Camelia, the Perl 6 bug

IRC log for #cdk, 2010-04-06

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All times shown according to UTC.

Time Nick Message
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09:13 egonw grmph...
09:13 egonw found rendercontrol classes in the renderextra module :(
09:19 jbrefort joined #cdk
09:30 sneumann egonw: CDKitty @ metabolom-aholics is not calculating my mwOf: Kitten went asleep ?
09:30 sneumann ah, didn't work with cut&paste
09:34 egonw it's triggered by some events...
09:34 egonw and adding a space behind the MF is important
09:35 egonw otherwise, it will replace a mass when you just finished typing 'C'
09:35 egonw replace *with* a mass
09:44 egonw I'd need to check if mwOf: does the molecular mass
09:44 egonw or monoisotopic mass
09:45 egonw I think that explains .8 versus .35
09:45 egonw think = guess
09:45 egonw the rest might be the used isotopic masses...
09:45 egonw not sure what list of isotopic masses is used by chemcalc
10:27 egonw Gpox: ping
10:28 egonw o, sushi
10:28 egonw mmm...
11:38 Gpox egonw: pong
11:38 egonw ah, hej :)
11:39 egonw I set up a stub module for control-impl-swt
11:39 egonw and was wondering if there is easy to port to CDK-JChemPaint code for SWT mouse events
11:40 Gpox SWTMouseEventRelay
11:44 egonw ack
11:45 egonw I'll try to do that for CDK-JChemPaint 10
11:45 egonw just released 9
11:45 egonw nigthly is rerunning
11:46 egonw enough JChemPaint for now
12:28 CIA-45 cdk: Egon Willighagen master * r8142ae5 / src/test/org/openscience/cdk/in​terfaces/AbstractBondTest.java : Fixed a typo in the test method name - http://bit.ly/9W5D5b
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13:59 s9asad Hi All
13:59 zarah ni hao s9asad
13:59 s9asad Can anyone help me to parse this smile in the CDK
13:59 s9asad SmilesParser sp = new SmilesParser(DefaultChemObj​ectBuilder.getInstance());
13:59 s9asad IAtomContainer target = sp.parseSmiles("C\C=C/OCC=C");
14:01 egonw hi s9asad
14:01 s9asad Hi Egon
14:03 egonw s9asad: try:
14:03 egonw sp.parseSmiles("C\\C=C/OCC=C");
14:04 s9asad you basically pre-process the input?
14:05 egonw only if you have the SMILES string hardcoded in the java source
14:06 egonw as a \ in Java source code is an escape character
14:07 s9asad hmm thanks
14:08 s9asad is there a way to parse stereo information in the CDK via SMILEs?
14:09 stain egonw: hi, are you still working on that XMPP execution thingie?
14:09 stain you were making a Taverna plugin at some point..?
14:10 egonw yeah, I wrote a Taverna plugin...
14:10 stain was that for 2.0?
14:10 egonw need to port that to 2.1, but no time and no student to work on it
14:11 stain all right :)
14:11 egonw yes: http://github.com/egonw/xws-taverna
14:11 zarah egonw's link is also http://tinyurl.com/ye9o8al
14:11 stain I could have a look
14:14 egonw patches most welcome :)
14:14 egonw seriously... when I requested commit rights, I was hoping to push things to the Taverna repository...
14:14 stain but time is always an issue, right.. ;)
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15:05 egonw IBond bond = new Bond();
15:06 egonw Assert.assertEquals(2, bond.getAtomCount()); // WTF ?!?!
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15:52 stain egonw: can you have a bond with a single atom?
15:52 stain Alan asks if you had a ock at the Smack library
15:52 stain look
15:52 stain no c..
15:52 egonw Smack?
15:52 egonw no, don't think so...
15:52 egonw URL?
15:52 egonw a single atom bond?
15:52 egonw no, that does not exist
15:52 stain http://www.igniterealtime.org/projects/smack/
15:52 zarah stain's link is also http://tinyurl.com/n99bha
15:53 egonw it would be lone pair, or single electron (aka radical orbital)
15:53 egonw does it support the IO-DATA XEP?
15:54 stain that's too technical for me ;)  I don't know why Alan mentioned that library
15:56 egonw johannes wrote a library for the IO-DATA XEP, but forgot what XMPP library he was using underneath
16:04 stain http://xmpp.org/extensions/xep-0244.html
16:04 zarah stain's link is also http://tinyurl.com/49jly3
16:11 egonw stain: that's the one
16:12 egonw ok, dinner time here in Sweden
16:12 egonw bbl
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