Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-07-25

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
07:11 sneumann__ joined #bioclipse
09:26 egonw joined #bioclipse
09:36 olass joined #bioclipse
09:37 olass hi
09:37 zarah oh hai olass
09:37 olass hi egonw
09:37 olass you got my email on the SMILES bug?
09:37 olass serious
09:37 olass and not so good
09:39 egonw no, still browsing my email
09:39 egonw got email from Maris, no DragonX license
09:40 egonw ok, I got it in front of me now
09:49 olass ok
09:49 * egonw just woke up... half an hour ago...
09:49 egonw finally some decent sleep
09:55 egonw BBQ today :)
10:31 * olass is in Trosa
10:36 * stain is in Bergen
10:37 * egonw is in Eindhoven
11:01 egonw olass: bug is not present in CDK 1.2.x in Git
11:07 olass but you could reproduce in bioclispe, right?
11:07 egonw did not try that yet
11:07 egonw I tend to work bottom up
11:07 egonw with these kind of bugs
11:17 egonw lunch time
11:23 sneumann__ joined #bioclipse
11:56 * olass is back from a lunch
12:38 * egonw suggests to remove 'bioclipse' from the SF download site...
12:38 egonw and rename 2.0.0.alpha02 to bioclipse2.0-alpha02
12:53 olass egonw: yes
12:53 olass egonw: any news on the critical bioclipse bug?
12:53 olass I really want to submit a patch
12:54 egonw looking at it...
12:54 olass egonw++
12:54 egonw yeah, feel free to submit a patch :)
12:54 olass :)
12:54 olass a bugfix on the update site :)
13:12 CIA-63 bioclipse.cheminformatics: Egon Willighagen 2.0.x * r969f831 / (2 files in 2 dirs):
13:12 CIA-63 bioclipse.cheminformatics: Fix for inconsistent atom typing from CML files created the FromSMILES wizard (closes #1434).
13:12 CIA-63 bioclipse.cheminformatics: * wizards now performs atom type perception
13:12 CIA-63 bioclipse.cheminformatics: * CDKMolecule.toCML() now saves atom type information, just like the CDKManager equivalent
13:13 CIA-63 bioclipse.cheminformatics: * atom types are correctly perceived from the SMILES (see upstream CDK patch #2826961),
13:13 CIA-63 bioclipse.cheminformatics:  and the problem is with atom typing starting from the CML (to be explored) - http://bit.ly/h3oiC
13:13 * egonw is now leaving for the BBQ
15:25 rajarshi joined #bioclipse
15:25 rajarshi hi olass
15:25 olass hi rajarshi
15:25 olass thanks for our reply
15:25 rajarshi np
15:25 olass replying as we speak :)
15:26 rajarshi I figured irc would be faster :)
15:26 olass SMILES handling was broken in Bioclipse 2 :(
15:26 olass yes
15:26 olass Egon fixed some things today
15:26 rajarshi aah ok
15:26 olass but this is clearly an error in Bioclipse
15:27 olass I will file another bug for egon if this second matter still persists
15:27 olass but he said something about a N fix in CDK atom typing...
15:27 rajarshi it might be as simple as making sure that the use aromaticity flag is set in the SMilesGenerator
15:28 rajarshi yes, that seems to have gone away in 1.2.x - I just add a unit test for it
15:28 olass great
15:29 olass oh, could you send me the bibtex entry for [YOUNG] Are the Chemical Structures in Your QSAR Correct? Douglas Young 1 *, Todd Martin 1, Raghuraman Venkatapathy 2, Paul Harten 1 QSAR & Combinatorial Science,Volume 27 Issue 11-12, Pages 1337 - 134
15:29 olass it is not in pubmed
15:29 olass else I need to type it
15:29 olass and I figured you probably had it in bibtex...
15:29 * olass is migrating to latex
15:29 rajarshi @article{Young:2008ab,
15:29 rajarshi Author = {Young, D. and Martin, T. and Venkatapathy, R. and Harten, P.},
15:29 rajarshi Journal = {QSAR Comb.~Sci.},
15:29 rajarshi Number = {11--12},
15:29 rajarshi Pages = {1337--1345},
15:29 rajarshi Title = {Are the Chemical Structures in Your {QSAR} Correct},
15:29 rajarshi Volume = {27},
15:29 rajarshi Year = {2008}}
15:29 rajarshi sorry
15:30 rajarshi mailed it
15:30 rajarshi aah, the joys of latex :) Serioisly, you're life will become *much* easier
15:31 olass oh, no, I always use latex
15:31 olass was just talking about this project form google docs :)
15:31 olass and while e are at it:
15:31 rajarshi aah, got it
15:31 olass Todeschini2002] please?
15:31 olass I only find the ref from 2000
15:31 rajarshi which one?
15:31 rajarshi handbook?
15:32 olass yes
15:32 rajarshi sent
15:32 olass thx
15:32 olass that should be it for now I think
15:32 rajarshi cool
16:45 wins joined #bioclipse
17:15 olass @pz 1436
17:15 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1436
18:02 sneumann__ joined #bioclipse
18:38 sneumann joined #bioclipse
21:47 * olass is tired
22:11 olass joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary