Camelia, the Perl 6 bug

IRC log for #cdk, 2009-03-18

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All times shown according to UTC.

Time Nick Message
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08:37 masak egonw: rednael, right?
08:37 egonw it's rednael
08:37 egonw masak: you know Zarah Leander, right?
08:37 egonw that's the link to zarah :)
08:37 masak egonw: yes. ah, I see.
08:37 masak an homage of sorts.
08:38 egonw leander nick was already registered
08:38 masak bet it was.
08:44 masak egonw: a good move, in case you haven't done so already, is to commit the bot to the cdk repo.
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09:19 egonw shk3: http://pele.farmbio.uu.se/​nmrshiftdb/?moleculeId=234
09:19 zarah egonw's link is also http://tinyurl.com/c4x36y
09:19 masak pele++
09:27 jbrefort joined #cdk
09:31 shk3 egonw: any particular purpose of that?
09:31 shk3 sorry for asking stupid questions
09:36 jpansanel moin
09:36 zarah ni hao jpansanel
09:50 egonw shk3: yes, Linked Open Drug Data
10:05 jpansanel egonw : what is Open Drug Data ?
10:05 egonw a group of people who want to make a RDF network of drug related data
10:06 jpansanel good idea
10:06 jpansanel it's about approved drugs, new drugs or both ?
10:07 egonw I think just about anything remotely relevant
10:08 egonw they are even linking potions...
10:08 egonw chinese medicine, that is
10:08 jbrefort joined #cdk
10:08 jpansanel ok
11:12 maclean joined #cdk
11:13 egonw shk3: http://chem-bla-ics.blogspot.com/2009/03/n​mrshiftdb-enters-rdfopenmoleculesnet.html
11:13 zarah egonw's link is also http://tinyurl.com/ddprcx
11:13 egonw shk3: that provides some context
11:17 shk3 egonw++
11:22 maclean egonw : around?
11:24 egonw yes
11:25 egonw well... in 10 minutes, OK?
11:25 maclean ok
11:33 egonw back
11:33 maclean ah, right
11:33 maclean it's about cloning of IAtomContainers
11:34 maclean I reused (copy/pasted) the code from the clone method of cdk.AtomContainer
11:34 maclean and it wasn't working
11:34 maclean so, I altered the line that looked like
11:34 maclean newAtoms[j] = clone.getAtom(getAtomNumber(bond.getAtom(j)));
11:35 maclean to lookup using a unique ID rather than '=='
11:35 maclean and that worked
11:36 egonw define unique ID
11:36 maclean I have a gist of this
11:36 egonw and what's not working?
11:36 egonw ok
11:36 maclean http://gist.github.com/81069
11:37 maclean unique ID is a stringified number - each atom is given a sequential numerical ID
11:37 egonw I guess that works if you have IDs
11:37 egonw which is not generally the case...
11:37 maclean I know
11:37 egonw but what exactly was not working?
11:38 maclean the atom references returned by getAtomByEquals were not right
11:38 maclean which I could tell by the string ids when I printed them out.
11:39 egonw your code is not working because you ask at what position the cloned atom is in the original molecule
11:39 maclean the atoms are in the same order
11:39 egonw yes
11:39 maclean this is how the code in AtomContainer.clone works
11:40 egonw but the getAtomByEquals() method is passed a cloned atom
11:40 egonw which will never be part of the source IAtomCotnainer
11:40 egonw I sure hope the AtomContainer.clone() is not doing that...
11:40 maclean no it isn't
11:40 egonw sure?
11:40 maclean for (IBond bond : source.bonds()) {
11:40 maclean 'bond' is from source
11:41 egonw ah, indeed
11:41 egonw sorry
11:41 maclean it's weird - the code in AtomContainer /should/ work
11:42 maclean it uses '==' to check for referential equality
11:42 egonw yes, indeed
11:42 maclean So I assume that I have done something wrong, but I can't see how.
11:42 maclean I'm trying to make a test case for it, so that I can check this
11:42 egonw ok
11:43 maclean Maybe I should get back to you when I know more :)
11:43 egonw please do
11:43 maclean tack
11:57 shk3 egonw: how do I get the code of the 1.2 branch from git?
11:57 shk3 would be great if you can just tell me the command or so
11:58 egonw git clone git://cdk.git.sourceforge.net/gitroot/cdk
11:58 egonw git checkout -b local-cdk-1.2.x cdk-1.2.x
12:00 shk3 sorry
12:00 shk3 first one works
12:01 shk3 second doesn't
12:01 egonw try:
12:01 egonw git branch -a
12:01 shk3 do I need to be in the new directory
12:01 shk3 ?
12:01 egonw the last may be something like:
12:01 egonw git checkout -b local-cdk-1.2.x origin/cdk-1.2.x
12:01 shk3 yes
12:01 egonw no, no new directory
12:01 shk3 * master
12:01 shk3 origin/HEAD
12:01 shk3 origin/cdk-1.2.x
12:01 shk3 origin/master
