Camelia, the Perl 6 bug

IRC log for #cdk, 2007-08-10

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All times shown according to UTC.

Time Nick Message
06:42 jbrefort joined #cdk
07:11 carsten joined #cdk
07:17 carsten egonw: wow, very very cool blo
07:17 carsten g
07:25 laszlof joined #cdk
09:03 laszlof left #cdk
09:21 steinbeck joined #cdk
09:24 steinbeck egonw:  around?
09:37 CIA-1 cdk: steinbeck * r8673 /trunk/cdk/src/org/openscience/cdk​/renderer/AbstractRenderer2D.java: Check for "null" in atom.getHydrogenCount() fixes NullPointerException in AbstractRenderer.
09:37 steinbeck never mind
09:59 egonw steinbeck: yes, I am now...
09:59 lambdabot2 egonw: You have 1 new message. '/msg lambdabot2 @messages' to read it.
09:59 egonw steinbeck: but it seems you already found the problem
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10:28 CIA-1 blueobelisk: egonw * r79 /cb/trunk/get_cid_images.pl: Ignore CID -1, and don't say what we already got; it's getting volumenous
10:29 CIA-1 blueobelisk: egonw * r80 /cb/trunk/get_cids.pl: Don't tell me what you already know about
10:48 steinbeck joined #cdk
11:10 egonw hi steinbeck
11:10 egonw you solved the problem, I saw...
11:11 steinbeck thanks
11:11 steinbeck yes
11:11 steinbeck but there may be plenty of others of that kind :-)
11:12 steinbeck I'm really pi**ed off by screw-up of the SDG in CDK. There have been changes to the code so strange that I cannot understand them.
11:12 egonw :(
11:12 egonw yes, that's annoying...
11:12 egonw how can I help?
11:12 steinbeck Or better it'll take me ages.
11:12 steinbeck dunno
11:13 steinbeck Stefan split GeometryTools and some of the new code relies on renderer coordinates supplied from out of space.
11:13 steinbeck No idea what that is used for
11:13 steinbeck anyway, will have to debug that step by step
11:14 egonw steinbeck: yes, that's rather ugly code indeed...
11:15 egonw the new renderer will make that completely obsolete...
11:15 egonw give Nielsout some more weeks...
11:15 steinbeck great
11:15 egonw and then we can remove all that code again
11:15 steinbeck I already learned a lot from Niel's code
11:16 steinbeck strange thing is that he also introduced this "rendererCoordinates" thing into StructureDiagramGenerator.
11:17 egonw Nielsout: you did what ?!?!
11:17 * egonw is not really angry...
11:18 egonw steinbeck: which commit?
11:18 steinbeck no
11:18 egonw OK, need to come back on that later today...
11:18 steinbeck egonw: not Niels
11:18 steinbeck Stefan did that
11:18 egonw ah, phew...
11:18 steinbeck hehe :-)
11:18 Nielsout huh?
11:18 steinbeck no
11:18 steinbeck Nielsout:
11:18 egonw hi Nielsout
11:18 steinbeck you did nothing
11:18 Nielsout hi :)
11:18 steinbeck nothing wrong
11:18 steinbeck that is
11:19 Nielsout renderercoordinates in structurediagramgenerator.. that's weird
11:19 steinbeck right
11:19 egonw that's laziness...
11:20 steinbeck public void distributePartners(IAtom atom, IAtomContainer placedNeighbours, Point2d sharedAtomsCenter,
11:20 steinbeck            IAtomContainer unplacedNeighbours, double bondLength, HashMap renderingCoordinates)
11:20 egonw stefan is a rather talented programmer (he gets things done, quickly, working...)...
11:20 steinbeck that was a very nice method, until ...
11:20 egonw he had to add this workaround to fix a number of bugs...
11:20 egonw *had to*... because the renderer code was so dirty...
11:20 steinbeck yes, Stefan is great
11:20 egonw Nielsout: you are fixing that renderer code
11:21 egonw so that when that is done, the SDG code can be cleaned again too
11:21 egonw and the GeometryTools classes
11:22 Nielsout aye
11:25 olas joined #cdk
11:27 egonw olas: you got a DOI for details on BioMoby?
