Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-18

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All times shown according to UTC.

Time Nick Message
06:05 egonw joined #bioclipse
07:15 egonw joined #bioclipse
07:29 Gpox joined #bioclipse
08:33 masak joined #bioclipse
08:34 olass joined #bioclipse
08:35 olass moin
08:35 zarah privet olass
08:36 masak y0
08:36 zarah hello masak, you fantastic person you
08:36 masak :)
08:36 egonw masak: over at #cdk I have a bot running that posts RSS items to IRC
08:36 egonw masak: so that we can monitor development in Git
08:36 egonw hi olass
08:36 masak egonw: great.
08:36 masak egonw++
08:37 olass egonw: that would be nice here too
08:39 egonw olass: yes... the code needs some updates, to support multiple channels and multiple RSS feeds
08:39 egonw that will happen 'at some point' (tm)
08:40 olass who has that tm? Must be a very rich man...
08:41 masak well, the guy who owns "Real Soon Now" is richer.
08:44 egonw it's a shame my "ASAP" patent ran out, just before started using it in Hollywood
08:44 masak oh, a patent even? :)
08:45 masak reminds me of the time I lost my exclusive rights to the term "O RLY?"
08:45 masak people have been using it en masse ever since.
09:04 jonalv joined #bioclipse
09:12 shk3 joined #bioclipse
09:14 masak jonalv-- # the real villain
09:14 * olass is updating the wiki and removing all bc1 material
09:14 masak Gpox++ # innocent :)
09:14 egonw olass++
09:14 masak in the end, karma is always just.
09:19 CIA-33 bioclipse: goglepox * r9356 /bioclipse2/trunk/plugins/net.bioclipse.script​ing/src/net/bioclipse/scripting/JsThread.java: Moved initations of 'LinkedList actions' to declarations. removed "BIG UGLY HACK". :)
09:20 olass Gpox++ //removing ugly hacks is always worthy of karma
09:23 jonalv olass: when is our next sheduled status meeting?
09:23 olass thursday maybe?
09:24 jonalv olass: yea that sounds like a plan
09:25 olass jonalv, egonw, masak, Gpox: Would be great if we could clean up all our bug lists for tomorrow's staus meeting. E.g. do the small and easy bug fixes that clutter our lists (if we can)
09:25 olass and clean out tasks that are finished or 2.1
09:26 olass so please verify your bug lists prior to thestatus meeting
09:26 * olass will do his right away
09:27 shk3 is bioclipse release plan still for 23rd?
09:27 egonw olass: I have exam tomorrow :)
09:27 olass hahaha
09:27 olass what time?
09:27 egonw olass: planned to work from home
09:28 egonw the whole day, Fri too...
09:28 olass oh
09:28 olass ok
09:28 egonw I guess assignment?
09:28 olass egonw: 2 days for that?
09:28 egonw dunno
09:28 egonw I will not get the 'exam' until tomorrow
09:28 egonw olass: ask Maris
09:28 olass egonw: you're in for a surprise
09:28 egonw yes
09:29 egonw well, my first test got 5 out of 5, so I think I'll do fine
09:29 egonw but there was some interesting new stuff...
09:29 egonw it was worthwhile...
09:29 egonw did the course in about a day... but useful nevertheless
09:42 masak olass: gotcha.
09:47 olass_ joined #bioclipse
09:47 olass_ strage
09:47 olass_ strange too
09:50 olass_ I'd be happy if more persons checked the BC wiki now
09:50 olass_ I've tried to remove most links to bc1 pages
09:53 olass_ it's an easy fix pending MW upgrade but looks much better now IMO
09:55 egonw MW upgrade?
09:55 * masak checks the BC wiki
09:59 masak olass_: perhaps we should have more coloured boxes on the Main Page. compare http://wiki.bioclipse.net/​index.php?title=Main_Page with http://en.wikipedia.org/wiki/Main_Page
09:59 zarah masak's link is also http://tinyurl.com/dhonqj
09:59 olass_ masak: that wouldbe nice
09:59 masak it would be nice to have pretty URL's, too. but that's not a priority.
09:59 olass_ can you assist?
09:59 masak olass_: sure!
09:59 olass_ see bug 257
09:59 olass_ wiki upgrade is planned
09:59 masak @pz 257
09:59 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=257
10:00 olass_ but will not have tim before 2.0
10:00 masak right.
