Camelia, the Perl 6 bug

IRC log for #cdk, 2010-08-14

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All times shown according to UTC.

Time Nick Message
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11:27 maclean ahhhh. git revert -n HEAD. ahhh.
11:40 maclean egonw : reviewed/signoff-ed on a javadoc patch (with a tiny fix) - what now?
11:40 egonw super!
11:40 egonw git format-patch -1
11:40 egonw or
11:40 egonw git format-patch -2
11:41 egonw and attached those to the patch report
11:41 maclean ok
11:52 maclean er... egonw : I don't seem to have permission to add stuff to patches. Or, at least not those ones...
11:52 egonw mom
11:54 egonw ok, can you try again?
11:55 maclean aha. works now, takk.
12:23 CIA-50 cdk: Egon Willighagen cdk-1.2.x * r38873dc / src/main/org/openscience/cdk​/tools/CDKHydrogenAdder.java :
12:23 CIA-50 cdk: Updated the JavaDoc for the atoms() Iterable API change (fixes #3034824)
12:23 CIA-50 cdk: Signed-off-by: maclean <gilleain.torrance@gmail.com> - http://bit.ly/b1KbZr
12:24 egonw maclean: please use the 'Group' field next time to mark the patch as 'Accepted'
12:24 maclean ok
12:24 egonw otherwise, thanx for the review!
12:24 egonw very, very much appreciated
12:25 * maclean is now On branch patch-3043782
12:26 egonw got to reboot my KDE session
12:26 egonw brb
12:28 egonw joined #cdk
12:29 egonw and I'm back
13:12 egonw maclean: oh, and if you need the patch author to make changes, please mark it as 'Needs Revisions"
13:12 maclean ah, ok.
13:12 egonw replied to your comment on the DeduceBondSystemTool patch
13:12 egonw that failing unit test is not new
13:12 egonw see: http://pele.farmbio.uu.se/nig​htly/test/result-smiles.html
13:12 zarah egonw's link is also http://tinyurl.com/2dzmlex
13:12 egonw but not fixed either
13:14 maclean I suspect that it is testing for one of the possible bond systems, and not another.
13:17 egonw good point
13:17 egonw I have not checked that
13:21 maclean It's assuming C1(=O)C=CC(=O)C=C1 and getting C1(O)=CC=C(O)C=C1
13:23 egonw you could update the test to see if the ring has the right number of DOUBLE and SINGLE bonds instead
13:24 egonw and that the alternate or so
13:24 maclean Hmm. Actually these two forms have different numbers of single/double bonds.
13:25 egonw oh... ah indeed...
13:25 egonw yeah, this is tautomerism...
13:25 egonw correct
13:25 egonw well, then it should be the first
13:25 maclean I guess the form with singly-bonded oxygens has charges on the oxygens?
13:25 egonw this is the well known example...
13:25 egonw this compound is not aromatic
13:26 maclean Ah
13:26 egonw benzoquinone
13:26 maclean 1,4-
13:26 egonw http://pubchem.ncbi.nlm.nih.gov/summar​y/summary.cgi?cid=4650&amp;loc=ec_rcs
13:26 zarah egonw's link is also http://tinyurl.com/3xl7m8t
13:30 maclean So, this test relates to my question of what the DeduceBondSystemTool is actually trying to do...
13:31 egonw given hybridization information, resolve where the double bonds should be
13:31 egonw basically comes down to:
13:31 egonw for linear systems, start at one end and alternate
13:31 egonw for ring systems, make a arbitrary cut
13:31 egonw and mix the lot
13:35 maclean_ joined #cdk
13:36 maclean_ Well, from a code point of view, it will take 1,4-BZQ and generate 3 bonds for the benzene ring.
13:36 maclean_ There's really no possibility for the code to pass the test - it's not really a bug.
13:41 maclean Actually, no that's not true. It generates all sorts of possibilities:
13:41 maclean [[[0-1, 2-3, 4-5], [1-2, 3-4, 5-0], [0-1, 2-3], [0-1, 4-5], [1-2, 3-4], [1-2, 0-5], [2-3, 4-5], [0-5, 3-4], [0-1, 3-4], [1-2, 4-5], [2-3, 0-5], [0-1], [1-2], [2-3], [3-4], [4-5], [5-0], []]]
13:46 maclean Ah, ok, which is all orbits of the colorings of the line graph :)
