Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-26

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All times shown according to UTC.

Time Nick Message
03:04 cpyang joined #cdk
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07:12 steinbeck joined #cdk
07:12 steinbeck moin
07:13 egonw hi steinbeck
07:13 egonw steinbeck: more nice CDK/Bioclipse news...
07:13 egonw the QSAR wizard is doing quite well now...
07:14 egonw you can select multiple molecules in the BioResource browser, and then calculate QSAR descriptors for the selected items :)
07:14 steinbeck woa - cool
07:14 egonw will set up a tutorial for CompLife
07:49 CIA-31 bioclipse: ospjuth * r3836 /trunk/playground/plugins/net.bioclipse.taverna/: Initial import.
07:50 olas joined #cdk
07:51 CIA-31 bioclipse: ospjuth * r3837 /trunk/playground/plugins/net.bioclipse.taverna/ (180 files in 87 dirs): Initial import to be able to run Taverna WF from within Bioclipse. Does not work yet.
07:51 cpyang joined #cdk
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08:16 CIA-31 cdk: egonw * r8963 /trunk/cdk/src/org/openscience/c​dk/tools/CDKHydrogenAdder.java: Added example code in the JavaDoc.
08:25 CIA-31 cdk: egonw * r8964 /trunk/cdk/src/org/openscience/c​dk/tools/CDKHydrogenAdder.java: Fixed JavaDoc: the constructor is private; getInstance() should be used.
08:29 CIA-31 cdk: egonw * r8965 /trunk/cdk/src/org/openscience/cdk/tools/m​anipulator/AtomContainerManipulator.java: Added a convenience method to convert implicit to explicit hydrogens.
08:31 CIA-31 cdk: egonw * r8966 /trunk/cdk/src/org/openscience/cdk/tools/m​anipulator/AtomContainerManipulator.java: Typed a few Iterators and Lists.
08:38 CIA-31 cdk: egonw * r8967 /trunk/cdk/pluginjar/: Removed obsolete plugins; Bioclipse is the standard now
08:43 CIA-31 cdk: egonw * r8968 /trunk/cdk/ (3 files in 3 dirs): Removed the complete plugin architecture. Bioclipse is favored instead, and the code was unmaintained.
08:54 CIA-31 cdk: egonw * r8969 /trunk/cdk/src/org/openscience/cdk/test/tools/​manipulator/AtomContainerManipulatorTest.java: Added some test methods for the new convenience method convertImplicitToExplicitHydrogens.
08:55 CIA-31 cdk: egonw * r8970 /trunk/cdk/src/org/openscience/cdk/tools/m​anipulator/AtomContainerManipulator.java: WTF was I thinking ?!?! That will teach me to write JUnit tests...
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09:06 CIA-31 cdk: egonw * r8971 /trunk/cdk/src/org/openscience/c​dk/tools/CDKHydrogenAdder.java: Added missing and crucial atom typing steps.
09:07 thomas_ku joined #cdk
09:07 egonw thomas_ku: I got the SOAP working in Taverna
09:08 thomas_ku oh great
09:08 thomas_ku I am so sorry
09:08 egonw whatfor??
09:08 thomas_ku I forgot it...
09:08 egonw no worries :)
09:09 egonw I forget things all the time :)
09:09 thomas_ku yeah but I hate such things
09:12 olas what things? CDK?
09:12 olas or taverna?
09:12 olas (or both)?
09:13 egonw I think he means 'forgetting something'
09:13 olas aah
09:14 thomas_ku oh yes I hate to forget something but I love taverna and the cdk
09:15 thomas_ku sometimes more sometimes less ;-)
09:15 egonw thomas_ku: olas is going to the Taverna meeting too
09:16 thomas_ku oh great
09:18 egonw OK, only 499 compile problems to go :(
09:20 cpyang joined #cdk
09:29 CIA-31 cdk: egonw * r8972 /trunk/cdk/src/org/openscience/c​dk/smiles/SmilesGenerator.java: Fixed a NPE with UNSET formal charges.
