Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-13

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All times shown according to UTC.

Time Nick Message
03:48 CIA-16 jmol: hansonr * r8612 /trunk/Jmol/src/org/jmol/ (10 files in 3 dirs): (log message trimmed)
03:48 CIA-16 jmol: version=11.3.44_dev new boundbox features
03:48 CIA-16 jmol: # new feature: boundbox {atomExpression} [on|off]
03:48 CIA-16 jmol: # sets the bound box around the specified atom expression
03:48 CIA-16 jmol: # default ON/OFF is to NOT change current setting
03:48 CIA-16 jmol: # new feature: boundbox {centerExpression} {centerExpression} [on|off]
03:48 CIA-16 jmol: # sets the bound box to encompass the two center points
06:13 jbrefort joined #cdk
07:23 rojasm joined #cdk
07:39 CIA-16 blueobelisk: cjames53 * r154 /smiles-spec/trunk/ (5 files):
07:39 CIA-16 blueobelisk: More changes, working towards completion of the second major version. Lots
07:39 CIA-16 blueobelisk: of corrections and clarifications. Work on aromaticity definition. Fixed
07:39 CIA-16 blueobelisk: various broken links.
07:52 CIA-16 blueobelisk: cjames53 * r155 /smiles-spec/trunk/open-smiles.html: Updated the table of contents.
07:56 EskilA left #cdk
08:09 egonw joined #cdk
08:09 egonw moin
08:16 LaserJock hi egonw
08:16 egonw hi LaserJock
08:16 LaserJock egonw: you work on Jmol right?
08:17 egonw yes, not so much anymore, but yes
08:17 LaserJock a friend of mine at uni uses it a ton
08:17 LaserJock and he would like to show crystal structures with it
08:17 egonw yeah, no problem
08:17 LaserJock but he'd like to be able to show the ellipsiods
08:18 egonw ah...
08:18 egonw I will ask Bob
08:18 LaserJock so I told him I'd ask you about it
08:18 egonw that we will need is a file format...
08:18 egonw or Bob, really...
08:18 LaserJock he has CIF files
08:18 egonw then he knows what data he has to render them
08:19 egonw OK, excellent
08:19 egonw please ask him to send one which we may freely distribute...
08:19 egonw for testing and development purposes...
08:19 LaserJock ok
08:22 LaserJock has anybody tried running jmol or cdk on icedtea?
08:23 egonw I have been running both using Classpath... but have not tried against icedtea...
08:23 egonw but since icedtea is Sun + Classpath, I assume it will work nicely...
08:23 egonw Jmol + Classpath was slow, though...
08:23 egonw a run with IcedTea would be nice...
08:24 LaserJock yeah, we have icedtea now in Ubuntu
08:24 LaserJock so we can work towards getting stuff packaged up an in the repos
08:24 egonw yes, dleidert has some more time for packaging things too...
08:24 LaserJock great
08:24 egonw I do not have much time, but around for consulting...
08:25 egonw but Jmol is ready to enter main
08:25 egonw so is the CDK
08:29 egonw LaserJock: http://www.mail-archive.com/jmol-develop​ers@lists.sourceforge.net/msg06400.html
08:29 egonw so, Bob did already do some work on ORTEP atoms...
08:30 LaserJock ok
08:31 LaserJock so maybe I just need to poke to see what the status is?
08:31 egonw so, things may go fast :)
08:31 egonw yeah, sure...
