Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-09

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All times shown according to UTC.

Time Nick Message
06:26 olass joined #bioclipse
06:34 Gpox joined #bioclipse
06:36 CIA-40 bioclipse: ospjuth * r11149 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Moved deleteVirtualProject from core to ui.business.Activator.start(). Solves #1192.
07:08 egonw joined #bioclipse
07:10 egonw moin
07:10 zarah oh hai egonw
07:10 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
07:10 egonw @msg
07:10 zarah egonw: 20 h 47 m 46 s ago, sneumann said "Last time my java/Eclipse was sluggish I had an inexistent printer server in /etc/cups/client.conf"
07:48 CIA-40 bioclipse: goglepox * r11150 /bioclipse2/trunk/plugins/net.bioclipse.co​re.tests/src/net/bioclipse/managers/tests/ (3 files): Added tests for bug #1213
07:48 zarah bug #1213 | http://tinyurl.com/lycvu3
07:52 olass egonw: I just filed 1230 and 1231 for your convenience
07:53 egonw ok, thanx
07:53 egonw the more, the marrier
07:53 egonw the more, the merrier
07:53 egonw ah, whateever
07:54 egonw masak and maclean are not around anyway
07:54 olass what for?
07:54 olass oh
07:54 olass for marking the words
07:54 olass let's hoep thwy don't read logs
07:54 olass if they do, they will pick on us
07:54 olass YOU HEAR THAT, MASAK?
07:55 olass ;)
07:55 olass now we'll know for sure if they do read the logs
07:55 * olass suspects not
07:55 olass egonw: is the molecule in bug 1230 really that strange that inchi cannot be calculated?
07:56 olass if so, how common is it that inchi cannot be calculated?
07:56 egonw @pz 1230
07:56 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1230
07:57 CIA-40 bioclipse: ospjuth * r11151 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (model/TestRun.java ui/views/DSView.java): Updated algorithm for consensus voting in TestRun and ConsensusCanvas.
07:58 egonw I'll explore
08:08 olass thanks
08:08 olass egonw: I also stumbled upon this case, bug 1232
08:08 olass these are very important issues
08:08 olass We should put all these molecules in Sample Data to make sure we test everything with them
08:09 egonw no, use them for unit tests
08:09 olass yes, even better
08:09 egonw then we are sure they are tested
08:09 olass if we can unit test context menu options
08:09 olass that is not trivial
08:09 egonw we can test the stuff for the manager
08:10 egonw thje context menu stuff must be non-critical
08:10 jonalv joined #bioclipse
08:10 olass bug 1232 is about the context menu option
08:10 shk3 joined #bioclipse
08:10 egonw olass: ok
08:10 CIA-40 bioclipse: goglepox * r11152 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.standard/src/org/opens​cience/cdk/geometry/GeometryTools.java:
08:10 CIA-40 bioclipse: Changed int to double
08:10 CIA-40 bioclipse: This make it behave much better and switch direction
08:10 CIA-40 bioclipse: when a bond is straight down or up.
08:10 CIA-40 bioclipse: Not patched in cdk
08:11 egonw yes, context menu content is really hard to test
08:11 egonw there is a bug report for testing which content-types are recognized for files
08:12 olass for now, we just have to hunt them down on a case by case basis
08:12 olass I think we are doing well
08:12 olass but there are some corner cases left
08:12 olass 1230 - 1232 are such corner cases
08:19 CIA-40 bioclipse: egonw * r11153 /bioclipse2/trunk/plugins/net.biocli​pse.reaction/src/net/bioclipse/react​ion/view/ReactionOutLinePage.java: Removed @Override which caused a compile error here
08:21 jonalv shk3: ping
08:22 shk3 jonalv: pong
08:22 jonalv shk3: I am looking at generate3dCoordinates...
08:22 shk3 ah
08:22 jonalv shk3: Do you know what you ahve done wrong?
08:22 shk3 wrong?
08:22 shk3 no :-(
08:23 jonalv shk3: as far as I can see you are not updating the monitor at all...
08:23 shk3 ah well, realized that
08:23 shk3 will look at it
08:23 jonalv shk3: okey good
08:28 shk3 ahm, ola found that as well
08:30 jonalv (shk3 I saw olass)
08:37 olass egonw: ping
08:37 egonw pong
08:37 olass what happens if you open a mol with no coords in JCP, edit it, and save?