10:01 masak a Main_Page redesign need not take long, however. and it's independent of upgrading, really.
10:01 olass_ yes
10:01 masak upgrading usually causes enough problems on its own.
10:01 olass_ can I file you a bug?
10:01 * masak creates ticket for 'nicer Main_Page'
10:01 olass_ ah
10:01 olass_ you do it:)
10:08 * masak did it
10:10 masak also creating a ticket for the nice URLs.
10:13 masak http://www.aftonbladet.se/nojesbladet/​melodifestivalen2009/article4664919.ab
10:13 zarah masak's link is also http://tinyurl.com/c9zhsm
10:39 egonw http://github.com/egonw/bioclipse/graphs/impact
10:39 zarah egonw's link is also http://tinyurl.com/cxmscg
10:40 egonw http://github.com/egonw/bi​oclipse/graphs/punch_card
10:40 zarah egonw's link is also http://tinyurl.com/63gddo
10:46 olass_ egonw: nice graphs
10:46 * olass_ is annoyed with versioned dependencies in plugins
10:47 egonw http://rdf.openmolecules.net/?InChI=1/C15H22O3/c1​-13(2)7-4-8-14(3)12(13)6-5-11(9-16)15(14,18)10-17​/h5,9-10,12,18H,4,6-8H2,1-3H3/t12-,14-,15+/m0/s1
10:47 zarah egonw's link is also http://tinyurl.com/c3hy6j
10:47 egonw links to Pele
10:48 CIA-33 bioclipse: ospjuth * r9357 /bioclipse2/trunk/plugins/net.bioclip​se.cdk.business/META-INF/MANIFEST.MF: Removed bundle versions
10:48 olass_ are you all OK withy me removing "bundle-version XX.XX" for all plugins?
10:48 olass_ right now I cannot export...
10:49 egonw if the cdk plugins have those, please keep those in
10:49 egonw that is...
10:49 egonw cdk.data version X, should depend on cdk.interfaces version X
10:50 olass_ I am talking about eclipse deps
10:50 olass_ not cdk deps
10:50 CIA-33 bioclipse: ospjuth * r9358 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.debug/META-INF/MANIFEST.MF: Removed bundle versioning and cleaned up manifest.
10:50 olass_ those I will leave
10:50 olass_ egonw: ok?
10:50 egonw ok
10:52 CIA-33 bioclipse: ospjuth * r9359 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.jchempaint/META-INF/MANIFEST.MF: Removed bundle versioning and cleaned up manifest. Left cdk bundle version constraints.
10:53 CIA-33 bioclipse: ospjuth * r9360 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Removed bundle versioning and cleaned up manifest. Left cdk bundle version constraints.
10:54 CIA-33 bioclipse: ospjuth * r9361 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui/META-INF/MANIFEST.MF: Removed eclipse bundle versioning and cleaned up manifest.
10:54 CIA-33 bioclipse: ospjuth * r9362 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.ui.sdfeditor/META-INF/MANIFEST.MF: Removed eclipse bundle versioning and cleaned up manifest.
11:16 CIA-33 bioclipse: ospjuth * r9363 /bioclipse2/trunk/plugins/ (7 files in 7 dirs): Removed eclipse bundle versioning and cleaned up manifest.
11:30 olass_ *phew* finally got export to work again
11:30 * olass_ is building an infocenter, see bug #732
11:31 olass_ egonw: about 742, would that be possible to do soon?
11:33 egonw @pz 742
11:33 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=742
11:35 egonw dunno
11:35 egonw I do not know how to publish something in the Help center
11:35 egonw just toc.xml?
11:40 olass_ yes
11:41 olass_ http://wiki.bioclipse.net/index.php?title=Writi​ng_documentation_and_help_for_Bioclipse_plugins
11:41 zarah olass_'s link is also http://tinyurl.com/cne2sb
11:41 olass_ egonw:  especially http://wiki.bioclipse.net/index.php​?title=How_to_add_help_to_a_plugin
11:41 zarah olass_'s link is also http://tinyurl.com/chsmnz
11:41 olass_ @
11:41 olass_ ?
11:41 olass_ (where did that @ come from?)
11:41 egonw and the plugin would just contain static dumps, correct?
11:44 olass_ yes
11:44 olass_ that we can update with scripts prior to a release
11:44 olass_ but please put all scripts in there
11:45 egonw the scripts in the plugin folder?