08:31 egonw already doing that :)
08:31 LaserJock heh
08:31 egonw btw: https://wiki.ubuntu.com/Lapt​opTestingTeam/HPCompaq6720s
08:34 LaserJock cool
08:34 egonw I requested joining the debichem team
08:35 jonalv joined #cdk
08:50 egonw LaserJock: lidaobing approved me :)
08:54 LaserJock egonw: great
10:34 CIA-16 bioclipse: jonalv * r4190 /branches/bioclipse2/ (playground/ testing/): rename testing -> playground
10:35 jonalv joined #cdk
10:38 masak joined #cdk
10:44 CIA-16 bioclipse: jonalv * r4192 /branches/bioclipse2/chemoinformatics/:
10:45 CIA-16 bioclipse: jonalv * r4193 /branches/bioclipse2/bioinformatics/:
10:46 CIA-16 bioclipse: jonalv * r4194 /branches/bioclipse2/core/:
10:47 CIA-16 bioclipse: jonalv * r4196 /branches/bioclipse2/ (Tools/ tools/):
12:28 egonw joined #cdk
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12:47 jonalv joined #cdk
13:02 masak joined #cdk
13:03 dleidert joined #cdk
13:20 jonalv joined #cdk
13:25 CIA-16 bioclipse: ospjuth * r4197 /branches/bioclipse2/core/features/: Added Features dir
13:26 CIA-16 bioclipse: ospjuth * r4198 /branches/bioclipse2/core/plugins/: Added plugins dir
13:30 CIA-16 bioclipse: ospjuth * r4199 /branches/bioclipse2/core/plu​gins/net.bioclipse.core.ui/: Initial import.
13:31 CIA-16 bioclipse: ospjuth * r4200 /branches/bioclipse2/core/pl​ugins/net.bioclipse.core.ui/ (37 files in 10 dirs): Initial import.
13:34 CIA-16 bioclipse: carl_masak * r4201 /branches/bioclipse2/core/plugin​s/net.bioclipse.core.scripting/:
13:34 CIA-16 bioclipse: [net.bioclipse.core.scripting]
13:34 CIA-16 bioclipse: * initial import
13:35 CIA-16 bioclipse: carl_masak * r4203 /branches/bioclipse2/core/plugins/n​et.bioclipse.core.scripting.tests/: Initial import.
14:18 masak joined #cdk
14:20 masak` joined #cdk
14:25 CIA-16 bioclipse: ospjuth * r4206 /branches/bioclipse2/core/plu​gins/net.bioclipse.logging/: Initial import of new logging plugin.
14:25 CIA-16 bioclipse: ospjuth * r4207 /branches/bioclipse2/core/pl​ugins/net.bioclipse.logging/ (13 files in 7 dirs): Initial import of new logging plugin.
14:32 steinbeck joined #cdk
14:33 steinbeck greetings everybody from the 3rd GCC in Goslar
14:34 * steinbeck has problem to compile CDK due to missing classes in SMARTSParser.
14:34 steinbeck any idea why that could be? known problem?
14:39 egonw not long enough here...
14:47 CIA-16 bioclipse: carl_masak * r4208 /branches/bioclipse2/core/plugins/​net.bioclipse.core.scripting.tests​/src/net/bioclipse/core/scripting/ (ScriptingTestCase.java tests/):
14:47 CIA-16 bioclipse: [net.bioclipse.core.scripting.tests]
14:47 CIA-16 bioclipse: * renamed to net.bioclipse.core.scripting
14:47 CIA-16 bioclipse: * this is because of the benefits re increased
14:47 CIA-16 bioclipse:  access to protected methods and fields
14:47 CIA-16 bioclipse:  in class being tested
14:59 CIA-16 bioclipse: carl_masak * r4209 /trunk/plugins/net.bioclipse.rhino/​src/net/bioclipse/plugins/bc_rhino/ (JarClasspathLoader.java ScriptingTools.java):
14:59 CIA-16 bioclipse: [JarClasspathLoader.java]
14:59 CIA-16 bioclipse: * extracted into convenience method
14:59 CIA-16 bioclipse: [ScriptingTools.java]
14:59 CIA-16 bioclipse: * corrected typos
15:02 CIA-16 bioclipse: ospjuth * r4210 /branches/bioclipse2/core/plugin​s/net.bioclipse.core.ui.tests/: Initial import of test plugin for core UI.
15:02 CIA-16 bioclipse: ospjuth * r4211 /branches/bioclipse2/core/plugi​ns/net.bioclipse.core.ui.tests/ (14 files in 9 dirs): Initial import of test plugin for core UI.
15:03 CIA-16 bioclipse: ospjuth * r4212 /branches/bioclipse2/core/pl​ugins/net.bioclipse.core.ui/ (META-INF/MANIFEST.MF src/net/bioclipse/core/ui/views/): Added package to match JUnit4
15:22 CIA-16 bioclipse: carl_masak * r4213 /branches/bioclipse2/core/plugin​s/net.bioclipse.core.scripting/ (6 files in 4 dirs):
15:22 CIA-16 bioclipse: [net.bioclipse.core.scripting]
15:22 CIA-16 bioclipse: * added js scripting
15:33 CIA-16 cdk: rajarshi * r9426 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Updated to use the latest aromaticity detector and cleaned up the code
15:34 CIA-16 bioclipse: jonalv * r4214 /branches/bioclipse2/core/plugin​s/net.bioclipse.core.business/: Initial import.
