Camelia, the Perl 6 bug

IRC log for #cdk, 2007-10-19

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
00:03 carsten joined #cdk
02:35 CIA-31 jmol: hansonr * r8468 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): version=11.3.35_dev # PDB remediated atom name upgrade -- NEEDS CAREFUL CHECKING
03:28 CIA-31 jmol: hansonr * r8469 /trunk/Jmol/src/org/jmol/ (modelsetbio/NucleicMonomer.java viewer/JmolConstants.java): version=11.3.35_dev # PDB remediated atom name upgrade -- NEEDS CAREFUL CHECKING
03:56 CIA-31 jmol: hansonr * r8470 /trunk/Jmol/src/org/jmol/ (modelset/ModelCollection.java viewer/Jmol.properties): version=11.3.35_dev # bug fix: getproperty atominfo returning string to Integer()
04:00 CIA-31 jmol: hansonr * r8471 /branches/v11_2/Jmol/src/org/jmol/ (modelset/ModelManager.java viewer/Jmol.properties): 11.2.15 # bug fix: getproperty atominfo returning string to Integer()
04:26 CIA-31 jmol: hansonr * r8472 /trunk/Jmol/src/org/jmol/ (shapespecial/IsosurfaceRenderer.java viewer/Jmol.properties): version=11.3.35_dev # POV-Ray cleaner for Molecular Orbitals
06:11 egonw joined #cdk
07:17 jpansanel moin
07:50 CIA-31 cdk: egonw * r9130 /trunk/cdk/src/org/openscience/cdk/test/aromat​icity/CDKHueckelAromaticityDetectorTest.java: Testing the new arom framework (based on old tests).
08:02 jonalv joined #cdk
09:06 egonw joined #cdk
09:13 masak joined #cdk
09:46 CIA-31 cdk: egonw * r9131 /trunk/cdk/src/org/openscience/cdk/aromat​icity/CDKHueckelAromaticityDetector.java: Fixed detection of ring bonds.
11:15 CIA-31 cdk: egonw * r9132 /trunk/cdk/src/org/openscience/cdk/aromat​icity/CDKHueckelAromaticityDetector.java: Eliminated a NPE source.
11:20 CIA-31 bioclipse: ospjuth * r3996 /trunk/playground/plugins/net.bio​clipse.biomoby/src/net/bioclipse/ (7 files in 3 dirs): Complete rewrite of service invocation wizard and action that finally works. Currently does not take secondary parameters as input but uses default.
11:26 CIA-31 cdk: egonw * r9133 /trunk/cdk/src/org/openscience/cd​k/templates/MoleculeFactory.java: Added InChIs.
11:32 CIA-31 cdk: egonw * r9134 /trunk/cdk/ (javadoc.xml src/net/sf/cdk/tools/doclets/CDKInChITaglet.java): Added InChI RDFa markup support to the JavaDoc, as used in the MoleculeFactory.
11:33 * egonw is going offline for a while... bbl
11:42 jbrefort joined #cdk
11:56 carsten joined #cdk
11:56 CIA-31 bioclipse: ospjuth * r3997 /trunk/playground/plugins/net.bio​clipse.biomoby/src/net/bioclipse/ (2 files in 2 dirs): Initializes secondaryData in wizard
12:00 CIA-31 bioclipse: ospjuth * r3998 /trunk/playground/plugins/net.bio​clipse.biomoby/src/net/bioclipse/ (9 files in 3 dirs): Some refactoring of classes
12:00 CIA-31 bioclipse: ospjuth * r3999 /trunk/playground/plugins/net.bio​clipse.biomoby/src/net/bioclipse/ (7 files in 3 dirs): Some more refactoring of classes
12:04 CIA-31 bioclipse: ospjuth * r4000 /trunk/playground/plugins/net.bio​clipse.biomoby/src/net/bioclipse/ (10 files in 4 dirs): Package cleanup
12:05 CIA-31 bioclipse: ospjuth * r4001 /trunk/playground/plugins/net.bioclip​se.biomoby/src/net/bioclipse/biomoby/ (8 files in 2 dirs): Moved tests to correct package
