Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-12

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All times shown according to UTC.

Time Nick Message
07:48 edrin joined #bioclipse
07:50 jonalv joined #bioclipse
07:56 olass joined #bioclipse
07:56 olass good morning
07:57 * olass is enjoying a cup oj hot Java
07:58 * jonalv has a cupatea
07:59 olass sounds like we're all set then
07:59 jonalv yea I am sort of having breakfest :)
08:00 olass jonalv: early breakfast?
08:00 olass or second breakfast?
08:00 olass (11ies?)
08:00 jonalv actually normal breakfast
08:00 olass oh
08:00 olass with tatoes?
08:02 jonalv nope
08:03 jonalv have you seen Lord of the Rings lately? ;)
08:03 edrin good morning
08:03 jonalv morning
08:06 olass what's the cmd to send priv msg in irc?
08:07 olass jonalv?
08:07 olass you use slemacs?
08:08 jonalv /msg nick
08:08 olass yup
08:09 jonalv "slemacs"? btw
08:09 olass :-)
08:16 egonw joined #bioclipse
09:03 olass jonalv: time for second breakfast?
09:03 edrin :)
09:03 edrin cu
09:03 jonalv yea I guess :)
09:04 jonalv actually I am waiting for masak
09:04 jonalv He was gonna come over and do his home exam in chinese from my place
09:04 jonalv we are gonna try to set up a writing shop here :)
09:05 shk3 joined #bioclipse
09:06 olass writing shop!?
09:06 olass what are you going to sell?
09:06 jonalv oh that was as a workshop for writing
09:07 * jonalv should probably choose his words better... :)
09:11 egonw might be wise for a writingshop
09:21 olass egonw: I'll now try to color a molecule open in JCP
09:21 olass will ask you if I run into problems :-)
09:21 olass (or need help)
09:21 olass Gpox said he thought it would work
09:22 olass since atoms/bonds now has colors and we can just change that color
09:22 olass anyway, will try
09:27 olass egonw: around?
09:27 olass guess not :-(
09:35 edrin joined #bioclipse
09:57 jonalv joined #bioclipse
10:33 egonw joined #bioclipse
10:43 olass egonw: sent you an email
10:43 olass made good progress
10:44 olass please comment when you have time
10:47 egonw just did
10:47 egonw very brief, very quick
10:49 olass thx
11:04 egonw joined #bioclipse
11:13 * jonalv heads for lunch. We will try to get some table space at Yukikos :)
11:13 jonalv bbl
11:28 olass egonw: around?
11:28 egonw physically... yes
11:29 egonw well, as much as you can speak about physically at IRC..
11:29 egonw point is, mentally is more difficult...
11:29 olass I suggest we move all cdk10 plugins to a dedicated folder named something like "outdated"
11:29 olass you still not feeling well?
11:29 olass or rather deprecated
11:30 olass rdfeditor (my miguel) is not yet refactored
11:30 olass but IMO we should move it
11:30 olass you agree?
11:30 olass can you do it?
11:30 olass subclipse is not good at these things...
11:30 olass will try to use CL asap, also git
11:31 olass next wek that is
11:31 olass egonw?
11:31 egonw ok, sounds good
11:31 olass thanks
11:40 egonw olass: this is the RDF editor in action:
11:40 egonw http://chemistry-to-informatics.blogspot.com/​2008/06/editor-for-rdfiles-in-bioclipse.html
11:40 zarah egonw's link is also http://tinyurl.com/5rhydg
11:43 egonw olass: btw, I got the bus ticket... I'll pay you next week for the remaining rides (400 SEK)
11:48 olass thanks
11:58 Gpox joined #bioclipse
11:59 egonw good morning Gpox!
12:12 olass hi Gpox
12:35 CIA-32 bioclipse: goglepox * r8032 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (3 files in 3 dirs): Implemented external highlights form the outline
12:54 CIA-32 bioclipse: goglepox * r8033 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Fixes selections in JCPEditor and should enable tooltips for atoms (see bug #172)
12:54 zarah bug #172 | http://tinyurl.com/5ejuya
12:55 egonw Gpox++
12:55 egonw Gpox++
13:04 jonalv Gpox++ // jonalv has no idea about what he has done but commits during vacation is definilty worth karma
13:14 shk3 hi all
13:14 zarah hi shk3
13:14 shk3 how is jcp in swt progressing?
13:16 egonw quite well
13:16 egonw there are some minor bugs
13:16 egonw but integration is good
13:16 egonw e.g. with the Outline
13:17 egonw as well as integration into the SD file 'editor' (which is mostly a viewer)
13:17 egonw and access from the JavaScript console is online too
13:17 shk3 good to hear that
13:17 egonw Oultine allows you to select atoms and bond which get highlighted
13:18 shk3 swing also looks ok
13:18 egonw and Ola got atom coloring working, using a 3rd party library
13:18 egonw I will look at it next week...
