Camelia, the Perl 6 bug

IRC log for #cdk, 2008-06-06

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All times shown according to UTC.

Time Nick Message
04:09 egonw joined #cdk
04:44 jbrefort joined #cdk
04:53 malick joined #cdk
05:25 rojasm joined #cdk
05:46 egonw joined #cdk
06:32 rojasm joined #cdk
06:33 carsten joined #cdk
07:06 rojasm joined #cdk
08:26 jpansanel moin
08:27 jpansanel Open Source Award on Source Forge.
08:28 jpansanel Could w propose Bioclipse ?
08:28 jpansanel s/w/we
08:29 egonw yeah, please do
08:29 egonw I proposed a few project last year
08:29 egonw without nomination
08:29 egonw likely because they are too specialistic
08:30 jpansanel I'll try Bioclipse
08:37 jpansanel egonw : which category ?
08:37 jpansanel Best Project for Educators ?
08:39 egonw yes, think so...
08:39 jpansanel egonw : we should add the following link on Bioclipse :
08:39 jpansanel http://sourceforge.net/communi​ty/cca08-badge?group_id=150681
08:39 jpansanel (a call for nomination !)
08:40 egonw jpansanel: ok, talk to Uppsala
08:40 jpansanel we could may be post the news on Bioclipse ML ?
08:42 egonw please email the devel list about this...
08:43 egonw afk
10:06 egonw joined #cdk
12:01 CIA-31 jmol: hansonr * r9466 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties Viewer.java):
12:01 CIA-31 jmol: version=11.5.40_dev signed applet security
12:01 CIA-31 jmol: # new feature -- signed applet shows frank "Jmol-S" which is NOT removable.
12:01 CIA-31 jmol: # possibly to come: signed applet will send confirmation first time it reads a local file?
12:05 carsten joined #cdk
14:55 CIA-31 jmol: hansonr * r9467 /trunk/Jmol/src/org/jmol/ (popup/PopupResourceBundle.java viewer/Jmol.properties): version=11.5.40_dev # bug fix: popup menu had stereo reversed
16:12 rojasm joined #cdk
17:25 CIA-31 jmol: nicove * r9468 /trunk/Jmol-FAH/projects/p785.xyz.gz: Folding@Home
17:25 CIA-31 cdk: rajarshi * r11290 /cdk/trunk/src/test/org/openscience​/cdk/smiles/SmilesParserTest.java:
17:25 CIA-31 cdk: Added test cases for parsing of aromatic and kekule forms of indole SMILES. The
17:25 CIA-31 cdk: kekule form is parsed correctly and when aromaticity is percieved, all atoms are
17:25 CIA-31 cdk: aromatic. When the aromatic SMILES is parsed, all atoms are not aromatic and
17:25 CIA-31 cdk: even manual prception of aromaticity does not seem to fix this
17:51 rojasm joined #cdk
17:52 egonw joined #cdk
17:56 rojasm joined #cdk
18:21 CIA-31 jmol: aherraez * r9469 /trunk/Jmol/src/org/jmol/tr​anslation/Jmol/Jmol-es.po: Spanish
18:22 CIA-31 jmol: aherraez * r9470 /branches/v11_4/Jmol/src/org/jmo​l/translation/JmolApplet/es.po: Spanish
20:16 CIA-31 cdk: rajarshi * r11291 /cdk/trunk/src/main/org/openscience/​cdk/templates/MoleculeFactory.java: Added a method to return an indole molecule in the form that is obtained after SMILES parsing of an aromatic SMILES form, that is, all atoms are marked as SP2 and all bonds are single
20:21 CIA-31 cdk: rajarshi * r11292 /cdk/trunk/src/test/org/openscience/cdk​/atomtype/CDKAtomTypeMatcherTest.java:
20:21 CIA-31 cdk: Added a unit test to check whether the typer can match the indole N as planar3
20:21 CIA-31 cdk: when the molecule is represeted as all sp2 atoms with all single bonds (to
20:21 CIA-31 cdk: simulate the strcture obtained from the parsing the aromatic SMILES of indole,
20:21 CIA-31 cdk: where no explicit H is given)
20:46 CIA-31 cdk: rajarshi * r11293 /cdk/trunk/src/ (2 files in 2 dirs): Removed code that was testing for an invalid molecule scenario
20:48 CIA-31 cdk: rajarshi * r11294 /cdk/trunk/src/test/org/openscience​/cdk/smiles/SmilesParserTest.java: Updated to test for the proper form of an aromatic indole SMILES
20:49 CIA-31 cdk: rajarshi * r11295 /cdk/trunk/src/test/org/openscience/cdk/sm​iles/smarts/parser/SMARTSSearchTest.java: Updated to test for the proper form of an aromatic indole SMILES
21:06 CIA-31 cdk: rajarshi * r11296 /cdk/trunk/src/ (2 files in 2 dirs): Updated SMILES generator code to output explicit H on aromatic N's with a PLANAR3 atom type, so that indole and pyrrole get properly generated
21:07 CIA-31 cdk: egonw * r11297 /cdk/trunk/src/ (2 files in 2 dirs): Added missing test unit tests
21:18 CIA-31 cdk: rajarshi * r11298 /cdk/trunk/src/test/org/openscience/cdk/​smiles/smarts/SMARTSQueryToolTest.java: Added a test for bug 1985811 which enures that a indole SMILES generated from a molecle will match against the molecule.
21:18 CIA-31 cdk: egonw * r11299 /cdk/trunk/ (5 files in 2 dirs): Upgraded to 4.2.2

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