Camelia, the Perl 6 bug

IRC log for #cdk, 2007-08-17

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Time Nick Message
02:03 CIA-1 jmol: hansonr * r8106 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties): 11.3.10 write JPG n # where n <= 100, the quality
05:21 CIA-1 jmol: nicove * r8107 /trunk/Jmol/src/org/jmol/translation/Jmol/ (11 files): Update of .po files
05:22 CIA-1 jmol: nicove * r8108 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
06:16 jbrefort joined #cdk
06:51 jbrefort joined #cdk
06:58 thomas_ku joined #cdk
06:58 thomas_ku moin
07:09 jpansanel moin
07:18 carsten joined #cdk
07:32 jonalv joined #cdk
07:51 neksa joined #cdk
08:10 egonw moin
08:14 jpansanel moin
08:14 jpansanel neksa : I was in meeting last afternoon
08:15 jpansanel can you make an Open Babel test ?
08:29 neksa jpansanel: hi, Jerome. sure, tell me what to do
08:32 CIA-1 bioclipse: jonalv * r3701 /trunk/plugins/net.bioclipse.statistics/s​rc/net/bioclipse/editors/GridEditor.java:
08:32 CIA-1 bioclipse: The grid editor now shows column labels and a somewhat broken row label. It
08:32 CIA-1 bioclipse: shows the same row label on each row... This seems to be due to a bug in the
08:32 CIA-1 bioclipse: Grid widget and I have contacted the Grid developers so a solution should turn
08:32 CIA-1 bioclipse: up in the not to distant future.
08:39 jpansanel neksa : can you convert this file :https://blueobelisk.svn.sourceforge.​net/svnroot/blueobelisk/structures/t​runk/src/ethers/1-butoxybutane.cml
08:39 lambdabot2 http://tinyurl.com/24yysz
08:39 jpansanel to a mol file
08:40 egonw works with OB 2.0.2
08:41 jpansanel egonw : do you have any bond type set to 14 ?
08:42 egonw no, all single bonds
08:42 jpansanel where is your copy from OB comming from ?
08:43 egonw 2.0.2-1 from kubuntu feisty
08:44 jbrefort 1-Butoxybutane
08:44 jbrefort OpenBabel08170710483D
08:44 jbrefort 27 26  0  0  0  0  0  0  0  0999 V2000
08:44 jbrefort    1.6892   -0.6260    1.5713 C   0  0  0  0  0
08:44 jbrefort    0.6265    0.3666    1.1086 C   0  0  0  0  0
08:44 jbrefort    0.0555   -0.1616   -0.0787 O   0  0  0  0  0
08:44 jbrefort   -0.9495    0.6740   -0.6323 C   0  0  0  0  0
08:44 jbrefort   -1.4771   -0.0301   -1.8791 C   0  0  0  0  0
08:44 jbrefort    2.4517   -0.7704    0.7798 H   0  0  0  0  0
08:44 jbrefort    2.3512   -0.1395    2.8504 C   0  0  0  0  0
08:44 steinbeck joined #cdk
08:44 jbrefort    1.0691    1.3632    0.9102 H   0  0  0  0  0
08:44 jbrefort   -0.1572    0.5035    1.8803 H   0  0  0  0  0
08:44 jbrefort   -0.5247    1.6668   -0.8822 H   0  0  0  0  0
08:44 jbrefort   -1.7593    0.8402    0.1060 H   0  0  0  0  0
08:44 jbrefort   -0.6513   -0.2175   -2.5945 H   0  0  0  0  0
08:44 jbrefort   -2.5616    0.8034   -2.5424 C   0  0  0  0  0
08:44 jbrefort    1.2383   -1.6256    1.7334 H   0  0  0  0  0
08:44 jbrefort   -1.8742   -1.0313   -1.6169 H   0  0  0  0  0
08:44 jbrefort    3.4093   -1.1091    3.3262 C   0  0  0  0  0
08:44 jbrefort    1.5870    0.0039    3.6402 H   0  0  0  0  0
08:45 jbrefort    2.8007    0.8603    2.6866 H   0  0  0  0  0
08:45 jbrefort   -3.1043    0.1197   -3.7769 C   0  0  0  0  0
08:45 egonw jbrefort: please use a pastebin website for these kind of dumps...
