Camelia, the Perl 6 bug

IRC log for #cdk, 2010-10-08

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All times shown according to UTC.

Time Nick Message
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06:42 CIA-98 cdk: Rajarshi Guha master * r851f899 / (11 files in 6 dirs):
06:42 CIA-98 cdk: New package for fragmentation algorithms - currently exhaustive and Murcko.
06:42 CIA-98 cdk: Added unit tests and updated code to use the new Murcko fragmenters. Removed old
06:42 CIA-98 cdk: murcko fragmenter which was unmaintainable. Additional unit tests have been
06:42 CIA-98 cdk: added and Javadocs have been improved
06:42 CIA-98 cdk: Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://bit.ly/9Y2MO3
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08:46 maclean hi
08:46 zarah hello maclean, you fantastic person you
09:06 egonw hej maclean
09:06 maclean hej egonw
09:10 egonw maclean: do you think you have time to look at this patch once more: 3043569 CIP subset implementation ?
09:10 egonw and let me know if I need to make further revisions?
09:10 maclean Hmm. Possibly over the weekend.
09:10 maclean Has it changed?
09:11 egonw see my comment
09:11 maclean Ok.
09:11 maclean Thanks for reviewing the aromaticity patch, btw.
09:13 maclean Oh, right. It changed months ago. Sorry, the cycle of change/re-review is easily broken.
09:20 egonw indeed...
09:20 egonw I got several older patches still in the queue :(
09:20 egonw such as RDF support ...
09:22 maclean That's because no-one understands RDF :P
09:22 egonw possibly...
09:22 egonw but reviewing the patch should still be possible...
09:23 maclean yes and no. It's quite hard to review others code - especially so if you don't understand what it is doing.
09:23 maclean I mean, you can catch typos but not much else.
09:25 egonw well, the JavaDoc should explain things a bit...
09:25 egonw the exact algorithm is something else...
09:26 maclean I suppose. And the 'user interface' of the code (method calls, and such).
09:27 egonw it's great if that is carefully reviewed too, but we are not entirely in the state yet, I think
09:27 egonw indeed.. a clear API is particularly important
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11:01 maclean http://vis.cs.ucdavis.edu/~​ogawa/research/storylines/
11:02 maclean (quick, before it gets /.ed :)
11:09 egonw already too late
11:09 maclean :( oh well.
11:10 egonw they posted at 5:11am
11:10 maclean was a visualisation of software projects as lines.
11:10 egonw so, I guess about an hour ago
11:10 maclean as graphs, that is.
11:26 egonw but the 'y axis' is not really reflecting something, right?
11:26 egonw or is it...
11:26 egonw would be cool of that would be Java package or so...
11:27 maclean time, I think.
11:27 egonw that's the horizontal axis, not?
11:27 maclean oh, right yes.
11:28 maclean (this is probably part of the reason why cdk-jcp used to draw molecules upside-down...)
11:34 egonw hehehehe
11:34 egonw ok, lunch time
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13:44 egonw http://chem-bla-ics.blogspot.com/​2010/10/100th-cdk-2003-paper.html
13:45 maclean Hah. Fantastic (but completely unrelated) paper title:
13:45 maclean "On being fired: experiences of patient-initiated termination of the patient-physician relationship in palliative medicine"
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13:50 egonw MorganNaming ... as in Morgan numbering?
13:52 maclean Er.. yes.
13:52 maclean Also a SignatureTree inner class... sigh.
13:55 maclean Heheh. Vindicated by a code comment : "NOTE: Apparent contradiction in paper at this point...." :D
13:57 maclean On-line papers should really have a mechanism that makes href links from author names to websites.
13:59 maclean sorry, I'll stop going on about this now, and get back to work.
14:00 egonw :)
14:00 egonw http://chem-bla-ics.blogspot.com/​2010/10/cdk-book-in-progress.html
14:00 egonw maclean: that's what the output looks like :)
14:00 maclean oooh.
14:01 maclean "herefore" should have been "therefore", I guess? (Rather than "heretofore" :)
14:01 egonw yes, tack
14:02 maclean Nicht zu denken.
14:03 maclean Is "it" in groovy like $_ in perl? Or self/this?
14:04 egonw yeah, like $_
14:04 egonw I could also write
14:04 egonw foreach (list) { it -> print it }
14:04 maclean right, yes.
14:05 egonw foreach (list) { whatever -> print whatever }
14:06 egonw foreach (atoms) { atom -> print atom }
14:07 maclean Yes, much like ruby's foreach |x| { print x }
14:07 maclean Anyway, what does this mean:
14:07 maclean Recent papers posted to egonw's library by the author Crabtree:JD.
14:07 egonw where do you see that?
14:07 maclean Other people post stuff to your library?
14:07 egonw that sounds like CiteULie...?
14:07 egonw no, I hope not
14:08 maclean I googled the author of the 100th paper, and naturally enough you appear on the first page :)
14:08 maclean sorry, the lead author.
14:08 maclean http://www.citeulike.org/us​er/egonw/author/Crabtree:JD
14:09 egonw the 'by' refers to the paper, not the process
14:09 egonw indeed not too clear
14:09 maclean No, oh well.
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18:18 CIA-98 cdk: Rajarshi Guha master * r9b81123 / src/test/org/openscience/cdk/fra​gment/MurckoFragmenterTest.java : Added another unit test - http://bit.ly/cLYHjd
18:18 CIA-98 cdk: Rajarshi Guha master * rdf15ed7 / src/test/org/openscience/cdk/fra​gment/MurckoFragmenterTest.java : removed debug code and add another check in the unit test - http://bit.ly/aX4kZA
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19:30 egonw hej s9asad
19:30 egonw seen my blog?
19:30 s9asad Hi Egon
19:31 s9asad np
19:31 s9asad Just a min
19:31 s9asad let me check, today I was baby sitting..no time :-)
19:31 s9asad CDK Book in progress?
19:32 egonw no, the other one
19:32 s9asad The 100th CDK 2003 paper?
19:32 egonw about the 100th paper
19:32 egonw yeah, that one
19:32 egonw that's the 100th according to Web of Science
19:32 s9asad I see make sense
19:32 egonw but in particular, look at the paper itself..
19:32 s9asad good paper
19:34 s9asad This would be a good add on to the CDK
19:35 egonw yeah, I hope they will consider contributing back...
19:40 s9asad thanks for the SMSD review
19:40 s9asad any help on the orbital
19:41 egonw no, not yet...
19:41 egonw still working on reducing backlog
19:41 s9asad I see
19:43 s9asad did you read Rajarshi blog on the Fingerprint, very interesting
19:43 s9asad http://blog.rguha.net/?p=814#comments
19:44 egonw yes, I did
19:46 egonw had not seen your reply until just now
19:46 s9asad well just a thought
19:51 s9asad I was wondering if we can create a CDK FP based on the combination of SMARTs and hashed set
19:53 s9asad say 512 bits hashed and rest 512 as SMARTS with fixed bits
19:53 s9asad faster and powerful
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