15:35 CIA-16 bioclipse: jonalv * r4215 /branches/bioclipse2/core/plugi​ns/net.bioclipse.core.business/ (12 files in 7 dirs): Initial import.
15:38 CIA-16 bioclipse: jonalv * r4216 /branches/bioclipse2/core/plugins/n​et.bioclipse.core.business.tests/: Initial import.
15:40 CIA-16 cdk: egonw * r9427 /branches/egonw/remove-non-cdkatomtype-code/ (11 files in 8 dirs): Synched with trunk up to rev 9426
15:40 CIA-16 bioclipse: jonalv * r4217 /branches/bioclipse2/core/plugins/​net.bioclipse.core.business.tests/ (11 files in 8 dirs): Initial import.
15:47 masak` joined #cdk
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16:13 CIA-16 bioclipse: jonalv * r4218 /branches/bioclipse2/core/plugins/spring/: Initial import.
16:16 CIA-16 bioclipse: jonalv * r4219 /branches/bioclipse2/core/plugins/spring/ (16 files in 8 dirs): Initial import.
16:26 CIA-16 blueobelisk: cjames53 * r156 /smiles-spec/trunk/ (6 files): More fixes and clarifications.
16:34 CIA-16 bioclipse: jonalv * r4221 /branches/bioclipse2/core/plug​ins/net.bioclipse.core.domain/ (11 files in 7 dirs): Initial import.
16:35 CIA-16 bioclipse: jonalv * r4222 /branches/bioclipse2/bioinformatics/features/:
16:36 CIA-16 bioclipse: jonalv * r4223 /branches/bioclipse2/bioinformatics/plugin/:
16:36 CIA-16 bioclipse: jonalv * r4224 /branches/bioclipse2/bioinformatics/ (plugin/ plugins/):
16:47 CIA-16 bioclipse: jonalv * r4225 /branches/bioclipse2/bioinformatic​s/plugins/net.bioclipse.biojava/: Initial import.
16:47 CIA-16 bioclipse: jonalv * r4226 /branches/bioclipse2/bioinformati​cs/plugins/net.bioclipse.biojava/ (7 files in 4 dirs): Initial import.
17:00 CIA-16 bioclipse: jonalv * r4227 /branches/bioclipse2/bioinformatics/plugins/ne​t.bioclipse.bioinformatics.biojava.business/: Initial import.
17:00 CIA-16 bioclipse: jonalv * r4228 /branches/bioclipse2/bioinformatics/plugins/n​et.bioclipse.bioinformatics.biojava.business/ (13 files in 8 dirs): Initial import.
17:01 CIA-16 bioclipse: jonalv * r4229 /branches/bioclipse2/core/plug​ins/net.bioclipse.core.domain/ (3 files in 2 dirs): changed name ISequence -> Sequence
17:04 CIA-16 bioclipse: jonalv * r4230 /branches/bioclipse2/bioinformatics/plugins/net.b​ioclipse.bioinformatics.biojava.business.tests/: Initial import.
17:05 CIA-16 bioclipse: jonalv * r4231 /branches/bioclipse2/bioinformatics/plugins/net.​bioclipse.bioinformatics.biojava.business.tests/ (11 files in 8 dirs): Initial import.
