Camelia, the Perl 6 bug

IRC log for #cdk, 2007-12-03

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All times shown according to UTC.

Time Nick Message
00:15 rojasm left #cdk
00:57 CIA-16 jmol: hansonr * r8720 /trunk/Jmol/src/org/jmol/ (8 files in 2 dirs):
00:57 CIA-16 jmol: version=11.3.52_dev variables
00:57 CIA-16 jmol: # bug fix: set of many more (but not all) parameters can accept mathematical expressions
00:57 CIA-16 jmol: # bug fix; set strandCount not properly handled
00:57 CIA-16 jmol: # new feature: set strandCountForStrands
00:57 CIA-16 jmol: # new feature: set strandCountForMeshRibbon
00:57 CIA-16 jmol: # note --- set strandCount sets BOTH, but now each is independent
06:23 CIA-16 jmol: hansonr * r8721 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java StateManager.java Viewer.java): version=11.3.52_dev variables # bug fix: set of many more (but not all) parameters can accept mathematical expressions
06:30 CIA-16 cdk: miguelrojasch * r9552 /branches/miguelrojasch/mf/src/org/openscience/c​dk/formula/MolecularFormulaSetManipulator.java: added remove
06:53 jbrefort joined #cdk
07:03 CIA-16 jmol: hansonr * r8722 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.52 VERSION
07:24 rojas1 joined #cdk
08:16 CIA-16 cdk: miguelrojasch * r9553 /branches/miguelrojasch/mf/src/org/openscience/cd​k/test/formula/MolecularFormulaCheckerTest.java: some breaks by the commit
08:17 CIA-16 cdk: miguelrojasch * r9554 /branches/miguelrojasch/mf/src/org/openscience/cd​k/test/formula/MolecularFormulaCheckerTest.java: some breaks by the commit
08:18 CIA-16 cdk: miguelrojasch * r9555 /branches/miguelrojasch/mf/src/org/openscience/cd​k/test/formula/rules/IsotopePatternRuleTest.java: some breaks by the commit
08:18 steinbeck joined #cdk
08:25 thomas_ku joined #cdk
08:27 thomas_ku moin
08:27 thomas_ku hi steinbeck
08:28 thomas_ku steinbeck: where should we meet us on Friday? At your old office?
08:29 steinbeck thomas_ku: not sure yet. We may just go for the cafe we took last time.
08:29 steinbeck When do we meet again?
08:29 steinbeck At what time, I mean?
08:30 thomas_ku at 11 o'clock
08:31 steinbeck I'll mail to you and Achim regarding the place.
08:31 thomas_ku ok that the best solution! thanks
08:57 jonalv joined #cdk
09:00 egonw moin
09:31 CIA-16 jmol: nicove * r8723 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
09:42 masak joined #cdk
09:55 jpansane1 moin
10:32 CIA-16 blueobelisk: pansanel * r218 /structures/trunk/src/amino_acids/ (L-4-nitrophenylalanine.cml index.xml): New structure : L-4-nitrophenylalanine.cml
10:34 CIA-16 blueobelisk: pansanel * r219 /structures/trunk/src/aromatics/ (4 files):
10:34 CIA-16 blueobelisk: New structures:
10:34 CIA-16 blueobelisk:  - 1H-1_2-benzodiazepine.cml
10:34 CIA-16 blueobelisk:  - 1H-1_4-benzodiazepine.cml
10:34 CIA-16 blueobelisk:  - 5-phenyl-1_3-dihydro-2H-1_​4-benzodiazepin-2-one.cml
10:35 CIA-16 blueobelisk: pansanel * r220 /structures/trunk/src/drugs/ (diazepam.cml index.xml):
10:35 CIA-16 blueobelisk: New structure:
10:35 CIA-16 blueobelisk:  - diazepam.cml
10:37 CIA-16 blueobelisk: pansanel * r221 /structures/trunk/src/polycyclic_alkanes/ (index.xml norbornane.cml):
10:37 CIA-16 blueobelisk: New structure:
10:37 CIA-16 blueobelisk:  - norbornane.cml
10:57 CIA-16 bioclipse: biocoder * r4368 /trunk/plugins/net.bioclips​e.chart/src/net/bioclipse/ (6 files in 3 dirs):
10:57 CIA-16 bioclipse: Added functionality for highlighting selected points, fixed a problem with a call that needed to be run on SWT's thread.
10:57 CIA-16 bioclipse: Created ScatterPlotRenderer which is in charge of handling the highlighting of points in scatter plots
11:49 steinbeck thomas_ku: around?
11:50 thomas_ku steinbeck: yes
11:51 steinbeck what would be a good download link for CDK/Taverna?
