Camelia, the Perl 6 bug

IRC log for #cdk, 2007-08-03

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All times shown according to UTC.

Time Nick Message
06:12 topic for #cdk is: The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 3597 test, 43 fails + 68 errors (3.09%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
07:54 olas joined #cdk
09:08 egonw joined #cdk
09:21 egonw moin
09:28 Nout yo
09:28 Nout hm noone has commented my funky colors blog yet at http://progz-jchem.blogspot.com/ :(
09:28 lambdabot2 Title: Dutch summer of code - jchempaint
09:29 egonw_ joined #cdk
09:44 carsten joined #cdk
10:32 olas joined #cdk
10:58 egonw_ jbrefort: around?
10:59 egonw_ changed the nick to egonw
11:02 jbrefort egonw, I'll be back in an hour or so
11:02 jbrefort time for lunch
11:03 egonw jbrefort: ack
11:04 CIA-34 cdk: egonw * r8649 /trunk/cdk/src/org/openscience/cdk/config/data/ (cdk_atomtypes.xml html.xsl): Trying to get the HTML going
11:06 CIA-34 cdk: egonw * r8650 /trunk/cdk/src/org/openscience/cd​k/config/data/cdk_atomtypes.xml: Full URL to SVN web interface
11:12 CIA-34 cdk: egonw * r8651 /trunk/cdk/src/org/openscience/cd​k/config/data/cdk_atomtypes.xml: Use a better SF URL, so have the MIME type set, so that FireFox picks it up as XML
11:14 thomas_ku joined #cdk
11:15 thomas_ku moin
11:18 egonw hi thomas_ku
11:18 CIA-34 cdk: egonw * r8652 /trunk/cdk/src/org/openscien​ce/cdk/config/data/html.xsl: Fixed stylesheet
11:18 CIA-34 cdk: egonw * r8653 /trunk/cdk/src/org/openscience/cd​k/config/data/cdk_atomtypes.xml: Use HEAD not a specific revision
11:18 egonw http://cdk.svn.sourceforge.net/viewvc/*checkout​*/cdk/trunk/cdk/src/org/openscience/cdk/config/​data/cdk_atomtypes.xml?content-type=text%2Fxml
11:19 lambdabot2 http://tinyurl.com/yrjg9u
11:19 * egonw is happy
11:19 egonw lambdabot2: that was CML you were reading
11:19 * egonw is trying to educate that lambdabot2
11:19 * egonw feels like he is talking to the wall
11:20 thomas_ku ;-)
11:22 shk3 joined #cdk
11:27 CIA-34 cdk: egonw * r8654 /trunk/cdk/src/org/openscien​ce/cdk/config/data/html.xsl: More facts on the atom types
11:27 egonw shk3: check out -> http://cdk.svn.sourceforge.net/viewvc/*checkout​*/cdk/trunk/cdk/src/org/openscience/cdk/config/​data/cdk_atomtypes.xml?content-type=text%2Fxml
11:27 lambdabot2 http://tinyurl.com/yrjg9u
11:28 * egonw notices that lambdabot2 has some sort of rudimentary memory ;)
11:34 shk3 egonw: didn't follow the discussions on atomtypes
11:35 egonw no worry...
11:35 egonw I'm just happy with the setup :)
11:35 shk3 good
11:40 CIA-34 cdk: egonw * r8655 /trunk/cdk/src/org/openscience/cdk/config/data/ (6 files): Added XSLT to other atom type lists too
11:40 egonw so, now I can easily browse them :)
11:57 egonw shk3: around?
12:00 shk3 yes
12:01 egonw was looking into mass calculation, and wanted to close the getCanonicalMass() issue...
12:01 egonw you added that, correct?
12:02 egonw IIRC, the argument was that people wanted to use IUPAC masses, correct?
12:02 egonw but the BODR data uses IUPAC masses for isotopes...
12:02 egonw actually, more recent masses than the 2003 lists mentioned in MFAnalyzer
12:02 egonw can I remove that code?
12:03 egonw or were there other reasons why that code is in there?
12:12 shk3 hm
12:13 shk3 if bodr data are latest iupac masses, this should be ok
12:14 egonw it's conform the 2006 publication of the IUPAC
12:14 egonw ok, will remove the code then
12:18 jonalv joined #cdk
12:20 CIA-34 cdk: egonw * r8656 /trunk/cdk/src/org/openscienc​e/cdk/tools/MFAnalyser.java: Removed redundant and code using outdated data (IUPAC masses from 2003 instead of 2006 from BODR data, closes #1647096)
12:27 jbrefort egonw, I'm back
12:27 egonw jbrefort: check http://cdk.svn.sourceforge.net/viewvc/*checkout​*/cdk/trunk/cdk/src/org/openscience/cdk/config/​data/cdk_atomtypes.xml?content-type=text%2Fxml