08:37 olass does it save in 2D?
08:38 olass and
08:38 olass what happens if you open a mol with 3D coords only in JCP, edit it, and press save?
08:38 egonw it should
08:38 egonw that depends on the format
08:38 olass if mol
08:39 olass now it looks like it saves, but loading it back does not contain the changes
08:39 egonw it should cause a saveAs
08:39 egonw for .mol
08:39 olass ok
08:39 olass I'll file a bug
08:43 egonw WARN - inchi.generate is not void or returning a BioclipseJob. But implementation takes a progress monitor.  Can not run as Job. Running in same thread.
08:43 egonw WARN - The MonitorContainer could not find a monitor connected to current thread so returning a NullProgressMonitor
08:43 egonw jonalv: we need to talk
08:45 jonalv egonw: funny I am just looking at the same warnings here
08:45 egonw :)
08:45 * olass is happy to have egonw back
08:46 jonalv egonw: talk now?
08:46 egonw yes
08:47 jonalv egonw: where?
08:48 CIA-40 bioclipse: ospjuth * r11154 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (2 files in 2 dirs): Return correct icon upon INCONCLUSIVE.
08:55 olass shk3: is it possible for 2 molecules to have different fingerprint length?
08:55 olass I get: Caused by: org.openscience.cdk.exception.CDKException: Bisets must have the same bit length
08:55 olass how can this happen?
08:56 masak joined #bioclipse
09:05 shk3 odd
09:05 shk3 shouldn't happen
09:05 olass egonw, shk3: What is the size of a CDK FP?
09:05 shk3 can you give me the examples?
09:05 shk3 1024
09:06 olass I get one that has 1536
09:06 shk3 by default and that should be used
09:06 shk3 hm, that rings a bell
09:06 shk3 somebody had something similar
09:06 shk3 but I don't fully remember
09:06 shk3 please file me a bug with examples
09:06 olass yes, this is really not good
09:06 olass will dig out the example
09:07 shk3 have some nmrshiftdb stuff to do, but will continue with bc the afternoon
09:07 olass ok
09:07 olass is it safe to assume if FP size differs that the FP are different?
09:07 olass I assume so
09:07 olass very different I mean
09:07 shk3 yes
09:07 shk3 you can't compare them
09:08 olass shk3: what is a very different tanimoto?
09:08 shk3 given they are really different and not just truncated or so
09:08 shk3 0
09:08 olass shk3: what is a very similar tanimoto value?
09:08 shk3 1
09:08 olass ok
09:08 shk3 easy
09:08 olass thx
09:08 shk3 isn't it?
09:08 olass not really
09:08 olass how similar is 0.8?
09:08 olass in a chemical sense?
09:08 shk3 pretty good
09:09 shk3 uuh, chemical sense
09:09 olass define 'pretty'
09:09 shk3 now that's hard to say
09:09 olass you see, not trivial ;)
09:09 shk3 no
09:09 olass ok, thx for the help
09:09 shk3 the concept of similarity is not easy
09:09 shk3 the range being 0 to 1 is easy
09:22 egonw yeah, bug 1234
09:26 shk3 joined #bioclipse
09:37 CIA-40 bioclipse: ospjuth * r11155 /bioclipse2/trunk/plugins/net.bioclips​e.ds.dblookup/src/net/bioclipse/ds/dbl​ookup/impl/ExternalMoleculeMatch.java: Implement adapter for ExternalMoleculeMatch to show up in JChemPaintView
09:41 CIA-40 bioclipse: ospjuth * r11156 /bioclipse2/trunk/plugins/ (3 files in 2 dirs):
09:41 CIA-40 bioclipse: * Use IMolecule.Property.USE_CALCULATED for InChI and FP since structural changes do not clear this
09:41 CIA-40 bioclipse: * Reverted criteria for tanimoto comparison
09:41 CIA-40 bioclipse: * Omit and do not compare molecules where fingerprints are not of same size (treat them as very different)
09:44 egonw shk3: that patch you wrote about on Apr 23
09:44 egonw is that for cdk-1.2.x or master?
09:44 egonw it does not seem to work on cdk-1.2.x
09:45 shk3 it was made against 1.2.x
09:45 egonw but not on master either
09:45 egonw ok
09:45 shk3 what means "it does not work"?