08:45 jbrefort   -2.1610    1.8020   -2.8084 H   0  0  0  0  0
08:45 jbrefort   -3.3837    0.9947   -1.8242 H   0  0  0  0  0
08:45 jbrefort    2.9860   -2.1011    3.5330 H   0  0  0  0  0
08:45 jbrefort    3.8863   -0.7568    4.2496 H   0  0  0  0  0
08:45 jbrefort    4.2014   -1.2431    2.5775 H   0  0  0  0  0
08:45 jbrefort   -3.5400   -0.8598   -3.5387 H   0  0  0  0  0
08:45 egonw jbrefort: 3-4 lines is OK, but this is a bit much...
08:45 jbrefort   -2.3188   -0.0471   -4.5260 H   0  0  0  0  0
08:45 jbrefort   -3.8894    0.7210   -4.2527 H   0  0  0  0  0
08:45 jbrefort  1  2  1  0  0  0
08:45 jbrefort  1  6  1  0  0  0
08:45 jbrefort  1  7  1  0  0  0
08:45 jbrefort  1 14  1  0  0  0
08:45 jbrefort  2  3  1  0  0  0
08:45 jbrefort  2  8  1  0  0  0
08:45 jbrefort  2  9  1  0  0  0
08:45 jbrefort  3  4  1  0  0  0
08:45 jbrefort  4  5  1  0  0  0
08:45 jbrefort  4 10  1  0  0  0
08:45 jbrefort  4 11  1  0  0  0
08:45 jbrefort  5 12  1  0  0  0
08:45 jbrefort  5 13  1  0  0  0
08:45 jbrefort  5 15  1  0  0  0
08:45 jbrefort  7 16  1  0  0  0
08:45 jbrefort  7 17  1  0  0  0
08:45 jbrefort  7 18  1  0  0  0
08:45 jbrefort 13 19  1  0  0  0
08:46 jbrefort 13 20  1  0  0  0
08:46 jbrefort 13 21  1  0  0  0
08:46 jbrefort 16 22  1  0  0  0
08:46 jbrefort 16 23  1  0  0  0
08:46 jbrefort 16 24  1  0  0  0
08:46 jbrefort 19 25  1  0  0  0
08:46 jbrefort 19 26  1  0  0  0
08:46 jbrefort 19 27  1  0  0  0
08:46 jbrefort M  END
08:46 jbrefort 1 molecule converted
08:46 jbrefort 16 audit log messages
08:46 jbrefort yes, sorry
08:46 jbrefort np
08:46 jpansanel thx
08:47 jpansanel egonw : can you convert from mol to inchi with your version ?
08:47 egonw mom, don't think so, but let me try
08:48 egonw no
08:48 egonw I need 2.1 for that...
08:48 egonw in gutsy, expected in october...
08:48 egonw installed it at home, can try tonight...
08:48 egonw neksa: can you?
08:51 neksa egonw, jpansanel: yes, it works with Open Babel 2.2.0b1
08:51 jpansanel egonw : there's no deb package for OB >= 2.1
08:51 jpansanel ?
08:52 egonw there is... for gutsy...
08:52 egonw not for feisty, AFAIK
08:52 egonw http://packages.ubuntu.com/cgi-bin/searc​h_packages.pl?searchon=names&amp;version​=all&amp;exact=1&amp;keywords=openbabel
08:52 lambdabot2 Title: Ubuntu -- Package Search Results, http://tinyurl.com/2zldfh
08:53 neksa btw, output here if you need http://pastebin.com/m5c0e7385
08:53 * neksa trying mol 2 inchi
08:53 egonw jpansanel: so what version are *you* using? that you get bond type 14??
08:54 jpansanel OB 2.0.2 on DEbian etch
08:54 neksa mol 2 inchi works as well on OB SVN
08:54 jpansanel neksa : thx
08:55 jpansanel 13 19 14  0  0  0
08:57 jpansanel I've reinstall OB
08:57 jpansanel I've always the same pb
08:57 jbrefort 0B 2.1.1 should be available for debian quite soonish
08:58 egonw jbrefort: with or without inchi?
