Camelia, the Perl 6 bug

IRC log for #cdk, 2010-09-28

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

All times shown according to UTC.

Time Nick Message
01:09 s9asad latest paper citing the CDK http://www.ncbi.nlm.nih.gov/pubmed/20850456
01:09 s9asad happy anniversary !
01:09 s9asad left #cdk
03:02 azeem_ joined #cdk
03:04 azeem left #cdk
03:54 sneumann_ joined #cdk
03:59 azeem joined #cdk
04:01 azeem_ left #cdk
04:01 sneumann_ left #cdk
05:05 egonw joined #cdk
05:25 egonw left #cdk
05:32 egonw joined #cdk
05:37 sneumann joined #cdk
05:58 bag__ joined #cdk
06:04 jbrefort joined #cdk
06:16 egonw left #cdk
06:17 egonw joined #cdk
06:51 Gpox joined #cdk
06:56 bag__ left #cdk
07:27 mgerlich joined #cdk
07:59 s9asad joined #cdk
08:09 egonw moin
08:09 zarah hi egonw
08:18 s9asad left #cdk
09:10 s9asad joined #cdk
09:30 jbrefort left #cdk
09:51 kml joined #cdk
09:52 kml hi
09:52 zarah privet kml
09:52 kml happy birthday CDK!
09:52 egonw thanx kml
09:53 kml I'm just a fan, but I can leave if this is private...
09:54 egonw oh, no... please stay around...
09:54 egonw this channel is not private at all...
09:54 egonw actually... everything is logged and put publicly online at:
09:54 egonw http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
09:54 egonw can you elaborate on 'fan' ?
09:54 kml wow, nice
09:54 egonw are you using the CDK? or using some piece of software that uses the CDK?
09:55 egonw or promoting other open source cheminformatics software?
09:55 kml I'm just a casual usur of CDK
09:55 egonw cool
09:55 egonw we always welcome any feedback very much...
09:55 kml I use other tools more though
09:55 egonw particularly if we do something really wrong :)
09:56 egonw what's your scientific domain?
09:56 kml oh, by the way, I'm Karol... the same as on the shapado QA
09:56 kml from cclib
09:56 kml :)
09:56 egonw ah, ic... welcome :)
09:57 egonw cclib is also noel, right?
09:57 egonw he was here yesterday
09:57 kml yeah, mainly Noel, Adam T. and me
09:58 egonw I saw there was a strong interest in seeing a CML output
09:58 egonw would love to see that too...
09:58 egonw then #cdk and #bioclipse can focus on just supporting CMLComp
09:59 kml yes... but cclib has been mostly idle for 1-2 years, maybe that will change in the future
09:59 kml I'm also on the BO mailing list, but don't really participate
10:00 kml anyway... as far as CDK is concerned, the fact it is Java discourages me most
10:00 egonw fair...
10:00 egonw well, there are python and ruby wrappers too :)
10:00 egonw and groovy, clojure, ...
10:00 kml it's ok to use, but in my job I often need to modify the source, and I don't like dabbling in java
10:01 kml yes, of course, there are wrappers
10:01 egonw seriously... I understand...
10:01 egonw I speak fortran, C, C++, perl too...
10:01 egonw but languages get rusty, and doing stuff in your native language is just so much quicker...
10:02 kml sure
10:03 kml assembler ;)
10:03 egonw yeah, did that too, a very, very long time ago...
10:03 egonw felt kind of cool, to program the CPU directly...
10:10 kml I think I've used CDK mostly for looking at active sites
10:10 kml any plans in that direction?
10:11 egonw I do not know if someone is actively working in that area right now...
10:11 egonw not seen any publications in that domain either...
10:11 egonw you could ask on cdk-user...
10:12 kml okay
10:24 zarah left #cdk
10:24 zarah joined #cdk
10:51 s9asad left #cdk
12:06 maclean joined #cdk
12:09 maclean egonw : 2pm CET?
12:09 egonw yes
12:09 egonw which is now
12:09 maclean oh!
12:09 maclean sorry.
12:10 egonw 2pm CEST
12:10 egonw but Lars is not online yet...
12:11 maclean yes, I saw. that's why I assumed it was 3pm GMT, not 1pm GMT (or BST, or whatever)
