignore any .class file; none should ever reach SVN
11:55 CIA-62 cdk: egonw * r12707 /cdk/branches/egonw-jchempaint/src/main/org/open​science/cdk/renderer/IRenderingParameters.java: Each rendering modula has separate parameter set
11:56 CIA-62 cdk: egonw * r12708 /cdk/branches/egonw-jchempaint/src/main/org​/openscience/cdk/renderer/JCPAction2D.java: Removed obsolete class
11:56 CIA-62 cdk: egonw * r12709 /cdk/branches/egonw-jchempaint/src/​main/org/openscience/cdk/renderer/ (5 files in 2 dirs): Java2DRenderer is currently the only renderer, and labeled it basic ('molecule' might be a better name
11:57 CIA-62 cdk: egonw * r12710 /cdk/branches/egonw-jchempaint​/src/main/org/openscience/cdk/ (2 files in 2 dirs): Highlight radius is really a parameter for the controller
11:58 CIA-62 cdk: egonw * r12711 /cdk/branches/egonw-jchempaint​/src/main/org/openscience/cdk/ (7 files in 2 dirs): Fixed several compile errors due to architectural changes
11:58 CIA-62 cdk: egonw * r12712 /cdk/branches/egonw-jchempaint/src/​main/org/openscience/cdk/renderer/ (6 files in 3 dirs): Example stubs for the rendering module idea
12:00 egonw Ah, there finally are the interesting commits... :)
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12:56 CIA-62 cdk: miguelrojasch * r12713 /cdk/branches/miguelrojasch-reactions/src/te​st/org/openscience/cdk/qsar/descriptors/atom​ic/PiElectronegativityDescriptorTest.java: Invalid smiles string
13:56 CIA-62 cdk: rajarshi * r12714 /cdk/branches/cdk-1.2.x/src/main/org/opensci​ence/cdk/smiles/smarts/SMARTSQueryTool.java: Fixed javadoc
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14:29 christa hey all
14:30 christa can anyone help me with this question? Initially a mixture contains 0.769 mol each of N2 and O2 in an 6.61 L vessel. Find the composition of the mixture when equilibrium is reached at 3900�C. For the reaction below, the Kc = 0.0123 at 3900�C. N2(g) + O2(g) <--> 2 NO(g)
14:31 christa N2 conc is 0.1163M and O2 and 2NO is 0.2327M for the initial but not sure where to go from there
14:40 christa anyone?
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15:28 * gilleain learns of the quadruple bond, and stands amazed...
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22:34 CIA-62 cdk: miguelrojasch * r12715 /cdk/branches/miguelrojasch-reactions/src/ (95 files in 10 dirs): Added dictionary which reads from a reaction-process.owl the mechanism for specific type reaction.

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