Camelia, the Perl 6 bug

IRC log for #cdk, 2008-09-12

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All times shown according to UTC.

Time Nick Message
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09:56 jpansanel moin
09:56 zarah hi jpansanel
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10:59 thomas_ku moin
10:59 zarah hi thomas_ku
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14:06 steinbeck thomas_ku: around?
14:07 steinbeck Would anyone have the number of descriptor classes and the total number of descriptors implemented therein?
14:07 steinbeck in CDK, that is?
14:13 thomas_ku yes
14:13 thomas_ku I am here
14:13 thomas_ku sent it to you via mail
14:13 thomas_ku QSAR descriptors (76, distributed into 42 molecular / 6 bond / 1 atom pair / 27 atomic)
14:13 thomas_ku QSAR descriptors (76, distributed into 42 molecular / 6 bond / 1 atom pair / 27 atomic)
14:14 thomas_ku not sure if this is what you want to know
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16:04 CIA-14 cdk: rajarshi * r12294 /cdk/branches/cdk-1.2.x/src/main/org/opens​cience/cdk/fingerprint/Fingerprinter.java:
16:04 CIA-14 cdk: Updated the method that converts 2-letter atom symbols to 1-letter symbols to
16:04 CIA-14 cdk: cover more 2-letter symbols. Also rewrote the code so that it's a little faster
16:04 CIA-14 cdk: and should take into account the fact that some elements will be more common
16:04 CIA-14 cdk: than others (but not rigorously tested)
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17:30 egonw moin
17:30 zarah hi egonw
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20:58 CIA-14 cdk: rajarshi * r12295 /cdk/branches/cdk-1.2.x/src/ (2 files in 2 dirs): Added missing test annotations and made the test a little more rigorous
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21:13 steinbeck Cheers
21:13 rguha hi
21:13 zarah hi rguha
21:13 rguha it's getting in good shape
21:13 steinbeck :-)
21:13 rguha I think I'm done with the prelim work section - I'll see about massaging the page limits tomorrow
21:13 steinbeck I still have hope
21:14 steinbeck ack
21:14 rguha regarding markush - is there any more to add? I didn't write in any details of what/how we'd do stuff
21:14 steinbeck I'll drop in tomorrow afternoon again. Will be online for the next 45 min to fix the spreadsheet in case we need it
21:14 steinbeck Markush...
21:14 rguha ok
21:15 steinbeck I'm studying an old article from 1991
21:15 steinbeck to see how what feature are there.
21:15 rguha the poster from ChemAxon might also provide pointers
21:15 steinbeck I hope to add something later
21:15 steinbeck which one was that again?
21:16 rguha OK, but after tonight I'll stop working on the GoogleDocs  -so if you need to add stuff it'd be best to send me the text in Word etc so I an put it in
21:16 rguha http://www.chemaxon.com/conf/Representation​_searching_and_enumeration_of%20Markush_str​uctures-from_molecules_towards_patents.pdf
21:16 steinbeck yes, with later I mean: In the next 45 min - in case I find the time
21:16 rguha http://www.chemaxon.com/conf/Representation​_searching_and_enumeration_of%20Markush_str​uctures-from_molecules_towards_patents.pdf
21:16 steinbeck ack
21:17 rguha ok
21:24 steinbeck rguha: do you remember how much percent of your time charged?
21:28 rguha 10%
21:28 rguha btw, do th CDK citations be an appendix?
21:31 steinbeck I thought they might be part of preliminary studies, but if there is an appendix, fine. I guess it will count as part of the 25 page in any case.
21:31 rguha hmm, tricky
21:31 rguha we should check with Barabara/Cindy
21:31 steinbeck yes, I thought so
21:32 rguha I think it's a good candidate for an appendix otherwise we might need to drop it
21:32 steinbeck ok. Why don't we try the appendix.