11:52 thomas_ku I would say you can take www.cdk-taverna.de this links direktly to the cdk-taverna site on the cubic server which contains the installation instruction and the links for the download
11:52 steinbeck ack
12:20 carsten joined #cdk
12:46 egonw thomas_ku: around?
12:50 thomas_ku egonw: yes
12:52 egonw hi thomas_ku
12:52 egonw got a question...
12:53 egonw does cdk-taverna support converting InChI to a 2D diagram?
12:53 egonw and, how would I go about and visualize that?
12:53 egonw is JCP integrated as view?
12:53 thomas_ku no currently not
12:53 egonw neither of the two?
12:54 thomas_ku I havent implemented a Inchi reader writer up to now (I have no idea why I haven't done this ....)
12:54 thomas_ku for the rendering part
12:54 thomas_ku JCP is available but not as viewer in the "normal" sense
12:54 egonw ok, just as input right?
12:54 egonw you told me...
12:54 thomas_ku it is used to draw a mol and to use it as imput for a workflow
12:54 egonw was not sure anymore...
12:55 thomas_ku but you can view your molecule using the pdf creater which creates a pdf with the mols
12:56 thomas_ku I will up the InChi IO to my to do list
13:07 egonw thomas_ku: I might want to do some more CDK-Taverna development too...
13:07 egonw as a side job, nothing big...
13:07 thomas_ku you are welcome everytime....
13:07 egonw can you tell me something on how you current develop and test it?
13:08 egonw (since we are slowly moving towards Taverna in metabolomics world)
13:08 carsten egonw: got my mail about density?
13:08 carsten in bodr
13:08 egonw no, dont' think so
13:09 thomas_ku egonw: I normally write for each new processor junit tests
13:09 thomas_ku or what do you mean?
13:09 egonw you're using Eclipse?
13:09 egonw do you have docs on how to build it?
13:09 thomas_ku ah yes I am using eclipse!
13:09 egonw maybe also on how to set up a update server?
13:10 thomas_ku how to build what? the jar file?
13:10 egonw (a local one, for testing purposes)
13:10 egonw thomas_ku: well... anything...
13:10 egonw if one final jar is the end product...
13:10 thomas_ku for the building I am using maven
13:10 thomas_ku with the normal maven commands
13:11 thomas_ku like mvn test or mvn compile or mvn package depending on what you want to have...
13:12 thomas_ku I have no docs on how to set up an update server but as far as I remember this was also on the Taverna help site! There is also a help on how to build new plugins and a default start plugin (as far as I remember...)
13:13 thomas_ku http://www.mygrid.org.uk/u​sermanual1.6/plugins.html
13:13 egonw OK, excellent! thanx
13:14 thomas_ku no problem
13:14 thomas_ku I you need further help please ask
13:15 egonw will branch
13:15 egonw so that you can monitor what I do
13:15 thomas_ku That is a good idea...
13:16 thomas_ku what are your plans
13:17 CIA-16 cdk: egonw * r9556 /branches/egonw/cdk-taverna-mb/: Made a branch to bridge CDK-Taverna with my metabolomics work.
13:17 egonw advertize CDK-Taverna :)
13:17 thomas_ku that a good point ;-)
13:20 egonw it's cdk-1.0.x based, correct?
13:20 thomas_ku yes
13:20 thomas_ku it uses a relative new version of the cdk-1.0.x branch from the beginning of November
13:29 CIA-16 cdk: egonw * r9557 /branches/egonw/cdk-taverna-mb/.project: Personalized project name
13:44 dleidert joined #cdk
13:44 egonw thomas_ku: how do I 'install the cdk-svn-DATE.jar into my local maven repos' ?
13:46 thomas_ku mom
13:47 CIA-16 cdk: egonw * r9558 /trunk/cdk/src/org/openscienc​e/cdk/io/ReaderFactory.java: Use a typed List.
13:47 egonw thomas_ku: please update the README for that...
13:55 egonw ha, there it is: http://www.rsc.org/chemistryworld/Is​sues/2007/December/SurfingWeb20.asp
13:55 egonw mentions Chemical blogspace
14:04 thomas_ku egonw: I have commited update for the README
14:04 egonw oi
14:05 * egonw is glad thomas_ku added that to the README
14:05 egonw would have never come up with that :)
14:05 thomas_ku I was a hard time at the beginning of using maven.... for me
14:05 thomas_ku +t
14:06 * egonw hates downloading on the fly
14:06 thomas_ku ;-)
14:12 * egonw issued 'mvn test'
14:15 egonw thomas_ku: several compile issues for the test classes
14:16 egonw seems to be missing 'execute'
14:16 egonw /home/egonw/var/Projects/SourceForge/cdk/branches​/egonw/cdk-taverna-mb/src/test/java/org/openscien​ce/cdk/applications/taverna/qsar/model/weka/Gener​ateMultilayerPerceptronModelTest.java:[142,23] cannot find symbol
14:16 egonw symbol  : method execute(java.util.Map)
14:16 egonw location: class org.openscience.cdk.applications.tavern​a.qsar.descriptors.molecular.AtomCount
14:16 egonw JUnit missing or so?
