Camelia, the Perl 6 bug

IRC log for #cdk, 2007-08-11

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All times shown according to UTC.

Time Nick Message
07:15 jbrefort joined #cdk
07:31 egonw joined #cdk
07:39 jbrefort joined #cdk
07:48 carsten joined #cdk
08:46 olas left #cdk
08:56 CIA-1 jmol: nicove * r8065 /trunk/Jmol-FAH/projects/p2427.xyz.gz: Folding@Home
08:56 jbrefort egonw, I tested my space groups file and found various errors, seems it's ok now, may I propose it for inclusion in bodr?
08:57 egonw absolutely...
08:57 jbrefort I wrote a test program and verified the groups are actually groups ;)
08:58 egonw cool :) blog about that...
09:03 jbrefort Hmm, I have no blog ;)
09:04 egonw maybe time to start one ? :)
09:04 jbrefort I'm not very inclined too
09:04 jbrefort to
09:05 * jbrefort does n ot like writing in general
09:05 egonw :)
09:31 * carsten thinks egonw or he should blog instead of jb :)
09:31 egonw yes, guess so :)
09:40 carsten egonw: could you paste "svn info elements.xml" for me?
09:40 carsten only the URL line
09:41 egonw http://cb.openmolecules.net/inchis.php -> 205 molecules now
09:41 lambdabot2 Title: Chemical blogspace - Chemical Compounds
09:43 edrin joined #cdk
09:50 egonw carsten: mom
09:58 jbrefort joined #cdk
09:58 egonw https://bodr.svn.sf.net/svnroot/bodr/trunk/bodr
10:02 jpansanel moin
10:04 egonw hi jpansanel
10:05 jpansanel egonw : the convention attribut is not yet qualified
10:05 jbrefort salut Jérôme
10:05 jpansanel salut Jean
10:05 jpansanel excellent les données pour les groupes spaciaux
10:06 jbrefort :)
10:06 jpansanel egonw : but is the synthax right ?
10:07 jbrefort changing the syntax is easy anyway
10:08 egonw not, stricly speaking you need to say which dictionary the entry points to...
10:09 jpansanel ok
10:09 jpansanel what would you suggest ?
10:11 egonw add xmlns:unit="http://url.for.units.dicts/" etc
10:15 jpansanel ok
10:18 jpansanel into molecule tag ?
10:25 egonw yes
10:27 egonw away for lunch
11:25 steinbeck joined #cdk
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14:12 jpansanel egonw : http://www.openscience.org/blog/?p=208
14:12 lambdabot2 Title: The OpenScience Project » Embedding Jmol applet in Wordpress posts
14:12 jpansanel did you know ?
14:12 jpansanel hehe
14:13 jpansanel lamdabot2
14:13 egonw yes, I think I've seen this
14:13 egonw I'm not using wordpress myself...
14:15 jpansanel and do you know the status of Jmol in Wikipedia ?
14:16 egonw no, good question...
14:27 jpansanel Nicolas is watching it ?
14:27 egonw ask him
14:27 egonw or blog about it...
14:28 egonw anything with wikipedia and Jmol in the title will get useful attention
14:30 jpansanel Ok
14:30 jpansanel I'll do it at least on monday
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20:15 egonw neksa: nice analysis of OSRA
20:17 neksa egonw: if only it was a library.
20:17 egonw yes... I guess it will be just that in the future...
20:17 neksa Strigi is a nice testbed for OSRA
20:17 egonw yeah, you could give the author a call...
20:18 egonw but I think this is too much for your GSoC work...
20:18 neksa yes, at least to ask him to put the code in a RCS
20:18 egonw right... propose SF
20:18 egonw then everyone can provide patches... for exmaple, to have it use autotools or cmake
20:19 egonw that's really important...
20:20 neksa egonw: it's very slow to analyze all the images. But it won't take much time to support OSRA once it becomes a library
20:20 egonw that's why threaded analyzing of jstreams would be nice...
20:21 egonw in addition to the 'only do chemical images' suggestion
20:21 neksa I'm not sure.
20:22 neksa if you have one CPU core it makes no difference
20:22 neksa and even if you have 2 CPU cores it makes no difference again. Because Strigi can run in threads.
20:24 egonw better would be a set up where one could run individual analyzers independently...
20:24 egonw is that not possible at this moment, already?
20:24 neksa the only reason for building a dependency tree could be sharing the data between analyzers
20:24 neksa It is possible
20:25 neksa all you need is a custom analyzerconfiguration, an example would be:
20:26 neksa xmlindexer/peranalyzerxml.cpp
20:28 egonw right, quite so...
20:29 egonw btw, did you see my commit with that SDF file, which cause a core dump with the current code in SVN?
20:32 neksa egonw: yes I did. atm I have a broken code, when I'm done I'll make a testcase for this file immediately.
20:33 egonw http://cb.openmolecules.net/inde​x.php?category=Summer%20Projects
20:33 lambdabot2 Title: Chemical blogspace - Summer Projects
20:39 shk3 joined #cdk
20:39 shk3 hi egonw
20:39 egonw hi shk3
20:39 egonw I was about to log out...
20:39 shk3 one question
20:40 egonw no problem
20:40 shk3 the smiles generator in nmrshiftdb no longer generates aromatic smiles
20:40 shk3 i. e. CC=CC=CC= instead of ccccccc
20:40 shk3 any idea about this?
20:40 shk3 any change you remember?
20:40 shk3 any flag in smilesgenerator I need to set?
20:41 egonw there is no flag at this moment, I think...
20:41 shk3 hm, so should work?
20:41 egonw yes, it now outputs CC=CC=CC=
20:42 shk3 oh, but that's wrong
20:42 shk3 :-(
20:42 egonw ... for my application
20:42 shk3 why that?
20:42 egonw you forgot to add that to your statement :)
20:43 shk3 no
20:43 shk3 it's wrong per se
20:43 shk3 in many cases, that gives different smiles for the same aromatic compound
20:44 egonw true, but see email list for rationale
20:44 shk3 hm, must have missed this
20:44 shk3 probably too much trouble with moving
21:55 CIA-1 cdk: shk3 * r8677 /branches/cdk-1.0.x/src/org/openscie​nce/cdk/smiles/SmilesGenerator.java: added a trigger to user aromaticity for smiles. Note this is important since without this the smiles generator will generate different smiles for identical molecules.
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