11:32 olas DOI?
11:35 egonw document object identifier...
11:35 egonw never heard of that??
11:35 olas ah, you mean for articles
11:35 olas right...
11:35 olas let me check
11:36 carsten joined #cdk
11:37 olas egonw: http://biomoby.open-bio.org/inde​x.php/what-is-moby/publications
11:37 lambdabot2 Title: BioMoby » Publications and Press
11:37 egonw OK, thanx
11:37 olas Have you tried the plugin?
11:37 egonw no, but looked at the screenshot...
11:38 egonw any chemical services in there?
11:38 olas no, but we should add them
11:38 olas we are setting up a server here
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14:59 CIA-1 bioclipse: ospjuth * r3692 /trunk/playground/plugins/net.bio​clipse.biomoby/src/net/bioclipse/ (4 files in 2 dirs): Started implementing primitive data types as GUI components. Currently not working...
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15:19 CIA-1 bioclipse: ospjuth * r3693 /trunk/playground/plugins/net.bio​clipse.biomoby/src/net/bioclipse/ (2 files in 2 dirs): Working on getting results from wizard
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15:32 steinbeck_ changed the nick to steinbeck
15:35 thomas_ku joined #cdk
15:35 thomas_ku moin
15:36 steinbeck_ joined #cdk
15:36 steinbeck_ wow. This sucks. Do others also experience these frequent reconnect to Freenode?
15:37 thomas_ku up to now I do not have any problems
15:38 egonw steinbeck_: yes, I do
15:38 steinbeck_ ah, good. Thought it was me :-)
15:39 * steinbeck_ fixed the bug which messed up 2D structure layout. now chasing remaining one which is less severe
15:39 egonw really? screenshot, screenshot, ...
15:39 thomas_ku that's great
15:40 steinbeck_ egonw: dunno what I should show in a screenshot :-)
15:40 egonw before and after bug fix?
15:40 steinbeck_ thomas_ku: could send me an example smiles which looks bad and I'll send how it looks now
15:41 thomas_ku can I sent you also a mol file?
15:44 thomas_ku steinbeck: y've got mail
15:53 shk3 joined #cdk
16:01 shk3 joined #cdk
16:01 shk3 hi all
16:02 thomas_ku hi shk3
16:02 shk3 just wanted to announce:
16:02 shk3 this is me
16:02 shk3 from my new computer
16:02 shk3 with new kubuntu
16:02 shk3 and my new dsl flatrate
16:02 thomas_ku ;-)  
16:02 shk3 installing eclipse now...
16:02 shk3 time to do some hacking
16:03 thomas_ku so there will be a lot of things to install...
16:04 shk3 apt-get install eclipse
16:04 shk3 seems to work...
16:04 shk3 java 1.4 it seems
16:05 steinbeck_ joined #cdk
16:05 steinbeck_ changed the nick to steinbeck
16:05 shk3 hi steinbeck
16:06 steinbeck hi shk3
16:06 thomas_ku steinbeck: it seems like you have really problems with the freenode connection...
16:06 steinbeck yes
16:06 shk3 so you missed the news?
16:06 steinbeck which one?
16:06 shk3 I have got a dsl flatrate
16:07 steinbeck hehe
16:07 steinbeck at home?
16:07 shk3 yes
16:07 steinbeck did not know you even had a private computer
16:07 steinbeck :-)
16:07 shk3 hm, problems installing java 1.5 ...
16:07 shk3 yeah, I have one
16:07 shk3 upgraded it
16:07 steinbeck cool
16:07 shk3 pretty much everything
16:07 shk3 except hd
16:07 shk3 even the netzteil needed to be changed ...
16:08 steinbeck sure, I can imagine that.
16:08 thomas_ku you are a lucky man... :-)
16:08 steinbeck And it was still cheaper than buying a new one?
16:08 shk3 well, yes
16:08 shk3 the cd drive could be kept as well
16:09 shk3 and I did not need to buy a windows licence...
16:09 steinbeck right
16:09 steinbeck but dell now sells ubuntu pc's
16:09 shk3 what's weired with ubuntu: it doesn't have a root user
16:10 steinbeck sure it has
16:10 shk3 does it?