21:33 rguha OK, I'll keep it as a separate document for now
21:33 rguha and we can check with Barabara on Monday
21:34 rguha btw, when you regenerate the ChEbI FP's it'd be interesting to get some performance results
21:35 rguha hmm, no stereochemistry means that a good chunk of the SMARTS proposal has to be cut :(
21:43 steinbeck Ok, don't you think that a short paragraph on stereo will do?
21:43 steinbeck Not sure what exactly is missing.
21:44 steinbeck Another question: We are applying for  student and a developer indiana, right? How much time will the student take up?
21:45 rguha re: stereo, wht would the hort para indicate?
21:45 rguha At the very least, it'd have to layoutwhat we want to do - I was thinking of the Dietz rep, but I don't know enough
21:45 rguha regarding, what is missing: as far as I can see, there is no section on stereo!
21:47 rguha grad student will be 50%
21:47 rguha developer will be 100%
21:48 steinbeck Ack regarding the student - thanks.
21:48 rguha np
21:49 steinbeck I know it is not nice, but given the tight timing, I would probably just add the sentence that we are going to implement the stereo impl of the Dietz model. I can add the Diet citation now and you add the sentence :-)
21:50 rguha OK :)
21:55 steinbeck Ok, it is [Dietz1995]
21:55 rguha thanks
22:08 steinbeck rguha: I've finished the project time sheet (you should have access to it via http://spreadsheets.google.com/ccc?ke​y=pHbOE9fWI-6vF6JJWR5JlIw&hl=en)
22:09 steinbeck I think I'll drop all the "effort" lines in the "methods" part and reference this sheet. What do you think
22:09 steinbeck ?
22:10 rguha looks good
22:10 rguha ys, good idea
22:10 rguha btw, what are the units of numbers under my, david, your names?
22:10 rguha also what is david managing?
22:10 steinbeck This should be weeks in all cases
22:10 rguha aah ok
22:10 rguha can you add an entry for stereochemistry somewhere?
22:10 steinbeck dunno - I just assumed that he would also doing 10% of whatever
22:11 rguha aah ok
22:11 steinbeck stereochem done by indiana developer or student or EBI?
22:11 rguha I'd suggst EBI
22:11 steinbeck ack
22:11 rguha IU will be covering smmart/smikrs/pcores
22:12 rguha also Egon had started on a Dietz branch
22:12 rguha btw, a total week count of 712 means 13 years :)
22:12 rguha is that what is meant?
22:14 steinbeck I counted four full time developers 52 weeks per year time 3 time 4 plus our and the students part time.
22:14 steinbeck Maybe wrong :-)
22:14 steinbeck this is man-weeks
22:14 rguha aah, OK
22:14 rguha might want to mention that somewhere - could lead to shock for the reviewers :)
22:14 steinbeck hehe
22:15 * steinbeck is getting very tired. Too many numbers.  Will drop in tomorrow again.
22:16 rguha ok, good night
22:16 steinbeck good night. And thanks :-)
22:16 steinbeck left #cdk
22:19 CIA-14 cdk: rajarshi * r12299 /cdk/branches/cdk-1.2.x/src/test/org/opensc​ience/cdk/coverage/SmilesCoverageTest.java: Updated SMILES coverage test to use annotations
22:19 CIA-14 cdk: rajarshi * r12298 /cdk/branches/cdk-1.2.x/src/main/org/op​enscience/cdk/smiles/SmilesParser.java: added test annotations, added Javadocs
22:20 CIA-14 cdk: rajarshi * r12296 /cdk/branches/cdk-1.2.x/src/main/org/openscien​ce/cdk/tools/manipulator/BondManipulator.java: Cleaned up Javadocs
22:20 CIA-14 cdk: rajarshi * r12297 /cdk/branches/cdk-1.2.x/src/ (3 files in 3 dirs): Updated tests to JUnit4, added test annotations, added Javadocs
22:31 CIA-14 cdk: rajarshi * r12302 /cdk/branches/cdk-1.2.x/src/ (2 files in 2 dirs): Added more unit tests and test annotations
22:34 CIA-14 cdk: rajarshi * r12303 /cdk/branches/cdk-1.2.x/src/ (3 files in 3 dirs): Added more unit tests and test annotations

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