09:39 CIA-31 bioclipse: jonalv * r3838 /trunk/playground/plugins/​net.bioclipse.structuredb/ (6 files in 3 dirs): Persisting is starting to work. Delete works for all objects. All objects get's somewhat persisted but not all fields are persisted yet.
09:59 egonw lunch time
11:07 thomas_ku_ joined #cdk
11:29 egonw OK, that will be one big bad patch
11:29 egonw only took me 2.2 hours to work out that patch...
11:29 egonw not even run the tests yet :)
11:34 olas joined #cdk
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11:35 egonw results look quite OK
11:37 steinbeck joined #cdk
11:38 egonw steinbeck: have not had time for the screenshot yet...
11:38 egonw when do you need it?
11:39 steinbeck until 3 pm, or so
11:39 egonw ack
11:41 thomas_ku_ hi steinbeck
11:41 steinbeck hi thomas_ku_
11:46 egonw OK, here's one super patch coming (in terms of size):
11:46 egonw (takes a while to hit the server ... :)
11:47 egonw steinbeck: no, no Copyright line update...
11:47 CIA-31 cdk: egonw * r8973 /trunk/cdk/src/org/openscience/cdk/ (82 files in 29 dirs): Removed the old, redundant HydrogenAdder
11:48 steinbeck woa - wonder if it is safe to upgrade before my EBI visit :-)
11:48 steinbeck Not that everthings breaks now
11:48 egonw I don't think more things are broken than before that patch...
11:48 egonw but best to use the branch
11:48 egonw I think the get/setFormalCharge() broke more things :)
11:49 egonw not all of those are fixed in trunk/ yet
11:49 steinbeck hehe
12:02 jpansanel moin
12:02 egonw hi jpansanel
12:49 jpansanel quick question
12:49 jpansanel is the IUPAC name for D-Arabinose:
12:49 jpansanel (2R,3S,4S)-2,3,4,5-Tetrahydroxypentanal
12:50 jpansanel or D-Arabinose ?
12:50 egonw no idea
12:51 jpansanel fr.wikipedia has D-Arabinose and en.wikipedia has (2R,3S,4S)-2,3,4,5-Tetrahydroxypentanal
13:01 CIA-31 bioclipse: jonalv * r3839 /trunk/playground/plugins/ne​t.bioclipse.structuredb/src/ (sqlMap.xml sqlMapConfig.xml): Introduced more fields in the resultmaps but have not updated them in the select statements. Need to write reusable paramatermaps for the object types to be used in the insert statements.
13:07 CIA-31 bioclipse: egonw * r3840 /trunk/playground/plugins/net.bioclipse.​seneca/src/net/bioclipse/plugins/jobs/De​terministicStructureElucidationJob.java: Be a bit more verbose in the Bioclipse console.
13:13 CIA-31 bioclipse: biocoder * r3841 /trunk/playground/plugins/net.bioclipse.dat​a.test/data/testData/GridEditordataset.csv: Added GridEditorDataset.csv as test data for MatrixGridEditor
13:15 CIA-31 bioclipse: egonw * r3842 /trunk/playground/plugins/net.biocl​ipse.seneca/src/net/bioclipse/senec​a/judges/WCCNMRShiftDBJudge.java: Fixed extraction of the molecular formula.
13:41 CIA-31 bioclipse: egonw * r3843 /trunk/playground/plugins/net.biocl​ipse.seneca/src/net/bioclipse/senec​a/judges/WCCNMRShiftDBJudge.java: Now really take into account both possibilities.
13:42 steinbeck updated...
13:42 steinbeck testing ...
13:42 steinbeck first check passed :-) ...
13:43 steinbeck this DetGen is so darn bloody slow
13:43 steinbeck did not even return the first 500 in more than 20 seconds.
13:43 steinbeck That really cannot be
13:43 steinbeck but I know it is
13:43 steinbeck I think I can write something faster without all this fuzz
13:43 steinbeck :-)
13:46 steinbeck egonw: is still supposed to come back after 500 with the first batch?
13:46 steinbeck cannot understand the code properly
13:46 egonw it still does batches of 500
13:51 steinbeck ah, it could be the instantiation of the HOSE code generator in the beginning, which is so slow, right?
