Camelia, the Perl 6 bug

IRC log for #cdk, 2009-08-03

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All times shown according to UTC.

Time Nick Message
00:34 CIA-72 cdk: Egon Willighagen cdk-1.2.x * r4bf822d / src/main/net/sf/cdk/tools/MakeJavafilesFiles.java :
00:34 CIA-72 cdk: Added support for 'public enum's
00:34 CIA-72 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/7FgnT
01:20 CIA-72 cdk: Rajarshi Guha cdk-1.2.x * rc888773 / (2 files in 2 dirs): Fixed a wrong javadoc tag. Also removed svn tag in the SMARTS parser JJT file, replaced with git tag - http://bit.ly/1H3RCr
01:20 CIA-72 cdk: Rajarshi Guha cdk-1.2.x * re0304bf / src/main/org/openscience/cdk/tools/manip​ulator/AtomContainerSetManipulator.java : Fixed Javadocs error - http://bit.ly/u0eOI
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08:10 CIA-72 cdk: egonw * r14693 /cdk-taverna-paper/trunk/cd​k-taverna/bmc_article.tex: Updated my address to UU, and removed CUBIC for all of us
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11:15 jonalv After some heavy testing of my database built upon CDK I find myself looking at Bond.contains
11:15 jonalv I spend a huge amount of execution time in that method.
11:17 jonalv it seems to want to have a hash somehow. Can anyone comment?
11:41 egonw I looked at that over the holidays...
11:41 egonw and used Map
11:42 egonw because the most use of contains() is from getConnectedFoo()
11:42 egonw using Map there, however, does not seem to increase performance really :(
11:43 egonw suggested patched that do improve are most welcome!
11:46 jonalv egonw: but the array in Bond is protected and (probably) used by a zillion children classes.
11:46 jonalv egonw: what approach do cdk have to equals and hashcode?
11:47 egonw not :(
11:48 egonw there is some use, but onconsistent...
11:48 jonalv egonw: oh you used a Map in getConnectedAtomsList?
11:48 egonw also the array may be protected, but not supposed to be used directly
11:48 jonalv egonw: I was just about to test that...
11:48 egonw yes, tried that
11:48 egonw but with no success
11:48 egonw did not improve things
11:48 jonalv but I don't think that will give much of a boost
11:48 jonalv the loop is still there...
11:48 egonw I can send you the patches, though
11:50 jonalv egonw: I would like to see that array as private
11:50 jonalv egonw: is that possible or impossible?
11:50 jonalv if it were private we could keep a Map beside it cashing things and maybe speeding things up a bit...
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11:54 egonw well, try it.. and see if things still compile
11:54 egonw please use from the command line:
11:54 egonw ant clean dist-all test-dist-all
11:55 egonw (or the equivalent from inside eclipse)
11:55 jonalv egonw: I am going to try a crazy thing with a LinkedHashSet instead and see if I can get in compiling...
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11:56 egonw ack
11:56 egonw jonalv++
12:35 jonalv egonw: I went from 60s to 208s. Not exactly what I would call an optimization... :(
12:36 egonw hehehehe
12:36 jpansanel moin
12:36 zarah ni hao jpansanel
12:36 egonw yeah, code performance is not really an intuitive science
12:36 egonw hi jpansanel
12:58 jonalv hm I made a mistake. correct was more lie 100s. Still not an optimization though :(
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20:17 CIA-72 cdk: thomaskuhn * r14694 /cdk-taverna-paper/trunk/cdk-taverna/ (9 files in 2 dirs): Done some work
21:12 CIA-72 cdk: egonw * r14695 /cdk-taverna-paper/trunk/cd​k-taverna/bmc_article.bib: Fixed syntax: and between each author
21:13 CIA-72 cdk: egonw * r14696 /cdk-taverna-paper/trunk/cd​k-taverna/bmc_article.tex: Added remark with extra info on the claim of being the first open source cheminfo workflow environment

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