13:46 maclean So, [1-2, 4-5] is the one that is wanted.
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13:53 egonw maclean++
13:54 maclean Well, this doesn't really fix it...
14:11 egonw btw, the x in front of the method name indicates that under a JUnit3 world it was not actually run...
14:11 egonw perhaps the test was flawed for a very long time already...
14:11 egonw then again... someone wrote it for some reason at some point, I guess...
14:15 maclean ah, I see.
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17:08 CIA-50 cdk: maclean master * r7959947 / .classpath :
17:08 CIA-50 cdk: Exporting the signatures jar
17:08 CIA-50 cdk: Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://bit.ly/cejKPk
17:08 maclean ta
17:08 egonw yeah, some patches are really easy to review :)
17:09 maclean well, true.
17:14 maclean egonw: What do you think of : "interface ChemicalFilter<T extends IChemObject> { public boolean accept(T); }"
17:14 egonw sounds like something olas would be happy with
17:14 egonw any planned implementations?
17:14 egonw prefiltering for QSAR?
17:15 maclean For the multiple bond stuff.
17:15 egonw ok
17:15 egonw cdk.filter ?
17:15 egonw ok, going to have dinner now
17:15 egonw bbl
17:15 maclean You generate possibilities, and filter out those that don't work, chemically.
17:15 maclean ok, cu.
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18:28 maclean egonw : My blog post was wrong, I think. It doesn't generate B as the C-O bonds are not considered.
18:29 egonw I was only slightly worried about that
18:29 maclean :)
18:30 maclean Well, I'm re-writing the DBST and the ring bonds are fine.
18:30 egonw you will make very many people happy
18:30 maclean But working out what other bonds should be considered is more tricky.
18:31 egonw true
18:32 maclean Isn't phenol an example of where the ring bonds delocalise with the C-O?
18:32 maclean Because, bonds attached to the ring could be considered. Then there's the problem of bonds that connect rings...
18:33 maclean Aargh.
18:33 egonw yes, non-trivial
18:33 egonw this is why I was thinking about SINGLE_OR_DOUBLE
18:33 egonw set by the SMILES parser
18:33 egonw because then one would know which atoms should be considered...
18:33 egonw but that was correctly rejected
18:34 egonw order = UNKNOWN
18:34 egonw that would still work
18:34 egonw then the DBST would only look at bonds with UNKNOWN bond order
18:35 maclean Hmmm. That could be okay.
18:40 egonw but that does require some hacking on the SMILESParser...
18:40 egonw if you would consider it...
18:40 egonw make sure to make that a separate patch, with proper tests etc...
18:41 egonw I will consider doing it when I am back from Boston, but not before
18:42 maclean Totally fine.
18:42 maclean At the moment, it's all in a separate project, not even a cdk branch.
18:56 egonw maclean: related to functional and unit tests... http://chem-bla-ics.blogspot.com/2010/08/s​pecifying-unit-test-dependencies-with.html
18:56 zarah egonw's link is also http://tinyurl.com/38smwq3
18:57 maclean Hah : "I don't know how useful it is, but if you try it, please come back to tell us whether it was useful."
18:57 maclean :D
18:58 maclean This reminds me of a family member's tendency to take things from the fridge and say "I think this has gone off - will you try it and see?"
19:01 egonw :)
19:22 egonw maclean: http://www.fatvat.co.uk/2009/​05/jvisualvm-and-clojure.html
19:22 zarah egonw's link is also http://tinyurl.com/n7nqdr
19:22 egonw should likely work with any Java program, not just clojure
19:25 maclean hmmm. interesting. seems like it's already installed with my jdk. nice interface.
19:26 egonw sudo apt-get install visualvm
19:52 * maclean is off to get some food. bye
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