11:45 olass_ why not in the plugin net.bioclipse.doc ?
11:45 egonw that's what I meant :)
11:45 olass_ oh :)
11:46 egonw I see the ambiguity
11:56 egonw olass_: are you exporting with 3.4.2 ?
11:56 olass_ yes
11:56 egonw olass++
11:57 egonw that will mean beta4 on SF, correct?
11:57 olass_ no
11:57 egonw core_patch will do?
11:57 olass_ ??
11:57 * olass_ is not doing a release
11:57 olass_ no reason to do so
11:57 egonw ah, ic
11:57 egonw just exporting for fun, you are...
11:57 olass_ building standalone documentaion
12:09 olass_ ok, apache2 is down on pele for a few mins
12:09 olass_ meaning bugzilla too
12:10 egonw minutes??
12:21 CIA-33 bioclipse: jonalv * r9364 /bioclipse2/trunk/plugins/​net.bioclipse.ui.business/ (5 files in 2 dirs): begun moving ui manager into the new world order
12:21 CIA-33 bioclipse: jonalv * r9365 /bioclipse2/trunk/plugins/net.bioclip​se.scripting/src/net/bioclipse/script​ing/business/JSJobCreatorAdvice.java: rewrote JSJobCreatorAdvice to convert from String to IFile for methods that does not contain progressmonitors as well
12:22 CIA-33 bioclipse: jonalv * r9366 /bioclipse2/trunk/plugins/net.bioclipse.u​i.business/src/net/bioclipse/ui/business/ (IUIManager.java UIManager.java): made ui.remove take a progressmonitor
12:23 CIA-33 bioclipse: jonalv * r9367 /bioclipse2/trunk/plugins/net.bioclipse.u​i.business/src/net/bioclipse/ui/business/ (IUIManager.java UIManager.java): attempt to make ui.open use @GuiAction
12:23 CIA-33 bioclipse: jonalv * r9368 /bioclipse2/trunk/plugins/net.bioclips​e.scripting.ui/src/net/bioclipse/scrip​ting/ui/business/GuiActionAdvice.java: GuiActionAdvice should check for @GuiAction not @Recorded
12:24 CIA-33 bioclipse: jonalv * r9369 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added RetentionPolicy.RUNTIME to @GuiAction. I consider the ui manager to be done according to the NEW WORLD ORDER now :)
12:36 CIA-33 bioclipse: jonalv * r9370 /bioclipse2/trunk/plugins/net.bioclip​se.usermanager/src/net/bioclipse/user​manager/business/IUserManager.java: Removed a few @Recorded from usermanager. This one needs to be locked into regarding recording but as for now I say this fixes bug: #643
12:38 olass_ jonalv: where should the IUserManager be locked into?
12:38 olass_ a box?
12:39 olass_ a basement?
12:39 olass_ *brr*
12:39 * jonalv warns olass that jonalv is in a terrible mood today
12:39 * olass is trembling
12:39 olass why?
12:40 olass you found tabs in code?
12:40 jonalv I am tired and my hand hurts. I feel like to little butter spread upon to much bread.
12:40 olass oh :(
12:40 olass maybe you should check that hand...
12:41 olass seriously, go to Sara at the hospital
12:41 jonalv it's actually going i nthe right direction. It's a bit better today...
12:41 olass ask meklund
12:41 olass ok
12:41 olass maybe just let it heal then
12:41 jonalv but it's in no way good
12:41 olass kept you awake too?
12:41 jonalv I don't think so
12:41 jonalv but I am tired
12:41 olass eve?
12:41 olass :)
12:42 jonalv that's the strange thing I have slpet many hours tonight...
12:42 olass jonalv: you drink to little coffee
12:42 olass +o
12:42 jonalv I am considering taking a long weekend. Perhaps take monday or friday off...
12:42 olass and just sleep?
12:42 olass jonalv: do that
12:43 jonalv yes, but no. I am going to visit my parents this weekend...
12:43 olass take the day off I mean
12:43 olass you should think about your well being
12:43 jonalv yea...
12:43 olass I write bad code when I am tired
12:44 olass (with tabs...)
12:45 jonalv aha
12:45 jonalv :)
12:46 jonalv I am thinking about 745
12:46 jonalv @pz 745
12:46 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=745
12:47 jonalv I am not sure that we want an exception when running a JavaScript script just because we are removing a faile which is already removed. But on the other hand when running he command from the console an error message would be nice...
