Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-31

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All times shown according to UTC.

Time Nick Message
00:27 jpansane1 joined #cdk
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07:32 rojasm joined #cdk
07:32 rojasm Moin
08:30 Annzi joined #cdk
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09:25 CIA-18 cdk: egonw * r9980 /trunk/cdk/ (javadoc.xml pmd-migrating.xml pmd-unused.xml pmd.xml): Added missing lines for the formula module (closes #1882918)
09:26 CIA-18 bioclipse: ospjuth * r4852 /branches/bioclipse2/core/plugins/net.bioclipse.c​ore/src/net/bioclipse/core/domain/IMolecule.java: Added IMolecule to core
09:40 jbrefort joined #cdk
09:48 egonw_ rojasm: can I sync reaction/ with trunk/ ?
09:50 CIA-18 bioclipse: ospjuth * r4853 /branches/bioclipse2/chemoinforma​tics/net.bioclipse.cdk.business/: Initial import of CDK business plugin.
09:50 CIA-18 bioclipse: ospjuth * r4854 /branches/bioclipse2/chemoinforma​tics/net.bioclipse.cdk.business/ (21 files in 9 dirs): Initial import of CDK business plugin.
09:51 CIA-18 bioclipse: ospjuth * r4855 /branches/bioclipse2/chemoinformatic​s/net.bioclipse.cdk.business.test/: Initial import of CDK business test plugin.
09:52 CIA-18 bioclipse: ospjuth * r4856 /branches/bioclipse2/chemoinformati​cs/net.bioclipse.cdk.business.test/ (18 files in 9 dirs): Initial import of CDK business test plugin.
09:55 CIA-18 cdk: egonw * r9981 /trunk/cdk/src/META-INF/tes​t-valencycheck.cdkdepends: Added missing dependency
10:01 CIA-18 bioclipse: carl_masak * r4857 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (5 files in 2 dirs):
10:01 CIA-18 bioclipse: [Database -> DatabaseImplementation]
10:01 CIA-18 bioclipse: * even in different packages, synonymous class names
10:01 CIA-18 bioclipse:  was a bit too cumbersome
10:01 CIA-18 bioclipse: * note to the Java design people: qualified imports would be nice
10:02 de_maas joined #CDK
10:02 egonw_ hi de_maas
10:02 de_maas He Egon,
10:02 carsten joined #cdk
10:02 de_maas de_maas als in Peter Maas
10:03 egonw_ already saw the 'specs' in the domain :)
10:03 egonw_ --> de_maas has joined this channel (n=de_maas@host-2.specs.demon.nl).
10:04 de_maas Ik heb nog nooit IRC geprobeerd maar je mailtje trok mijn aandacht
10:05 de_maas left #CDK
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10:07 CIA-18 cdk: egonw * r9982 /trunk/cdk/src/org/openscience/cdk/t​est/smiles/SmilesGeneratorTest.java: Added unit test for bug #1875946, but it does not give the error... too simple, I guess
10:07 de_maas joined #cdk
10:07 egonw_ that's a shame...
10:07 egonw_ you just mist a commit message by seconds...
10:08 egonw_ [2008-01-31 11:09:54] <CIA-18> cdk: egonw * r9982 /trunk/cdk/src/org/openscience/cdk/t​est/smiles/SmilesGeneratorTest.java: Added unit test for bug #1875946, but it does not give the error... too simple, I guess
10:08 de_maas Still fighting this thing :(
10:09 egonw_ IRC?
10:10 de_maas Yep
10:10 egonw_ ah, ic
10:11 de_maas Are you always online here or is it just for the upcoming event?
10:13 egonw_ I tend to be here all day
10:13 egonw_ but often just monitoring...
10:13 egonw_ hours can go past without any actual chatting...
10:13 de_maas Why am I not surprised
10:14 egonw_ but sometimes when I need to ask someone something, I can easily ping him/her...
10:15 de_maas Soons like a sensible thing, we use it like this for collegues over sess
10:15 de_maas sees
10:17 annzi-olas egonw_: around?
10:17 egonw_ annzi-olas: yes
10:18 annzi-olas How many molecules do you input into MOSS?
10:18 annzi-olas commonly?
10:18 egonw_ as many as possible...
10:18 annzi-olas approx?
10:18 annzi-olas >1000?
