Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-19

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All times shown according to UTC.

Time Nick Message
04:45 thomas_ku joined #cdk
05:37 thomas_ku joined #cdk
06:14 rojasm joined #cdk
06:25 carsten joined #cdk
06:52 Nout joined #cdk
07:22 rojasm left #cdk
07:36 egonw joined #cdk
07:36 egonw moin
07:41 thomas_ku hi egonw
07:41 thomas_ku egonw: did you saw my emails?
07:42 egonw no, only just booted my email client
07:45 jonalv joined #cdk
07:48 olas joined #cdk
07:53 thomas_ku egonw: did you got them already? Or didn't they come through?
07:54 egonw mom, going through my email...
07:54 thomas_ku ok no prob, I am just asking because I got some problems with my emails in the past week...
07:54 egonw ok, good to hear you got funding...
07:55 egonw for the rest, no idea yet...
07:55 egonw have not had a reply from Tom yet, after my email that I would like to accept the invitation...
07:55 egonw will call him by phone tomorrow
08:02 thomas_ku ok and than you write my a mail?
08:03 egonw yes
08:15 egonw hi Nout
08:41 jonalv joined #cdk
09:12 rojasm joined #cdk
09:17 CIA-31 bioclipse: jonalv * r3773 /trunk/playground/plugins/ (7 files in 5 dirs):
09:17 CIA-31 bioclipse: The hsqldb server currently starts from the structuredb Activator and shuts down
09:17 CIA-31 bioclipse: from the stop method in the hsqldb Activator class. It probably won't be started
09:17 CIA-31 bioclipse: always when the strucutredb plugin is run but rather the structuredb plugin (and
09:17 CIA-31 bioclipse: any other plugins needing it) should start it when needed.
10:03 CIA-31 bioclipse: jonalv * r3774 /trunk/playground/plugins/​net.bioclipse.structuredb/ (12 files in 8 dirs): Created domain objects. No references among them implemented yet.
10:04 jonalv how do I calculate smiles, smarts and fingerprints from an AtomContainer?
10:42 jbrefort joined #cdk
11:17 CIA-31 bioclipse: biocoder * r3775 /trunk/playground/plugins/net.bi​oclipse.chart/src/net/bioclipse/ (chart/ChartUtils.java plugins/views/ChartView.java): Added time series and code comments
11:18 nout joined #cdk
11:19 nout hey
11:20 * nout is at uni on a stupid mac with a weird irc client
11:21 carsten joined #cdk
11:32 nout egoonw around?
11:33 nout *egonw, this stupid client doesn't event have nick-completion :/
11:36 egonw nout: yes I am
11:36 egonw olas: you hear that? "stupic mac"
11:37 egonw :)
11:39 olas grrr
11:40 olas nout: use fire or psi
11:41 nout :p
11:41 egonw has christoph been spotted online today?
11:43 nout i'm afraid not
12:22 jonalv Can CDK generate a name for a molecule?
12:23 egonw no
12:23 jonalv okey
12:23 CIA-31 bioclipse: biocoder * r3776 /trunk/playground/plugins/n​et.bioclipse.chart.testing/ (5 files in 2 dirs): The chart testing plugin can now test line plot, scatter plot, histogram and time series using sample data
12:23 egonw jonalv: but you could use code to look up a name in PubChem
12:23 jonalv Is that impossible to do?
12:24 jonalv ah
12:24 egonw no, just very many rules...
12:24 egonw I once started an architecture...
12:24 egonw but it's tricky...
12:25 jonalv So maybe it's something that will exist sometime in the future if one get's into the dreaming state of mind...
12:47 egonw olas: just replied Rajarshi with a suggested IMarkushContainer API
12:47 egonw and IMarkushAtom
12:49 CIA-31 cdk: rajarshi * r8953 /trunk/cdk/src/org/openscience/cdk/d​ict/data/descriptor-algorithms.owl: When back to the version with all desc even though the CDK does nt implement them
12:57 olas cool
12:57 * olas is afk
13:01 CIA-31 bioclipse: jonalv * r3777 /trunk/playground/plugins/​net.bioclipse.structuredb/ (13 files in 7 dirs): created test cases for the domain class structure
13:11 nout hm I think i'll go home.. not doing anythign usefull at uni :/
13:16 CIA-31 bioclipse: egonw * r3778 /trunk/playground/plugins/net.bioclip​se.structuredb/META-INF/MANIFEST.MF: Fixed pointer to the HSQLDB plugin.