12:47 jonalv olass: what do you think?
12:47 olass hmm
12:48 olass tricky
12:48 olass if trying to remove a non-existing file we should get a message IMO
12:49 olass on the other hand, this is not a severe error
12:49 olass what do you think=
12:49 olass ?
12:49 * olass is writing a cheatsheet
12:49 jonalv I just don't know...
12:49 egonw http://pele.farmbio.uu.se/bioc​lipse/help/2.0beta4/index.jsp
12:49 zarah egonw's link is also http://tinyurl.com/cdngsu
12:49 egonw egonw++
12:49 zarah shame on you, egonw, giving yourself karma like that
12:50 jonalv egonw++ :)
12:51 jonalv hm I especially like the bla bla bla texts...
12:51 olass egonw: thanks for that
12:51 olass bla bla bla?
12:52 egonw jonalv: file bug reports
12:52 egonw bla bla bla in official help is not good
12:52 jonalv "Bioclispe at a glance"
12:52 olass haha
12:52 olass I have a bug
12:52 olass but seriously, I have spent MANY hours on writing docu for bc2
12:53 jonalv olass++
12:53 olass if someone wants to assist, please PLEASE do
12:54 olass I appreciate help in docu much more than bug reports
12:54 olass you want it, you write it
12:55 jonalv olass: that only works for core plugins which all of us know how they work...
12:56 olass jonalv: you know much more than you want to admit
12:56 jonalv maybee :)
12:56 egonw or marchbee ?
12:56 egonw anyway...
12:56 egonw olass: better to remove the link to the bla bla bla text
12:56 jonalv march bee march!
12:57 egonw fixing is even better, sure
12:57 olass egonw: no, it should be updated
12:57 olass it MUST be
12:57 egonw yes, that's what I see
12:57 egonw so, a bug should be filed
12:57 egonw blocking the release
12:57 olass I have one already
12:57 olass blocking the release
12:57 olass so you donät need to worry
12:57 egonw ack
12:58 olass egonw: but as you see, much needs to be added
12:58 egonw ack
12:58 olass the content right now is just not enough
12:58 egonw almost finished with NMRShiftDB-RDF
12:58 egonw (next would be PubChem)
12:58 olass ack
12:58 egonw will do .doc and .doc.devel after that
12:58 olass ack
12:59 olass egonw: I see no reason havinf two plugins for this...
12:59 olass why so?
12:59 olass it's just a topic in the help...
12:59 olass but by all means
12:59 egonw the more documentation, the more noise, the more difficult to find what you really are interested in
12:59 egonw ?
12:59 olass ok
12:59 egonw maybee?
13:00 olass you decide :)
13:00 olass if we ever get a Bioclipse SDK, then devel docu would be nice to have there
13:00 olass available from inside Eclipse
13:00 olass what devel doc do we have now?
13:00 egonw docs on extension points
13:00 olass right
13:00 egonw provided by Bioclipse
13:01 olass not much, but a start
13:01 egonw indeed
13:01 olass they are quite poorly documented...
13:06 CIA-33 bioclipse: goglepox * r9371 /bioclipse2/trunk/cdk-externals/trunk/o​rg.openscience.cdk.control/src/org/open​science/cdk/controller/MoveModule.java: Refactored mergeMolecule to get a better understaning of what it dose.
13:07 CIA-33 bioclipse: goglepox * r9372 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Centers molecules when first rendered fixes bug #699
13:07 zarah bug #699 | http://tinyurl.com/cvkuwt
13:45 CIA-33 bioclipse: jonalv * r9373 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/IUIManager.java: annotated ui.open(bioobject) (should have done that before, uups...:)
13:49 CIA-33 bioclipse: ospjuth * r9374 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.smartsmatching/src/net/bioclipse/cdk/sma​rtsmatching/views/SmartsMatchingView.java: On dispose, unregister listening on parts.
13:58 CIA-33 bioclipse: ospjuth * r9375 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.smartsmatching/ (html/smartstheory.html html/toc.html toc.xml): Added missing help page.
13:59 egonw masak: where do the ilogger2 logs go to?
13:59 egonw http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse
14:00 egonw or is of ilbot2 ?