12:01 egonw shk3: you can though
12:01 egonw if you really want
12:01 egonw cd ..
12:02 shk3 Branch local-cdk-1.2.x set up to track remote branch refs/remotes/origin/cdk-1.2.x.
12:02 shk3 Switched to a new branch "local-cdk-1.2.x"
12:02 shk3 does that mean it was done?
12:02 egonw git clone cdk <secondFolder>
12:02 shk3 ah yes
12:02 egonw then: cdk <secondFolder> and do the branch swtich there
12:02 egonw shk3: yes
12:02 shk3 git log gives me your new changes
12:02 egonw good :)
12:03 shk3 now I need to import to eclipse
12:05 maclean shk3 : that google also turned up this site:
12:05 maclean http://www-cs-students.stanford​.edu/~blynn/gitmagic/index.html
12:05 zarah maclean's link is also http://tinyurl.com/64gy5z
12:07 maclean heh, including a chapter on "Git shortcomings" - I thought they didn't exist :p
12:07 egonw sure, it doesn't cure cancer yet
12:08 maclean what!? Bah. I'm moving to Hg, then.
12:08 egonw no, no...
12:08 egonw you do not understand...
12:08 egonw Hg causes cancer
12:08 maclean Ohhh.
12:08 maclean :)
12:08 egonw hahahah
12:08 maclean Cures syphillis, though *cough*.
12:09 egonw http://cheat.errtheblog.com/s/gitsvn/
12:09 zarah egonw's link is also http://tinyurl.com/4rnmh3
12:09 egonw oh... wrong one...
12:09 egonw oops
12:09 egonw http://cheat.errtheblog.com/s/git/
12:09 zarah egonw's link is also http://tinyurl.com/28naxk
12:10 egonw oh no...
12:19 maclean wow, that's an impressive surname : "Cihan Kamil Öğüt"
12:19 maclean near-maximal diacritic density
12:37 maclean egonw : false alarm on that cloning thing - it was my fault :( sorry
12:37 * maclean mutters bloody structure generation...
12:54 egonw yeah, structgen is not simple material
12:58 maclean I was fusing two atom containers, so it wasn't surprising that using the count wasn't working :)
13:00 egonw ok :)
13:00 egonw yeah, writing unit tests is quite useful
13:00 egonw helps you understand in detail what is going on
13:18 maclean lol egonw you have a feature request here:
13:18 maclean http://sourceforge.net/tracker/ind​ex.php?func=detail&amp;aid=927585&​amp;group_id=20024&amp;atid=370024
13:18 zarah maclean's link is also http://tinyurl.com/dzkgda
13:18 maclean about a SMARTs visual editor
13:18 maclean where you say " I've got
13:18 maclean this planned for early May."
13:18 egonw hahaha
13:19 egonw well, that gives a bit of time :)
13:19 maclean submit date :2004-04-01 15:43
13:19 egonw doesn't say which May, does it :)
13:19 maclean true
13:19 egonw seriously... this shows how long the JCP design was overdue
13:19 maclean this is so
14:55 egonw shk3: ping
14:55 egonw shk3: do spectra also have unique URLs in NMRShiftDB, like molecules have:
14:56 egonw http://nmrshiftdb.ice.mpg.de/portal/​js_pane/P-Results/nmrshiftdbaction/s​howDetailsFromHome/molNumber/NUMBER
14:56 zarah egonw's link is also http://tinyurl.com/deuts8
14:59 shk3 no
14:59 shk3 only via molecule
14:59 egonw ack
14:59 shk3 would not be a problem to add
15:03 egonw would be nice
15:03 egonw it would give spectra their own URLs
15:03 egonw but not crucial
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15:22 rednael [cdk-1.2.x] Applied patch #2675819 (Stefan Kuhn): Patch to add a removeReaction to reactionSet  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=42646​250294ac7c3c7f2afc54da4118f2fe50f0b
15:23 egonw rednael++
15:24 maclean type(rednael) == bot?
15:24 egonw bot rdf:type bot
15:24 egonw umm
15:24 maclean :)
15:24 egonw rednael rdf:type bot
15:24 egonw rednael is a hack up to monitor the Git RSS feed
15:24 egonw to get commit messages here
15:25 maclean ahh
15:25 maclean careful you don't create a feedback loop somewhere : irc->blog->svn->bot->irc
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15:46 masak maclean: how would a blog commit to SVN?
15:46 maclean you never know...
15:46 maclean *waves hands* javascript!
15:46 sneumann where is zarah today ?
15:47 sneumann Day off ?
15:47 jonalv joined #cdk
15:47 jonalv oh hai
15:47 maclean ohai
15:47 maclean (tm)
15:48 sneumann ;-)
15:48 jonalv isn't zarah here?
15:49 egonw no, she left at some point
15:49 masak that's odd.
15:51 zarah joined #cdk
15:51 jonalv zarah: hi
15:51 zarah hello jonalv :)
15:51 masak zarah: you're welcome.
15:51 zarah masak: that was not so easy for a little bot to understand
15:52 egonw hi zarah
15:52 masak she doesn't reply to that.
15:52 masak zarah: you're the quiet one!
15:52 zarah masak: no, YOU'RE the quiet one!
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