Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-11

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All times shown according to UTC.

Time Nick Message
07:15 egonw joined #bioclipse
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09:35 CIA-32 bioclipse: ospjuth * r8019 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Fixes to bug #70. Egon, please verify.
09:35 zarah bug #070 | http://tinyurl.com/5u7vag
09:36 edrin hello
09:36 zarah hi edrin
09:51 CIA-32 bioclipse: goglepox * r8020 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jche​mpaint/src/net/bioclipse/cdk/jchempaint/widgets/ (JChemPaintEditorWidget.java SWTRenderer.java): Fixed changes to selections jchempaint-primary@13522
09:55 olass egonw: http://nobelprize.org/nobelfoundation/press/
09:55 zarah olass's link is also http://tinyurl.com/5v4xng
10:03 shk3 hi olass
10:03 olass hi shk3
10:04 shk3 enjoyed your holiday?
10:06 * shk3 is for coffee
10:07 CIA-32 bioclipse: egonw * r8021 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Code was OK, but as you said, there actually is no need to cast to a CDK IMolecule first
10:29 CIA-32 bioclipse: egonw * r8022 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): A few fixes for Ola's recent API change: 'perceive' atom types
10:34 gilleain joined #bioclipse
10:34 gilleain
10:35 * shk3 is back
10:36 egonw gilleain: do selections have identifiers?
10:36 egonw we are right now working on something like:
10:36 egonw setSelection(ID, IChemModel)
10:36 egonw setColor(ID)
10:36 egonw maybe in one call?
10:37 egonw so that at the same time we can have different substructures with different colors?
10:37 egonw they ID would be needed to 'change' a particular selection...
10:38 gilleain wow. that's exactly what I was thinking about making.
10:38 gilleain so : no, not yet :)
10:38 egonw ok
10:39 egonw I did note the commit with LogicalSelection.ALL
10:39 gilleain there are still two types of selection : atomcontainers wrapped in a selection object (LogicalSelection, ShapeSelection), and 'bare' atomcontainers
10:40 gilleain Yeah, LogicalSelection.ALL is not quite as good as I thought it would be :(
10:40 egonw have not looked at the inner code...
10:40 egonw gilleain: btw, tried to upload my slides to slidesshare.com
10:40 gilleain you still have to fill up the selection at the point of creation, rather than lazily with the select method...
10:40 egonw but it messed up the fonts of the PDF...
10:40 gilleain oh yeah? oh no :(
10:41 gilleain so it's unreadable?
10:41 egonw yeah :(
10:42 egonw will need to think of something better
10:42 egonw slideshare is not working for me
10:42 egonw I have a few presentation PDFs it just fails on...
10:42 egonw it's a stupid service...
10:42 egonw bad software, dunno
10:42 egonw way too buggy from my perspective at least
10:42 gilleain yeah, sounds it.
10:43 gilleain when do you need this selection stuff for?, as I should really be doing something else this morning, but could work on it over the weekend.
10:45 egonw we need it by next monday
10:45 egonw but Gpox is here with us right now
10:45 egonw so we're going to have a go at it now
10:45 gilleain ok, cool.
10:45 egonw as he is formally on holiday :)
10:45 gilleain yeah, I thought that he was...
10:46 shk3 is the new renderer rendering isotopes?
10:47 gilleain well : my thoughts are that you could have some map of selections in the rendermodel, keyed by ID -for lasso_selection, rectangle_selection..
10:47 gilleain shk3 : no
10:47 gilleain ...external_selection, and so on.
10:48 shk3 and radicals?
10:48 egonw no
10:48 egonw and no reactions
10:48 egonw nore lone pairs
10:48 egonw and no curly arrows for electron movement either
10:48 gilleain nor atom-atom mappings
10:48 gilleain ohh. I saw that the old jcp code had curly arrow code.
10:49 gilleain that is prime reuse material! :)
10:49 egonw :)
10:50 egonw yes, that's a rather interesting renderer module indeed
10:50 egonw though I have never actually seen it in live action
10:50 egonw ask Christoph... it's his code
10:50 gilleain oh i know
10:50 gilleain I can sortof tell by now who wrote what
10:50 egonw :)
10:51 egonw yeah, that should be trivial
10:51 gilleain gpox has a characteristic "method( args )" style
10:51 egonw but it is not really at this moment
10:51 gilleain christoph uses serializable and fully-qualified imports a lot
10:51 gilleain shk3 method chains everywhere :)
10:52 egonw "fully-qualified imports" -> that's actually a must for CDK SVN :)
10:52 gilleain What, really?