13:51 egonw maybe
13:52 egonw but don't think so...
13:52 egonw from what I've seen it's memory usage
13:52 egonw too much cloning of objects
13:52 steinbeck hm, the CDK version in Biolcipse should be updated. There are still these old layout bugs
13:52 egonw ha...
13:52 egonw ummm... yes
13:53 egonw are those fixes backported to the 1.0.x branch yet?
13:54 steinbeck dunno
13:54 steinbeck btw, did you see on the fien pages that the SMOG generator is free
13:54 steinbeck http://ccl.net/cca/softwar​e/MS-DOS/SMOG/README.shtml
13:54 steinbeck it is darn old. Dunno if it is usable
13:54 steinbeck and how much faster it is
13:56 egonw TobiasK was writing a technical report on those things
14:00 steinbeck ack
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14:29 thomas_ku_ A question:
14:29 CIA-31 bioclipse: steinbeck * r3844 /trunk/playground/plugins/net.biocl​ipse.seneca.examples/data/example4/ (. a-pinen-case.sjs data.cml): Added deterministic CASE for alpha-pinene with the NMRShiftDB judge
14:30 thomas_ku_ Where should I store calculated QSAR values especially the values of the atompair descriptors
14:31 thomas_ku_ the molecule descriptors I store as property of the IMolecule, the atomic desciptors as property of the atom etc
14:31 egonw good point
14:31 thomas_ku_ but where should I store the atompair values?
14:31 egonw no idea
14:31 egonw please send email to the list
14:31 thomas_ku_ ok
14:38 CIA-31 bioclipse: biocoder * r3845 /trunk/playground/plugins/net.bioclipse.chart/ (4 files in 4 dirs): Made a dialog for constructing charts. Made a model class for handling axis data.
14:38 CIA-31 bioclipse: egonw * r3846 /trunk/playground/plugins/net.bioc​lipse.seneca/src/net/bioclipse/plu​gins/views/BestStructureView.java: Fixed a NPE when the view is not shown
14:39 CIA-31 bioclipse: biocoder * r3847 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Working on integrating charting capabilities withj MatrixGridEditor
14:46 CIA-31 bioclipse: egonw * r3848 /trunk/playground/plugins/net.bioclipse.seneca/ (3 files in 3 dirs): Added a DEPT-based judge (only works with DetGen)
15:10 carsten joined #cdk
15:23 * egonw is going home
17:45 egonw joined #cdk
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19:06 egonw crap... the new CDK atom typer is pin pointing artificial dummy molecules for testing other stuff :)
19:07 egonw like: [C-]C[C+][C+]C
19:10 CIA-31 cdk: egonw * r8974 /trunk/cdk/src/org/openscience/cdk/test/tools/​manipulator/AtomContainerManipulatorTest.java: Somewhat more acceptable molecules :) Two positively charge carbons next to each other?? Of course the atom typer will trip over that :)
19:14 CIA-31 cdk: egonw * r8975 /trunk/cdk/src/org/openscience/cd​k/test/tools/MFAnalyserTest.java: Replaced SMILES parser for hard coded structure, because the SMILES parsing fails because of the unrecognized boron and bridging hydrogen atom types.
19:55 steinbeck joined #cdk
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21:08 CIA-31 jmol: nicove * r8317 /trunk/Jmol-FAH/projects/p3734.xyz.gz: Folding@Home
21:25 CIA-31 jmol: hansonr * r8318 /branches/v11_2/Jmol/src/org/jmol/ (modelset/ModelManager.java viewer/Jmol.properties): 11.2.13 bug fix: within(chain,xxx) not working
21:33 CIA-31 jmol: hansonr * r8319 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs):
21:33 CIA-31 jmol: version=11.3.26_dev
21:33 CIA-31 jmol: # new feature: _1 parameter for "first atom" in second expression of connect:
21:33 CIA-31 jmol: # connect 3.0 (_H and connected(_N) (_O and not within(chain,_1)) hbond
21:33 CIA-31 jmol: # bug fix within(chain,xxx) not working
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