14:00 egonw nvm
14:00 egonw found it
14:18 egonw I think Jarl has given his presentation: http://chembl.blogspot.com/2009​/03/bioactivity-databases.html
14:18 zarah egonw's link is also http://tinyurl.com/dd9fsc
14:18 egonw ah, no... that blog is of yesterday...
14:18 egonw anyway... cites Helena
14:21 CIA-33 bioclipse: ospjuth * r9376 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (3 files in 2 dirs): Added a cheatsheet: "Using the Bioclipse Workbench".
14:23 CIA-33 bioclipse: goglepox * r9377 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/editor/SWTMouseEventRelay.java: Reversed zoom fixes bug #701
14:23 zarah bug #701 | http://tinyurl.com/c4tqjx
14:25 CIA-33 bioclipse: goglepox * r9378 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Doesn't try to render when atomcontainer is null resolves bug #748
14:25 zarah bug #748 | http://tinyurl.com/cckloy
14:34 CIA-33 bioclipse: ospjuth * r9379 /bioclipse2/trunk/plugins/n​et.bioclipse.scripting.ui/ (html/ html/scriptingBioclipse.html toc.xml): Added a stub for a scripting help topic.
14:34 CIA-33 bioclipse: ospjuth * r9380 /bioclipse2/trunk/plugins/n​et.bioclipse.scripting.ui/ (4 files in 3 dirs): Added a tutorial cheatsheet for the Javascript console.
14:39 CIA-33 bioclipse: ospjuth * r9381 /bioclipse2/trunk/plugins/net.b​ioclipse.scripting.ui/toc.xml: Added missing slash to close topic tag.
14:40 olass masak: I've filed bug 750 for you, with a context
15:01 CIA-33 bioclipse: ospjuth * r9382 /bioclipse2/trunk/plugins/net.bioclips​e.qsar/schema/descriptorProvider.exsd: Updated pluginID of QSAR descriptors EP.
15:03 masak olass: thanks.
15:04 olass de nada
15:04 olass we need that doc for 2.0
15:04 olass scripting is central :)
15:08 CIA-33 bioclipse: ospjuth * r9383 /bioclipse2/trunk/plugins/​net.bioclipse.usermanager/ (2 files in 2 dirs): Login/logout menus now only visible if extension for EP accountType exist. Solves #585.
15:08 rajarshi joined #bioclipse
15:10 olass hi rajarshi
15:10 rajarshi hi
15:10 zarah hi rajarshi
15:10 rajarshi if I want to play with the latest QSAR stuff in bioclipse which download should I use?
15:10 rajarshi beta3?
15:10 olass yes
15:10 shk3 does anybody know if/how it is possible to find out if a certain file is open in editor and get the editor (IEditorPage or so)?
15:10 olass then download QSAR feature from experimental update site
15:11 olass in software update
15:11 olass shk3: PlatformUI.. .. .. .getActivePage().getEditors
15:11 olass something like that
15:12 shk3 ah, and then look through them or so?
15:13 olass something like that
15:14 olass rajarshi: I am doing a complete rewrite of the QSAR project building now
15:14 olass but it does work in teh release
15:14 rajarshi aah, ok
15:14 olass it's just not optimized
15:14 rajarshi I was planning to try it out on a smal problem and provide some feedback
15:14 olass (always calculates all descriptors for all mols, and so)
15:14 olass yes
15:14 olass would be really great
15:14 rajarshi I figured I should use what I'm writing about :)
15:14 * olass wants feedback
15:17 shk3 olass: thanks
15:17 olass rajarshi: ;)
15:17 olass that is the way to improve things
15:18 * olass should do a screencast for using the QSAR feature
15:18 olass all in time
15:18 olass rajarshi: will you come to the cdk workshop?
15:18 rajarshi olass: unfortunately not - visa issues
15:18 olass oh no
15:18 olass :(
15:18 rajarshi yeah, sucks
15:19 rajarshi hopefully, I can follow by audio streaming
15:19 olass yes
15:20 olass since centering of mols is fixed I'll throw out a new update on update site now
15:20 olass it is sort of bad to have un uncentered out...
15:24 rajarshi what do I need to do in Bioclipse to install the QSAR update? I can see that my update site list has the experimental site included in there
15:25 CIA-58 joined #bioclipse
15:25 olass rajarshi: can you see the QSAR feature?
15:26 rajarshi where would I see that? Via Preferences?