09:45 egonw Applying: Better excpetion handling in builder3d
09:45 egonw error: patch failed: src/main/org/openscience/cdk/modeling/bu​ilder3d/ForceFieldConfigurator.java:240
09:45 egonw error: src/main/org/openscience/cdk/modeling/​builder3d/ForceFieldConfigurator.java: patch does not apply
09:45 egonw error: patch failed: src/main/org/openscience/cdk/modeli​ng/builder3d/ModelBuilder3D.java:33
09:45 egonw error: src/main/org/openscience/cdk/model​ing/builder3d/ModelBuilder3D.java: patch does not apply
09:46 egonw Patch failed at 0001.
09:47 shk3 i will look at this later
09:48 shk3 it might just be the patch is old
09:48 shk3 i don't know
09:48 egonw could be
09:48 egonw but nothing much happened in between
09:48 egonw svnrev -> githash
09:48 egonw and some other seemingly unrelated stuff
09:49 egonw ah... wait
09:49 egonw I think I found something
09:52 egonw ok, one prob solved
09:54 egonw ok, one patch fixed
09:55 CIA-40 bioclipse: ospjuth * r11157 /bioclipse2/trunk/plugins/net.biocl​ipse.ds.dblookup.bursi/plugin.xml: Added exact db test that was uncommented by mistake.
10:01 shk3 joined #bioclipse
10:04 egonw joined #bioclipse
10:08 rojasm joined #bioclipse
10:11 egonw shk3: http://cdk.git.sourceforge.net/git/​gitweb.cgi?p=cdk;a=commit;h=bc5837d​848267f8ed7896cbb8a6281b2de6d443b
10:11 zarah egonw's link is also http://tinyurl.com/kudlnn
10:12 shk3 thanks
10:14 maclean joined #bioclipse
10:30 olass hi maclean
10:30 maclean hi
10:30 zarah privet maclean
10:30 maclean I do read the logs :)
10:30 olass lol
10:30 egonw rojasm: ping
10:30 jonalv o/
10:31 egonw rojasm: please add the patches to the patch tracker report
10:54 CIA-40 bioclipse: ospjuth * r11158 /bioclipse2/trunk/plugins/net.biocl​ipse.ds/src/net/bioclipse/ds/model/ (SimpleResult.java TestRun.java): Set correct icon upon error in results.
11:01 olass egonw: ping
11:01 egonw pong
11:01 olass I get this: Error while generating InChI: Accepted unusual valence(s): C(3); Cannot process aromatic bonds
11:01 olass what does that mean?
11:01 olass and how can I work around it?
11:01 egonw incomplete input
11:02 olass I had a mol
11:02 egonw that message should be ignored byt the code
11:02 olass then I removed a CL
11:02 olass then inchi generation fails
11:04 egonw inchi is more picky
11:04 egonw ask sam
11:04 olass egonw: could we add a method in JCP in context menu: Satisfy valency with hydrogens?
11:04 egonw that would be called something like:
11:04 egonw add explicit hydrogens
11:04 olass ok
11:05 olass will file a bug
11:14 CIA-40 bioclipse: jonalv * r11159 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: method taking BioclipseUIJob should not be published
11:16 CIA-40 bioclipse: jonalv * r11160 /bioclipse2/trunk/plugins/net.biocli​pse.core/src/net/bioclipse/managers/ (2 files in 2 dirs): only output the same warning to logger once every 2 minute. fixes bug: #1229
11:16 zarah bug #1229 | http://tinyurl.com/kjrf6b
11:36 jonalv egonw: do you have a bug ticket for that inchi / properties stuff?
11:36 egonw @pz 1196
11:37 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1196
11:37 egonw @pz 1230
11:37 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1230
11:37 egonw @pz 1235
11:37 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1235
11:38 jonalv okey so basically out inchi suppoirt sucks...
11:38 Gpox @pz 711
11:38 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=711
11:38 Gpox @pz 1208
11:38 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1208
11:39 egonw I'll make a wrapper report
11:39 jonalv egonw: yes please
11:41 egonw @pz inchi support
11:41 zarah [1240] Fix InChI support                 http://tinyurl.com/mmtlt7
11:41 zarah [1001] Calculate properties for large... http://tinyurl.com/md5n6t
11:41 zarah Entire list at http://tinyurl.com/n8g2uj
11:42 egonw OK, lunch time
12:00 CIA-40 bioclipse: ospjuth * r11161 /bioclipse2/trunk/plugins/net.bioclipse.ds/​src/net/bioclipse/ds/ui/views/DSView.java: Commented out ViewerSorter to allow for sorting by implementors.