08:58 egonw I saw on the InChI mailing list that the source tar.gz has license issues...
08:58 jbrefort damned
08:58 egonw missing license statement... some conflict...
08:58 jbrefort bad
08:58 egonw yes...
08:58 jpansanel :(
08:59 egonw someone from red hat asked about that...
08:59 egonw or the open owl:sameAs variant of which I lost the name
08:59 neksa egonw: Michael Banck from debichem wants to know if anybody is using libinchi except for OB
08:59 neksa egonw: otherwise he will drop the libinchi package and ship inchi libs within the OB bundle
09:00 egonw CDK would be...
09:00 egonw but still no package for that
09:00 egonw neksa: I think that would make perfect sense at this moment...
09:00 egonw OB is not that large anyway
09:01 neksa egonw: I have no contr-examples to argue with Michael, so if you leave it with no feedback he drops libinchi as a separate package.
09:01 jpansanel neksa , egonw , jbrefort : http://pastebin.com/m77b787f6
09:02 neksa egonw: debian guys really work in a relaxed manner, no tight release constraints applied. I'm not yet a .deb wizard to help out there
09:02 jbrefort clearly a bug in OB-2.0 but fixed in later versions
09:03 egonw neksa: making deb packages is really easy...
09:03 jbrefort jpansanel, fill a bug report against debian package
09:03 egonw easpecially, if the system does ./configure; make; make install (or the cmake variant...(
09:04 neksa egonw: ok, I'll be able to try after SoC
09:04 egonw indeed... after SoC
09:05 neksa egonw: if Blue Obelisk does no use SVN at cubic (it moved to sf), would it make sense to remove that repo from cubic servers?
09:08 * jpansanel building a OB2.1.1 package for Debian based on Ubuntu Gutsy
09:09 egonw neksa: yes
09:09 egonw they will dissappear within one/two months, likely...
09:10 neksa jpansanel: is the latest cml2 format of chem-file now stable?
09:11 neksa btw, for a Google candy, try this query:  latest release OpenBabel
09:11 neksa it seems that Google recognizes wikipedia templates
09:13 egonw how so?
09:13 egonw I don't see anything special
09:14 neksa egonw: with www.google.com I see this:
09:14 neksa OpenBabel ? Latest Release: 2.0 / November 26, 2005
09:14 neksa According to http://en.wikipedia.org/wiki/OpenBabel
09:14 lambdabot2 Title: OpenBabel - Wikipedia, the free encyclopedia
09:14 neksa on top of google search results
09:14 egonw ok,not here...
09:14 egonw but I get redirected to google.nl
09:15 jpansanel neksa : I need to add  informtation for dict namespace
09:16 neksa jpansanel: yes, that's important for correct parsing
09:17 neksa jpansanel: especially if embedded in and another XML (e.g. SVG)
09:18 egonw neksa: not the CML namespace...
09:18 egonw but regarding the use of QNames in attributes
09:19 egonw why the f**k is still so much broken on 64bit distribs ?!?!? :(
09:30 * egonw regrets not having installed the 32bit ubuntu release...
09:46 jpansanel he he
09:47 * jpansanel has now openbabel-2.1.1
09:48 jpansanel and it works fine
09:49 dleidert joined #cdk
09:54 jpansanel mychem works great :)
09:54 jpansanel select molfile_to_molecule(peptiglycan_mol.mol,0) from peptiglycan_mol;
09:54 jpansanel returns :
09:54 jpansanel InChI=1/C20H39N7O7/c1-10(22)16(29)26-14(7-8-1​5(23)28)19(32)27-13(6-4-5-9-21)18(31)24-11(2)​17(30)25-12(3)20(33)34/h10-14H,4-9H2,1-3,21-2​2H3,(H2,23,28)(H,24,31)(H,25,30)(H,26,29)(H,2​7,32)(H,33,34)/t10-,11+,12+,13-,14+/m0/s1
09:55 jpansanel (I store molecule as inchi string)
09:55 egonw mychem is your compound database?
09:55 egonw it's opensource, not?
09:55 jpansanel yes
09:55 egonw what tools are you using?
09:55 jpansanel GPL-v2
09:55 egonw LAMP + what?