13:16 nout left #cdk
13:25 jerome_ joined #cdk
13:26 jpansanel hi
14:04 CIA-31 bioclipse: ospjuth * r3779 /trunk/playground/plugins/net.bioclipse.s​tructuredb/tests/testData/TestData.java: Soves classloading problem in Junit test
14:05 CIA-31 bioclipse: ospjuth * r3780 /trunk/playground/plugins/net.bioclip​se.structuredb/META-INF/MANIFEST.MF: Fixed manifest
14:14 CIA-31 bioclipse: biocoder * r3781 /trunk/playground/plugins/net.biocli​pse.chart/src/net/bioclipse/dialogs/ (. ChartDialog.java): Designing charting dialog
14:15 CIA-31 bioclipse: jonalv * r3782 /trunk/playground/plugins/ (net.bioclipse.database.hsqldb.runner/ net.bioclipse.hsqldb/): Renamed my hsqldb plugin. Next step will be to remove the hsqldb.jar and use the one in net.bioclipse.database.hsqldb instead
14:42 egonw rojasm: oh, let's take this atom type stuff to this channel
14:42 rojasm ok
14:42 Nout joined #cdk
14:43 egonw hi Nout
14:43 rojasm what you mean about learn my code, what class exactaly :(
14:44 egonw how to do that fragmentation reactions...
14:44 egonw the new atom types have lone pairs...
14:44 egonw and counts on pi bonds
14:44 Nout hey
14:44 egonw I think useful for what you did with the fragmentation...
14:45 egonw Nout: what's the deal with tomorrow? have you heard anything about it?
14:45 egonw like where??
14:45 Nout location is on the website
14:45 Nout it's in amsterdam
14:45 Nout at the Wibautstraat
14:45 Nout like.. 0 minutes away from a metrostation :)
14:46 Nout http://www.hollandopen.nl/agendaevent.jsp?nr=6661
14:46 egonw OK
14:47 Nout kinda weird.. according to 9292ov.nl Wibautstraat 150 IS the metrostation :D
14:48 Nout and well.. that's about all I know
14:48 Nout Jo had sent me an e-mail asking me what i'm gonna tell tommorrow.. haven't answered that one yet, will ask for more info when I answer it ;)
14:52 CIA-31 cdk: nielsout * r8954 /trunk/cdk/src/org/openscience/cdk/ (6 files in 3 dirs):
14:52 CIA-31 cdk: Thought I did this submit last night.. guess that failed somehow
14:52 CIA-31 cdk: Simple version of Controller2DModuleAddAtom added (used to add atoms on mouseclick)
14:52 CIA-31 cdk: To be added: if an atom is selected: change that atom instead of adding one
14:54 egonw Nout: at what time do the presentations begin?
14:54 Nout no clue :/
14:54 Nout think during one of our meetings ~17:30 was mentioned.. but perhaps it was 18:00
14:55 Nout aw, one of the files was out of date according to the svn, that's why the previous submit failed :)
14:56 CIA-31 cdk: nielsout * r8955 /trunk/cdk/src/org/openscience/cdk/ren​derer/progz/JCPActionChangeMode.java: now it works
15:13 carsten joined #cdk
15:19 egonw Nout: what's the state of your work?
15:20 egonw that is... I guess you are preparing your presentation now, not?
15:20 olas left #cdk
15:23 Nout yup, gonna prepare for presentation
15:23 Nout once that's done i'll see what more I can code ;)
15:23 * egonw just booked a train ticket to London :)
15:23 Nout well.. files I just submitted are most recent ones
15:24 egonw we got a SWT version yet?
15:24 Nout nope :/
15:24 egonw ack... will work on that tonight
15:24 Nout and haven't been able to make the 'bond-adding' yet
15:24 egonw ack, asked Christoph for help on that...
15:24 egonw he originally wrote that code...
15:24 egonw that's fine...