17:12 CIA-16 bioclipse: jonalv * r4232 /branches/bioclipse2/bioinformatics/plugins/ (net.bioclipse.bioinformatics.biojava/ net.bioclipse.biojava/): rename
17:48 jbrefort joined #cdk
18:53 CIA-16 jmol: hansonr * r8613 /trunk/Jmol/src/org/jmol/ (13 files in 4 dirs): (log message trimmed)
18:53 CIA-16 jmol: version=11.3.44_dev boundbox command, getProperty() function
18:53 CIA-16 jmol: # new feature: Jmol math getProperty() function
18:53 CIA-16 jmol: # allows FULL math access to ALL getProperty types
18:53 CIA-16 jmol: #
18:53 CIA-16 jmol: # syntax: getProperty(propertyType,{atomset}, itemSelector, propertyName1, propertyName2)
18:53 CIA-16 jmol: #
19:17 CIA-16 jmol: hansonr * r8614 /trunk/Jmol/src/org/jmol/viewer/Eval.java:
19:24 shk3 joined #cdk
20:00 CIA-16 jmol: hansonr * r8615 /trunk/Jmol/src/org/jmol/sha​pebio/BioShapeRenderer.java:
20:00 CIA-16 jmol: version=11.3.44_dev
20:00 CIA-16 jmol: # bug fix: nuisance "render mesh error" console report
20:07 rojasm joined #cdk
20:18 shk3 hi rojasm
20:37 CIA-16 jmol: hansonr * r8616 /trunk/Jmol/src/org/jmol/ (shape/Text.java viewer/Jmol.properties): version=11.3.44_dev # bug fix: labels cannot be resized
20:59 jbrefort joined #cdk
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22:15 edrin joined #cdk
22:24 rojasm hi stefan
22:24 rojasm sorry too late the answere
22:26 CIA-16 cdk: miguelrojasch * r9428 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (2 files in 2 dirs): Modified calculation of the isotopes pattern.
22:31 rojasm hi shk3: Egon said me that you have found a new Job
22:31 rojasm congratulations
22:31 shk3 rojasm: yes, I felt like I neede to try industry
22:31 shk3 what about your thesis?
22:32 rojasm I am with that!
22:32 rojasm But I need to rewrite the bc_medea
22:32 rojasm there is not Thesis without publications
22:32 shk3 So you did not submit it for November?
22:32 rojasm according Christoph and (I)
22:33 rojasm nop
22:33 rojasm :(
22:33 shk3 Hm
22:33 shk3 How is bc_medea going?
22:33 shk3 I try to work on the spectrum stuff in bc a bit
22:33 rojasm I am trying what Egon proposed
22:33 rojasm with experimental data
22:33 rojasm and compare
22:33 shk3 sounds good
22:33 shk3 do you have data?
22:34 rojasm but now I have to finish some stoff about isotopes pattern
22:34 rojasm Yes I have
22:34 rojasm Too much I think
22:34 rojasm And you where are exactly now
22:34 shk3 There can never be too much
22:34 rojasm In what company?
22:35 shk3 Software company called Osthus
22:35 shk3 in Aachen
22:35 shk3 Almost in the Netherlands :-)
22:35 rojasm oo
22:36 rojasm And dedicated too research or more programmating
22:36 shk3 more programming
22:37 rojasm but you like, don't you?
22:37 shk3 es
22:37 shk3 yes
22:38 shk3 and it's good to be an an industry environment
22:38 shk3 for experience
22:38 rojasm And the contract indefined?
22:38 rojasm unbefristet
22:38 shk3 yes
22:39 shk3 how are you doing?
22:39 shk3 some new exciting research?
22:40 rojasm I am with the same issue. Identification of metabolites
22:40 shk3 and you work in bioclipse?
22:40 rojasm and Egon works as well with me or I work with him
22:41 rojasm I tried to integrate all algorithms into cdk first
22:41 rojasm and after to bioclipse of course
22:41 rojasm All for opensource :)
22:41 shk3 good
22:41 rojasm and you still working with cdk
22:42 shk3 I try to do some things
22:42 rojasm o good
22:42 shk3 I still try to do an nmrshiftdb-bioclipse-release
22:43 rojasm and you are still the responsible of nmrshiftdb
22:43 shk3 yes
22:44 rojasm perfect
22:44 rojasm :)
22:52 shk3 Will you be here for Pascals disputation?
22:54 rojasm I didn't speak with him
22:54 rojasm when is it?
22:58 shk3 Tobias said Nov 30th
22:59 shk3 but don't trust that
23:02 rojasm ok
23:02 rojasm I will sent a email
23:04 shk3 I think I will be there
23:04 shk3 should be possible
23:06 rojasm I will also try
23:08 shk3 I think Tobias will be there
23:41 shk3 ok, see you

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