Camelia, the Perl 6 bug

IRC log for #cdk, 2008-05-27

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
04:16 egonw joined #cdk
05:06 CIA-31 cdk: egonw * r11177 /cdk/trunk/src/ (2 files in 2 dirs): Partial rewrite to make use of IAtomType.Hybridization, but it seems not all atom types have proper hybrid info yet??
05:14 CIA-31 jmol: hansonr * r9432 /trunk/Jmol/src/org/jmol/ (17 files in 5 dirs): (log message trimmed)
05:14 CIA-31 jmol: version=11.5.39_dev
05:14 CIA-31 jmol: # bug fix: better reporting of script commands and comments
05:14 CIA-31 jmol: # new feature: reading COMPND and HEADER records of PDB file
05:14 CIA-31 jmol: # new feature: set messageStyleChime
05:14 CIA-31 jmol: # -- No atoms selected!
05:14 CIA-31 jmol: # -- <n> atoms selected!
05:16 jbrefort joined #cdk
05:37 rojasm joined #cdk
06:19 malick joined #cdk
06:40 rojasm joined #cdk
06:40 CIA-31 jmol: hansonr * r9433 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties:
06:40 CIA-31 jmol: version=11.5.39_dev new show features
06:40 CIA-31 jmol: # new features:
06:40 CIA-31 jmol: # show info
06:40 CIA-31 jmol: # show residue(s)
06:40 CIA-31 jmol: # show chain(s)
06:40 CIA-31 jmol: # show sequence
06:40 rojasm moin
07:22 thomas_ku joined #cdk
07:22 thomas_ku moin
07:25 thomas_ku rojarm: do you know if the current cdk can render reactions?
07:26 rojasm hi thomas
07:26 rojasm yes I am trying
07:26 rojasm but what you mean render?
07:26 rojasm handling!
07:27 thomas_ku no I mean get a picture of a reaction
07:27 CIA-31 jmol: hansonr * r9434 /trunk/Jmol/src/org/jmol/mo​delset/AtomCollection.java: version=11.5.39_dev show residue
07:27 rojasm I don't know exactly but it was possible
07:28 rojasm and as well with eclipse
07:28 rojasm bioclipse
07:28 rojasm ups
07:29 thomas_ku I knew that it was possible but I fear that the new cdk renderer2d did not suppurt it up to now
07:29 rojasm maybe
07:29 thomas_ku I will ask egon
07:29 rojasm better if you ask egon
07:29 rojasm exactly
07:46 jpansanel moin
07:47 rojasm moin
08:00 jonalv joined #cdk
08:08 jpansanel who's going to Goslar this year ?
08:12 egonw joined #cdk
08:13 egonw moin
08:13 jpansanel moin egonw
08:14 egonw hi jpansanel
08:14 egonw what came out of the chemdb renaming thing?
08:14 jpansanel I'm waiting more comments about the name
08:17 jpansanel rnst-Georg did not reply
08:18 egonw maybe ping the discussion some more?
08:18 jpansanel yes
08:18 jpansanel egonw : did you see the mail on CCL about this Drug Databank ?
08:19 egonw yes, already was wondering if you were going to reply
08:19 jpansanel how far is Bioclipse to fit all the requirements ?
08:19 egonw close, I think...
08:19 egonw there is a structuredb that needs testing...
08:19 egonw and an SDF editor
08:20 egonw the latter with one or two bugs, because of AWT/SWT integration complexity
08:20 jpansanel I've to test Mychem in a win32 platform
08:21 jpansanel I'd like to work a lot on Bioclipse. It's a very important project.
08:22 jpansanel but my work takes me a lot of time
08:22 egonw yeah, that's a situation I recognize
08:36 thomas_ku egonw: A question does the current cdk supports the rendering of reaction?
08:37 egonw thomas_ku: yes
08:37 egonw cdk10 version that is...
08:37 egonw trunk not
08:57 egonw joined #cdk
09:01 CIA-31 cdk: miguelrojasch * r11178 /cdk/branches/miguelrojasch-Reaction​Ontology/src/test/org/openscience/cd​k/modulesuites/MreactionTests.java: removed abstract test from the MReaction modulesuites
09:03 CIA-31 cdk: miguelrojasch * r11179 /cdk/branches/miguelrojasch-ReactionOntology/src/ (6 files in 4 dirs): Added proton affinity prediction based on learning models extracted from weka software. Ajusted better the models for IP prediction.
09:16 CIA-31 bioclipse: jonalv * r5703 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: added some whitespace and fixed some indentation
09:35 egonw joined #cdk