12:01 CIA-40 bioclipse: ospjuth * r11162 /bioclipse2/trunk/plugins/net.bioclipse.ds​/src/net/bioclipse/ds/model/IDSTest.java: Changed <ITestResult> to <? extends ITestResult> so it is possible to return list of implementations.
12:03 CIA-40 bioclipse: ospjuth * r11163 /bioclipse2/trunk/plugins/net.bioclipse.ds.d​blookup/src/net/bioclipse/ds/dblookup/impl/ (3 files):
12:03 CIA-40 bioclipse: * Added field 'similarity' on ExternalMoleculeMatch to allow for sorting
12:03 CIA-40 bioclipse: * Sort on similarity field when returning results from DBNNTest
12:03 egonw back
12:06 CIA-40 bioclipse: ospjuth * r11164 /bioclipse2/trunk/plugins/net.bioclips​e.ds.dblookup/src/net/bioclipse/ds/dbl​ookup/impl/DBNearestNeighborTest.java: Replaced 'Math.round(x*100.0) / 100.0' with DecimalFormat class per advice by masak++ and Gpox++.
12:07 olass egonw: you will be at BMC tomorrow?
12:07 olass we need to have a status meeting
12:07 olass it is important to get RC2 out
12:07 olass I woudl like RC2 tomorrow if possible
12:07 olass but we need to sort out quite some bugs for this
12:08 egonw no, meeting at school
12:08 edrin joined #bioclipse
12:08 edrin hi
12:08 zarah privet edrin
12:08 egonw hi edrin
12:08 edrin hi egonw
12:14 olass oh no
12:16 edrin hi olass
12:16 olass hi edrin
12:18 jonalv hi
12:18 zarah privet jonalv
12:19 masak hi
12:19 zarah ni hao masak
12:19 masak ni hao zarah
12:37 shk3 jonalv: can you advise me on the monitor stuff?
12:37 jonalv shk3: what about it?
12:38 shk3 if i initialize it to UNKNOWN, do I still need to call worked?
12:38 shk3 because for me, I get the bar, but no progress
12:38 shk3 it's just empty and stays empty
12:39 jonalv shk3: yea if you go UNKNOWN I don't think there is any point in  worked calls
12:39 shk3 think so as well
12:39 shk3 best would be that sort of progress bar where a section moves left and right
12:40 shk3 you know what I mean?
12:40 jonalv shk3: yea that's what you should get with UNKNOWN
12:41 shk3 hm, i don't
12:41 jonalv strange...
12:42 shk3 anything else then beginTask and done I need to call?
12:44 jonalv Gpox: do you have any idea?
12:45 Gpox about what?
12:45 CIA-40 bioclipse: goglepox * r11165 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfedi​tor/CDKFingerPrintPropertyCalculator.java: Fixed typos
12:45 CIA-40 bioclipse: goglepox * r11166 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
12:45 CIA-40 bioclipse: Added clear to substructure generator when structure changed.
12:45 CIA-40 bioclipse: Resolves bug #1055
12:45 shk3 how progrossmonitor with UNKNOWN works?
12:45 zarah bug #1055 | http://tinyurl.com/nyamkm
12:50 Gpox is this a SubProgressMonitor?
12:54 shk3 no
12:54 shk3 just normal progress monitor
12:54 shk3 I want it to "oscilate"
12:54 Gpox do you call monitor.worked
12:57 shk3 no
12:57 shk3 is this necessay with unknown?
12:59 CIA-40 bioclipse: jonalv * r11167 /bioclipse2/trunk/plugins/net.bioclipse.jmol/ (5 files in 3 dirs): brought jmol manager int NWO. fixes: 1077
12:59 zarah bug #1077 | http://tinyurl.com/n3k4zu
13:01 Gpox it can't hurt
13:05 olass egonw: ping
13:05 egonw pong
13:11 shk3 Gpox: no, doesn't make a difference
13:13 CIA-40 bioclipse: shk3 * r11168 /bioclipse2/trunk/plugins/net.bioclip​se.cdk.ui/src/net/bioclipse/cdk/ui/ha​ndlers/Create2dHandlerWithReset.java: added monitor and cancel to generate coordinates
13:13 CIA-40 bioclipse: shk3 * r11169 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: added monitor and cancel to generate coordinates
13:22 shk3 egonw: it seems you started converting validatecmlmanager to nwo.
