Camelia, the Perl 6 bug

IRC log for #cdk, 2008-07-14

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All times shown according to UTC.

Time Nick Message
04:20 egonw joined #cdk
04:25 CIA-33 cdk: egonw * r11572 /cdk/branches/egonw-atowl/src/ma​in/org/openscience/cdk/atomtype/ (SybylAtomTypeMatcher.java mapper/ mapper/AtomTypeMapper.java): Set up infrastructure for mapping CDK atom types 2 sybyl atom types
04:26 CIA-33 cdk: egonw * r11573 /cdk/trunk/src/main/org/openscience/cdk/modelin​g/builder3d/AtomTetrahedralLigandPlacer3D.java: Fixed NPE due to double 2 Double transition
04:44 CIA-33 cdk: egonw * r11574 /cdk/trunk/build.xml: Fixed building of sourcedist: removed elements.xml, included *.owl
04:50 CIA-33 cdk: egonw * r11575 /cdk/trunk/src/main/org/openscience/cdk/m​odeling/builder3d/TemplateHandler3D.java: A bit of code clean up: typed List; don't silently catch Exceptions; removed unused field
04:51 CIA-33 cdk: egonw * r11576 /cdk/trunk/src/test/org/openscience/cdk/mod​eling/builder3d/TemplateHandler3DTest.java: Whitespace cleanup
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05:06 CIA-33 jmol: hansonr * r9591 /trunk/Jmol/src/org/ (24 files in 6 dirs): (log message trimmed)
05:06 CIA-33 jmol: 11.5.46 VERSION
05:06 CIA-33 jmol: # bug fix: remove the skipping of semicolons if parentheses or braces have been closed. (11.5.43 bug)
05:06 CIA-33 jmol: # bug fix: set picking on broken in 11.5.39
05:06 CIA-33 jmol: #
05:06 CIA-33 jmol: # new feature: measure {atomExpression or point} {atomExpression or point} ...
05:06 CIA-33 jmol: # measurements to POINTS, including using the mouse (set drawPicking on)
06:20 masak joined #cdk
06:23 egonw joined #cdk
06:32 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 7113, 73 fails + 58 errors (1.84%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk | CDK News paper online on pharmacophores: http://www.cdknews.org/
06:35 masak joined #cdk
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07:12 rojasm moin
07:41 olas joined #cdk
07:44 carsten joined #cdk
08:20 olas hi all
09:03 CIA-33 jmol: nicove * r9592 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
09:57 masak egonw: there are many collections without generics in CDK. is that something that you are working on, or are there reasons not to add generics?
09:57 egonw first
09:57 egonw do you have an exhaustive list?
09:57 masak I'm in o.os.cdk.protein.data.PDBPolymer now, and e.g. getStructures() only returns a Collection
09:58 egonw if so, please file a bug report and add it
09:58 masak egonw: I could look around a bit
09:58 masak egonw: oki
09:58 egonw or, if you like to work on it, that would be even nicer :)
09:58 masak egonw: I'll have to ask olas :)
09:59 egonw otherwise, just file bug reports
09:59 egonw in general fine with that
09:59 masak anyway, the Collection in the return type of getStructures() should really be List<Something>
09:59 masak I'll file a bug report
09:59 masak lunch &
10:00 egonw ok, thanx!
11:08 egonw masak: we do have these reports: http://cheminfo.informatics.indiana.edu/~​rguha/code/java/nightly/pmdmsummary.html
11:08 shk3 joined #cdk
11:09 egonw masak: but not sure if your problems are in there too
11:09 egonw hi shk3
11:09 egonw shk3: please check my email on the builder3d
11:09 egonw I fixed on problem
11:09 egonw but there is more
11:09 masak egonw: I'll have a look. thanks
11:23 shk3 egonw: three of the remaining failing tests look like the file is not found.
11:23 shk3 no idea why.
11:23 shk3 any change in trunk with respect to this from cdk 1.0?
11:24 egonw try:
11:24 egonw jar tvf dist/jar/cdk-test-builder3d.jar | grep data
11:24 egonw that shows the test files
12:29 steinbeck joined #cdk
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12:33 zarah joined #cdk
12:33 egonw hi zarah
12:33 masak zarah: hi
12:33 zarah hello masak :)
12:37 olas karma olas
12:37 zarah olas has a karma of 2
12:37 olas hi all
12:37 zarah hi olas
12:59 shk3 egonw: looks like all files are there
12:59 zarah shk3: You have new messages. Write '@messages' to read them.
12:59 shk3 @messages
12:59 zarah shk3: jonalv said Go for the eclipse version 3.4 alternative when creating new plugin. Also consider using the example plugin if you are doing a plugin that will contribute a manager
13:11 shk3 egonw: works now - no idea why
13:11 shk3 just some ring templates not found left
13:11 shk3 will look at these
13:11 egonw oh...
13:12 shk3 do you have an idea what could be the difference to cdk 1.0
13:12 shk3 ?
13:12 egonw no, not at this moment
13:12 egonw some ring templates are not found, or none?
13:13 shk3 some, it seems
13:13 shk3 some ring tests work
13:15 egonw this is the problem of lack of unit tests
13:15 egonw the builder3d is using a lot of stuff...
13:15 egonw including some atom typing code
13:15 egonw and only a small bit is tested
13:15 egonw no clue what is now working differently
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15:17 malick left #cdk
18:52 egonw joined #cdk
18:53 egonw hi all
18:53 zarah hi egonw
19:03 bag joined #cdk
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19:36 rojasm joined #cdk
20:27 bag hi any openbabel developer around :)
20:27 bag is it possible to generate a 2d or 3d structure from a smile/inchi string?
21:12 CIA-33 joined #cdk

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