Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-13

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All times shown according to UTC.

Time Nick Message
05:35 Nout joined #cdk
06:23 rojasm_ joined #cdk
06:25 carsten joined #cdk
07:00 edrin joined #cdk
07:18 Rhadamanthysp joined #cdk
07:29 jonalv joined #cdk
07:45 egonw joined #cdk
07:47 egonw moin
07:47 rojasm moin egonw
07:48 egonw hi rojasm
08:00 egonw rojasm: can you send me your and Piotr's NMC proposals?
08:00 egonw rojasm: I have not sent mine to you, did I?
08:02 rojasm I don't have the Piotr but my of course I send you. One Moment
08:03 rojasm You sent me one proposal but not (I think) the proposal that will be shown tomorrow
08:03 egonw no, that would be be larger internal proposal...
08:06 rojasm sent
08:06 rojasm Could you send me your proposal too
08:09 thomas_ku joined #cdk
08:09 thomas_ku moin
08:09 egonw rojasm: sent
08:10 egonw thomas_ku: any news? I haven't heard from Tom yet
08:10 rojasm perfect
08:10 egonw rojasm: Ooo is fine
08:10 egonw perfect really...
08:10 egonw that's what I used too :)
08:10 thomas_ku egonw: currently no good one! Up to now I have no funding...
08:10 egonw rojasm: though I saved it as .doc
08:11 rojasm sorry a mistake I meant not in Ooo
08:11 egonw :)
08:11 egonw no worry
08:11 rojasm but in doc
08:11 thomas_ku egonw: But we try to get some... not sure if I will get some...
08:11 CIA-31 jmol: hansonr * r8256 /trunk/Jmol/src/org/jmol/viewer/ (5 files): (log message trimmed)
08:11 CIA-31 jmol: 11.3.21 new feature: fully functional user-defined functions:
08:11 CIA-31 jmol: #
08:11 CIA-31 jmol: # MACROS (no parameters)
08:11 CIA-31 jmol: #
08:11 CIA-31 jmol: # function mymacro
08:11 CIA-31 jmol: # background red
08:12 jpansanel coin
08:12 jpansanel moin
08:13 egonw hi jpansanel
08:19 jpansanel hi egonw
08:56 olas joined #cdk
08:59 CIA-31 jmol: hansonr * r8257 /trunk/Jmol/src/org/jmol/ (shapespecial/Isosurface.java viewer/Jmol.properties):
08:59 CIA-31 jmol: 11.3.21 bug fix: isosurface of MOs not properly displaying color in saved state
08:59 CIA-31 jmol: #
09:07 egonw hi Nout, olas
09:10 Nout egonw I think i'll be around saturday
09:11 egonw I'll be on the train then... so no IRC
09:15 Nout 0kay
09:17 Nout bleh, eclipse is taking ages to start up :(
09:18 Nout wonder why the nightly build failed.. thought I commited all files I changed
09:18 carsten Question: In LaTeX I have a bibliography. But I need to have a chapternumber for it... Any clue? Google doesn't help
09:20 carsten bibtotocnumbered...
09:22 egonw use a appendix
09:23 carsten not allowed
09:23 carsten the bib has to be chapter 10
09:24 carsten \documentclass[a4paper,11pt,smallhe​adings,bibtotocnumbered]{scrartcl}
09:24 carsten That works
09:45 Nout what's the problem with the nightly build failed? I don't understand why it cannot find the symbol because it works fine here and I did commit all those files last night.
09:47 egonw build deps...
09:48 egonw ummm...
09:48 egonw I'll fix that mom...
09:48 Nout 0kay
09:48 egonw the Ant build.xml compiles things i na module way
09:48 egonw and each module has explicit deps on other modules...
09:49 egonw the class you use is in a module that the progz module does not depend on
09:49 Nout ah ok, that makes sense :)
10:34 CIA-31 jmol: hansonr * r8258 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Eval.java):
10:36 neksa joined #cdk
10:51 CIA-31 jmol: hansonr * r8259 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Jmol.properties StateManager.java): 11.3.21 -- fix for state saving of @
10:54 edrin joined #cdk
10:54 CIA-31 jmol: hansonr * r8260 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.21 version
11:10 dleidert joined #cdk
11:11 dleidert egonw: around?
11:17 egonw dleidert: yes
11:17 dleidert hi
11:17 dleidert I finished my first Debian Java package
11:18 dleidert it's easier than I thought ;)
11:18 dleidert so I'm going to package cdk very soon
11:18 dleidert my question:
11:18 egonw oh cool
11:18 egonw using ...
11:18 dleidert will you help, at least if I have questions about the build system and when bug reports arrive?
11:18 egonw what's the name again... that helper
11:18 egonw c-something..?
11:19 dleidert cdbs
11:19 egonw dleidert: absolutely
11:19 egonw right
11:19 dleidert I would put it into the debichem project together with the other scientific applications and libraries, not into the pkg-java package
11:19 dleidert s/package/project
11:20 egonw ok, the cdk/debian is in pkg-java now, right?
