Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-10-23

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All times shown according to UTC.

Time Nick Message
06:33 miguelrojasch joined #bioclipse
07:02 egonw joined #bioclipse
07:11 Gpox joined #bioclipse
07:17 egonw moin
07:17 zarah saluton egonw
07:38 olass joined #bioclipse
07:51 olass moin
07:51 zarah hello olass, you fantastic person you
07:58 egonw_ joined #bioclipse
08:04 edrin joined #bioclipse
08:07 edrin hi
08:07 zarah oh hai edrin
08:07 edrin olass: and finished you PhD thesis?
08:08 olass well, it's for print now
08:08 olass will have my defence on November 27th
08:13 edrin ok
08:13 edrin so everything fine
08:43 sneumann joined #bioclipse
08:50 jonalv joined #bioclipse
08:50 jonalv oh hai
08:50 zarah saluton jonalv
08:55 egonw moin
08:55 zarah oh hai egonw
09:20 masak joined #bioclipse
11:02 egonw olass: http://www.myexperiment.org/workflows/934
11:02 zarah egonw's link is also http://tinyurl.com/ygucchx
11:08 olass egonw: looks nice
11:13 CIA-51 bioclipse.cheminformatics: Egon Willighagen 2.2.x * r967ea45 / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/CDKManager.java : Fixed method to work with ICDKMolecule contains an IAtomContainer instead of an IMolecule - http://bit.ly/3F5oq7
11:13 CIA-51 bioclipse.cheminformatics: Egon Willighagen 2.2.x * rb0a8e73 / (3 files in 2 dirs): Added a method to determine the MCSS for a List<IMolecule>; see http://www.myexperiment.org/workflows/934 - http://bit.ly/2KoCsn
11:13 zarah CIA-51's link is also http://tinyurl.com/ygucchx
12:06 samuell joined #bioclipse
12:07 egonw hi samuell
12:07 egonw finished with your examination?
12:07 samuell Hello
12:07 zarah hello samuell, you fantastic person you
12:07 zarah samuell: You have new messages. Write '/msg zarah @messages' to read them.
12:07 samuell Yep
12:08 samuell No sleep this night...
12:08 samuell :)
12:09 samuell But I hope this was the last time for this exam.
12:13 egonw :)
12:20 olass egonw: ping
12:20 olass egonw: you got a pull request from me for cheminfo 2.2.x implementing 1675
12:20 egonw ack
12:21 olass let me know if I messed things up :)
12:21 olass egonw: ping again
12:21 egonw pong
12:22 olass I need to move the plugin net.bc.webservices to core
12:22 olass do I duplicate it and request you to drop it from cheminfo?
12:22 olass or can you move it for me?
12:23 * samuell will need a little bit of rest and will be back online later (~17-18)
12:23 egonw I can move it...
12:23 egonw please give me a full list...
12:24 egonw I have to do subfolder one by one
12:24 egonw samuell: no worries
12:24 egonw samuell: get some sleep
12:24 samuell yep :)
12:24 samuell will need that. bye
12:24 olass egonw: the entire net.bc.webservices plugin
12:25 egonw olass: it's just one commit, right?
12:25 olass egonw: and the entire net.bc.webservices.test plugin
12:25 olass egonw: yes
12:25 olass a big one
12:25 egonw SmartsMatchingConstants does not have copyright header
12:26 egonw the -Helper does not too...
12:26 egonw please check that
12:26 olass ah
12:26 egonw well, and if possible...
12:26 egonw JavaDoc
12:26 olass I'll give you a new pull req
12:27 egonw manifest has versioned depends
12:27 olass thx for pointers
12:28 olass was probably unclean before
12:28 * olass will clean it up
12:28 olass egonw: is it not OK to have versioned deps to cdk plugins?
12:28 olass that should be fine IMO
12:29 egonw someString.equals("") -> better someString.length() == 0
12:29 egonw 3.5 was giving a lot of trouble with versions...
12:29 olass egonw: you can probably improve a lot
12:29 egonw and removing them seemed the only option to solve that...
12:29 olass egonw: that was eclispe plugin deps
12:29 egonw no, not just
12:29 olass right?
12:30 olass ok
12:30 egonw anyway
12:30 egonw we can remove it when/if it actually gives trouble
12:31 olass egonw: will you move the ws and ws.tests plugins to core now?
12:31 olass while I clean up smartsmatching?
12:32 egonw ok
12:35 egonw oh. had not seen samuel's new front page had already gone online :)
12:39 egonw damn, christoph is getting some really good hands in his already good ChEBI team...
12:39 egonw Nico Adams joins soon, and just heard that Duncan Hull also joined
12:40 olass egonw: why the 'damn'? To me it sounds like good news!
12:40 egonw as in, damn impressed
12:40 olass egonw: ok, you have a new pull request
12:42 egonw foo
12:42 egonw can't find that page on bioclipse / git
12:42 egonw searching for git
12:42 egonw directs to a page without giving *all* hits :(
12:43 egonw btw, those templates are really damn good
12:43 egonw and meanwhile my brains stops working...
12:50 CIA-51 bioclipse.cheminformatics: Ola Spjuth 2.2.x * r3ce78ba / (14 files in 7 dirs): (log message trimmed)
12:50 CIA-51 bioclipse.cheminformatics: Added support for SmartsMatching on MolTable.
12:50 CIA-51 bioclipse.cheminformatics: * Added checkbox for SmartsMatchingView
12:50 CIA-51 bioclipse.cheminformatics: * Rewrote models to support SmartsFiles
12:50 CIA-51 bioclipse.cheminformatics: * Added import SMARTS from file
12:50 CIA-51 bioclipse.cheminformatics: * Running SmartsMatching with MolTable open highlights hits in chemical structures.
12:50 CIA-51 bioclipse.cheminformatics: Smartsmatching in MolTable is very slow, mainly because results are not persisted among redraws (see bug 1676).
12:50 zarah bug #1676 | http://tinyurl.com/ykhujzf
12:50 CIA-51 bioclipse.cheminformatics: Ola Spjuth 2.2.x * rf483c0a / (5 files in 4 dirs):
12:50 CIA-51 bioclipse.cheminformatics: Code cleanup.
12:50 CIA-51 bioclipse.cheminformatics: * Added missing copyright headers
12:50 CIA-51 bioclipse.cheminformatics: * Removed versioned plugin deps - http://bit.ly/19eFfj
13:05 jonalv` joined #bioclipse
13:13 olass egonw: is the move of net.bc.ws progressing?
13:13 egonw slowly
13:13 egonw still struggling to find the wiki page
13:13 olass I see
13:13 olass wiki page?
13:13 egonw and doing some other stuff in parallel...
13:13 olass ok, ping me
13:14 egonw http://wiki.bioclipse.net/ind​ex.php?title=Git_Development
13:14 zarah egonw's link is also http://tinyurl.com/mqpa8m
13:14 egonw that one
13:14 egonw got it !
13:31 egonw olass: can I commit to bioclipse.core ?
13:31 olass egonw: yes please
13:31 egonw here comes
13:32 egonw there it is
13:32 egonw I think the CIA will ignore it
13:32 egonw but it is in the repos now
13:32 sneumann Hi, I have been following bioclipse development loosely in two roles:
13:32 sneumann as a user, looking for mostly stable devel releases, also to provide feedback
13:33 sneumann and as developer of some MS functionality (not too much, though)
13:33 * egonw is holding his breadth for the verdict....
13:33 sneumann (here it is :-) I found it a nightmare to have a working, buildable workspace in eclipse,
13:33 sneumann even in the days of svn
13:34 sneumann and I haven't dared to try the same in git world.
13:34 sneumann Too many different locations IMHO.
13:34 egonw yes, that's an area where Eclipse unfortunately excels ... :(
13:34 egonw we are working on improving that
13:34 egonw using Buckminster
13:34 sneumann Currently, I am more the "simple user" role
13:34 egonw once that is operational, it can be used to pull together all the requirements
13:35 sneumann hence looking for a mostly working bioclipse installation,
13:35 sneumann runtime only -- no sources.
13:35 egonw binary download?
13:35 CIA-51 bioclipse.cheminformatics: Egon Willighagen 2.2.x * rb760c89 / (73 files in 21 dirs): Removed plugins which are now found in bioclipse.core - http://bit.ly/2ZCr8D
13:35 sneumann would I download 2.1.1 and try to continuously use the update sites ?
13:35 sneumann during the early days it was usually a new full install.
13:35 sneumann has that improved ?
13:36 sneumann during the early (beta1-beta4) days it was usually a new full install.
13:36 egonw we have had 2.0.1 and 2.0.2 on an update site
13:36 egonw yeah, it depends on changes to the target platform, I think
13:36 egonw but I think 2.1.0 and 2.1.1 are separate binary download too...
13:37 sneumann so with 2.1.x it will be new installs most of the time ?
13:37 egonw olass: how did this work again? when does one need to create a new binary bioclipse core, instead of putting updates on the update site?
13:37 olass egonw: when we change platform-specific plugins
13:37 olass or core deps
13:38 olass liek a new Eclipse 3.5 version
13:38 olass over 3.4
13:38 egonw 3.5.1 over 3.5 not?
13:38 olass maybe, not sure. Hopefully not
13:38 egonw indeed
13:38 olass but until we havea release on SF I will build new binaries
13:38 olass devel version will not be supported
13:38 egonw ... with update sites
13:39 olass right
13:39 egonw :)
13:39 olass it isa pain managing multiple versions on an update site with deps
13:39 olass it tends to grow very large
13:39 olass egonw: can I pull core now and find webservices?
13:39 egonw yes, you should
13:40 egonw 2.2.x branch
13:40 olass yup
13:40 sneumann Next question: is there a way to calculate an AM1 or PM3 structure optimisation in Bioclipse ?
13:40 sneumann Like MOPAC does ?
13:40 olass we really should add MOPAC support to Bioclipse
13:41 olass bug 1672 is about MOPAC
13:41 olass sneumann: do you have experience with mopac?
13:41 olass egonw: do you have exp with mopac?
13:41 sneumann yes and no.
13:41 sneumann I want some structure minimised, including their protonated form.
13:42 sneumann So I have the uncharged molfile, and next I need to (manually for now)
13:42 egonw olass: I have very little mopac experience
13:42 sneumann protonate them, that's where I want to use the Bioclipse editor for ;-)
13:42 sneumann We have Sybyl here, which can launch MOPAC.
13:43 sneumann And finally I need to get MOPACs / Sybyls result.txt into some form
13:43 sneumann to continue with CDK.
13:43 * sneumann does not like proprietary packages
13:44 olass sneumann++
13:45 olass sneumann: I like your use case
13:45 olass could we formulate that in a bug or on a wiki page?
13:45 olass right now it's not possible for me to assist
13:45 olass egonw: ping
13:45 egonw pong
13:46 olass egonw: the packages swt.render.extra do not have any src
13:46 egonw I suggest we port the ghemical plugins from bc1
13:46 egonw ghemical uses mopac, IIRC
13:46 egonw olass: no, not yet... they will...
13:46 olass they do not compile
13:47 egonw I know
13:47 egonw need to talk with Gpox about this...
13:47 olass you have non-compiling stuff in 2.2.x?
13:47 olass why not a branch?
13:47 egonw I was hoping we'd make the moving of that code before the 2.2 release
13:47 egonw laziness
13:48 jonalv laziness--
13:48 egonw yes, the bastard
13:51 * sneumann just aptitude install ghemical mopac7-bin
13:51 sneumann see you next week
13:51 sneumann bye
13:55 olass sneumann: bye
13:56 olass egonw: damn, I forgot how to retrieve new branches from git remote :(
13:56 olass git fetch does not seem todo it?
13:56 egonw git branch -r
13:56 egonw git checkout -b foo remote/branch
13:56 egonw possibly first: git fetch remote
13:56 egonw or
13:56 olass does not masak have a 2.2.x branch in bioinformatics?
13:56 egonw git fetch remove branch
13:56 egonw dunno
13:58 egonw no, he has not
14:00 CIA-51 bioclipse.core: Ola Spjuth 2.2.x * r7b44917 / features/net.bioclipse.core_feature/feature.xml : Added net.bc.webservices to core feature. - http://bit.ly/1aNl40
14:11 olass egonw: can we read PDBs with CDKmanager for now?
14:11 egonw no
14:11 olass egonw: does CDK support reading multiple concatenaded PDBs from file?
14:11 egonw not sure
14:11 egonw let me check
14:11 olass thx
14:12 egonw olass: it might
14:12 olass :)
14:12 olass PDBReader?
14:12 egonw not entirely sure
14:12 olass I'll give it a try
14:12 egonw the API indicates it could be possible
14:12 olass lol
14:12 egonw allows reading a ICHemFile
14:12 egonw but that might simply because of the PDB data model
14:13 egonw it's very much oriented at PDB entries...
14:13 egonw so, I'd say it would not
14:14 egonw but it may just be a handy spin off...
14:14 egonw hard to tell
14:16 olass egonw: PDBReader is not in cdk.io?
14:16 olass ah, found module pdb
14:16 egonw right
14:16 olass strange that the writer is in io
14:19 egonw :)
14:19 egonw indeed
14:19 egonw but I am pretty sure the are mutually incompatible
14:20 egonw so in some wicked kind of way, it actually makes sense :)
14:36 olass egonw: what is the regexp to query for END and arbitrary spaces+newline?
14:37 egonw END\s+[\n|\r]+
14:37 olass thx
14:40 olass egonw: how does CDK treat a PDB with several models? several ACs?
14:40 egonw should be a list of IChemModel's
14:42 olass what is the superstructure?
14:42 olass An IAtomContainer or IMolecule?
14:42 egonw I would go for IAC
14:42 olass so an IAC can contain multiple chemmodels?
14:42 olass ok
15:38 olass egonw: about RMSD and multiple tanimoto, how much time do you expect? I am just asking since you said you might be away entire next week...
15:40 egonw dunno yet
15:40 egonw will keep you informed
15:41 bjonnh joined #bioclipse
15:41 bjonnh Hi there
15:41 bjonnh I'm writing a mass spectrometry database for my lab purposes
15:41 bjonnh and I'm looking for a format for the database
15:41 olass bjonnh: interesting
15:42 olass egonw is probable the one to ask
15:42 olass I am not so much into MS
15:42 bjonnh I thinked about mzxml, but I don't know if it's really fine for treated datas (no spectrum, only peaks m/z and amplitude)
15:43 olass egonw: is sneumann not working with mzxml?
15:43 egonw bjonnh: where are you from?
15:43 egonw there is also a group in Leiden involved in mass spec in bioclipse
15:43 bjonnh egonw, France
15:44 egonw metabolomics ?
15:44 bjonnh not really
15:44 bjonnh phytochemistry
15:44 bjonnh especially polyphenols
15:49 bjonnh but I don't know anything about java
15:49 bjonnh I'm a python coder
15:49 olass joined #bioclipse
15:50 bjonnh ERROR - Widget disposed too early!
15:50 bjonnh ???
15:50 egonw yeah, that happens to me sometimes too...
15:50 bjonnh need to restart ?
15:51 bjonnh doesn't work
15:51 olass bjonnh: can you reproduce that?
15:51 olass it is a bug that needs to be fixed
15:51 bjonnh every time I try to start bioclips
15:51 bjonnh :p
15:51 egonw how did you get here? are you running the binary, or from eclipse?
15:51 bjonnh x86_64
15:51 bjonnh the binary
15:52 olass could you paste a stacktrace in a pastebin?
15:52 bjonnh bioclipse.2.0.0.20090520.linux.gtk.x86_64.zip
15:52 olass hopefully solved in 2.2.x branch
15:53 olass RC1 will be out on tuesday
15:53 olass if all goes well :)
15:53 bjonnh http://www.bjonnh.net/share/trace.txt
15:53 zarah bjonnh's link is also http://tinyurl.com/yjq5bfb
15:54 bjonnh http://this.is.a.test
15:55 bjonnh so I need to install eclipse and everything to use 2.2
15:55 bjonnh :(
15:59 egonw 2.0 is known to work on 64 linux
16:00 egonw I have that setting too
16:00 egonw bjonnh: I know that stack trace...
16:01 egonw google for "XPCOM error -2147467262"
16:01 zarah egonw: http://rbtech.blogspot.com/2009/01/sti​ck-with-masses-eclipse-341-xpcom.html
16:01 egonw there is an idea at http://dev.eclipse.org/newslists​/news.eclipse.birt/msg29253.html
16:02 zarah egonw's link is also http://tinyurl.com/ygru6og
17:05 edrin left #bioclipse
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18:03 sneumann hi, are there any hidden 64bit versions of bioclipse-2.1.1.v20091002-linux.gtk.x86.tar.gz ?
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