Camelia, the Perl 6 bug

IRC log for #cdk, 2010-09-27

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All times shown according to UTC.

Time Nick Message
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08:27 egonw moin
08:54 sneumann Hi, is cdk using junit3 or junit4 ?
08:54 sneumann I am preparing a bugreport with attached unit test
08:54 egonw hi sneumann
08:54 egonw junit4
08:54 sneumann thx
09:20 prcek joined #cdk
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09:29 sul joined #cdk
09:29 sul hello
09:30 egonw hi sul
09:31 egonw that's been a very long time?
09:31 egonw still at VTT?
09:31 egonw oh wait...
09:31 egonw no you are not, right?
09:31 egonw it was one of the baltic states, or?
09:31 egonw or are you just a completely different Sul? :)
09:31 egonw anyway.... welcome to the party!
09:32 egonw sneumann: thanx for your bug report...
09:32 * sneumann is currently trying to find some reference solution to the MCS
09:32 sneumann with the two molecules at hand to see whether the problem might be ill-posed
09:33 egonw sneumann: I'm hoping that asad will show up today too
09:36 sul I'm from University of Tartu (in Estonia)
09:37 sul still the same old "sul" :)
09:37 egonw right... well, it has been a long time... great that you joined!
09:38 * egonw should really keep a good contact notebook
09:38 egonw and could have then just quickly looked it up :)
09:39 sul I don't use IRC much these days. but after the announcement in the list joined in
09:42 egonw several developers still do a lot...
09:42 egonw but certainly not all...
09:42 egonw and we have others here too...
09:45 zarah joined #cdk
09:56 egonw hi zarah
10:08 baoilleach joined #cdk
10:08 egonw hi baoilleach!
10:09 baoilleach Could I have some champagne please?
10:09 egonw zarah: if you could be so kind...?
10:09 zarah egonw: eh... wha'?
10:09 baoilleach Look - I'll have it easy. Here's my glass...
10:09 baoilleach (Typo: "have" = "make")
10:10 egonw ... glok glok glok ...
10:10 egonw baoilleach: cheers!
10:10 egonw To Open Source Cheminformatics!
10:10 baoilleach Skol
10:10 baoilleach !Viva la revolution!
10:11 egonw baoilleach: btw, azeem is the person to talk to about making .deb packages
10:11 baoilleach Are you involved with Debichem azeem? Or just with the CDK side of things?
10:12 egonw baoilleach: /whois azeem
10:12 egonw he's indeed on the Debian side
10:12 egonw and often just listening in on #cdk, but busy with other stuff :)
10:13 baoilleach Well - it all comes down to the versions available. I'll look into this (with time...).
10:14 baoilleach Quick IRC question (this is pretty much my first time on IRC). How do you automatically log?
10:14 egonw depends on the client...
10:14 egonw konversation does it automatically
10:14 egonw but not entirely sure where the logs show up...
10:15 egonw oh, and this channel is also logged by _ilbot2
10:15 baoilleach I was hoping that I could log without running a client...:-/
10:15 egonw see channel topic
10:15 baoilleach oh - that sounds like what I am talking about..
10:15 egonw http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
10:15 azeem cdk is maintained by the java group though
10:16 egonw azeem: baoilleach wrote cinfony, python wrapper for CDK and other cheminfo software
10:16 azeem ah
10:16 egonw using jpype and/or jython
10:16 egonw we were discussion on #friendfeed that it would be great if there was a .deb for it...
10:16 baoilleach Problem is...too many dependencies (by its nature).
10:16 egonw I ran into a problem that the ubuntu/debian jython version is too outdated
10:18 azeem baoilleach: does it need/use rdkit, or was that a different project yet again?
10:18 baoilleach (Sorry - someone just popped in in real life...)
10:18 egonw azeem: yeah, cinfony also wraps rdkit
10:18 egonw use at least... baoilleach: is it optional?
10:19 baoilleach The big dependencies are optional. If RDKit isn't there, it will still work, but you can't use the rdkit.py part.
10:20 baoilleach It's basically a lightweight wrapper around OpenBabel, RDKit and CDK (and maybe more).
10:20 azeem ok, so they can be packaged in paralle
10:20 azeem l
10:20 baoilleach That's true.
10:20 egonw azeem: yeah, nice idea... cinfony-openbable, cinfony-cdk, with appropriate deps for each of them
10:21 egonw but we would need to update the CDK too, I guess...
10:21 egonw btw... next stable CDK 1.4 should arrive this year...
10:21 baoilleach If I were to progress with this, e.g. the cinfony-cdk, should I start using debian unstable or so, and connect with someone at Debichem?
10:23 egonw http://lists.alioth.debian.org/​mailman/listinfo/debichem-devel
10:23 baoilleach Sorry - I just figured out who you are azeem. :-)
10:24 azeem hi
10:24 zarah ni hao azeem
10:26 azeem baoilleach: there's an #openbabel channel as well by the way - but it is not very active
10:26 baoilleach Ok - I'd better finish this champagne and get back to work. Hopefully my computer will tell me if someone mentions my name...