15:26 olass in teh update site > experimental category?
15:26 rajarshi or do I need to create a Project first?
15:26 CIA-58 bioclipse: ospjuth * r9385 /bioclipse2/trunk/plugins/net.biocl​ipse.scripting.ui/build.properties: Added docu to build.props.
15:26 olass did you install QSAR?
15:26 olass from teh update site?
15:26 rajarshi I havenm't installed anything - do I need to that outside of Bioclipse?
15:27 olass no
15:27 olass go to software updates
15:27 olass expand experimental update site
15:27 olass check "QSAR feature"
15:27 olass click install
15:27 olass report here if you don't see QSAR feature
15:27 rajarshi ok, let me restart
15:27 olass sure
15:28 * olass is verifying that this works here too
15:28 rajarshi hmm. Where do I find s/w update? When I start up I see the Navigator panel, Outline panel etc
15:29 olass Help menu
15:29 rajarshi aah! got it
15:29 olass after checking QSAR, click "add required"
15:30 olass this also checks the CDK plugin (which is a dep for QSAR)
15:30 olass I'll be here and talk you through this
15:30 olass I should really write a cheatsheet for QSAR
15:30 rajarshi thanks a lot, I think I'm getting the hang of it
15:30 olass :)
15:30 rajarshi very nice to have data collections in there already
15:31 olass yes
15:32 rajarshi it would be good to have some default JVM settings in Info.plist - I see it starts with 24M as the max heap size?
15:34 olass that should be more...
15:34 shk3 did anybody ever get an error like:
15:34 shk3 Attempted to beginRule: L/Sample Data/Maaranolide_G.xml, does not match outer scope rule: L/Virtual/sid_51c9184d3467398​9f6a5b668e4f91667335cf2bd.cml
15:35 rajarshi so I created a new QSAR Project
15:35 olass rajarshi: Go to menu About, click "Configuration details"
15:35 olass here it says: update2_beta4_0318
15:35 olass ha
15:35 olass -Xmx512M
15:36 rajarshi aah ok, can I start it with Xms512M or something? Basically start up with a good amount of ram
15:37 olass would you like Xms also, not only Xmx ?
15:38 rajarshi yes - that way if I have RAM I can start up with a good size
15:38 rajarshi e.g., for IDEA I start up with 512M and go to a max of 1024M
15:38 olass there is a config file, mom
15:39 olass bioclipse.ini
15:39 olass you can edit this
15:39 rajarshi oh ok, thanks. not a big deal at this point.
15:39 olass hmm, maybe we should add an -Xms128M or so
15:40 rajarshi might be useful
15:40 rajarshi how can I import an SD file?
15:41 olass drag it into the molecules windo
15:42 olass or copy it into the molecules folder in a QSAR project
15:42 olass rajarshi: have you created a QSAR project?
15:42 rajarshi yes
15:42 olass Doubleclick qsar.ml
15:42 olass go to page molecules
15:43 olass qsar.xml
15:43 rajarshi aah, got it
15:44 rajarshi drag and drop works like a charm
15:44 olass :)
15:44 olass egonw, jonalv: there's a new update available from update site
15:44 olass for chemoinfo
15:44 jonalv olass: cool
15:44 olass solving the centering problem that Gpox++ fixed today
15:44 jonalv w00t
15:44 olass jonalv: please verify that it works
15:44 jonalv oh
15:44 jonalv uhm
15:45 jonalv okey...
15:45 olass please?
15:45 rajarshi how can I view the depictin of a molecule?
15:45 olass please explain
15:45 olass the 2D?
15:45 rajarshi yes
15:45 olass in the Navigator, doubleclick the file
15:45 rajarshi i had thought double clicking on a molecule would show it
15:45 olass the mol in the QSAR window is limited
15:45 rajarshi yes, I did so, but nothing happens
15:46 olass in the Left navigator, not teh QSAR editor panel?
15:46 olass in the project?
15:46 olass in folder molecules?
15:46 rajarshi correct
15:46 olass is your SDFile there?
15:46 rajarshi BoilingPoints/molecules/big.​sdf/Molecules/[1]dan001.sdf
15:47 rajarshi yes, I see my 277 molecules in a list
15:47 jonalv -join cdk
15:47 olass so nothing happens when you doubleclick the file?
15:47 rajarshi correct
15:47 olass very very strange
15:48 olass just to confirm: you doubleclick teh file, not any of its children?