11:20 dleidert AFAIK right
11:21 dleidert but we will not be able to use much things from it I guess - aren't there my old Debian packaging files or did you update them?
11:21 egonw I did work on them
11:21 * dleidert is currently looking
11:22 egonw dleidert: would be best of we would do a hack session...
11:22 egonw then we should be able to complete it in a couple of hours...
11:23 dleidert I see ... you did a lot of work - looks good
11:23 egonw I did not have time to complete it...
11:23 egonw and still don't :(
11:23 egonw that is...
11:23 egonw don't have time to keep up with policies etc
11:24 egonw anyway... the build.xml should now be such that one can build from a very clean tar.gz
11:24 egonw that is, a tar.gz without any third party libs
11:24 egonw per your request
11:24 dleidert I see ... seems you reworked it ... perfectly
11:25 egonw likely needs some polishing...
11:25 egonw I simply don't have time to get pbuilder up and running
11:26 dleidert No problem, I have a working system for pbuilder and stuff (unfortunetly kaffe is broken atm, so it's impossible to use it in a pbuilder session)
11:27 egonw why not ecj
11:27 egonw ?
11:28 dleidert your rules file defines kaffe and kaffe afaik automatically pulls in ecj and also uses ecj to compile the package - but kaffe doesn't install in pbuiler atm
11:28 dleidert BTW: Ondrej Certik is working on a nice server-based system to compile packages in a pbuilder environment and test them with piuparts - really a nice idea - I will ask him, how far he got - maybe we can already use it
11:28 egonw thomas_ku: around? didn't you do some Markush structure generation? or was that reactions?
11:30 thomas_ku egonw: I used markush structures for a reaction enumeration
11:31 egonw thomas_ku: OK, please talk to olas
11:31 olas thomas_ku; How well do CDK support markush structures now?
11:32 egonw olas wants to use markush structures for structure enumeration
11:32 olas Is there a JUnit test?
11:32 dleidert egonw: What about a hack session at saturday afternoon/evening - we could use the debichem channel for discussion?
11:32 egonw will be on the train to germany then
11:32 egonw going to Ulm, next week
11:33 olas thomas_ku: can you write an example on the CDK wiki or similar?
11:33 thomas_ku I have not defined a class for markush structures I loaded molecules from sd files which contains different R-Groups and these R-Groups get replaced with different Molecules
11:33 thomas_ku olas:
11:33 olas start from a markush and use one or more fragments to build a molecule
11:34 dleidert egonw: ah ok - I will them probably simply begin with checking your work and we will find another day to check it together
11:34 thomas_ku take a look at the following junit test:
11:34 egonw dleidert: ack
11:34 egonw late afternoon I might have connectivity...
11:34 egonw and sunday morning possibly...
11:34 egonw send me email, when you need input
11:35 egonw or things done
11:35 thomas_ku olas: http://cdk.svn.sourceforge.net/viewvc/cdk/tr​unk/cdk-taverna/src/test/java/org/openscienc​e/cdk/applications/taverna/reactionenumerato​r/ReactionEnumeratorTest.java?view=markup
11:36 olas thomas_ku: could you comment on it? it is not documented at all
11:36 olas no javadoc, no nothing
11:36 thomas_ku Ok sorry
11:36 thomas_ku yes of course
11:36 thomas_ku olas: It is currently not designed for single structures! It is designed for reactions
11:37 thomas_ku so the enumerator gets a reaction
11:37 thomas_ku each reactant contains at least one R-Group
11:37 egonw thomas_ku: is there a data structure in CDK to hold a Markush structure?
11:37 dleidert egonw: k (I'm away during saturday and sunday morning - I will be back at sunday afternoon, so replace saturday with sunday in my earlier question).
11:37 thomas_ku no, not as far as I now
11:37 olas so that needs to be done
11:37 egonw dleidert: ack
11:38 olas how hard would that be for one of you to implement?
11:38 thomas_ku olas: yes
11:38 olas I have no knowledge in this, just want to use the API...
11:38 thomas_ku I depends on what it should do?
11:38 olas hold markush structures for single structures
11:39 olas and allow to add fragments to any R-groups
11:39 egonw that would include the lists of attached fragments...
11:39 olas whatever you say
11:40 jonalv joined #cdk
11:40 olas I want to be able to draw a markush structure in JCP, and from that create many virtual molecules by taking fragments from a fragment library and positioning them on R-groups
11:40 jonalv_ joined #cdk
11:40 olas based on some algorithm
11:40 egonw olas: I need some days to hack this up
11:41 thomas_ku yeh
11:41 olas excellent!
11:41 thomas_ku The question is where is the bindingsite of the fragments
11:41 egonw thomas_ku: right, that's the difficult part
11:41 egonw I looked at this in the past... but need to get things together
11:41 thomas_ku If I have a given reaction it is no prob
11:42 thomas_ku but if you have no reaction defined I fear it is quite hard or I fear it will not work!
11:42 egonw how so?
11:43 thomas_ku If the fragment library contains also R-groups as binding site it would be easy again
11:43 egonw thomas_ku: it must
11:43 egonw otherwise it can't work indeed
11:43 egonw coffee, then meeting... bbl
11:44 egonw olas: I will email shortly...
11:44 olas if I want to download a fragment library from a company, how do they provide their molecules digitally?
11:44 olas in a big SDF file probably
11:44 thomas_ku if both the org. mol and then fragment libs mol contains R groups that I should be quite easy to do
11:44 olas but also probably without an R site...
11:45 olas ok, looking forward to the email!
11:45 * olas is off for a meeting with jonalv
11:56 thomas_ku olas: I send you a mail which contains a description of the reaction enumerator
11:57 egonw thomas_ku: thanx
11:58 thomas_ku no prob
11:58 CIA-31 cdk: egonw * r8914 /trunk/cdk/src/org/openscience/cdk/renderer/progz/ (SomeToolBar.java TestEditor.java): Placed into jchempaint module to fix CDK Nightly build
11:59 egonw Nout: sorry... had many other things to do in between... CDK Nightly is fixed again
11:59 egonw or should be
12:03 CIA-31 cdk: thomaskuhn * r8915 /trunk/cdk-taverna/src/main/java/org/ope​nscience/cdk/applications/taverna/qsar/ (4 files): Same small changes to using correct java 5 generic's
12:04 CIA-31 cdk: thomaskuhn * r8916 /trunk/cdk-taverna/src/main/java/org/openscie​nce/cdk/applications/taverna/qsar/IQSAR.java: Add an interface for the qsar worker
12:05 CIA-31 cdk: thomaskuhn * r8917 /trunk/cdk-taverna/src/main/java/org/openscience/c​dk/applications/taverna/qsar/QSARDescriptor.java: Rewrite of the QSAR worker, it now uses the new registry which contains the available qsar worker
12:06 CIA-31 cdk: thomaskuhn * r8918 /trunk/cdk-taverna/src/main/java/org/o​penscience/cdk/applications/taverna/qs​ar/action/QSARDescriptorAction.java: Rewrite of the UI for the QSAR worker, how the choosing of collection of different qsar worker with the help of the ui is possible
12:08 CIA-31 cdk: thomaskuhn * r8919 /trunk/cdk-taverna/src/main/java/org/op​enscience/cdk/applications/taverna/reac​tionenumerator/ReactionEnumerator.java: Update the Exception handling a bit
12:09 CIA-31 cdk: thomaskuhn * r8920 /trunk/cdk-taverna/src/main/java/org/opens​cience/cdk/applications/taverna/registry/ (. QSARRegistry.java RegistryInitializer.java): Initial commit of the new QSARRegistry and a initializer class.
12:10 CIA-31 cdk: thomaskuhn * r8921 /trunk/cdk-taverna/src/main/java/org/​openscience/cdk/applications/taverna/​scuflworkers/cdk/CDKLocalWorker.java: Same small changes to using correct java 5 generic's
12:11 CIA-31 cdk: thomaskuhn * r8922 /trunk/cdk-taverna/src/test/java/or​g/openscience/cdk/applications/tave​rna/qsar/QSARDescriptorTest.java: Update the unit test of the qsar worker
13:37 Nout egonw ok cool :)
13:43 egonw Nout: what is?
13:43 * egonw is really doing too much at the same time...
13:46 egonw ah, the compile fix... right
13:52 jbrefort joined #cdk
13:59 jonalv joined #cdk
14:07 CIA-31 cdk: egonw * r8923 /trunk/cdk/src/org/openscienc​e/cdk/interfaces/IBond.java: Added the IBond.Order enumaration. Not used yet.
15:15 rojasm joined #cdk
15:16 egonw rojasm: cu tomorrow
15:16 rojasm yes
15:16 rojasm see you tomorrow
16:12 rojasm left #cdk
16:36 olas left #cdk
16:45 carsten joined #cdk
16:51 Nout yeah the compile fix egonw :)
16:51 Nout <- back to beers
19:04 shk3 joined #cdk
20:46 CIA-31 jmol: nicove * r8261 /trunk/Jmol-FAH/projects/p2966.xyz.gz: Folding@Home
20:53 CIA-31 jmol: nicove * r8262 /trunk/Jmol/src/org/jmol/translation/JmolApplet/ (11 files): Update of .po files
20:55 CIA-31 jmol: nicove * r8263 /trunk/Jmol-FAH/projects/p3853.xyz.gz: Folding@Home
21:03 CIA-31 jmol: nicove * r8264 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
21:14 CIA-31 jmol: nicove * r8265 /trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java: Folding@Home
21:17 CIA-31 jmol: nicove * r8266 /trunk/Jmol-web/ (3 files in 2 dirs): Folding@Home

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