16:10 steinbeck you can just "su" as usual
16:10 steinbeck but you can also "sudo" things
16:10 shk3 yeah, but that's not root as a such
16:10 shk3 do you think it should install java 1.6?
16:10 steinbeck right, but the passwords are different
16:11 steinbeck try "sudo passwd root" and set the password for "root" to something different
16:11 steinbeck are you on ubuntu now?
16:11 shk3 yes
16:11 egonw shk3: sun-java6-jre
16:11 steinbeck are "sudo passwd root" you can "su" or log in as root.
16:11 steinbeck are == after
16:12 shk3 if I use the ubuntu install,
16:12 * egonw need some time to adjust, but *never* missed the root account
16:12 shk3 is it possible to find the directory for java_home etc?
16:12 steinbeck right, me neither
16:12 egonw shk3: yes
16:12 shk3 that's a problem sometimes
16:12 shk3 if not using sun install
16:12 shk3 ok, I will ask you if necessary
16:12 egonw $ more /usr/local/bin/eclipse3.2
16:12 egonw #!/bin/sh
16:12 egonw /usr/bin/eclipse -vm /usr/lib/jvm/java-6-sun-1.6.0.00/jre/bin/java -vmargs -d64 -Xmx512M
16:14 shk3 installing...
16:17 * egonw is going home
16:17 egonw shk3: if you are interesting in hacking...
16:17 egonw might I interest you in an RDF interface to NMRShiftDB?
16:17 shk3 what's that?
16:17 egonw resource description format
16:18 egonw a semantic web technology to link different sources of information...
16:19 egonw would be great (very novel) to see NMR spectra available as RDF resources...
16:19 egonw shk3: just think about it...
16:20 shk3 sounds good
16:20 shk3 it seems this firefox plugin is not included in java for ubuntu.
16:20 shk3 you know, that libjavabla you need to set a link to.
16:20 shk3 any idea?
16:21 egonw are you running the 64bit version?
16:21 egonw then it is a problem...
16:22 egonw but Konqueror+Java still works then
16:22 shk3 "To get later versions of Java working with Firefox on amd64, you need to install the 32-bit version of Firefox and run 32-bit Java 1.5 or 1.6." :-(
16:22 shk3 hm, ok, will come back later to that...
16:22 shk3 lets see how eclipse is doing
16:23 egonw ok, so you're running x86_64 indeed... so am I
16:23 egonw don't have Java running in Firefox either...
16:23 shk3 yeah, the processor was the most expensive part of my computer...
16:23 shk3 btw: I get a dvd player for 19 euro
16:23 egonw dual core? or 4 cores?
16:23 shk3 I needed some sort of cable, that was 12 Euro
16:24 shk3 so if you want to make money, go for accessoires...
16:24 egonw :)
16:24 egonw ok, really leaving now
16:24 egonw bye
16:24 shk3 bye
16:31 thomas_ku I will leave now too!
16:31 thomas_ku cu
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16:37 shk3 what egon told me is jre only...
16:38 shk3 not too good for development...
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17:01 CIA-1 cdk: steinbeck * r8674 /trunk/cdk/src/org/openscience/cdk/layout/ (3 files): Fixes bug which causes folding of molecule parts back onto rest of molecule
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18:52 CIA-1 jmol: nicove * r8063 /trunk/Jmol-FAH/projects/p2563.xyz.gz: Folding@Home
19:02 CIA-1 jmol: nicove * r8064 /trunk/Jmol-FAH/projects/p2563.xyz.gz: Folding@Home
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20:59 CIA-1 cdk: steinbeck * r8675 /trunk/cdk/src/org/openscienc​e/cdk/layout/AtomPlacer.java: Fixed misplacement of ligands in certain situations (like a ring substituent in the lower right corner of a cyclobutane ring)
21:15 CIA-1 cdk: steinbeck * r8676 /trunk/cdk/src/org/openscience/cdk/test/l​ayout/StructureDiagramGeneratorTest.java: Added few tests, visual and not, for the recent bug fixes.
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