12:05 CIA-31 bioclipse: ospjuth * r4002 /trunk/playground/plugins/net.bioclipse.​biomoby/src/net/bioclipse/biomoby/tests/ (3 files): Added more tests that currently fails
12:35 egonw joined #cdk
13:20 CIA-31 cdk: egonw * r9135 /trunk/cdk/src/org/openscience/cdk/test/aromat​icity/CDKHueckelAromaticityDetectorTest.java: Some clean up (note: expected values are given as first argument in assertX() methods.)
13:22 carsten joined #cdk
13:33 CIA-31 bioclipse: ospjuth * r4003 /trunk/playground/plugins/net.bioclip​se.biomoby/src/net/bioclipse/biomoby/ (4 files in 2 dirs): Implemented secondaryParameters in service invocation.
13:50 CIA-31 cdk: egonw * r9136 /trunk/cdk/src/org/openscie​nce/cdk/tools/manipulator/ (RingManipulator.java RingSetManipulator.java): Added markAromaticRings() convenience methods that mark IRing's with the flag CDKConstants.ISAROMATIC when all atoms and all bonds in the ring are flagged aromatic.
14:13 egonw joined #cdk
14:45 CIA-31 cdk: egonw * r9137 /trunk/cdk/src/org/openscience/cdk/tools/m​anipulator/AtomContainerManipulator.java: Added a convenience method to perceive atom types for the IAtomContainer and configure the atoms accordingly.
14:49 CIA-31 cdk: egonw * r9138 /trunk/cdk/src/org/openscience/cdk/test/aromat​icity/CDKHueckelAromaticityDetectorTest.java: Forgot to add the atom type perception prior to aromaticity detection. Outcome: 12/16 tests succeed! Not bad at all for a first go :)
15:10 CIA-31 cdk: egonw * r9139 /trunk/cdk/src/org/openscience/cdk/test/aromat​icity/CDKHueckelAromaticityDetectorTest.java: Better feedback: indicate which atoms fails.
15:14 CIA-31 cdk: egonw * r9140 /trunk/cdk/src/org/openscience/c​dk/test/MexperimentalTests.java: Added test suite for the new Hueckel aromaticity detector.
15:27 CIA-31 blueobelisk: cjames53 * r135 /smiles-spec/trunk/ (5 files):
15:27 CIA-31 blueobelisk: open-smiles-3-input.html
15:27 CIA-31 blueobelisk: open-smiles.html
15:27 CIA-31 blueobelisk: open-smiles.css
15:27 CIA-31 blueobelisk: open-smiles-1-intro.html
15:27 CIA-31 blueobelisk: open-smiles-4-output.html
15:27 CIA-31 blueobelisk:  Ongoing work...
16:10 CIA-31 bioclipse: ospjuth * r4004 /trunk/playground/plugins/net.bioclip​se.biomoby/src/net/bioclipse/biomoby/ (5 files in 2 dirs): Adapted to work with DB retrieval (added namespaces). ResultWizard is hardcoded to one object, but works for single retrieval services (e.g. getKeggPathwayAsGif).
17:52 CIA-31 jmol: hansonr * r8473 /trunk/Jmol/src/org/jmol/ (5 files in 4 dirs): 11.3.35 POV-Ray slab/depth ooooooooo :)
20:12 CIA-31 cdk: dleidert * r5 /trunk/bodr/ (ChangeLog bodr.pc.in):
20:12 CIA-31 cdk: 2007-10-19 Daniel Leidert <daniel.leidert@wgdd.de>
20:12 CIA-31 cdk:  * bodr.pc.in: Re-added pkgdatadir (closes #1713504 sf.net).
20:29 CIA-31 cdk: rajarshi * r9141 /trunk/cdk/doc/refs/cheminf.bibx: Fixed bad xml in refs
20:49 CIA-31 cdk: rajarshi * r9142 /trunk/cdk/src/org/openscience/cdk/tool​s/manipulator/RingSetManipulator.java: Fixed a typo to the markAromatic method
21:25 CIA-31 cdk: rajarshi * r9143 /branches/cdk-1.0.x/doc/refs/cheminf.bibx: Fixeda typo in the xmls refs
22:32 CIA-31 cdk: rajarshi * r9144 /trunk/cdk/tools/nightly.py: Added a links section

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary