Camelia, the Perl 6 bug

IRC log for #cdk, 2008-02-13

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All times shown according to UTC.

Time Nick Message
00:30 dleidert joined #cdk
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07:08 rojasm joined #cdk
07:11 egonw joined #cdk
07:11 egonw bbl
07:12 rojasm moin egonw
07:15 rojasm egonw: could you give me !again! the command that I have to write for merging from trunk to branches. Is it correct
07:15 rojasm svn merge -r 10046:1081 https://cdk.svn.sourceforge​.net/svnroot/cdk/trunk/cdk "Synched with trunk; merged 10046:10081"
07:26 CIA-18 cdk: miguelrojasch * r10082 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (9 files in 8 dirs): Synched with trunk; merged 10046:10081
07:54 egonw rojasm: I'll wait with fixing radical atom types, pending the @cdk.bug lines in the JavaDoc...
07:54 egonw will look at CMLSpect now
08:00 masak joined #cdk
08:00 rojasm egonw ok
08:15 rojasm egonw: to create a branch:
08:16 egonw svn copy http://bla/trunk/cdk http://bla/branches/miguelrojash/removemfa/
08:16 egonw possibly with -m, as in:
08:16 rojasm svn copy https://cdk.svn.sourceforge.net/svnroot/cd​k/branches/miguelrojasch/mfTools-removing
08:16 egonw svn copy -m "Set up branch for ..." http://bla/trunk/cdk http://bla/branches/miguelrojash/removemfa/
08:17 rojasm ok, thanks
08:17 egonw rojasm: no, better use my command
08:17 egonw to copy directly in the SVN repos
08:17 egonw instead of local checkouts
08:17 rojasm ok
08:17 rojasm I didn't read your comment before I was finishing writing :(
08:18 rojasm I do how you said
08:18 egonw ack :)
08:24 CIA-18 cdk: miguelrojasch * r10083 /branches/miguelrojasch/removemfa/: Set up branch for removing the MFAnalyser class. It will be replaced for MolecularFormulaManipulator class
08:26 de_maas joined #cdk
08:30 egonw de_maas: jpansanel has started working on JJs...
08:31 egonw de_maas: so, if you plan to work on JJs too... please make sure to update the JJ tracking system to indicate that you started working on a particular JJ
08:53 egonw jpansanel: ping
08:56 jonalv joined #cdk
09:06 egonw hi jonalv
09:06 jonalv hi egonw
09:07 jpansanel pong
09:08 jpansanel egonw : do you want that I start JJ 1802589 again, so I can send you a more simple patch ?
09:10 egonw yes, please do
09:10 egonw jpansanel: you could simple do this:
09:10 egonw edit with a plain text editor your current patch...
09:10 egonw and remove those bits not related to spelling errors...
09:10 egonw though they might overlap...
09:10 egonw in which case a fresh start is indeed ebtter...
09:10 egonw jpansanel: you can also use a branch for that...
09:11 egonw then your work is even more visible to the world...
09:11 egonw because you can then commit your patches yourself...
09:12 egonw and you get some repository fame
09:14 egonw but you need to email your SF account name to the cdk-devel ML
09:15 jpansanel ok
09:19 jpansanel it's certainly a good idea for a task like spelling
09:19 jpansanel (many files to edit)
09:23 jpansanel subclispe plugin is really great
09:25 steinbeck joined #cdk
09:25 steinbeck moin
09:25 egonw hi steinbeck
09:26 jpansanel moin steinbeck
09:29 jpansanel egonw : if spelling fix, I thing we can replace constructured by constructor
09:29 jpansanel i.e. :
09:29 jpansanel Once instantiated all field not filled by passing parameters * to the constructured are null.
09:29 jpansanel Once instantiated all field not filled by passing parameters * to the constructor are null.
09:34 egonw looks good
09:36 jpansanel ok
09:42 egonw crappy R XML library...
09:46 egonw https://bugs.launchpad.net/ubunt​u/+source/r-cran-xml/+bug/191502
09:48 steinbeck left #cdk
09:55 egonw bloody hell...
09:55 egonw r-cran-xml is seriously broken...
09:56 egonw bbl
10:32 alexandros joined #cdk
10:40 jpansanel egonw : I've updated the patch
10:41 CIA-18 cdk: miguelrojasch * r10084 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (3 files in 3 dirs): added new mechanism, reactionProcess and tests for tautomerization.
11:13 steinbeck joined #cdk
12:21 CIA-18 cdk: miguelrojasch * r10085 /branches/miguelrojasch/reaction/src/​org/openscience/cdk/test/reaction/typ​e/TautomerizationReactionTest.java: added reverse process of the tautomerization in the test
12:25 egonw joined #cdk
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13:33 MarkFiers joined #cdk
13:34 egonw hi MarkFiers
13:34 MarkFiers Hi Egon,
13:35 MarkFiers To continue my previous question....
13:35 egonw was just about to spend some time with the kids...
13:35 egonw but please go ahaed :)
13:35 MarkFiers ah.. in that case I'll try later
13:35 egonw btw, please test that 'make' works for you
13:35 egonw no, go ahead...
13:35 egonw they're still busy...
13:36 MarkFiers ok.. was wondering about data formats...
13:36 egonw right
13:36 egonw mzData/mzXML has not enough scope...
13:36 MarkFiers I agree
13:36 egonw not sure about openMS... but supporting that would neither be difficult nor time consuming...
13:36 MarkFiers but a lot of support for some feeatures
13:36 egonw with respect to XCMS, I think that CMLSpect has the more features...
13:36 egonw yes, indeed
13:37 egonw will email details about CMLSpect tonight...
13:37 MarkFiers I don't understand cmlspect wel enough yet, We can get the data in there, but wouldn't we be the only ones doing so, at the moment?
13:38 egonw ah...
13:38 MarkFiers and, as you wrote, we can get experiment info in there using scalar/metadata, but that's not in a standardize manner
13:38 egonw to some extend, yes
13:38 egonw JSpecView and Bioclipse support CMLSpect too...
13:39 egonw not so many other programs, I guess...
13:39 MarkFiers but, do they support LCMS data in CMLSpect?
13:39 MarkFiers CMLSpect is a rather broadly defined standard
13:39 egonw to some extend, yes
13:39 egonw some tweaking might be needed...
13:39 egonw that said...
13:39 MarkFiers you're going to your kids.. right?
13:40 egonw not sure what programs support openms-consensus, other than openms
13:40 egonw yes, will go to the kids now...
13:40 egonw will email
13:40 MarkFiers good... speak to you tomorrow...
13:40 MarkFiers cheers
14:21 MarkFiers left #cdk
14:43 CIA-18 cdk: miguelrojasch * r10086 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (34 files in 4 dirs): To initiate a mechanism is necessary to add a IMoleculeSet instead of IMolecule
15:10 jbrefort joined #cdk
15:37 CIA-18 bioclipse: jonalv * r4883 /branches/bioclipse2/core/plugins​/net.bioclipse.recording.tests/: Deleted net.bioclipse.recording.tests. It contained some broken integration testing code that needs a later version of Spring DM to even have a chance to work. We might need to do some other sort of integration testing.
15:45 carsten joined #cdk
16:03 CIA-18 cdk: miguelrojasch * r10087 /branches/miguelrojasch/reaction/src/org/openscien​ce/cdk/test/atomtype/ReactionStructuresTest.java: test atomtype matching for metals
16:08 CIA-18 cdk: miguelrojasch * r10088 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (6 files in 4 dirs): added new mechanism, reactionProcess and tests for adduction (protonation).
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16:25 CIA-18 bioclipse: jonalv * r4884 /branches/bioclipse2/chemoinformatics/net.​bioclipse.cdk.business.test/src/net/biocli​pse/cdk/business/test/CDKManagerTest.java: clearifying comment
16:30 dleidert joined #cdk
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17:55 egonw moin
17:56 egonw steinbeck: are things settling down?
17:56 egonw or still damn busy? :)
17:57 steinbeck ah egonw
17:57 steinbeck well, don't think that's gonna settle down
17:57 steinbeck will get worse  :-)
17:57 egonw :)
17:58 steinbeck still waiting for new computer and office furniture
17:58 steinbeck these things take too long
17:58 egonw ah
17:59 egonw and research lines?
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19:02 CIA-18 jmol: hansonr * r8991 /trunk/Jmol/src/org/jmol/ (popup/JmolPopup.java viewer/Jmol.properties): version=11.5.7_dev # bug fix: menu select element missing SELECT command
19:04 CIA-18 jmol: hansonr * r8992 /branches/v11_4/Jmol/src/org/jmol/ (popup/JmolPopup.java viewer/Jmol.properties): version=11.4.RC5_dev # bug fix: menu select element missing SELECT command
20:04 CIA-18 cdk: miguelrojasch * r10089 /branches/miguelrojasch/reaction/src/o​rg/openscience/cdk/reaction/mechanism/ (4 files): cleaning concepts
20:25 CIA-18 cdk: miguelrojasch * r10090 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (8 files in 3 dirs): changed the name of Adduction to AdductionLP which specifies more specific according to adduction from LonePair orbitals.
20:27 egonw rojasm: what is adduction?
20:28 rojasm uff. Ok, is the mechanism for the protonation
20:29 egonw that is, what does adduction mean?
20:29 egonw is it related to:
20:29 rojasm come from adduct
20:29 egonw http://en.wikipedia.org/wiki/Adduction
20:30 egonw is it a real word?
20:30 egonw never seen it...
20:30 egonw but no MS expert yet :)
20:30 rojasm me either
20:31 egonw http://www.ingentaconnect.com/content/els​/00092797/1996/00000102/00000002/art03738
20:31 rojasm do you think should be other name?
20:31 egonw this last link suggests not
20:31 egonw seems a proper word :)
20:32 rojasm :)
20:32 egonw google seems quite a few hits on 'sodium adduction'
20:33 egonw http://www.sciencedirect.com/science?_ob=Art​icleURL&_udi=B6VND-4BKB71J-1&_user=1​0&_rdoc=1&_fmt=&_orig=search&amp​;_sort=d&view=c&_acct=C000050221&amp​;_version=1&_urlVersion=0&_userid=10​&md5=286a7603869ea4b2c7e52a7ac3402767
20:34 rojasm I will put too the Li+ and K+
20:35 rojasm they are the three used usually
20:35 egonw do you really need them as C=[O+]-Na ?
20:35 egonw why not simply: C=O.[Na+] ?
20:35 egonw I'm happier about the last... an ionic bond, rather than a convalent dative bond
20:36 rojasm ok, but with proton also?
20:37 egonw no
20:37 egonw there I'm happy with  C=[O+]-H
20:37 rojasm But then I need to have two different mechanisms
20:38 egonw hehehe
20:38 egonw ummm...
20:38 egonw well...
20:38 egonw which metals are this...
20:38 egonw O-Li is already supported...
20:38 egonw and R=[O+]-R too...
20:38 egonw so why not -Na...
20:38 egonw if that makes your live easier...
20:38 egonw maybe it is reasonable...
20:39 egonw I wish a was a bit more fluent with QM
20:39 rojasm The problem is that when you starts to predict reaction with the adduct Na depends a lot of where is the Na
20:40 rojasm if I put as adduct general
20:40 egonw well... it is true that kations are quite well located...
20:40 rojasm then I can not continue with the subsequent reactions
20:40 egonw as a student I studied prefered K2+ positions on DNA crystal structures...
20:40 egonw and they were quite fixed...
20:41 egonw indicating a strong, almost dative covalent bond...
20:41 egonw OK, I'm convinced...
20:41 rojasm :) buff
20:41 egonw let's see if we can back it up with MolBase...
20:46 egonw http://winter.group.shef.ac.uk​/molbase/compound.html?id=603
20:46 egonw but seems to be more like a salt
20:47 egonw mmm :(
20:57 rojasm may be there is a differences between description in organic or inorganic
20:57 egonw possibly...
20:57 egonw MolBase seems fairly accurate...
20:58 egonw I'd be happy with C=[O+]-Na
20:58 egonw add to that bug report you filed which counter ions you'd like covalently bound
21:00 rojasm ok
21:00 egonw btw, you were correct about the dates...
21:00 egonw just to make sure: I'll be there Tue/Wed, with a presentation on Wed when Thomas will be there
21:02 rojasm mm 26(Wednesday)-27(Thursday). Good it should be if you could do the presentation morning 27 Thursday
21:03 egonw now I'm confused...
21:03 rojasm We said 26-27, isn't it?
21:04 egonw feb, right?
21:04 rojasm ostres
21:04 rojasm now I see
21:04 egonw 26-27 Feb is Tues-Wed
21:04 rojasm stranges
21:05 rojasm you are correct
21:05 rojasm 26(Tues) 27 (Wed)
21:05 rojasm 27 morning
21:05 egonw ack :)
21:05 egonw right
21:06 rojasm Nevertheless I will sent you again mail tomorrow
21:06 rojasm but It was sure 26 27
21:10 rojasm I am creating a ontology description for all reactions and mechanisms. At the moment on the paper. How do you think I could do it
21:10 rojasm only in xml
21:11 egonw ummm...
21:11 egonw I have some ideas...
21:11 egonw but not so much now...
21:12 egonw cracking my brains on CMLSpect for XCMS output
21:13 rojasm ups.
21:16 egonw but I think I'm close to something sensible...
21:16 egonw not bad for one day of analysis...
21:17 rojasm that is good
22:27 egonw ok, bed time
22:27 rojasm cu egonw
22:28 egonw rojasm: forwarded you the email on CMLSpect for XCMS output
22:28 rojasm ok. I will have a look
22:28 egonw will look at CMLSpect for spectral trees in more detail on friday
22:28 egonw including the requirements you emailed
22:29 CIA-31 joined #cdk
22:30 rojasm thanks
22:38 CIA-31 cdk: miguelrojasch * r10092 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (7 files in 4 dirs): new Reaction for Adduction of protons in double bonds
22:54 Conrad joined #cdk
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23:18 CIA-31 cdk: miguelrojasch * r10093 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (14 files in 7 dirs): changed name of the class BrekingBond* to HeterolyticCleavage*
23:21 CIA-31 cdk: miguelrojasch * r10094 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (10 files in 5 dirs): changed name of the class CleavageBond* to HomolyticCleavage*
23:25 CIA-31 jmol: aherraez * r8993 /trunk/Jmol-web/source/doc/script/ (promotion1.es.txt promotion1.fr.txt promotion1.nl.txt): fix localization in promotion script
23:34 CIA-31 cdk: miguelrojasch * r10095 /branches/miguelrojasch/reaction/sr​c/org/openscience/cdk/reaction/type​/HeterolyticCleavageReaction.java: added ACTIVE_CENTER for atoms as well
23:37 CIA-31 cdk: miguelrojasch * r10096 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (2 files in 2 dirs): added the correct atom mapping
23:44 alexandros_ joined #cdk
23:45 CIA-31 cdk: miguelrojasch * r10097 /branches/miguelrojasch/reaction/s​rc/org/openscience/cdk/reaction/ty​pe/HomolyticCleavageReaction.java: added the correct atom mapping

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