Camelia, the Perl 6 bug

IRC log for #cdk, 2008-05-26

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All times shown according to UTC.

Time Nick Message
00:06 CIA-31 cdk: miguelrojasch * r11161 /cdk/branches/miguelrojasch-ReactionOntology/src/ (50 files in 9 dirs): added new functionality extracting information from the owl file
01:06 mansu_ joined #cdk
05:04 bag joined #cdk
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05:35 CIA-31 jmol: hansonr * r9430 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs):
05:35 CIA-31 jmol: version=11.5.39_dev PDB and debugScript reporting of script/comments
05:35 CIA-31 jmol: # bug fix: better reporting of script commands and comments
05:35 CIA-31 jmol: # new feature: reading COMPND and HEADER records of PDB file
05:39 malick joined #cdk
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06:38 thomas_ku moin
07:01 egonw joined #cdk
07:01 mansu_ hi egon
07:01 mansu_ hi egonw
07:01 egonw hi mansu_
07:01 egonw got your mail
07:01 egonw will reply later
07:02 egonw sounds like an interesting project
07:02 mansu_ egonw, thanks ... sorry for a very long mail
07:02 mansu_ egonw, thanks
07:02 egonw in addition to the unit tests, we've had more exhaustive quality testing...
07:02 egonw see http://cdk.svn.sourceforge.n​et/viewvc/cdk/cdk-qa/trunk/
07:03 mansu_ egonw, cool like what?
07:03 egonw a few are looking at QSAR descriptors...
07:03 egonw to see how well they calculate a certain molecular property
07:04 egonw by comparing predicted versus true value of the property
07:04 edrin joined #cdk
07:04 egonw the thing you propose is somewhere in between, I guess...
07:04 egonw hi edrin
07:05 mansu_ egonw, do you think it will be useful in general?
07:05 mansu_ egonw, i guess i will wait for your reply
07:05 egonw mansu_: yes, I think it is
07:05 mansu_ egonw, cool
07:06 mansu_ egonw, if you think it will take a lot of time, we can arrange some time to talk
07:06 mansu_ egonw, I have been waiting for you here
07:06 egonw it is actually one of the main sources of bug reports that people use algorithms on input with certain characteristics it was not aimed to work with
07:08 mansu_ egonw, ok cool
07:27 CIA-31 cdk: thomaskuhn * r11162 /cdk-taverna/trunk/src/test/java/org/opensc​ience/cdk/applications/taverna/tools/chebi/​ExtractDataFromChebiStructureTSVTest.java: Remove wrong path to test file
07:27 rojasm joined #cdk
07:29 rojasm moin all
07:30 egonw hi rojasm
07:30 rojasm moin egonw
07:30 egonw there is something weird with trunk/
07:30 rojasm ups
07:30 rojasm what is? I was checking it but I found all correct
07:30 egonw not sure what goes wrong...
07:30 egonw the HOSECodeGenerator does not get assigned to a module
07:31 egonw used to be in extra...
07:31 CIA-31 cdk: thomaskuhn * r11163 /cdk-taverna/trunk/src/ (6 files in 2 dirs): Remove some UTF8 problems with a german umlaut
07:31 egonw and now reaction does not compile, even though it depends on extra...
07:31 egonw rojasm: $ grep HOSECodeGen build/*.javafiles
07:31 egonw does that give you the class?
07:31 egonw it only lists the test class here
07:33 rojasm One moment I have the original in my laptop and it is still in back
07:39 egonw ok, found the problem
07:39 rojasm what was?
07:39 rojasm so I can know for the next time
07:40 egonw Nina assigned the unit test for the new random reader to 'extra' instead of 'test-extra'...
07:40 egonw this caused the extra.javafiles to overwrite the one for the non-unit tests...
07:40 rojas1 joined #cdk
07:40 egonw rojasm: it had nothing to do with your patching
07:49 CIA-31 cdk: egonw * r11164 /cdk/trunk/src/main/net/sf/cdk/​tools/MakeJavafilesFiles.java: Fixed default package for test classes to be 'test-extra'
07:49 CIA-31 cdk: egonw * r11165 /cdk/trunk/src/test/org/openscience/​cdk/io/random/RandomAccessTest.java: Fixed missing module assignment; cleaned up header.