12:27 lambdabot2 http://tinyurl.com/yrjg9u
12:28 egonw it is raw XML with an associated stylesheet to autocreate (in FF and IE) HTML on the fly for easier browsing...
12:28 egonw that would be useful for your spacegroup XML too
12:28 jbrefort yes, probably
12:49 CIA-34 cdk: shk3 * r473 /trunk/nmrshiftdb/src/java/​org/openscience/nmrshiftdb/ (AdminPanel.java om/DBMolecule.java): the fingerprint rebuilding works again
13:20 CIA-34 cdk: egonw * r8657 /trunk/cdk/src/org/openscienc​e/cdk/tools/MFAnalyser.java: Now uses Java5 syntax and fixed Copyright statement
13:20 CIA-34 cdk: egonw * r8658 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Fixed compile problems after removal of getCnanonicalMass().
13:40 CIA-34 cdk: shk3 * r8659 /trunk/cdk/src/org/openscience/cdk/fi​ngerprint/ExtendedFingerprinter.java: the sssrfinder as used if no ringset is given does not work in certain cases, must be all rings finder
13:41 CIA-34 cdk: shk3 * r8660 /trunk/cdk/src/org/openscience/cdk/test/fi​ngerprint/ExtendedFingerprinterTest.java: test for: the sssrfinder as used if no ringset is given does not work in certain cases, must be all rings finder
13:42 CIA-34 cdk: egonw * r8661 /trunk/cdk/src/org/openscience/c​dk/tools/MassToFormulaTool.java: Added a stub for the Mass2Formula code which needs porting to the CDK
13:50 jbrefort joined #cdk
13:54 egonw Nout: around?
14:12 CIA-34 cdk: egonw * r8662 /trunk/cdk/src/org/openscience/cdk/test​/atomtype/CDKAtomTypeMatcherTest.java: Fixed method name according to expected naming scheme.
14:33 CIA-34 bioclipse: ospjuth * r3624 /trunk/playground/plugins/net.biocli​pse.biomoby/src/net/bioclipse/action​s/BioclipseMobyRequestHandler.java: Added MobyResponseHandler (not working)
14:33 CIA-34 cdk: egonw * r8663 /trunk/cdk/src/org/openscience/cdk/​test/smiles/smarts/ParserTest.java: Fixed SMARTS to parse (closes #1760968).
14:33 CIA-34 bioclipse: ospjuth * r3625 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/acti​ons/ExecuteMobyServiceAction.java: Added action for invoking BioMoby services
14:34 CIA-34 bioclipse: ospjuth * r3626 /trunk/playground/plugins/net.bioclipse.biomoby/s​rc/net/bioclipse/actions/MobyServiceDialog.java: Added dialog to edit inputs to a MobyService
14:34 CIA-34 bioclipse: ospjuth * r3627 /trunk/playground/plugins/net.bioclipse.biomob​y/src/net/bioclipse/actions/testBiomoby.java: Updates to test
14:34 CIA-34 bioclipse: ospjuth * r3628 /trunk/playground/plugins/net.bioclip​se.biomoby/src/net/bioclipse/biomoby/ (Activator.java BioclipseMobyModel.java): Updated MobyModel to use cached CentralAll instead of Central
14:35 CIA-34 bioclipse: ospjuth * r3629 /trunk/playground/plugins/net.bioclipse.biomoby/​src/net/bioclipse/biomoby/BioMobyConstants.java: Added a constants class
14:35 CIA-34 bioclipse: ospjuth * r3630 /trunk/playground/plugins/net.bioclipse.b​iomoby/src/net/bioclipse/biomoby/wizards/ (. BioMobyResultWizard.java ReviewResultPage.java): Added a result wizard for storing resource in virtual foilder
14:36 CIA-34 bioclipse: ospjuth * r3631 /trunk/playground/plugins/net.bioclipse.​biomoby/src/net/bioclipse/biomoby/views/ (6 files): Updated model for MobyView
14:51 CIA-34 cdk: fichte01 * r474 /trunk/protonprediction/Data/ (109 files in 4 dirs):
14:59 CIA-34 cdk: mario_baseda * r8664 /trunk/cdk-taverna/ (3 files in 2 dirs): Changed to SpringLayout
15:56 dleidert joined #cdk
15:59 CIA-34 cdk: dleidert * r8665 /trunk/cdk/src/org/openscien​ce/cdk/config/data/html.xsl: Small clean-up.
16:39 carsten joined #cdk
17:16 jbrefort joined #cdk
18:13 CIA-34 cdk: fichte01 * r475 /trunk/protonprediction/Data/output2/Models/ (11 files in 2 dirs):
21:02 jbrefort joined #cdk

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