13:18 shk3 do you have an idea about undo/redo in eclipse?
13:18 egonw and see which action code snippets can go into the IChemModelRelay
13:18 egonw no
13:18 egonw maybe Gpox?
13:18 egonw but he is on holiday
13:19 egonw so don't like to ask him to much :)
13:19 egonw s/to/too/
13:20 shk3 we need a concept for that
13:20 shk3 sooner or later
13:21 egonw yes
13:22 shk3 I have some ideas for the sdf editor/viewer
13:23 shk3 but I still think it should integrate with qsar functions
13:23 egonw sure
13:23 egonw that's an important aim for it
13:23 egonw olass is working in that area
13:23 shk3 but they are separate right now, aren't they?
13:23 shk3 ah, olass works on it
13:24 olass well... not directly
13:24 olass just giving Gpox use cases
13:24 olass it really is him doing the coding
13:24 olass but I might dig into it
13:24 shk3 ah, but somebody works on it
13:24 olass yes
13:24 shk3 can you open an sdf an calculate qsar for it?
13:25 olass not yet
13:25 olass soon
13:25 olass qsar is my table :-)
13:26 olass anyway, about undo/redo
13:26 shk3 my ideas were
13:26 olass what did you want to know?
13:26 shk3 1) calculate similarity to a structure
13:26 shk3 so you open an sdf, choose some other structure from file system or so
13:26 shk3 and get tanimoto similarity as a new column
13:27 shk3 2) Do a substructure search
13:27 shk3 you open an sdf, chose some other structure and filter the sdf by it
13:28 shk3 or you are just told where this is a substructure in an additional column and filter on that
13:28 egonw option 2) -> structuredb manager
13:28 olass I agree with egonw
13:28 olass 1) is a good suggestion
13:28 shk3 a general filter mechanism would be good anyway
13:28 egonw shk3: http://gist.github.com/25713
13:28 olass file as RFE to me
13:28 shk3 never got structure db working
13:29 olass should work now, else sk jonalv
13:29 shk3 that is similar to sdfs in some respects, I think
13:29 olass shk3: http://publib.boulder.ibm.com/infocenter/​rsmhelp/v7r0m0/index.jsp?topic=/org.eclip​se.platform.doc.isv/guide/wrkAdv_undo.htm
13:29 zarah olass's link is also http://tinyurl.com/5auorf
13:29 shk3 will look at it
13:29 egonw shk3: or http://gist.github.com/23900
13:30 shk3 does the structuredb have a wizard to create a db from a collections of structure files?
13:31 * jonalv heard his name being uttered... :)
13:31 egonw a SD file is dragged onto your database
13:32 shk3 just sd file?
13:32 jonalv shk3: for the moment you can only create a db by dropping an sdf file to the database
13:32 jonalv I need use cases...
13:32 jonalv well you can use the console as well
13:32 jonalv But the only gui part is that...
13:32 shk3 I would like to have something where you select any sort of structure files (perhaps also recursivly, so you choose a diretory)
13:32 shk3 and they get combined to something
13:33 shk3 should also be possible for an sdf
13:33 shk3 which then could become a db
13:33 jonalv perhaps you could write up a wiki page with use cases for structuredb? :)
13:33 shk3 don't we have one?
13:33 shk3 we have use cases pages
13:33 jonalv Tha manager contains the needed code for that but there is no such gui parts
13:33 shk3 there should be one for structure db as well
13:34 jonalv I don't know
13:34 * jonalv afk bbl
13:35 shk3 is there documentation on how to use structure db?
13:38 egonw there is github
13:42 shk3 you mean http://gist.github.com/25713?
13:43 egonw and the other one too
13:43 egonw and there is help in the javascript console
13:44 olass grep (egonw && (git || gist)) in irc history ~ null
13:45 egonw or, check: delicious.com/tag/bioclips​e+git+manager:structuredb
13:45 olass sorry: grep (egonw && (git || gist)) in irc history = null
13:46 olass :-)
13:47 shk3 structuredb is still not running for me
13:47 shk3 !MESSAGE Missing required bundle org.springframework.bundle.spring.orm_0.0.0.
13:47 shk3 !MESSAGE Missing required bundle org.springframework.bundle.spring.jdbc_0.0.0.
13:49 shk3 ok, these seem to be gone
13:49 shk3 but
13:49 shk3 !MESSAGE Missing required bundle net.bioclipse.usermanager_2.0.0.
13:49 shk3 I have got usermanager
13:50 shk3 ah, this is missing encryption
13:51 shk3 and encryption is missing org.apache.commons.codec
13:51 shk3 where do I get that from?
13:57 shk3 anybody an idea?
13:57 shk3 olass
13:57 shk3 egonw
13:57 shk3 jonalv
13:57 shk3 ?