10:26 azeem I'm back in an hour or so
10:26 baoilleach To be honest, I don't like to be accessible to users in real time. I don't think I would be able to get any work done.
10:27 azeem heh
10:27 azeem there's not many users - Tim hangs out there and sometimes Geoff
10:28 baoilleach ok, joined - happy now :-)
10:28 baoilleach ?
10:28 azeem \o/
10:42 s9asad joined #cdk
10:43 s9asad Hi
10:43 zarah hello s9asad, you fantastic person you
10:43 s9asad Thanks!
10:43 egonw hi s9asad
10:43 egonw do you have a glass?
10:43 s9asad Hi Steffen, I have commented on your bug report please check it
10:43 s9asad glass?
10:44 s9asad Hi egon!
10:44 s9asad you mean the one to drink or wear?
10:44 egonw wear??
10:44 egonw yeah, a glass to drink from...
10:44 s9asad yes
10:44 egonw champagne to be precise
10:44 s9asad mate
10:44 s9asad wow!
10:44 s9asad yeah Cheers
10:44 egonw please hold it steady...
10:45 egonw .... glok glok glok ...
10:45 s9asad ...okies
10:45 egonw cheers!
10:45 s9asad cheers!
10:48 alchimiste moin
10:49 zarah privet alchimiste
10:49 alchimiste egonw : ok for cdk on fr_wikipedia, i will do it
10:49 egonw alchimiste: tack
10:49 egonw alchimiste: I tried to update it... but not sure about the syntax of French dates :)
10:51 sneumann zarah: and please champage for s9asad, too ;-)
10:51 zarah sneumann: excuse me?
10:51 s9asad :-)
10:52 s9asad left #cdk
10:55 pierre___ joined #cdk
10:55 egonw was just about to say that s9asad should really blog on how to use SMSD...
10:55 egonw hej pierre___!
10:55 egonw have a glass of champagne!
10:56 pierre___ just testing :-P
10:56 egonw ... glok glok glok ...
10:56 egonw there you go...
10:56 pierre___ thanks for the Champagne !
10:56 pierre___ and happy birthday CDK
10:56 pierre___ ciao :-)
10:56 pierre___ left #cdk
11:02 alchimiste egonw : I've fix the 'sep' issue.
11:03 egonw merci beauxcoup
11:26 egonw some spelling error... my written french is not good...
11:26 egonw my spoken french at tourist level...
11:26 egonw je voudrais deux baguettes
11:26 sneumann da hat aber jemand Hunger!
11:27 egonw ja, genau
11:27 egonw mycket
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12:39 s_wolf ckuhl: /mnt/VOL1/ABT/Alle/PhD_students/Gene​ral_Information/Satzung_20100915.pdf
12:39 maclean joined #cdk
12:39 s_wolf sry
12:39 s_wolf wrong window
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13:03 egonw s_wolf: :)
13:04 s_wolf too much champagne ;)
13:04 maclean egonw : ¥ø
13:05 maclean also : you weren't joking when you said that javadocs/junit for rendererbasic was "a big task".
13:05 maclean I'm only 1/2 way through just the docs...
13:08 maclean as well: sorry if I missed celebrations, but I was on a train from london-cambr.
13:10 azeem what's the celebration about anyway?
13:11 sneumann 10 yrs of CDK
13:11 sneumann everybody gets drunk here
13:11 sneumann http://blog.rguha.net/?p=790
13:12 azeem ah right
13:12 sneumann In real world, that means secondary school next year :-)
13:13 sneumann and only 8 years until it'll do a driving license
13:13 sneumann and 6 years (german law) until allowed to drink the own champagne :-)
13:20 egonw maclean: indeed
13:21 maclean the good news is that making javadocs can expose subtle errors, like defining a rectangle by its corner rather than its center :)
13:21 egonw indeed
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14:38 sneumann Interesting, we're currently running a large import from PubChem, and I just looked at the most frequent warnings:
14:38 sneumann 1554   #0 :Accepted unusual valence(s): N,d(3);
14:38 sneumann 1494   #0 :Metal was disconnected;
14:39 sneumann 1381   #0 :Metal was disconnected
14:39 sneumann So there are two *dfferent* instances of disconnected Metal, one with, one without ; at the end.
14:46 maclean does "disconnected;" have some distinct meaning to "disconnected" ?
14:46 maclean :)
14:46 maclean Also : oh my! "public <T extends IGeneratorParameter<S>,S> S get(Class<T> paramType) {"
14:47 maclean I actually don't understand that method signature.
15:06 egonw hi dlonie`
15:06 egonw sneumann: importing where?
15:07 egonw maclean: use /** {@inheritDoc} */
15:08 maclean egonw : it has documentation, I just mean that I can't mentally parse it. This is why I don't like reflection in java.