15:25 egonw you acchieved the goal of the project: rewrite the rendering engine
15:25 Nout yeh
15:25 egonw the editing functionality is proof of principle that the JChemPaint can be rewritten to make use of it
15:26 Nout also when hovering over a bond it looks somewhat odd atm, either setHighlightedBond isn't the right thing to use or it's wrong in the renderer
15:26 egonw bbl
15:26 egonw ack
15:27 egonw we'll talk later
15:27 Nout ah well.. just run the testeditor so you can see it yourself
15:27 Nout ack, i'll be here all night
15:48 CIA-31 bioclipse: jonalv * r3783 /trunk/playground/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/Structure.java: Made a fingerprint
15:55 CIA-31 bioclipse: jonalv * r3784 /trunk/playground/plugins/ (34 files in 9 dirs): reverted my renaming
16:00 CIA-31 bioclipse: jonalv * r3785 /trunk/playground/plugins/net.bioclipse.s​tructuredb/tests/testData/TestData.java: Spelling error on filename
16:21 Nout egonw how can I fix that nightly build failure?
16:42 egonw oh, is there a new one...
16:42 egonw will talk later...
16:53 CIA-31 jmol: hansonr * r8288 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Jmol.properties):
16:53 CIA-31 jmol: version=11.3.24
16:53 CIA-31 jmol: includes critical bug fix for 11.3.23
16:58 Nout ack
18:31 Nout egonw there is more info now at http://www.hollandopen.nl/agendaevent.jsp?nr=6661
18:32 rojasm egonw around?
18:35 egonw Nout: ack
18:35 egonw rojasm: yes
18:36 rojasm I have written the class MolecularFormula and its test could you make a look?
18:36 rojasm may be I can send you
18:37 rojasm And say what you think
18:40 rojasm I sent you a email, If you have time
18:41 egonw ack
18:49 CIA-31 jmol: nicove * r8289 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
18:58 rojasm left #cdk
21:19 CIA-31 jmol: hansonr * r8290 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties): 11.3.25 bug fix save state "axes = window"
21:54 Nout egonw are you able to bring your laptop tommorrow so I can use that to show the presentation and to show jchempaint?
21:55 egonw yes
21:55 Nout great!
21:55 Nout I suppose you do have the latest version from the svn? :)
21:56 Nout i'll put all files on a usb-stick for back-up btw just to be sure
21:56 egonw will update around noon tomorrow, OK?
21:56 Nout that's cool yeah
21:56 egonw yes, that sounds like a good idea
21:57 Nout i'll have college tommorrow from 9:00 till 11:00 and 13:00 till 15:00 so doubt I will be able to make many changes
22:02 Nout hm at the last meeting we spoke about meeting just before the presentation for last-minute things but we didn't spoke about a time, did we?
22:02 Nout ah well.. i'll just e-mail everyone about it and see if I get a response in time :)
22:06 egonw no, and I can't make it before 17:00...
22:06 egonw actually... I might be somewhat later...
22:06 Nout ok
22:06 Nout well then i'll be sure to have a backup in case you get too late :P
22:06 egonw Nout: add this clause to JCPActionChangeMode
22:07 egonw in the JavaDoc:
22:07 egonw @cdk.module jchempaint
22:07 egonw then Nightly will now in which CDK module it belongs...
22:07 Nout ack, that's enough to get rid of the compile failure? :o
22:07 Nout ah ok
22:07 egonw yeah
22:07 egonw the problem is the TestEditor is in the jchempaint module
22:08 egonw and the module extra does not depend on jchempaint, so does not have TestEditor in the classpath
22:08 Nout ah ok
22:08 egonw the full deps are defined in trunk/src/META-INF/jchempaint.cdkdepends
22:08 egonw or somethng like that
22:09 CIA-31 cdk: nielsout * r8956 /trunk/cdk/src/org/openscience/cdk/ren​derer/progz/JCPActionChangeMode.java: fixes nightly build errors for JCPActionChangeMode
22:12 egonw ok, will check if I can get a SWT version up and running
22:12 Nout ok
22:13 Nout don't forget to get some sleep ;)
22:13 CIA-31 jmol: hansonr * r8291 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Eval.java Jmol.properties): 11.3.25 bug fix compiler not recognizing XXX = as "set XXX" where XXX happens to be a command name (measure, axes, others?)