13:57 egonw check the META-INF of the usermanager bundle
13:58 shk3 the META-INF of the usermanager bundle?
13:58 shk3 that contains manifest.mv and a spring dir
13:58 egonw indeed
13:58 zarah egonw: You have new messages. Write '@messages' to read them.
13:58 egonw @msg
13:59 zarah egonw: 1 m 21 s ago, masak said :) -- language barriers are fun, and especially common between China and the west, of course -- since Chinese characters are so damn cool. see also http://www.boingboing.net/2008/​10/31/email-error-on-road.html
14:01 shk3 what's this directory supposed to tell me about org.apache.commons.codecs?
14:03 egonw it might give you clues which plugins you are missing
14:03 shk3 I am missing org.apache.commons.codecs
14:04 egonw I don't think I have that in my workspace...
14:04 egonw doesn't that come with eclipse?
14:05 egonw jonalv?
14:05 shk3 not for me, it seems
14:06 egonw my eclipse does:
14:06 egonw eclipse3.4/plugins/org.apache.comm​ons.codec_1.3.0.v20080530-1600.jar
14:06 egonw can't remember having to install this manually...
14:06 egonw btw, I note codecS versus codec
14:09 shk3 codec for me as well
14:09 shk3 i have eclipse 3.4.1
14:10 shk3 has 4 org.apache.commons plugins
14:10 shk3 no codec
14:10 shk3 can you send me yours?
14:12 egonw yes
14:13 * jonalv is back
14:13 egonw sent
14:13 * jonalv has backlogged and is quite honestly not sure
14:13 jonalv I thought it came with Eclipse...
14:13 egonw maybe one of the plugin you and I have installed?
14:13 egonw maybe Mylyn?
14:13 * jonalv is sort of semi online today... :)
14:14 jonalv egonw: could be...
14:14 jonalv I don't really know how to find that out but perhaps we need to include it target platform...
14:14 jonalv Once we get a buildserver we should find out about all these things...
14:14 jonalv probably not the easy way though...
14:18 egonw shk3: did you receive the jar?
14:19 charlgren joined #bioclipse
14:23 shk3 no
14:23 shk3 not by email
14:23 charlgren hi all
14:23 zarah hi charlgren
14:23 egonw hi charlgren
14:23 egonw shk3: mmm...
14:23 egonw I sent it to your ebi account
14:24 egonw 15:13
14:24 egonw 14:13 for you
14:24 egonw but it's a jar ==  zip, maybe spam filter?
14:25 charlgren You know the plugin that you need to press the "add required plugin"-button twice to add? Well, that's org.eclipse.team.core
14:27 shk3 it's not in my spam folder
14:29 egonw do you got another account I could email it to?
14:31 shk3 stefhk3@web.de
14:34 egonw sent
14:35 shk3 arrived
14:40 shk3 another question: net.bc.cdk.business.tests depends on cdk10
14:40 shk3 is that intended?
14:42 egonw mm... I thought I commits those fixes...
14:42 egonw let me check
14:43 egonw Date:   Thu Dec 11 11:09:51 2008 +0000
14:43 egonw Removed CDK10 specific code
14:43 egonw should be commit 8024 in SVN
14:44 shk3 i've got 8033
14:44 shk3 ah, wait
14:45 shk3 looks like the cdk10 problems were gone with my update
14:45 shk3 but others remain
14:45 egonw http://bioclipse.svn.sourceforge.net/viewv​c/bioclipse/bioclipse2/trunk/plugins/net.b​ioclipse.cdk.business.test/META-INF/MANIFE​ST.MF?r1=8024&r2=8023&pathrev=8024
14:45 zarah egonw's link is also http://tinyurl.com/69uyp8
14:45 shk3 I didn't check carefully enough after update, it seems
14:45 egonw ok, good
14:51 shk3 can the structuredb only be used from console?
14:51 shk3 or is there a structuredb browser or so?
14:54 egonw Service View
15:10 egonw shk3: what's a free lone pair?
15:10 egonw do they exist?
15:10 egonw I'd say they are always bound to an electron
15:10 egonw it that common working for LPs?
15:10 shk3 yeah, may be
15:11 shk3 I wanted to discuss that with somebody
15:11 egonw getImplicitLonePairCount() ?
15:11 egonw like implicit hydrogens?
15:11 shk3 sounds good
15:12 egonw btw, the JavaDoc speaks about lone pair electrons...
15:12 egonw whcih is twice the number of lone pairs
15:12 egonw please update that while your renaming the method
15:18 shk3 true
15:51 egonw bye all
15:51 egonw have a nice weekend!
18:07 edrin left #bioclipse
22:51 edrin joined #bioclipse
22:52 edrin hi jonalv
22:57 edrin still up?
23:12 jonalv edrin: yea :)

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