13:22 shk3 but ValidateCMLManager.java still implements IValidateCMLManager.
13:22 shk3 is this intended?
13:23 egonw no, not good
13:24 shk3 ok, i work on that
13:24 shk3 np
13:24 shk3 just wanted to make sure there isn't a plan behind it I didn't understand
13:24 egonw I'll fix it myself
13:24 egonw thanx for letting my now about that omission
13:27 egonw shk3: please ack...
13:29 shk3 go ahead
13:32 CIA-40 bioclipse: egonw * r11170 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Manager implementation should not implement the matching interface
13:32 Gpox joined #bioclipse
13:33 CIA-40 bioclipse: egonw * r11171 /bioclipse2/trunk/plugins/net.bioclipse.cml/src/ne​t/bioclipse/cml/managers/IValidateCMLManager.java: Added missing test annotation
13:42 shk3 jonalv: sorry, do you have a minute?
13:42 jonalv shk3: sort of maybe...
13:43 shk3 ok, i just ask, perhaps you have an idea:
13:43 jonalv shk3: I am looking at you error dialog problem for generating 3d coords...
13:43 shk3 thanks for that
13:43 shk3 if I do:
13:43 shk3 help nmrshiftdb.submitSpecmol
13:43 shk3 I get:
13:43 shk3 nmrshiftdb.submitSpecmol(CMLCml cmlcml, String serverurl,String username,
13:43 shk3 String password)
13:43 shk3 ok
13:43 shk3 then I do:
13:44 shk3 nmrshiftdb.submitSpecmol(x,"http://localhost:8080/axis","shk3","test");
13:44 shk3 which gives me:
13:44 shk3 java.lang.RuntimeException: Failed to find the method to run
13:44 jonalv shk3: Cmlcml?
13:44 shk3 and I get x via:
13:44 shk3 x=cml.parseFile("/Sample Data 1/Speclipse/specmol/Maaranolide_G.xml")
13:45 shk3 gvining me:
13:45 shk3 [org.xmlcml.cml.element.CMLCml: cml]
13:45 jonalv that's not a BioObject is it??
13:45 shk3 ah no
13:45 shk3 it's a jumbo object
13:45 jonalv it should probably work anyway though..
13:46 shk3 looks ok for me
13:46 shk3 do we need BioObjects as parameters always?
13:47 shk3 ah, wait
13:47 egonw @pz 519
13:47 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=519
13:47 jonalv so the method implementation of submitSpecmol has an identical method signature as the one in the interface?
13:47 shk3 I think signature is different in interface
13:47 jonalv shk3: no not really but it is better...
13:47 shk3 no, that's probably the reason
13:47 shk3 changed implementation but not interface
13:47 shk3 testing...
13:49 shk3 hm, no
13:50 shk3 well, anyway, I will find the reason
13:50 shk3 you better look at the dialog problem ;-)
13:57 CIA-40 bioclipse: shk3 * r11172 /bioclipse2/trunk/plugins/net.bioclips​e.cml/src/net/bioclipse/cml/managers/ (IValidateCMLManager.java ValidateCMLManager.java): added a method for parsing files
13:58 CIA-40 bioclipse: shk3 * r11173 /bioclipse2/trunk/plugins/net.bioclipse.nmrsh​iftdb/src/net/bioclipse/nmrshiftdb/business/ (INmrshiftdbManager.java NmrshiftdbManager.java): submit can now be done in javascript
14:17 jonalv zarah: tell shk3 when catching exceptions and throwing BioclipseExceptions please give the caught exception as casue paramater to the BioclispeException
14:17 zarah Consider it noted.