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08:19 rojasm what is the difference between TestCase and NewCDKTestCase
08:19 rojasm what should we use?
08:19 egonw preferably the latter
08:20 egonw or JUnit4 at least
08:20 rojasm I see in all descriptor that use still the first
08:20 egonw CDKTestCase adds a few convenience assert() methods on top of TestCase
08:20 egonw CDKTestCase is the JUnit3 version
08:20 egonw NewCDKTestCase the JUnit4 version
08:20 rojasm ok
08:21 egonw yeah, lot's of test classes need to still make that transition to JUnit4
08:27 rojasm but  should the NewCDKTestCase not be a extension of TestCase?
08:28 egonw no
08:28 egonw because JUnit4 works differently
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08:55 CIA-31 cdk: egonw * r11166 /cdk/trunk/META-INF/MANIFEST.MF: Added missing jars
09:33 CIA-31 bioclipse: egonw * r5696 /bioclipse2/trunk/plugins/net.bioclipse.cdk/:
09:33 CIA-31 bioclipse: Removed; use https://cdk.svn.sourceforge​.net/svnroot/cdk/cdk/trunk instead. See
09:33 CIA-31 bioclipse: http://wiki.bioclipse.net/index.php?title=Checking​_out_Bioclipse_2#Getting_the_CDK_Extension_Plugins
10:31 CIA-31 bioclipse: ospjuth * r5697 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk10.sdfeditor/ (2 files in 2 dirs):
10:31 CIA-31 bioclipse: Added action, toolbar item, and context menu for open and export actions. Export
10:31 CIA-31 bioclipse: action should allow to extract one or more entries from SDFile to another file,
10:31 CIA-31 bioclipse: but not implemented yet. Page switch also fails to update editor tab. Very
10:31 CIA-31 bioclipse: strange.
10:47 dleidert joined #cdk
10:48 dleidert egonw: around?
10:52 jpansanel moin
11:16 Andreas1 joined #cdk
11:16 Andreas1 Hi
11:35 CIA-31 bioclipse: ospjuth * r5698 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk10.sdfeditor/ (2 files in 2 dirs): Constructed a FileDialog to save files with workspace as root folder.
11:40 rojasm can CML parser reader the identifier inchi from a molecule?
11:41 rojasm yes it can :)
11:54 rojasm not it can not extract
11:54 rojasm mmm
11:56 CIA-31 cdk: miguelrojasch * r11167 /cdk/branches/miguelrojasch-ReactionOntology/src/ (2 files in 2 dirs): new test to test if it can extract the inchi id for certain molecule
12:17 CIA-31 cdk: miguelrojasch * r11168 /cdk/branches/miguelrojasch-ReactionOnto​logy/src/data/cml/moleculeWithINCHI.cml: Corrected the identifier scheme to <identifier convention="iupac:inchi" value="InChI=1/CH4/h1H4"/> and not as <identifier convention="iupac:inchi">InC​hI=1/CH4/h1H4</identifier>. Now it works
12:48 rojasm egonw around?
12:48 rojasm the specification in cml of lonepair electron or single electron for a given atom is not implemented, right?
12:51 CIA-31 cdk: miguelrojasch * r11169 /cdk/branches/miguelrojasch-ReactionOntology/src/m​ain/org/openscience/cdk/libio/cml/Convertor.java: implemented to write the count of single or lonepair electrons given a atom in the cml file.
13:08 egonw rojasm: I am now
13:08 egonw rojasm: I guess not
13:08 egonw let's hack up some unit tests for that
13:41 rojasm hi egonw
13:41 rojasm it was my fail
13:41 rojasm I put not correctly the convention
13:41 rojasm http://cmlexplained.blogspot.c​om/2006/09/inchis-in-cml.html
13:42 rojasm but I was lucky finding your blog :)
13:42 rojasm ups false thema
13:44 egonw but single electron and lps still apply, right?
13:44 rojasm that I implement some thing in convertor.java class
13:45 rojasm which puts in cmlAtom a scalar with DictRefer(cdk:SingleElectron) and its value
13:48 egonw yeah, possibly...