12:11 maclean It's not so hard to work out really :)
12:12 maclean oh, and BasicAtomGenerator is unit tested, the others will foolow. I guess I'll pull-request you when it's fully done?
12:12 egonw sounds good
12:13 egonw I'll look at it very soon
12:14 maclean well you have some time - my initial estimate of "finished on Sunday" was clearly wildly optimistic :)
12:17 jbrefort joined #cdk
13:15 Gpox left #cdk
13:16 Gpox joined #cdk
13:20 s9asad joined #cdk
13:21 Gpox left #cdk
13:31 s9asad hello
13:31 zarah privet s9asad
13:32 s9asad how can I calculate oxidation number of atom/molecule/atomcontainer using CDK
13:32 s9asad ?
13:33 egonw ummm...
13:34 egonw see http://github.com/egonw/odk/blob/master/src​/main/net/sf/cdk/tools/CreateAtomTypes.java
13:35 zarah egonw's link is also http://tinyurl.com/35cqdgm
13:37 maclean Is that ODK code making CDK code?
13:37 egonw no, it's ODK code creating ODK code :)
13:37 egonw but taking CDK atom types as input
13:37 s9asad thanks egon :-)
13:38 maclean egonw : Ah. I see. I think.
13:38 s9asad so basically int oxidationState = electronCount + formalCharge;
13:39 egonw yes
13:39 egonw for atom types...
13:39 egonw not necessarily for atoms
13:40 s9asad atomcontainer
13:40 egonw those do not have ox states anyway
13:40 egonw neither do molecules
13:41 s9asad how will I know that the oxidation number has changed in a reaction  (sorry for the query as I am not a chemist)
13:41 s9asad between reactant and product?
13:42 s9asad something to do with molecular formula?
13:43 egonw no, not at all...
13:43 egonw you'd do atom type perception on both sides
13:43 egonw and compare atom types
13:43 s9asad an exmp plz
13:43 s9asad in terms of cdk i mean
13:44 egonw Fe(II) -> Fe(III)
13:44 s9asad aha
13:44 egonw first would have Ox 2, latter Ox 3
13:44 s9asad yes
13:44 egonw Fe, no neighbors, 2+ for first
13:44 egonw Fe, no neighbors, 3+ for second
13:45 s9asad so one has to iterate over the atoms in the container
13:45 egonw sure
13:45 egonw oxidation state is a property of the atom type
13:46 s9asad get the formal charge and electron count and then difference between summation of reactant and product will show the change
13:47 s9asad awesome, thanks for increasing my chem knowledge
13:49 maclean heheh. to make a ring of size N : "for i in range(N): ring.addBond(i, ((i + i) % N))"
13:57 egonw Dan on the CDK history http://www.openscience.org/blog/?p=428
14:00 kml that whiteboard sessions looks fun :)
14:01 s9asad left #cdk
14:03 maclean I like RENDERER. That's a keyword for me at the moment.
14:03 egonw :)
14:06 maclean So what connection is there between Dan's group and Robert Hanson?
14:09 egonw the Dr. Who's of Jmol: Dan, Bradley, Egon, Miguel, Robert
14:10 maclean Right, yes.
14:11 egonw three blog posts on #cdk10 now...
14:11 egonw https://sourceforge.net/apps/mediaw​iki/cdk/index.php?title=10th_Annive​rsary#Coverage_of_10_years_of_CDK
14:14 maclean Ah, in fact one is in Indiana, the other in Miniapolis. Minni... well, 600 km away.
14:43 maclean hmmm. I actually used wolfram|alpha (tm etc) for a chemical question:
14:43 maclean http://www.wolframalpha.com/input/?i​=which+element+is+the+most+dense%3F
14:43 zarah maclean's link is also http://tinyurl.com/2u9clup
14:48 egonw lovely...
14:52 s9asad joined #cdk
15:28 s9asad left #cdk
15:43 maclean left #cdk
15:50 jbrefort left #cdk
16:11 s9asad joined #cdk
16:13 sneumann left #cdk
16:34 s9asad left #cdk
16:43 jbrefort joined #cdk
19:09 kml good night cdk'ers!
19:11 kml left #cdk
19:35 s9asad joined #cdk
19:44 s9asad left #cdk
19:57 bag__ joined #cdk
20:17 jbrefort left #cdk
20:51 bag__ left #cdk
21:23 egonw left #cdk

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