14:22 shk3 joined #bioclipse
14:33 CIA-40 bioclipse: jonalv * r11174 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: added cause param to BiocliseException creations
14:34 jonalv svn--
14:34 CIA-40 bioclipse: jonalv * r11175 /bioclipse2/trunk/plugins/net.bi​oclipse.core/src/net/bioclipse/ (4 files in 3 dirs): Fancier Exceptions. The Error dialog will now show a complete stack trace when clicking the reason button. Also fixed error reporting from within BioclipseJobs. Fixes bug: #1218
14:34 zarah bug #1218 | http://tinyurl.com/mdem9z
14:35 CIA-40 bioclipse: egonw * r11176 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (3 files in 2 dirs): Added jcp.addExplicitHydrogens() popup menu action (fixes #1242 and 1239)
14:36 zarah bug #1242 | http://tinyurl.com/krxyg2
14:37 CIA-40 bioclipse: jonalv * r11177 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: whitespace
14:38 egonw blackspace is better for the environment
14:40 jonalv egonw: why_
14:40 egonw less energy consumption
14:46 CIA-40 bioclipse: egonw * r11178 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Binds the JChemPaint editor to MDL molfile files with 3D coordinates (fixes #1232)
14:46 zarah bug #1232 | http://tinyurl.com/m7ogfe
14:58 olass nice progress today
14:58 * olass feels RC2 will be tomorrow
14:58 olass if no blocker remains...
15:01 egonw funny
15:01 jonalv olass: there that problem with permssions
15:01 egonw a .smi file opened in the JCP editor
15:01 egonw has no ICDKMolecule.getSMILES()
15:04 jonalv olass: or is that solved?
15:05 CIA-40 bioclipse: egonw * r11179 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: Return an zero-length String when there is no cached InChI and the cached version is requested; fixes a NPE
15:05 CIA-40 bioclipse: egonw * r11180 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/d​omain/CDKMoleculePropertySource.java: Added SMILES, InChI and InChIKey to the properties view; uses the cached version, and does not trigger calculation itself (fixes #1216)
15:05 zarah bug #1216 | http://tinyurl.com/kvlt7m
15:07 CIA-40 bioclipse: goglepox * r11181 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (2 files in 2 dirs):
15:07 CIA-40 bioclipse: Added 'Show Implicit Hydrogen' to jcp-context menu
15:07 CIA-40 bioclipse: Fixes bug #1175
15:07 zarah bug #1175 | http://tinyurl.com/mjdc8o
15:17 Gpox joined #bioclipse
15:17 egonw Gpox: is showAromaticity true by default?
15:17 egonw it seems not here
15:17 egonw not sure if that is default
15:17 egonw or my workspace setting
15:22 CIA-40 bioclipse: egonw * r11182 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: Create 2D/3D action menu is now also available for 0D CML and 0D MDL molfile (fixes #1231)
15:23 zarah bug #1231 | http://tinyurl.com/na3r7s
15:24 jonalv olass: ping
15:24 olass pong
15:24 jonalv olass: is the permissions trouble solved now?
15:24 olass no
15:25 olass we should probably zip outside of eclipse
15:26 olass how come you ask?
15:26 jonalv olass: maybe masak or egonw could write a little script for you that unzips your zip files, sets the permssions and rezips them?
15:26 olass would indeed be nice
15:26 jonalv olass: becasue you asked if there where any blockers left and that one is the only one I can think of...
15:26 olass let's talk about that tomorrow
15:26 olass jonalv: ok
15:27 jonalv olass: + I only have one 2.0 bug left and I am stuck on that one...
15:27 jonalv :(
15:27 olass which one?
15:27 olass the jmol + 2d view is important...
15:27 jonalv @1213
15:28 jonalv olass: the what?
15:28 jonalv @pz 1213
15:28 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1213
15:29 olass 1243
15:30 olass @tell jonalv: 1243 is a blocker...
15:30 zarah Consider it noted.
15:30 jonalv joined #bioclipse
15:30 jonalv @ping
15:30 zarah jonalv: pong
15:30 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
15:30 egonw olass: about 1241
15:30 jonalv zarah: just tell me...
15:31 zarah jonalv: 52 s ago, olass said 1243 is a blocker...
15:31 egonw getSMILES() was originally planned to always recalculate??
15:31 jonalv @1243
15:31 jonalv @pz 1243
15:31 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1243
15:31 olass egonw: I don't know
15:31 egonw who does?
15:31 olass egonw: what do you suggest here?
15:31 olass you hold the most experience...
15:31 egonw two issues:
15:32 egonw you cannot recalculate... makes BC sluggish
15:32 jonalv @pz 1241
15:32 egonw and
15:32 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1241
15:32 egonw we have no listening interface
15:32 olass egonw: 1) sluggish: agree
15:32 egonw only solution I see, is remove getSMILES() getInChI() etc
15:32 olass egonw: in favor of...?