10:52 egonw oh, or do you mean in the source code?
10:52 egonw and not in the 'import' section?
10:53 gilleain like new java.lang.Object()
10:53 egonw ah...
10:53 egonw no that's bad
10:53 egonw don't think there is much such code
10:53 egonw other than from the period
10:53 gilleain oh, it's old code.
10:53 egonw where we had cdk.interface.Molecule
10:53 egonw and cdk.Molecule
10:55 gilleain anyway, selections : each selection has certain properties, like colour, the shape of the selection, whether it auto-updates, and so on.
10:56 gilleain I think that it is up to the client of the renderer to make sure that different selection look different (have different properties).
11:02 egonw yes, think so too
11:04 shk3 what happened to org/openscience/cdk/config/d​ata/valency2_atomtypes.xml?
11:04 egonw check the svn logs
11:05 CIA-32 bioclipse: egonw * r8023 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.debug/src/net/bioclipse/cdkd​ebug/business/CDKDebugManager.java: Changed namespace (fixes #164)
11:06 zarah bug #164 | http://tinyurl.com/5gzz5h
11:09 shk3 how do I check the svn log of a deleted file?
11:09 gilleain grep the logs for the filename
11:10 CIA-32 bioclipse: egonw * r8024 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.business.test/ (2 files in 2 dirs): Removed CDK10 specific code
11:10 gilleain that will give you the revision number at which it was deleted
11:10 egonw and the relevant commit message
11:11 shk3 egonw: "Removed obsolete atom type lists"
11:11 shk3 not too great a commit message
11:11 egonw yeah, you can know :)
11:11 * egonw is away for making lunch
11:12 gilleain "you can know"? Parse error : unknown sentence construction.
11:15 shk3 looks like mm2 and mmff94_atomtypes.xml have valencies.
11:16 shk3 gilleain: do you understand atom typing now?
11:16 gilleain heh. hell no.
11:16 gilleain I understand it better than I did before, though.
11:16 gilleain what's the situation?
11:17 shk3 I need to get valency numbers for elements
11:32 egonw for elements?
11:32 egonw not for atom types?
11:32 egonw which have oxidation states?
11:32 egonw shk3: what are you trying to acchieve?
11:33 egonw maybe neighbor count does the job?
11:34 shk3 the converttoradicalactions does this:
11:34 shk3 nLonePair = (valency - (hcount + bondOrderSum) - charge) / 2;
11:34 shk3 valency came from that file
11:35 egonw try LonePairElectronChecker
11:36 egonw check the sature(IAtom, IAtomContainer) method for example code
12:03 CIA-32 bioclipse: egonw * r8025 /bioclipse2/trunk/plugins/net.bioclip​se.data.sampledata/data/2DStructures/ (emptyFile.cml emptyFile.mdl): Added two empty molecule template files
12:34 CIA-32 bioclipse: egonw * r8026 /bioclipse2/trunk/cdk-externals/trunk/ (14 files in 6 dirs): Synchronized with CDK's jchempaint-primary branch (rev 13534)
12:53 CIA-32 bioclipse: goglepox * r8027 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java: Fixed compact rendering
12:56 CIA-32 bioclipse: goglepox * r8028 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (2 files in 2 dirs): Selection do no longer assume Molecule as first element
13:04 jonalv joined #bioclipse
13:04 jonalv hi
13:04 zarah hi jonalv
13:12 CIA-32 bioclipse: goglepox * r8029 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Added visibleWhen for ring icon
13:15 CIA-32 bioclipse: goglepox * r8030 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculesEditor.java: Smaller margins in SDF editor and compact rendering
13:39 CIA-32 bioclipse: goglepox * r8031 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Moved visibility check to core expression
14:00 gilleain joined #bioclipse
14:52 egonw jonalv: http://chem-bla-ics.blogspot.com/2008/11/f​inding-commit-that-causes-regressions.html
14:52 zarah egonw's link is also http://tinyurl.com/683mhn
14:56 egonw ok, enough for me today
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