Camelia, the Perl 6 bug

IRC log for #cdk, 2008-11-04

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

All times shown according to UTC.

Time Nick Message
05:51 jbrefort joined #cdk
05:54 thomas_ku joined #cdk
08:04 thomas_ku moin
08:04 zarah hi thomas_ku
08:17 egonw joined #cdk
09:03 jonalv joined #cdk
10:37 gilleain joined #cdk
11:11 jonalv joined #cdk
12:21 gilleain joined #cdk
13:14 jonalv joined #cdk
14:42 jpansanel joined #cdk
15:02 CIA-38 cdk: egonw * r12997 /cdk/branches/cdk-1.2.x/src/META-​INF/test-fingerprint.cdkdepends: Added missing dep
17:27 CIA-38 cdk: rajarshi * r12998 /cdk/branches/cdk-1.2.x/src/test/org/openscience​/cdk/fingerprint/ExtendedFingerprinterTest.java: report the diff if there is one
18:16 carsten joined #cdk
18:42 jackygrahamez joined #cdk
18:45 egonw joined #cdk
18:45 jackygrahamez hi
18:45 zarah hi jackygrahamez
18:45 jackygrahamez hi zarah
18:46 jackygrahamez I'm trying to figure out if cdk does what I'm looking for
18:46 egonw zarah is a friendly bot
18:46 egonw what would you like to do?
18:47 egonw btw, hi :)
18:47 jackygrahamez Thanks, I want an interface where users can create molecules and I can generate files in some standard molecular formats such as xyz, mol2, pdb
18:47 jackygrahamez 3d molecular formats
18:48 jackygrahamez I got the jchempaint integrated
18:48 jackygrahamez though it looks like that can only generate 2d representations in mol format
18:49 egonw well, JChemPaint is a 2D editor...
18:49 egonw you might find Bioclipse interesting
18:49 egonw which integrates both JChemPaint and Jmol
18:50 egonw check: http://chem-bla-ics.blogspot.com/2008/10/b​ioclipse2-scripting-1-from-smiles-to.html
18:50 zarah egonw's link is also http://tinyurl.com/56pa7o
18:50 jackygrahamez I was looking at that briefly, any chance it integrates into webpages like an applet or java web start?
18:50 egonw though it is not web based
18:50 jackygrahamez I see
18:50 egonw no, unfortunately not
18:51 egonw 3D structure generation typically requires a DB with templates for the ring structures
18:51 egonw those are difficult
18:51 egonw CDK has one
18:51 egonw it's about 3.5MB
18:51 egonw so, difficult to use as applet
18:51 egonw you might want to use a webservice for hook up the 2D drawing with Jmol's 3D visualisation
18:52 egonw you should be able to call the SOAP service with JavaScript
18:53 jackygrahamez So if I understand you, it takes a 2d representation and makes a serries of guesses to transform it into a 3d?
18:57 egonw yes
18:57 egonw though it's not really trial and error
19:03 jackygrahamez I don't really see how it works, is there a java method that converts formats?
19:07 egonw no, not in the current applet
19:10 jackygrahamez I was playing with the jchempaint and trying to use those bond angles that are perpendicular to the plane and seeing if it creates 3d representations. Apparently it does not. It appears to me, Mol format only treats the z axis as zero when you getMolFile from the applet
19:11 jackygrahamez so I see how you can convert this using openbabel but it looks like it would make everything flat
19:12 egonw yes, JChemPaint is a 2D drawing applet, not 3D drawing
19:13 jackygrahamez I could always integrate either nci diversity set or pub chem as a source for templates
19:14 jackygrahamez if I wanted to modify existing structures, would there be a good web application?
19:14 egonw I think any template library would be too large for applet purposes
19:14 egonw 2D or 3D?
19:15 jackygrahamez 3D
19:15 egonw I'm not aware of a applet to edit 3D molecules
19:15 egonw though with some extras this is possible
19:15 egonw but not with a single applet
19:15 jackygrahamez which extras?
19:16 egonw mom
19:16 jackygrahamez ? are you talking about my mom :-)
19:16 egonw [mom]ent
19:17 egonw check this page:
19:17 egonw http://wetche.cmbi.ru.nl/cgi-bin/jm​oledit.pl?fname=/usr/local/home2/we​tche/organic/datfiles/ethane12.dat
19:17 zarah egonw's link is also http://tinyurl.com/5abkxl
19:18 jackygrahamez cool I will bookmark that
19:19 jackygrahamez That's a good idea. I just looked at the source. I did not think of having a text field linked to a jmol window.
19:20 jackygrahamez I'm off to vote
19:21 egonw ok, happy to hear that :)

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