13:49 egonw but please check the CML schema first...
13:49 egonw for radical there is some stuff I think
13:58 CIA-31 bioclipse: ospjuth * r5699 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Catch NPE if setDirty on non-initialized JCPModel.
14:00 CIA-31 bioclipse: ospjuth * r5700 /bioclipse2/trunk/plugins/net.bioclipse.cdk10​.sdfeditor/src/net/bioclipse/cdk10/sdfeditor/ (4 files in 2 dirs): Added extractAction that allows for exporting of selected entries in StructureTable and save as individual molfiles.
14:12 egonw mdleditor is working for me
14:20 CIA-31 bioclipse: ospjuth * r5701 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (2 files in 2 dirs): Added WSFileDialog.
14:42 rojasm I saw that in convertor file there is the concept spinMultiplicities! is that referred to singleElectron?
14:42 egonw rojasm: yes, thikn so
14:42 rojasm ok
14:45 egonw not sure about the lone pair stuff...
14:45 egonw but a DictRef("cdk:lonepairCount") would do
14:45 rojasm well I suppose that it is not necessary to add
14:45 rojasm if all rest agree
15:14 rojasm egonw  I found in CMLCoreModule line 1332 aproximatly the code extracting the singleElectronCount form spinMultiplicity Integer.parseInt((String)s​pinMultiplicity.get(i)-1) meaning that if I put 1 in spinMultiplicity="1" the result is 0
15:14 rojasm why?
15:14 rojasm maybe you know
15:15 egonw check the cml.xsd
15:15 egonw in cdk.io.cml.data or so
15:15 egonw cmlAll.xsd, I think...
15:18 rojasm doesn't say much only it is possible between 1 and 5
15:18 rojasm ok that I assume 1 is for us 0 single electron
15:22 CIA-31 cdk: egonw * r11170 /cdk/trunk/src/main/org/openscience/cdk/tool​s/manipulator/AtomContainerManipulator.java: Fix for NULL hydrogen counts: don't default to zero upon clone, when t was unset. If it was unset, then increase starting from zero
15:24 rojasm I forgot completely what was spin multiplicity
15:24 egonw :)
15:56 CIA-31 bioclipse: ospjuth * r5702 /bioclipse2/trunk/plugins/ (26 files in 6 dirs): Large experimental commit to get editing working in SDFEditor JCPPage. Now uses JCPMultiPageActionContributor.
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16:41 CIA-31 cdk: miguelrojasch * r11171 /cdk/branches/miguelrojasch-ReactionOntology/src/ (3 files in 3 dirs): The LonePair electron are extracted now from CML using dicRef:LonePair and singleElectrons are extracted from spinMultiplicity. Added Tests
16:41 CIA-31 cdk: miguelrojasch * r11172 /cdk/branches/miguelrojasch-ReactionOntology/src​/test/org/openscience/cdk/io/cml/CML2Test.java: And the test!
16:50 CIA-31 cdk: miguelrojasch * r11173 /cdk/branches/miguelrojasch-Reacti​onOntology/src/test/org/openscienc​e/cdk/io/cml/CML2WriterTest.java: added tests testing if the writerCML writer correctly the SingleElectron and LonePair information.
17:29 CIA-31 cdk: miguelrojasch * r11174 /cdk/branches/miguelrojasch-ReactionOntology/src/ (38 files in 5 dirs): adapted the reactions test to the ReactionProcessTest which extracts from the owl ontology file the parameter to be applied as example of reaction.
17:37 CIA-31 cdk: miguelrojasch * r11175 /cdk/branches/miguelrojasch-ReactionOntology/ (5 files in 5 dirs): Synchronized with trunk the branches.miguelrojasch-ReactionOntology, Rev=11158:11174
17:59 Andreas1 left #cdk
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19:44 CIA-31 jmol: nicove * r9431 /trunk/Jmol-FAH/projects/p1733.xyz.gz: Folding@Home
22:51 CIA-31 cdk: miguelrojasch * r11176 /cdk/branches/miguelrojasch-ReactionOntology/src/ (47 files in 9 dirs): update to the new ReactionProcess extracting the infomration from the owl file

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