15:09 egonw ah, this is not reflectiong...
15:09 egonw this is generics
15:09 egonw but your point remains...
15:10 maclean Yes, I do realise that T and S are due to generics, but the reason for this method is due to 'clever' use of reflection.
15:11 sneumann egonw: sorry, was menat for #openbabel :-(
15:11 maclean Anyway, it's no use me complaining about it now.
15:11 sneumann The difference is that there seem to be two codepaths to detect the disconnected metal
15:11 egonw ic
15:11 sneumann and import into pgchem Postgres database
15:12 sneumann three clients hammering the postgres server :-)
15:14 egonw maclean: well, it means that the JavaDoc should be clearer...
15:14 egonw maclean: and the generic stuff is more about strong typing and simpler code (hahahaha), than about dynamically discovery of functionality...
15:14 egonw the simpler code refers to where it is used:
15:15 egonw Double scale = model.get(Scale.class)
15:15 egonw instead of something like:
15:15 maclean Yes, yes, I know all this.
15:15 egonw Double scale = (Double)model.get(Scale.class).getValue()
15:16 maclean I understand generics. Also I am now pretty familiar with the renderbasic code...
15:16 maclean :)
15:17 egonw but now we have it documented in the logs too...
15:17 egonw useful for others, I hope...
15:18 maclean I'm just saying that many programmers less experienced than the CDK developers will look at the RenderModel.get method and think : "what!?".
15:19 maclean Specifically: http://tvtropes.org/pmwiki​/pmwiki.php/Main/FlatWhat
15:19 maclean Or possibly even, http://tvtropes.org/pmwiki/pmwiki.php/Main/BigWhat
15:19 egonw http://www.chemhacker.com/​2010/09/chemhackerstm-0-1/
15:19 egonw open source scanning tunneling microscopy
15:20 egonw maclean: yeah, we need good tutorials too...
15:20 egonw I'll see what I can do with my blog posts...
15:20 maclean Well, I did write one once.
15:20 egonw wanted to convert that into a document anyway (actually, chapter for the long overdue CDK book....)
15:21 egonw yes, I know... I used those and updated them in my blog for APi changes...
15:21 maclean Haha. "Put all of this stuff up on a Git repository (as soon as I learn how to use Git)" - and he thought making an STM from scratch was tricky....
15:21 egonw hehehehe
15:21 egonw yeah, see my tweet:
15:22 egonw http://twitter.com/#!/egonwi​llighagen/status/25695822344
15:22 egonw this is what opensource is about... someone else should do that git bit...
15:22 egonw I might even after I finished those two stupid book chapters...
15:22 maclean all he needs to do now is hook it up with a reprap somehow, and it will be awseome : http://reprap.org/wiki/Main_Page
15:24 egonw when I was still a student, the physics students made STMs themselves too...
15:24 egonw it's really not that tricky, apparently...
15:24 maclean Ah, also egonw : a less moany issue that's quite important - BasicBondGenerator and RingGenerator.
15:24 egonw the positioning is actually easy, by using the perpendicular grooves...
15:25 egonw (or so they told me :)
15:25 maclean The latter just makes the circles that go in aromatic...no wait.
15:25 maclean I remember now. It's to do with aromaticity detection.
15:25 egonw yuck
15:26 maclean BasicBondGenerator could be even simpler if it didn't detect rings...
15:26 maclean But that would mean having very ugly double bonds in rings
15:26 maclean As the inner ring bond would not be shorter.
15:27 maclean However, it would make your goal of a tiny applet more feasible :)
15:28 maclean What do you think?
15:29 egonw sounds reasonable to me... please bring it up on cdk-jchempaint@ so that Mark and the EBI people can give their opinion too
15:29 maclean Perhaps I'll file it as a feature request.
15:30 maclean (as well as, yes posting on the list)
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16:53 maclean right. javadocs for renderbasic finally done.
17:02 egonw oh, cool... impressive!
17:12 maclean Well, actaully I spoke too soon. Now that I've started on the junit tests, I realise the @TestClass and @TestMethods are missing.
17:42 sneumann_ joined #cdk
17:47 maclean bye
17:47 maclean left #cdk
19:34 slyrus__ joined #cdk
19:34 slyrus__ how's the party?
19:36 sneumann_ it went on all day,
19:37 sneumann_ and ppl had plenty of champagne
19:37 sneumann_ nicks I haven't heared of since I follow #cdk (only a year or so)
19:40 egonw slyrus__: slowing down a bit...
19:40 egonw not been too busy, honostly...
19:41 egonw there were indeed a few oldies around...
19:41 egonw sul joined in who used and contributed some years ago
19:41 egonw and noel showed up who uses the CDK in Cinfony
19:42 egonw and pierre dropped by
19:42 egonw but he's a bio sequence guy
19:42 egonw who just wanted to test the webchat functionality ;)
19:43 slyrus__ +1 for biosequence guys!
20:06 * egonw will be offline today, cu tomorrow
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