Camelia, the Perl 6 bug

IRC log for #cdk, 2012-02-19

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All times shown according to UTC.

Time Nick Message
08:22 egonw joined #cdk
10:18 CIA-121 cdk: John May cdk-1.4.x * r07bbbb2 / (3 files in 3 dirs): Added ability to read atom parity from Mol files (inc. junit test). - http://git.io/H8LuzQ
10:18 CIA-121 cdk: John May cdk-1.4.x * reae7598 / src/test/org/openscience/cdk​/io/MDLV2000ReaderTest.java : Added close to unit-test resource stream - http://git.io/M19Nbg
10:18 CIA-121 cdk: Egon Willighagen cdk-1.4.x * r8ff4584 / src/test/org/openscience/cdk​/io/MDLV2000ReaderTest.java :
10:18 CIA-121 cdk: Fixed unit test: because the implementation creates an IMolecule object, the original 'molecule' pointer does not get atoms, and the returned IMolecule object should be assigned to get a molecule with information
10:18 CIA-121 cdk: Change-Id: I480895ef8a0f308a279f80c869a6efb93c67cbee - http://git.io/prDu6g
11:04 sneumann joined #cdk
11:30 sneumann joined #cdk
12:26 mrsy joined #cdk
12:26 egonw hi mrsy
12:27 egonw .lv ?
12:27 mrsy hi
12:27 zarah oh hai mrsy
12:28 egonw (zarah is our friendly bot...)
12:28 mrsy ahaa, ok
13:04 mrsy any plans in the future of making some kind of integration with database? like a cartridge or something
13:04 egonw there are several solutions for that
13:04 egonw (based on the CDK)
13:05 mrsy hmm, i thought only rdkit supported database functions
13:05 egonw no, that would not be true
13:05 egonw for Oracle: http://orchem.sourceforge.net/
13:06 mrsy ou, how i did not find it
13:06 mrsy thanks, will try it out
13:06 egonw there should be a solution for MySQL too, but cannot directly find it...
13:06 egonw mmm... we should have a wiki page for that...
13:07 egonw you can browse the cdk-user mailing list archives...
13:07 mrsy currently I'm using chemaxon, but I don't feel that the price of licences is appropriate for functionality that they are providing
13:07 egonw oh, stupid me...
13:07 egonw of course there is AMBIT
13:08 egonw and NMRShiftDB uses the CDK with MySQL too, for structures
13:08 egonw sorry... it's sunday...
13:08 egonw stefan kuhn posted an update on his use of CDK / MySQL recently
13:09 egonw AMBIT -> http://www.jcheminf.com/content/3/1/18/abstract
13:09 egonw skip the RDF/OpenTox bits...
13:09 mrsy for me sunday is the only day I can get to peacefuly think about 'future developments and improvements' and not being distracted by day-to-day bugfixes etc :)
13:09 egonw at the core, it's MySQL with CDK
13:09 egonw yeah, I know that feeling :)
13:10 egonw this is also worth checking out: http://nar.oxfordjournals.org/​content/37/suppl_1/D284.short
13:13 egonw ask around in the cdk-user mailing list, if you like to make a full list...
13:13 egonw in fact, there is probably room for a good review of the field of open source structure database solutions...
13:13 egonw anyway... going to spend some time with the kids now...
13:13 egonw bbl
16:36 egonw joined #cdk
17:10 CIA-121 cdk: Egon Willighagen 361-14x-mdlPatchesJMay * r7199518 / src/test/org/openscience/cdk​/io/MDLV2000WriterTest.java :
17:10 CIA-121 cdk: Same as earlier: use the returned object, which is not the same as the passed IAtomContainer
17:10 CIA-121 cdk: Change-Id: I5c6424507a3bd691ce1824f64b555b643a608ff6 - http://git.io/-lQV_w
17:10 CIA-121 cdk: John May 361-14x-mdlPatchesJMay * rc7aa428 / (2 files in 2 dirs):
17:10 CIA-121 cdk: Write atom parity
17:10 CIA-121 cdk: Writes the atom stereo parity for MDLV2000 format - http://git.io/JJiWBA
17:10 CIA-121 cdk: John May 361-14x-mdlPatchesJMay * ra977e85 / src/test/org/openscience/cdk​/io/MDLV2000WriterTest.java :
17:10 CIA-121 cdk: Assertion error fix
17:10 CIA-121 cdk: Fixed error in new unit test assertion - http://git.io/hnNqsg
17:10 egonw oops
17:10 egonw wrong branch
17:11 CIA-121 cdk: John May cdk-1.4.x * ra977e85 / src/test/org/openscience/cdk​/io/MDLV2000WriterTest.java :
17:11 CIA-121 cdk: Assertion error fix
17:11 CIA-121 cdk: Fixed error in new unit test assertion - http://git.io/hnNqsg
17:11 CIA-121 cdk: John May cdk-1.4.x * rc7aa428 / (2 files in 2 dirs):
17:11 CIA-121 cdk: Write atom parity
17:11 CIA-121 cdk: Writes the atom stereo parity for MDLV2000 format - http://git.io/JJiWBA
17:11 CIA-121 cdk: Egon Willighagen cdk-1.4.x * r7199518 / src/test/org/openscience/cdk​/io/MDLV2000WriterTest.java :
17:11 CIA-121 cdk: Same as earlier: use the returned object, which is not the same as the passed IAtomContainer
17:11 CIA-121 cdk: Change-Id: I5c6424507a3bd691ce1824f64b555b643a608ff6 - http://git.io/-lQV_w
18:29 mrsy joined #cdk
19:15 egonw joined #cdk
19:59 CIA-121 cdk: John May cdk-1.4.x * re2eb007 / (5 files in 3 dirs): (log message trimmed)
19:59 CIA-121 cdk: Resolution for Bug 3485634
19:59 CIA-121 cdk: Adding test molecule data/mdl/bug3585634.mol. This molecule is from the
19:59 CIA-121 cdk: metlin database (http://metlin.scripps.edu/)
19:59 CIA-121 cdk: 1) MDLReader and MDLV2000Reader unit tests
19:59 CIA-121 cdk:  Unit test's to ensure the molecule is read.
19:59 CIA-121 cdk: 2) MDLV2000Reader empty atom properties fix
21:25 CIA-121 cdk: Egon Willighagen cdk-1.4.x * r7c7248a / src/main/org/openscience/cdk/io/PDBReader.java :
21:25 CIA-121 cdk: Fix for charge parsing in PDB files, based on the patch by Nils <nils@users.sf.net>
21:25 CIA-121 cdk: Change-Id: I7414228850ac87880febdebfc6e912647638f2c6
21:25 CIA-121 cdk: Signed-off-by: John May <john.wilkinsonmay@gmail.com> - http://git.io/IK7-9A
21:25 mrsy that ambit looks quality stuff, too bad documentation is very weak. But it's common for os projects

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