15:48 rajarshi in the cheminformatics perspective, if I double click an molecule, the Properties window gets focus
15:48 olass you cannot doubleclick molecules, you must doubleclick th file
15:48 rajarshi aaargh, duh!
15:48 olass big.sdf
15:49 rajarshi ok got it now
15:49 rajarshi yes, it shows up
15:49 olass *phew*
15:49 olass I agree, this is intuitive
15:49 olass will file a bug
15:50 rajarshi I agree - clicking on the sdf brings up the table as expected, but I should also see a molecule if I double click on a single entry within an SD file
15:51 zarah joined #bioclipse
15:52 shk3 yes, you should
15:52 shk3 I worked on a child editing,
15:52 shk3 but this is a sort of nasty workaround
15:52 rajarshi in the desc selection list, I see an entry called Molecular Descriptors under which I see a mix of topological, hybrid, constitutional descriptors. Is this nby design?
15:52 shk3 would be best to get the normal eclipse mechanism working for children
15:53 olass rajarshi: it's the ontology...
15:53 olass it reads from RDF/OWL
15:53 rajarshi hmm, there are two facts: descriptor type and descriptor class
15:54 rajarshi I haven't looked at the OWL recently, but one categorizes descriptors as molecule atomic bond
15:54 jonalv will somebody please think of the children
15:54 rajarshi and the other categorizes as topo, geo, hybrid etc
15:54 rajarshi so ideally, you'd have top levelnode as: atomic molecule bond
15:54 olass rajarshi: would be great if you could say how you like it to look like
15:54 rajarshi and then under molecular, you'd have topo, geom, const etc (like inthe CDKDescUI)
15:55 olass could you write this up in an email?
15:55 rajarshi sure
15:56 olass I haven't implemented "import response values" yet
15:57 rajarshi hmm, that was my next question - how do put in a Y?
15:57 olass but adding mols and adding descriptors (try setting parameters) and then clicking "save"
15:57 olass that makes clculation kick in
15:57 olass for Y: go to tab "responses"
15:57 jonalv olass: I am trying but it seems sourceforge is dead... :(
15:57 olass you have to do it manually for now...
15:57 olass jonalv: ok
15:57 rajarshi aah ok
15:57 jonalv can someone else confirm?
15:57 olass jonalv: you need to DL a new fresh beta3?
15:58 olass you have no stored one?
15:58 jonalv olass: yes I have not run Bioclipse in Windows on Nox for quite a while...
15:58 olass I only updated the update site today
15:58 olass and only cheminfo feature
15:58 * olass hopes that is enough, it worked here at least...
15:59 olass rajarshi: if you click "save", does it calculate the descriptors for all molecules?
15:59 rajarshi haven't got there yet, in a minute or two
15:59 olass :)
16:01 rajarshi desc calcs are running, sweet :)
16:01 rajarshi sent you the email
16:01 rajarshi I take it, descs are done in parallel?
16:01 jonalv gah sourceforge's website is totally downed...
16:02 rajarshi regarding response import - one useful thing would be to ask if an SD property field should be used as the Y
16:03 maclean joined #bioclipse
16:03 maclean hei olass - I've been trying out the QSAR feature just now
16:03 olass maclean: great
16:03 maclean two things:
16:04 olass just talking rajarshi through it
16:04 olass maclean: happy for feedback
16:04 maclean 1) it doesn't save the qsar.xml when you click 'run'
16:04 olass hmm, it should...
16:04 olass ok
16:04 * olass is taking notes
16:04 maclean 2) feature request : importing an sdf file could import all the molecules in it?
16:04 rajarshi one issue: after clicking on Edit molecules in qsar.xml and then adding big.sdf from my project, when I go back to qsar.xml / Overview, I see that it says Structures in analysis is N/A. Shouldn't this be the number of molecules in my file?
16:05 maclean (bit dangerous since I just tried to import a file called "C10H22.sdf" - guess how many structures :)
16:05 olass rajarshi: true, this is a known bug
16:05 olass maclean: can you not import an SDFile?
16:05 olass that should work...
16:05 rajarshi olass: aah, ok
16:05 maclean I can, but it ..oh wait
16:05 olass ok...
16:06 rajarshi when importing an SDF, is there a way to force all corrds to be read as 3D, even if they look 2D (i.e., zero Z-coord)
16:06 olass rajarshi: what is that good for?
