Camelia, the Perl 6 bug

IRC log for #cdk, 2010-08-17

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All times shown according to UTC.

Time Nick Message
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04:54 slyrus annoyingly CHEBI's SMILES strings and pubchem's dont match :(
04:56 slyrus I think trying to reproduce a supposedly canonical SMILES is a losing battle
04:57 slyrus and I'm annoyed that the INCHI spec seems to be so complex that no one has attempted to re-implement it
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07:40 s9asad Hi everyone, I was toying with pubchem fingerprint as implemented in the CDK
07:41 s9asad but for alot of molecules it takes ages
07:41 s9asad any clue?
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08:59 s9asad Hi egonw:
09:00 egonw s9asad: ask Rajarshi about the PubChem fingerprinter
09:00 s9asad aha
09:01 s9asad I was wondering, if can replace UIT with SMSD in the SMARTQueryTool
09:02 s9asad its seems to me thats the place where most of the computing time is spend
09:04 egonw please email cdk-devel to bring this up...
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15:04 maclean what's the difference between atom.formalCharge and atom.charge? (apart from Integer/Double...)
15:13 azeem_ Integer vs. Double would be quite a big difference already, no?
15:16 maclean :) This is true.
15:16 maclean I guess it means that you can specify fractional charges, but not fractional formal charges.
15:19 maclean Actually, wikipedia explains it quite well: http://en.wikipedia.org/wiki/Formal_charge
15:19 zarah maclean's link is also http://tinyurl.com/2dlqudh
15:39 egonw indeed... formal is [O-]
15:39 egonw getCharge() is for point charges e.g. from QM calculations
15:48 maclean Ah, indeed.
15:49 maclean public interface IChargeCalculator extends IElectronicPropertyCalculator {} - hmmm.... (tagging interface, I suppose)
15:51 maclean egonw : so what about oxidation state?
16:47 * slyrus decides that what the opensmiles spec calls canonical is completely bogus
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20:58 s9asad well some news to share, now CDK SMARTS used SMSD instead to UIT .
20:59 s9asad well as excepted the runtime is pretty impressive!
20:59 s9asad uses*
21:01 egonw s9asad: please blog!
21:01 egonw please, please, triple please
21:01 egonw that will certainly speed up the discussion
21:02 egonw it might even trigger Rajarshi to apply the current approved patches before the ACS meeting :)
21:02 s9asad :-)
21:02 s9asad sure
21:02 egonw s9asad: well done!
21:02 egonw you're get good CDK fame for this :)
21:03 s9asad Thanks, my pleasure
22:13 egonw s9asad: and feel free to RT this page too: http://egonw.github.com/acsrdf2010/
22:13 zarah egonw's link is also http://tinyurl.com/2475pon
22:13 egonw see the retweet button on the right hand side of that page

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