Camelia, the Perl 6 bug

IRC log for #cdk, 2009-05-25

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All times shown according to UTC.

Time Nick Message
04:16 bag joined #cdk
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09:42 egonw ok, release 1.2.3
09:42 rednael2 [CDK Twitter] me is wondering if #rednael is more happy about twits about #cdk #bioclipse and #metware now  http://twitter.com/egonwill​ighagen/statuses/1911120949
09:43 zarah rednael2's link is also http://tinyurl.com/o2mkdj
09:44 * egonw makes note that rednael should ignore bots as channel acitivity
09:46 maclean egonw : are we seriously going to have tweets re-broadcast to irc?
09:46 egonw sure
09:46 maclean because I really would prefer not to have that.
09:46 egonw as long as it keeps low traffic
09:46 egonw why?
09:47 maclean if I want to follow a twitter feed, I will sign up to twitter
09:47 maclean I don't, and I won't
09:47 maclean :)
09:47 maclean low traffic?
09:47 egonw fair point
09:47 maclean is it specific to certain things?
09:48 egonw it only RTs stuff with the #cdk hashtag
09:48 maclean hmmm. that's not so bad, I suppose.
09:49 egonw no, and if 'we' start to hate it, we just turn it off...
09:49 egonw life is one big experiment
09:49 maclean true
10:21 egonw CDK 1.2.3 being uploaded
10:25 maclean cool
10:32 egonw sent email to cdk-user
10:33 rednael2 [CDK Twitter] uploading #cdk 1.2.3 aka the 'Don't use this Renderer' release  http://twitter.com/egonwill​ighagen/statuses/1911343364
10:33 zarah rednael2's link is also http://tinyurl.com/pzp23r
10:34 * egonw is happy that rednael now only checks feeds when something happened on this channel
11:00 carsten joined #cdk
11:03 egonw hi carsten
11:05 carsten moin moin
11:05 egonw any new features in Kalzium in 4.3?
11:10 carsten no
11:11 carsten a couple of new things in 4.2, though
11:15 maclean egonw : I'm going to make a PVRNumberer class that will canonically number molecules according to a particular scheme
11:15 maclean do you think that it should take IMolecule s or IAtomContainer s?
11:16 * maclean should probably look at other cdk numbererers
11:17 egonw IMolecule
11:17 egonw because you require the input to be fully connected
11:17 egonw IMolecule does not enfore that, but imply it at least
11:17 egonw (recurrent theme :)
11:17 maclean indeed.
11:17 maclean well I guess it's a kind of documentation.
11:19 egonw right
11:19 maclean oh, and it should actually re-order the atoms, right?
11:19 maclean I mean, I can't think of a way of numbering using flags
11:20 maclean oh, no, there are properties, I suppose.
11:20 jpansanel moin
11:21 zarah hi jpansanel
11:25 egonw maclean: yes, reordering sound good
11:25 maclean ok, will do.
11:25 egonw btw, please a better name
11:25 egonw and an interface, perhaps
11:25 maclean Interface?
11:25 egonw PVRNumberer is a bit uninformative
11:25 egonw yeah, shared by your code
11:25 egonw and MorganNumbering tool
11:25 egonw or whatever it is called
11:25 maclean ahhh.
11:26 maclean Naming is important, but 'MaximalBitwiseNumberer' doesn't inform very much, either...
11:27 maclean But I'll try to come up with a better name, yes.
11:27 maclean "MorganNumbersTools"... :(
11:30 maclean hmm. that class does not re-number the atom container that it takes. no common interface there.
11:31 egonw maclean: do you see a refactoring to share interface?
11:31 egonw I mean the goal is the same, not?
11:31 egonw find a canonical numbering
11:32 maclean do you mean : extend the MorganNumbersTools class to provide a renumbering, as well as just the morgan numbers?
11:33 maclean because currently it supplies two methods, one of which provides the morgan numbers (as a long[]), and the other which provides the same, but 'labelled' by element type
11:34 maclean implementing new methods is not exactly the same as refactoring...
11:40 maclean now, refactoring out the numberer that smiles uses might be useful.
11:53 egonw yes, agreed
12:12 maclean d'oh. it's the CanonicalLabeler class that shares functionality with what I'm doing.
12:13 maclean although that class needs a re-write..
12:20 egonw ah, right
12:21 egonw a shared interface would definately be welcome
12:25 maclean I'm thinking 3 methods : 'public int[] getNumbering(IMolecule)', 'public IMolecule renumber(IMolecule)', and public void renumber(IMolecule)' where the last one destructively re-orders, while the second re-orders a clone.
13:02 rojasm egonw: did you apply the patch 2793070? about the charge in Molecular Formula!
13:02 rojasm I can not find in the git-browser cdk page
13:02 rojasm http://cdk.git.sourceforge​.net/git/gitweb.cgi?p=cdk
13:03 zarah rojasm's link is also http://tinyurl.com/dnyxao
13:03 egonw think so...
13:03 egonw checking
13:03 egonw rojasm: this one:
13:03 egonw http://cdk.git.sourceforge.net/git/​gitweb.cgi?p=cdk;a=commit;h=2f30841​07769f6634fe8a930d6984bf61f85943a
13:03 egonw ?
13:03 zarah egonw's link is also http://tinyurl.com/o9929f
13:04 rojasm oo thanks! My updating like always doesn't work properly mmm
13:06 egonw do a: git fetch
13:07 rojasm in trunk?
13:07 rojasm or it is from cdk.1.2
13:08 egonw 1.2.x
13:08 egonw did not sync with trunk yet
13:09 rojasm achso
13:09 rojasm ok
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13:45 rojasm sorry egonw: and the patch 2786201?
13:46 egonw does not seem to be reviewed yet
13:46 egonw and thus not applied
13:46 rojasm ok!
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15:12 egonw OK, 1.2.3 version bump commited to SF
15:12 rednael2 [cdk-1.2.x] Bumped version number  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=681b3​a129f34bbbb85264bfe92451918c395960e
15:12 zarah rednael2's link is also http://tinyurl.com/qs93yy
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