16:07 rajarshi well, my sd file has some entries which are flat and their z-coords are 0
16:07 olass but you want them as 3D?
16:07 rajarshi so when I look at them under processedMols, I can only view them in 2D and not in 3D
16:07 rajarshi olass: yes
16:07 egonw olass: there is an IO option for that
16:07 egonw oh wait...
16:07 maclean hmmm. I only get one result row, but there are 7 molecules in the sdf.
16:07 olass ok, how about a checkbox for this?
16:07 egonw not for the SD editor, I guess...
16:08 egonw rajarshi: please file a bug for CDK
16:08 * egonw has to make dinner now
16:08 olass maclean: that sounds bad
16:08 olass maclean: in the molecules tab, does it say that it contains 7 molecules?
16:08 maclean ja
16:08 egonw olass: please file a bug report for IO settings for SDF / MDL reading in pelezilla
16:08 rajarshi egonw: what is the CDK bug I should file here?
16:09 egonw that SDFReader should have the readAs3D IO options MDLV2000Reader has
16:09 olass maclean: try clicking "run" in toolbar again
16:09 maclean ok
16:10 olass anyway, I have rewritten the builder to be more stable and scalable
16:10 olass but unfinished
16:10 maclean no, wait - 'molecules tab' - I thought you meant the children in the navigator. no, in the tab, you get a single entry.
16:10 olass and what does it say, no mols?
16:11 olass maclean?
16:11 maclean hmm. it works for test.sdf
16:11 maclean it doesn't say "no molecules" anywhere, no
16:11 olass maclean: maybe you can send me the SDF per mail if it dosn't work
16:11 maclean ok.
16:11 olass does it say "contains 7 mols"?
16:12 maclean it's generated by molgen, so maybe ... I'll check
16:12 olass I have to run off :(
16:12 olass please send me more bug reports by email
16:12 olass I'll be back later tonight as well
16:12 rajarshi ok, thanks for the help
16:12 maclean ok
16:13 olass rajarshi, maclean: appreciate your feedback
16:13 olass keep em bugs coming!
16:13 maclean no problem
16:13 olass ok, be back in 2-3 hours or so
16:13 olass bye
16:20 maclean left #bioclipse
16:23 CIA-58 bioclipse: shk3 * r9386 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/src/net/bioclipse/spe​ctrum/editor/PeakTableViewer.java: fixes npe
16:24 CIA-58 bioclipse: shk3 * r9387 /bioclipse2/trunk/plugins/net.biocli​pse.specmol/src/net/bioclipse/specmo​l/actions/OpenInEditorAction.java: the child editing works
17:09 CIA-58 bioclipse: shk3 * r9388 /bioclipse2/trunk/plugins/net.bioclipse.nm​rshiftdb/cheatsheets/SubmitCheatSheet.xml: changed help to actual situation
17:11 CIA-58 bioclipse: shk3 * r9389 /bioclipse2/trunk/plugins/net.bioc​lipse.specmol/html/maintopic.html: changed help to actual situation
18:15 CIA-58 bioclipse: egonw * r9390 /bioclipse2/trunk/plugins/ (14 files in 4 dirs): Template for doc plugins
18:15 CIA-58 bioclipse: egonw * r9391 /bioclipse2/trunk/ (23 files in 3 dirs): Added EP documentation to doc.developers plugin
18:16 CIA-58 bioclipse: egonw * r9392 /bioclipse2/trunk/plugins/net.bioclips​e.doc.developers/META-INF/MANIFEST.MF: Fixed manifest: actual bundle name, and no activator
18:16 CIA-58 bioclipse: egonw * r9393 /bioclipse2/trunk/features/​net.bioclipse.sdk_feature/ (. .project build.properties feature.xml): Pretty emty feature right now: only the EP documentation
18:17 CIA-58 bioclipse: egonw * r9394 /bioclipse2/trunk/plugins/net.bioclipse.​ui.business.tests/src/net/bioclipse/ui/b​usiness/tests/UIManagerPluginTest.java: Compile fix for recent API change
18:19 CIA-58 bioclipse: egonw * r9395 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (html/workbench/editors/ed_xmlEditor.html toc.xml): Update help docs for name change of our local XMLEditor to XML-Lite Editor
18:24 steinbeck joined #bioclipse
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