09:46 CIA-31 bioclipse: Annzi * r5704 /bioclipse2/trunk/plugins/net.bioclipse.logg​er/src/net/bioclipse/logger/Activator.java: Created a workaround for reading OSGI properties on logger startup. It seems on windows we need to look up some paths via URL.
09:46 CIA-31 bioclipse: jonalv * r5705 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: SDF-editor. Fixed cashed swap between tabs with the same mol selected
10:41 egonw joined #cdk
12:05 CIA-31 bioclipse: jonalv * r5706 /bioclipse2/trunk/plugins/net.bioclipse.​structuredb.tests/META-INF/MANIFEST.MF: updated structuredb tests to use the new cdk solution
12:05 CIA-31 bioclipse: ospjuth * r5707 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.tests/src/ (2 files in 2 dirs): Added new test file (SDF) and test for getChildren().
12:05 CIA-31 bioclipse: ospjuth * r5708 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: Removed obsolete ref to JCP from cdk.ui.
12:21 CIA-31 bioclipse: ospjuth * r5709 /bioclipse2/trunk/plugins/net.bioclipse.logg​er/src/net/bioclipse/logger/Activator.java: Corrected case when OSGI property ends in slash (valid only on Mac it seems).
12:59 CIA-31 bioclipse: ospjuth * r5710 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.tests/src/ (3 files in 2 dirs): Updated test file mal.sdf.
14:05 CIA-31 bioclipse: ospjuth * r5711 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.ui.tests/src/net/bioclipse/cdk/ui/​tests/MoleculeContentProviderTest.java: Updated test to reflect latest testfile mal.sdf.
14:54 malick left #cdk
15:30 CIA-31 bioclipse: ospjuth * r5712 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (5 files in 4 dirs): MoleculesPage now asks for molecules using new WSFileDialog.
15:31 CIA-31 bioclipse: ospjuth * r5713 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/dialogs/WSFileDialog.java: Updated dialog with ability to filter out unwanted IResources.
16:27 CIA-31 bioclipse: jonalv * r5714 /bioclipse2/trunk/plugins/ne​t.bioclipse.structuredb/src/ (3 files in 3 dirs): Swapped fingerprintrepresentation in database from VARCHAR to BINARY as a first step in moving the fingerprint matching to the database layer
16:27 jbrefort joined #cdk
16:47 CIA-31 bioclipse: jonalv * r5715 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Wrote DAO test for fingerprint substructure search query. Moving this to the database should speed things up a bit.
17:49 carsten joined #cdk
17:52 rojasm joined #cdk
18:07 CIA-31 jmol: nicove * r9435 /trunk/Jmol-FAH/projects/p4549.xyz.gz: Folding@Home
18:11 CIA-31 jmol: nicove * r9436 /trunk/Jmol-web/ (4 files in 2 dirs): Folding@Home
19:30 CIA-31 cdk: miguelrojasch * r11180 /cdk/trunk/src/main/org/openscienc​e/cdk/qsar/descriptors/molecular/I​PMolecularLearningDescriptor.java: removed @cdk.bug 1628465. IPDescriptor works again fine. It was set a new model to predict the ionization potential using the software weka.
19:36 CIA-31 cdk: miguelrojasch * r11181 /cdk/trunk/src/main/org/openscience/cdk/qsar/d​escriptors/bond/IPBondLearningDescriptor.java: Closed @cdk.bug 1861626. Now the IBondLearningDescriptor is a extension of AbstractBondDescriptor
20:04 jbrefort joined #cdk
20:25 rojasm joined #cdk
20:51 rojas1 joined #cdk
21:21 CIA-31 cdk: miguelrojasch * r11182 /cdk/branches/miguelrojasch-Reaction​Ontology/src/main/org/openscience/cd​k/dict/data/reaction-processes.owl: added some reactive center and representation scheme in owl reaction file
21:48 CIA-31 cdk: miguelrojasch * r11183 /cdk/trunk/src/test/org/openscience/cdk/formula/ (3 files): correct name of the test to make have the junit test with '_IChemObjectBuilder'
21:56 CIA-31 cdk: miguelrojasch * r11184 /cdk/trunk/src/main/org/openscience/cdk/formula/ (2 files): correct name of the test reference to make happy the junit test with '_IChemObjectBuilder'
22:04 rojas1 cdk under 100 in the ranking
22:05 rojas1 http://sourceforge.net/project/stats/ran​k_history.php?group_id=20024&amp;ugn=cdk
22:37 dleidert joined #cdk
22:52 dleidert left #cdk

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary