Camelia, the Perl 6 bug

IRC log for #cdk, 2007-10-09

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All times shown according to UTC.

Time Nick Message
03:18 CIA-31 jmol: hansonr * r8391 /trunk/Jmol/src/org/jmol/ (60 files in 7 dirs): (log message trimmed)
03:18 CIA-31 jmol: all renderers now represented as export generators,
03:18 CIA-31 jmol: and all exporters ready for implementations.
03:18 CIA-31 jmol: This involved:
03:18 CIA-31 jmol: 1. creating interface JmolRendererInterface.
03:18 CIA-31 jmol: 2. abstracting much of Graphics3D.java to make Export3D.java
03:18 CIA-31 jmol: 3. adding code in Export3D that mirrors that in Graphics3D
04:06 CIA-31 jmol: hansonr * r8392 /trunk/Jmol/src/org/jmol/modelset/Atom.java: oops -- almost lost properties
05:19 jbrefort joined #cdk
05:43 rojasm joined #cdk
06:35 carsten joined #cdk
07:48 jonalv joined #cdk
08:18 egonw joined #cdk
08:19 egonw moin
08:20 carsten Moin Ego
08:20 carsten n
08:20 egonw hi carsten
08:21 carsten KDE 3.5.8 tagged, KDE 4.0b3 totday or something like that
08:21 egonw ha, will there be a 3.5.8, nice :)
08:21 carsten yes, and the ChangeLog is huge
08:21 carsten many improvements in khtml for example
08:22 carsten good for us, as I won't switch to kde4 until 4.1.x is out
08:23 carsten egonw: yesterday I finished my Referendariat. So I am officially done with that
08:23 egonw ah, excellent! congratulations!
08:24 carsten thanks :)
08:24 carsten Next week we are moving to Oldfenburg
08:25 masak joined #cdk
11:42 CIA-31 jmol: hansonr * r8393 /trunk/Jmol/src/org/jmol/ (modelset/ModelSet.java viewer/Jmol.properties): version=11.3.31 # bug fix: calculate aromatic for N and O refined
11:43 dleidert joined #cdk
12:06 egonw hi dleidert
12:06 * egonw is now going for lunch
12:06 egonw bbl
12:19 CIA-31 jmol: nicove * r8394 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
12:28 jpansanel hello
12:52 CIA-31 bioclipse: jonalv * r3936 /trunk/playground/plugins/net.bioclipse.database/ (7 files in 3 dirs): Created interfaces for database related items
12:52 carsten joined #cdk
12:58 jpansanel hi carsten
12:58 carsten moin
12:58 jpansanel carsten : I've added many saccharides
12:59 carsten carsten@moinmoin:~/svn> svn up blueobelisk/
12:59 carsten Revision 131.
12:59 carsten carsten@moinmoin:~/svn> svn up bodr/
12:59 carsten Revision 4.
13:21 egonw joined #cdk
13:31 carsten_ joined #cdk
14:45 CIA-31 bioclipse: jonalv * r3937 /trunk/playground/plugins/ (5 files in 5 dirs): Extension point for databases now works for structuredb.
15:46 carsten joined #cdk
15:47 CIA-31 bioclipse: jonalv * r3938 /trunk/playground/plugins/net.bioclipse.keyring.te​sts/tests/net/bioclipse/keyring/KeyRingTest.java: minor spelling change
18:16 egonw joined #cdk
18:17 egonw moin
18:33 egonw hi rojasm
18:33 egonw how are you?
18:33 rojasm Hi egonw
18:34 rojasm trying to finish a report for tomorrow
18:34 rojasm :(
18:34 egonw ah :)
18:34 rojasm und you how was the taverna worshop
18:34 egonw very nice
18:34 rapodaca joined #cdk
18:34 rojasm some new news
18:34 egonw taverna2 looks very good
18:34 egonw he rapodaca
18:34 egonw how did you end up here? :)
18:35 rapodaca hello, egon
18:35 egonw yes, taverna2 is really new..
18:35 rapodaca thought i'd give it a try
18:35 egonw with a horribly better design than taverna1
18:35 egonw rapodaca: you're most welcome here :)
18:35 egonw I'm happy to see you online
18:35 rojasm that means that you think it could be used for us
18:35 egonw it's a bit quite now...
18:35 rojasm ok
18:36 egonw during EU office hours some 10 people are normally online
18:36 egonw rojasm: there is a BioRange project in NL... which seems likely to be using Taverna for metabolomics...
18:36 rojasm you will present some think in you group about what you think
18:36 egonw our group is involved in that too...
18:36 rojasm ok
18:37 rapodaca i've been playing around w/ cdk inchi support via jruby
18:37 rapodaca looks very nice
18:38 egonw it works?
18:38 egonw I have not played with it much...
18:38 rapodaca beautifully
18:38 egonw had no time for that yet..
18:38 egonw I played with KNIME(.org)...
18:38 egonw and wrote my first node for that...
18:38 rapodaca only problem is InChI<->SMILES
18:38 rapodaca does cdk SMILES support stereochemistry yet?
18:38 egonw which gets a .mol file from ChemSpider using the InChIKey
18:39 egonw IIRC: writing yes, reading no
18:39 egonw or the other way around...
18:39 egonw rapodaca: would be easy to add...
18:39 egonw using it would be another thing...
18:39 egonw CDK has a IAtomParity interface...
18:39 egonw to store stereochemistry in the way SMILES does...
18:41 rapodaca molfile->inchi works great... even w/ stereo
18:41 egonw sorry... the WLAN in my hotel room is not so good...
18:41 egonw only in the bathroom it is workable...
18:41 egonw there is wiring too... but got no UTP cable :(
18:42 egonw am I back on IRC?
18:42 rojasm egonw: BioRange is not more or less forcussed in genomics and not metabolomics?
18:42 egonw rojasm: apparently not
18:42 egonw I do not know all the details though...
18:42 egonw am my messages reaching you?
18:43 rapodaca yes
18:43 egonw oh, good :)
18:43 egonw am=are
18:43 rojasm :) not
18:43 rojasm :(
18:43 egonw huh?
18:44 egonw anyway...
18:44 egonw ola sat down with a Taverna developer and is now able to run a taverna workflow...
18:44 egonw which will be part of Bioclipse...
18:44 rapodaca just wondering... does molfile->SMILES retain stereochemistry in cdk?
18:45 rojasm ok sounds great
18:45 rapodaca didn't look like it, but i'm not sure
18:45 egonw rapodaca: I think the molfile reader does not read stereochemistry...
18:45 egonw rapodaca: in many cases it's just wedge bonds...
18:46 rapodaca hmm... thx...
18:46 rapodaca if i wanted to convert from molfile w/ stereochemistry...
18:46 rapodaca oops...
18:46 egonw rojasm: and I had a crash course in BioMoby today...
18:46 egonw from Anika from MPI in Cologne
18:47 egonw oops?
18:47 egonw rm ~* ?
18:47 rojasm I think I remenber
18:49 rapodaca egonw: na, just started asking the wrong question...
18:49 egonw ah, ok :)
18:50 rapodaca i'm looking for a way to convert stereo inchis to smiles...
18:50 rapodaca sounds like cdk doesn't support that now...
18:50 egonw no, might not
18:50 rapodaca smiles reader/writer doesn't support stereo...
18:51 rapodaca so that's a bit of work that would need to be done...
18:51 rapodaca has anyone started something like tha before?
18:51 egonw why SMILES?
18:51 rapodaca molfile requires coordinates...
18:51 egonw the OpenSMILES discussion showed plenty of limitations of the spec
18:51 egonw CML?
18:51 egonw that does not require coordinates
18:52 rapodaca if you convert inchi->molfile, stereo info is lost...
18:52 rapodaca hmm.. can you point me to a cml file w/ tetrahedral stereo...
18:52 rapodaca not needing coordinates to interpet?
18:52 egonw w/ -> that's with or without?
18:52 rapodaca with
18:53 egonw mom
18:54 rapodaca re OpenSMILES - true... I was just looking for a quick way to do it...
18:54 egonw btw. will need to go offline soon...
18:55 egonw only WLAN in bathroom, but no power there...
18:55 egonw battery is almost empty :(
18:55 rapodaca no prob... me to let's catch up later...
18:55 egonw I'll look up the CML stereo example before going offline
18:55 rapodaca great
18:55 rapodaca left #cdk
18:55 egonw rojasm: btw, any luck with the bugs I reported?
18:56 rojasm I made some progress but it is not finish
18:56 rojasm sorry
18:56 egonw np
18:56 egonw anything I can help with?
18:57 rojasm I think it can handle it
18:57 rojasm I can
18:58 egonw OK :)
18:58 egonw (I know you can :)
19:00 egonw OK, will go offline now...
19:00 egonw not sure if I will be back online...
19:00 egonw might hit bed very soon now actually...
19:00 egonw bye
19:22 rojasm left #cdk
20:47 CIA-31 bioclipse: shk3 * r3939 /trunk/plugins/net.bioclipse.spectrum/sr​c/net/bioclipse/plugins/bc_spectrum/view​s/spectrumCharts/PeakSpectrumView.java: peak spectrum view shows up

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