10:18 egonw_ Jeroen Kazius did over 4000
10:18 egonw_ IIRC
10:18 de_maas Just put 80.000 in the using knime
10:18 egonw_ :)
10:18 egonw_ this is why this is so useful :)
10:19 annzi-olas In bioclipse, how would you envision the input to moss? A file of SMILES?
10:19 egonw_ de_maas: annzi is integrating MOSS into bioclipse
10:19 de_maas Small guy big numbers
10:19 annzi-olas I envisioned you select multiple molecules and click "MOSS"
10:19 egonw_ annzi-olas: no, don't think so
10:19 annzi-olas :-(
10:19 annzi-olas so, what would you prefer?
10:19 egonw_ the patterns become more meaningful for more molecules
10:19 annzi-olas a folder of mols?
10:19 egonw_ a database
10:20 annzi-olas yes
10:20 egonw_ SDF/SMILES file -> database -> MOSS
10:20 annzi-olas ok, but not multiple files?
10:20 annzi-olas of a folder?
10:20 annzi-olas or a folder?
10:21 egonw_ a folder with SDF files... yeah, why not...
10:21 annzi-olas ok, so basically collect many molecules and generate a list of SMILES
10:21 annzi-olas whatever the origin
10:21 annzi-olas right?
10:21 annzi-olas We have decided to just support SMIELS input into MOSS for the moment
10:21 annzi-olas ok, thanks
10:22 annzi-olas need to think about this a little
10:22 egonw_ yeah, makes sense... SMILES is primary input
10:23 de_maas Are SD-files already supported on BioClipse, last time I looked they were not
10:24 egonw_ no
10:24 egonw_ not in a 80k mols kind of way, at lesat
10:24 egonw_ least
10:24 de_maas :(
10:25 de_maas Will it be when the database part will be introduced?
10:26 egonw_ hopefully...
10:26 egonw_ I'm not fluent enough with Bioclipse2 yet...
10:26 egonw_ but I would say that the SDF would be loaded into a (temporary) database, of which the content can be explored...
10:27 egonw_ de_maas: there is too #bioclipse
10:27 de_maas I noticed from you account.
10:27 egonw_ :)
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10:50 CIA-18 bioclipse: carl_masak * r4858 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (5 files in 3 dirs):
10:50 CIA-18 bioclipse: [Base2Database.java]
10:50 CIA-18 bioclipse: [MockDatabase.java]
10:50 CIA-18 bioclipse: * simplified constructor parameters
10:50 CIA-18 bioclipse: [DatabaseImplementation.java]
10:50 CIA-18 bioclipse: * new method getName()
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12:23 rojasm sorry egonw: you can do it please
12:23 egonw_ rojasm: no worries... hang on
12:24 rojasm I am working still with the reaction staff
12:24 rojasm but I think it will not be a problem
12:24 rojasm I will make a update
12:25 egonw_ in progress: svn merge -r 9958:9982 https://cdk.svn.sf.net/svnroot/cdk/trunk/cdk
12:25 rojasm perfect
12:26 egonw_ ok, but go to go to a meeting first now...
12:26 egonw_ so, won't commit anytime soon, I guess...
12:26 egonw_ please hold off commits in reaction/
12:26 rojasm ok
12:27 egonw_ you can continue working, just don't commit :)
12:27 rojasm :)
12:27 rojasm not problem
12:27 olas joined #cdk
12:27 olas egonw_: around?
12:28 egonw_ no, sorry... got a meeting just around now...
12:28 egonw_ bbl
12:28 olas ttl then
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14:11 CIA-18 bioclipse: ospjuth * r4859 /branches/bioclipse2/chemoinformatics/net.bi​oclipse.cdk.business/src/net/bioclipse/cdk/ (5 files in 2 dirs): Loading of multiple molecules is now possible, also createMoleculeFromSMILES.
14:14 CIA-18 bioclipse: ospjuth * r4861 /branches/bioclipse2/chemoinformatics/n​et.bioclipse.cdk/META-INF/MANIFEST.MF: Added XOM jar to manifest to get cdk to compile in Eclipse.
14:14 CIA-18 bioclipse: ospjuth * r4862 /branches/bioclipse2/chemoinformatics/n​et.bioclipse.cdk.business/src/net/biocl​ipse/cdk/domain/CDKMoleculeList.java: Updated CDKMoleculeList to extend BioObjectList<IMolecule>
14:14 CIA-18 bioclipse: ospjuth * r4863 /branches/bioclipse2/core/plugins/net.bioclipse.c​ore/src/net/bioclipse/core/domain/IMolecule.java: Updated IMolecule with createSMILES()
14:46 CIA-18 bioclipse: ospjuth * r4864 /branches/bioclipse2/core/plugins/n​et.bioclipse.core/src/net/bioclipse​/recording/WrapInProxyAdvice.java: Removed unnecessary @override
15:05 CIA-18 jmol: hansonr * r8940 /branches/v11_4/Jmol/src/org/jmol/ (modelsetbio/AminoMonomer.java viewer/Jmol.properties): 11.4.RC3 # bug fix: PDB files with missing amino acid carbonyl O cause exception
15:06 CIA-18 jmol: hansonr * r8941 /trunk/Jmol/src/org/jmol/ (modelsetbio/AminoMonomer.java viewer/Jmol.properties): version=11.5.4_dev # bug fix: PDB files with missing amino acid carbonyl O cause exception
15:26 egonw_ rojasm: I'm compiling the patched reaction/ now...
15:27 egonw_ if I don't get compile errors, I'll commit the merge witrh turnk/
15:37 egonw_ it's on its way now
15:37 CIA-18 cdk: egonw * r9983 /branches/miguelrojasch/reaction/ (122 files in 23 dirs): Synched with trunk; merged 9958:9982
15:51 egonw_ $ sh compareBranchAndTrunk.sh                                                                           ></ant
15:51 egonw_ Summary:
15:51 egonw_ Fixed:
15:51 egonw_ 20
15:51 egonw_ New fails:
15:51 egonw_ 0
15:51 egonw_ that looks pretty promising :)
15:51 egonw_ rojasm: good work!
15:52 egonw_ oh... never mind...
15:52 egonw_ the reaction module did not run at all...
15:53 egonw_ then the tests can't ail either :)
15:53 egonw_ +f
16:00 CIA-18 bioclipse: ospjuth * r4865 /branches/bioclipse2/chemoinformatics/​net.bioclipse.cdk.business/src/net/bio​clipse/cdk/business/CDKManager.java: Cleanup of javadoc.
16:01 CIA-18 bioclipse: ospjuth * r4866 /branches/bioclipse2/misc/net.bioclipse.data​.sampledata/src/net/bioclipse/data/sampledat​a/wizards/NewSampleDataProjectWizard.java: Fixed so that folders only gets installed when checked.
16:05 CIA-18 bioclipse: ospjuth * r4867 /branches/bioclipse2/bioinformatics/plugins/n​et.bioclipse.biojava.ui/src/net/bioclipse/bio​java/ui/views/SequenceContentProvider.java: Some code cleanup.
16:06 CIA-18 bioclipse: ospjuth * r4868 /branches/bioclipse2/bioinformatics/plugins/net​.bioclipse.biojava.ui.test/src/net/bioclipse/bi​ojava/ui/test/SequenceContentProviderTest.java: Some more documentation in tests.
16:07 CIA-18 bioclipse: ospjuth * r4869 /branches/bioclipse2/chemoinfo​rmatics/net.bioclipse.cdk.ui/ (6 files in 5 dirs): Updated contentprovider and labelprovider to use and parse into IMolecule.
16:08 CIA-18 bioclipse: ospjuth * r4870 /branches/bioclipse2/chemoinforma​tics/net.bioclipse.cdk.ui.tests/: Initial import. Tests for CDK UI. Currently tests MoleculeContentProvider.
16:08 CIA-18 bioclipse: ospjuth * r4871 /branches/bioclipse2/chemoinforma​tics/net.bioclipse.cdk.ui.tests/ (21 files in 9 dirs): Initial import. Tests for CDK UI. Currently tests MoleculeContentProvider.
16:41 de_maas left #cdk
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16:46 CIA-18 bioclipse: carl_masak * r4872 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (5 files in 2 dirs): * CDF files are now shown alongside other files under a RawBioAssay
16:48 CIA-18 bioclipse: Annzi * r4873 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.moss/ (11 files in 4 dirs): Are now able to read molecules from input file and able to set basic parameters
16:49 Annzi left #cdk
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17:51 CIA-18 jmol: nicove * r8942 /trunk/Jmol-FAH/projects/ (p2451.xyz.gz p2587.xyz.gz): Folding@Home
18:11 Annzi left #cdk
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