14:16 egonw but Maven2 should take care of that, not?
14:23 thomas_ku egonw: sorry got a call
14:23 egonw no problem
14:24 thomas_ku one moment, you took a clean checkout ?
14:25 thomas_ku how do you start the mvn command? from within eclipse or from the command line?
14:31 masak joined #cdk
14:36 thomas_ku egonw: it looks like it has problems with your cdk version...
14:37 egonw typed: mvn test
14:37 egonw then mvn compile (which worked)... then again mvn test...
14:37 egonw btw, how do I set up the classpath in eclipse??
14:38 egonw is that written in that tutorial on mygrid.org too?
14:38 thomas_ku because I have just checked out your branch and did a mvn test on the command line and there it worked for me at least until an out of mem error was thrown...
14:38 thomas_ku the classpaht for what?
14:38 thomas_ku do you use the maven plugin for eclipse?
14:39 egonw no... me starts looking for the update site
14:39 egonw found
14:40 thomas_ku for the maven plugin?
14:40 egonw yes
14:40 thomas_ku ok so you found it right?
14:41 egonw yes, but complains about subclipse too old :)
14:41 egonw ok, for now...
14:41 egonw will let you know when I don't get this working...
14:41 thomas_ku ok have fun ;-=
14:41 thomas_ku ;-)
14:47 CIA-16 bioclipse: ospjuth * r4370 /branches/bioclipse2/chemoinformatics/net.b​ioclipse.cdk.ui/src/net/bioclipse/cdk/ui/ed​itors/JCPMultiPageEditorContributor.java: Uncommented toll bar as not used yet
14:49 CIA-16 bioclipse: ospjuth * r4371 /branches/bioclipse2/chemoinfo​rmatics/net.bioclipse.cdk.ui/ (8 files in 4 dirs): Hooked in CDK in the Navigator. Now you can expand SDF molecules and see multiple molecules.
14:51 egonw thomas_ku: crap... can't download subclipse 1.3.5 (or better)
14:52 thomas_ku why.... ?
14:55 egonw because there is no update site...
14:55 egonw I'm (so far) stuck with 1.2.x
14:56 thomas_ku ok i am using subcipse version 1.2.0
14:57 thomas_ku with maven intergration plugin v 0.0.10
15:05 CIA-16 bioclipse: ospjuth * r4372 /branches/bioclipse2/chemoinformatics/net.​bioclipse.cdk.ui/src/net/bioclipse/cdk/ui/ (3 files in 2 dirs): Made JCP remove JCP Tab (not implemented yet) and fixed name bug in MoleculeContent
15:15 egonw thomas_ku: giving up
15:15 egonw there does not seem to be a place to install subclipse 1.3.x
15:15 egonw while the maven2 plugin requires that version :(
15:16 thomas_ku can you please give me the link for the maven2 plugin site?
15:16 egonw http://m2eclipse.codehaus.org/index.html
15:16 egonw see Installation header
15:30 egonw thomas_ku:
15:30 egonw [2007-12-03 16:31:21] <markphip> it requires SVN 1.5, so you have to go here to get it:  http://merge-tracking.open.collab.net/
15:30 thomas_ku I have really no idea why it doesn't work for you I have installed the maven2 plugin on different machines
15:31 egonw no idea either...
15:32 egonw anyway... seem able to install the maven2 plugin now
15:32 thomas_ku ok thats good
15:36 egonw thomas_ku: ok, no errors anymore in Eclipse
15:36 egonw btw, warning about that maven/svn version
15:36 egonw svn 1.5 will break compatibility with 1.4
15:36 egonw so no command line utils can be used after subclipse 1.3.x touched it
15:37 egonw anyway
15:37 egonw back to those compile errors...
15:37 egonw it's now downloading more plugins
15:37 egonw seems the maven2/eclipse plugin did something?
15:38 egonw tests are running now
15:38 egonw exceptions and a JCP window
15:41 egonw thomas_ku: where are the results stored?
15:41 thomas_ku in the target folder...
15:47 egonw so, how do I create a plugin site?