22:14 CIA-31 jmol: hansonr * r8292 /trunk/Jmol/src/org/ (2 files in 2 dirs): 11.3.25 # bug fix for WebPageMaker creating uncompressed PNG
22:23 edrin joined #cdk
22:24 Nout hey edrin
22:32 edrin hi nout
22:33 edrin Nout: do I know you?
22:33 Nout not in real life I guess
22:33 Nout I just like to say hi to people who join every now and then ;)
22:34 edrin ah
22:34 edrin where are you from?
22:34 Nout from holland
22:34 Nout studying AI in Amsterdam and working on JChemPaint for the 'dutch summer of code'
22:35 edrin ah
22:35 edrin artificial intelligence?
22:36 Nout yeah
22:36 Nout basicly just computer science but somewhat broader
22:36 Nout at least for the bachelor i'm doing that is
22:56 egonw arghh....
22:56 egonw so damn close
22:56 Nout aw what's goign wrong?
22:56 egonw then I run into trouble because the CDK in bioclipse SVN is too old :(
22:56 Nout argh idd
22:57 egonw and cannot up bioclipse svn
22:57 egonw because that will break about everything else
22:57 egonw ok, hope is not up yet
23:01 egonw ok, now I give up
23:01 Nout aw
23:13 egonw OK, forget the SWT application
23:14 egonw cannot even build a simple SWT app
23:17 Nout ack
23:17 Nout i've never tried to build a SWT app :/
23:47 egonw Nout: just realized that it not really matters what the view shows...
23:48 Nout huh?
23:51 egonw what happens on line 112 of Java2DRenderer?
23:51 egonw get a Null pointer on that line:
23:52 Nout well it does the transform on the graphics object there
23:52 egonw Error: nulljava.lang.NullPointerException
23:52 egonw at java.awt.geom.AffineTransform.conc​atenate(AffineTransform.java:2213)
23:52 egonw at sun.java2d.SunGraphics2D.trans​form(SunGraphics2D.java:1483)
23:52 egonw at org.openscience.cdk.renderer.progz.Java2DRen​derer.paintMolecule(Java2DRenderer.java:112)
23:52 egonw at net.bioclipse.plugins.views.Java2DRendererV​iew.updateView(Java2DRendererView.java:156)
23:52 egonw at net.bioclipse.plugins.views.Java2DRendererView​.reactOnSelection(Java2DRendererView.java:103)
23:52 egonw at net.bioclipse.plugins.views.Java2DRendererView​.selectionChanged(Java2DRendererView.java:94)
23:52 Nout oh
23:52 Nout that's odd
23:52 Nout that paintmolecule should only be called when that transformation already exists
23:52 Nout normal procedure is to call paintMolecule(IAtomContainer atomCon, Graphics2D graphics,
23:52 Nout Rectangle2D bounds) {
23:52 Nout once
23:53 egonw ah... Rectangle2D...
23:53 Nout so it has the bounds and bases the transform matrix on that
23:53 egonw don't have that...
23:53 egonw how do I get that?
23:53 egonw renderer.paintMolecule(
23:53 egonw molecule,
23:53 egonw (Graphics2D)graphics
23:53 egonw );
23:53 egonw that's what I called
23:53 egonw how do I get that?
23:53 egonw the Rectangle2D that is
23:53 Nout well the bounds of the graphical object it's going to draw on
23:53 Nout in swing it's (Rectangle2D)getBounds()
23:54 egonw on what object?
23:54 egonw what do you need it for anyway?
23:54 Nout to calculate where the drawing will take place
23:54 Nout ie.. to convert from chemical coordinates to screen
23:55 Nout usually the bounds will be 0,0,width, height
23:55 egonw that's not just (0,0,width,hieght) or so?
23:55 egonw ok, that crossed...
23:55 egonw when would it not be that?
23:55 Nout if you want to draw two things in other coordinates mayb
23:55 egonw ack...
23:57 Nout i'll add soemthign to catch it in that line 112, although it won't have access to such coordinates at that place so Ig euss it'll just throw some error
23:57 egonw RendererModel has the width and height to which it must draw
23:57 egonw in screen coords
23:58 Nout it does?
23:58 egonw yes
23:58 Nout hm I don't see it in the renderer model
23:59 egonw getBackgroundDimension
23:59 egonw gives you width and height

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