15:33 egonw manager.getSMILES()
15:33 egonw where manager := {cdk, ...}
15:33 olass hmm
15:33 olass but IMO we should cache SMILES...
15:33 olass it is an expensive operation
15:33 olass or..?
15:33 egonw but what does the inventor of IMolecule.getSMILES() think about this
15:33 olass who cares
15:33 olass what do you thnk?
15:34 edrin left #bioclipse
15:34 egonw but caching only works when you know when the cache becomes too old
15:34 egonw which does not exist
15:34 olass how can that be resolved?
15:34 olass is it possible to have a listener for this?
15:36 olass the ICDKMol would in itself listen to changes on its AtomContainer and clear the SMILES/InChI upon need?
15:36 jonalv olass: there is no such listener in cdk
15:36 jonalv which sucks...
15:36 egonw the listener stuff for AtomContainer is giving trouble
15:36 olass hmm
15:36 egonw jonalv: huh? eplxain...
15:37 egonw there is IAtomContinare listener in the CDK
15:37 jonalv egonw: the changelistener in CDK triggers on flag changes and falgs changes even when drawing an atom container...
15:37 jonalv egonw: if there was a real changelistener in cdk that only triggered when the actual molecule was chagned then we could use that one
15:38 egonw ha, you mean the system is not fine graned enough
15:38 egonw a flag change is a change
15:38 jonalv egonw: actually it's too fine grained
15:39 egonw yes, depending on your perspective :)
15:39 jonalv egonw: drawing a molecule should not change a molecule in my oppinion :)
15:39 jonalv egonw: well another listener would be nice...
15:42 olass so there is no solution right now
15:42 olass what do we do?
15:42 olass in the short run and in the long run
15:43 olass egonw: you suggest to recalculate all times using cdk.createSMILES()
15:43 jonalv olass: I think we need an afk brainstorm on this...
15:43 olass yes
15:43 olass tomorrow would be good
15:44 olass but egonw will not be at bmc
15:44 jonalv yes
15:44 jonalv no :(
15:44 olass and he is central for this
15:44 jonalv definitly
15:44 jonalv egonw: when will you be @bmc next?
15:44 egonw Thu: 8:25 for day out
15:44 jonalv oh right thursday is utflykt
15:45 olass can we postpone this at all?
15:45 olass a skype call now?
15:45 olass we sort of need a conclusion...
15:45 egonw I should: file a bug report against JCPEditor for deleting the cached version upon any edit action
15:45 jonalv we do? My feeling was that this could wait...
15:46 olass egonw: sounds like a good idea
15:46 olass jonalv: we need to show SMILES in the properties view
15:46 olass that is a blocker
15:47 olass and editing the structure should update the SMILES
15:47 olass there is your use case
15:47 jonalv olass: okey well in that case we have to figure something out
15:47 olass yes
15:47 olass it is OK if it is not a super solution
15:47 olass but it should work relatively good
15:48 olass even if we calculate too much too many times
15:49 jonalv olass: well I don't know how to keep those values up to date. But I do know that they need to be calculated outside the gui thread
15:50 olass indeed
15:51 jonalv olass: as for 1243 that seems strange. I don't even underestand what is going on with that one...
15:51 olass but you can reproduce?
15:52 jonalv olass: yes
15:52 olass we need to solve that before RC2
15:54 * egonw needs to catch the bus
15:54 olass egonw: would be great if you got internet tomorrow
15:54 olass then we could discuss this further
15:55 egonw indeed
15:55 egonw otherwise in Gävle
15:55 jonalv egonw: in Gaevle?
15:55 olass ?
15:55 egonw Thu
15:55 * olass will not join
15:55 egonw bye
15:55 olass bye
15:55 egonw cu Thu!
15:56 jonalv egonw: are we going to gaevle on thuserday?
15:56 * olass had no idea
15:56 olass it's supposed to be a secret
15:56 jonalv yea
15:56 jonalv who told?
15:56 * olass wonders how egonw figured that out
16:03 olass jonalv: are you looking at 1243?
16:04 olass if you can't solve it let's hope Gpox can help tomorrow
16:04 jonalv olass: I gave up
16:04 olass aha
16:04 jonalv olass: I think I am giving up for tiday..
16:04 jonalv |today
16:04 olass oki
16:04 * olass will work late today
16:05 * jonalv is sort of stuck everywhere..
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