15:48 egonw ... retorical
15:51 thomas_ku you have to create two xml files which are quite easy these the first one descriptes the what plugins are available from this site (this is the pluginlist.xml file)
15:51 thomas_ku I will email you an example of these two files
15:52 thomas_ku beside the two files you need a maven repository
15:52 thomas_ku with contains the jars needed for your plugin
15:54 thomas_ku sent it to your gmail account
15:56 egonw ok, thanx
15:56 thomas_ku no prob
16:11 CIA-16 bioclipse: egonw * r4373 /trunk/plugins/net.bioclips​e.data.drugbank/plugin.xml: Fixed menu key; Fixed action class name
16:17 CIA-16 bioclipse: egonw * r4374 /trunk/playground/plugins/ne​t.bioclipse.nmrshiftdb/bin/: Removed autogenerated dir.
16:20 CIA-16 bioclipse: egonw * r4375 /trunk/playground/features/net.bioc​lipse.spectrum-feature/feature.xml: Added the tutorial
16:25 CIA-16 bioclipse: egonw * r4377 /trunk/ (2 files in 2 dirs): Moved to include in the update site.
16:26 olas joined #cdk
16:26 CIA-16 bioclipse: egonw * r4378 /trunk/ (2 files in 2 dirs): Also for the update website.
16:27 CIA-16 bioclipse: egonw * r4379 /trunk/ (2 files in 2 dirs): Also for the update website.
16:46 CIA-16 bioclipse: ospjuth * r4380 /branches/bioclipse2/chemoinfo​rmatics/net.bioclipse.cdk.ui/ (4 files in 3 dirs): Added a PopupManu that contributes CreateSmileAction from cdk.ui for Molecules. Only works for expanded files of type Molecule.
16:47 egonw thomas_ku: still here?
17:04 jonalv joined #cdk
17:12 CIA-16 cdk: egonw * r9560 /branches/egonw/cdk-taverna-mb/src/ (5 files in 3 dirs): Added plugin for parsing InChIs
18:30 carsten joined #cdk
20:16 egonw_ joined #cdk
20:37 jbrefort joined #cdk
20:58 CIA-16 cdk: egonw * r9561 /branches/egonw/lpchecker/.project: Customized project name, to fix project name conflict
21:41 rojasm joined #cdk
21:41 CIA-16 cdk: egonw * r9562 /branches/egonw/lpchecker/src/org/openscience/cdk/ (26 files in 8 dirs): Reworked the LPChecker to make use of CDK atom types: note that atom type perception is assumed to be performed on beforehand
21:41 egonw_ hi rojasm
21:41 egonw_ perfect timing !
21:41 rojasm hi egonw
21:41 egonw_ I had already pressed commit, and was just about the send you email...
21:42 egonw_ really, perfect timing... on the second
21:42 egonw_ literally :)
21:42 rojasm ok thanks
21:42 rojasm but not finish
21:42 rojasm But I think it should be more flexible
21:43 rojasm I have good results with the elemental formula from a tree
21:43 egonw_ rojasm: please check the LonePairElectronChecker in my branches/egonw/lpchecker branch
21:43 rojasm ok
21:43 rojasm I do it now
21:43 egonw_ you'll see that the code is *much* simpler...
21:44 egonw_ I haven't run a full test-all yet, but the reactions module is working properly...
21:44 egonw_ note that I did have to add atom type perception calls to the unit tests
21:47 rojasm updating
21:49 rojasm so in lpchecker is the implementation of reaction and lonepair?
21:50 egonw_ the LonePairElectronCHecker is doing the same thing as before
21:50 rojasm Now I realesed what you said in the beginning
21:51 egonw_ what's that?
21:53 rojasm Not important that I thought you said perfect tining about some thing but was other. My mistake. dont worry I am still tired from swimm I am not wake still :)
21:53 egonw_ :)
21:53 egonw_ no worries...
21:53 egonw_ I went through your patches...
21:53 egonw_ but was not able to review the new code in the branch
21:53 egonw_ will do that later this week...
21:54 rojasm not problem thanks
21:56 egonw_ ok, got to go now
21:56 egonw_ please let me know what you think of the code...
21:56 egonw_ I'm sure tests outside reaction still fail...
21:56 egonw_ as no atmo type perception is done for radicals...
21:56 egonw_ will email later
21:56 egonw_ bye
22:39 rojasm left #cdk
23:26 CIA-16 cdk: rajarshi * r9563 /trunk/cdk/src/org/openscience/cdk/qs​ar/descriptors/molecular/ALOGP.java: Fixed copyright
23:27 CIA-16 cdk: rajarshi * r9564 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Commited update for the EState atom typer and also a set of JUnit tests
23:32 CIA-16 cdk: rajarshi * r9565 /trunk/cdk/src/org/openscience/cdk/test/​atomtype/EStateAtomTypeMatcherTest.java: Cleaned up code so that test failure will show the actual failure location

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