09:56 jpansanel Mychem is only an extension for MySQL
09:56 egonw and the frontend?
09:56 jpansanel that provides OpenBabel tools
09:56 jpansanel On our Intranet, we are using LAMP
09:57 egonw someone was looking for an opensource, easy to use molecule database website software
09:57 egonw so PHP frontend?
09:57 jpansanel yes
09:57 egonw jpansanel: please blog about it, with a screenshot...
09:57 egonw then I can send the link to that guy
09:57 jpansanel egonw : I will do that next week
09:57 jpansanel We want to release Mychem today (v0.2)
09:58 egonw OK, send me the release URL then, please
09:59 jpansanel ok
10:33 Nout joined #cdk
10:44 egonw hi Nout
10:44 egonw any progress?
10:51 carsten joined #cdk
10:51 Nout hey egonw
10:51 egonw hi
10:51 Nout not much progress as in working stuff
10:52 Nout but I did figure out some stuff
10:52 egonw tell me...
10:52 Nout i'm back in Wognum btw, not that that really matters :P
11:13 CIA-1 jmol: hansonr * r8109 /branches/gutow-webmaker/src/org/openscience/jmo​l/app/webexport/script_button_instructions.html: proper height
11:13 CIA-1 jmol: hansonr * r8110 /trunk/Jmol/src/org/openscience/jmol/app/w​ebexport/script_button_instructions.html: proper height for image
11:13 Nout how to find out what the radicals of an atom are (if any)?
11:14 egonw if an atom is a radical... it should have a ISingleElectron attached
11:18 Nout ah oki
11:19 steinbeck joined #cdk
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13:05 steinbeck left #cdk
13:48 masak joined #cdk
13:49 masak is there something in cdk that can give a IUPAC name to an arbritarily chained alkane, or construct one from its IUPAC name?
13:57 egonw joined #cdk
14:00 masak is there something in cdk that can give a IUPAC name to an arbritarily chained alkane, or construct one from its IUPAC name?
14:01 egonw there are bits of code... nothing general though
14:01 masak ok
14:01 masak it's probably hard to go much more general than branching alkanes
14:02 masak but if I gave it a try, would you accept a patch?
14:03 jonalv masak has an exam in organic chemistry coming up   :)  
14:03 egonw masak: sure
14:03 masak jonalv: yes. I need to blow off some steam on a meaningful programming exercise
14:03 masak egonw: I have one question. which molecule file format should I target?
14:03 egonw CML
14:04 masak ok, great
14:22 jpansanel Mychem is released :)
14:23 jpansanel http://sourceforge.net/project​/showfiles.php?group_id=195099
14:23 lambdabot2 Title: SourceForge.net: Files
14:28 egonw get your free T-shirt at: http://network.nature.com/blogs/user/joa​nnascott/2007/08/17/save-the-giant-panda
14:28 lambdabot2 Title: Save the Giant Panda - Joanna Scott's blog - Joanna Scott's blog on Nature Netwo ..., http://tinyurl.com/2abqpc
14:48 jpansanel egonw : http://pansanel.blogspot.com/​2007/08/mychem-02-is-out.html
14:48 lambdabot2 Title: Jerome's Blog Space: Mychem 0.2 is out !
14:49 egonw what does the web front end look like?
14:50 jpansanel egonw : the web front-end is into another project : sciwork
14:50 jpansanel (Scientific Workbench)
14:50 egonw ah, ic
14:50 jpansanel The project is splitted into two parts
14:50 egonw yes, that sounds fine
14:51 jpansanel so people can only use the mysql extension or the both
14:51 jpansanel (sciwork depends on mychem)
14:51 * jpansanel need to catch a train
15:38 neksa egonw: r u subscribed to Debichem-devel?
15:38 egonw have been in the past...
15:38 egonw not sure about the now
15:38 egonw why?
15:39 neksa egonw: fwd. please comment
15:39 neksa egonw: I'm not sure I read it correctly about the exclusion of inchi
15:40 egonw I'm chatting with michael on #debichem just now
15:42 neksa egonw: thanks, I was not aware of this channel
15:43 neksa left #cdk
15:46 egonw thomas_ku: does the CDK website work for you?
15:46 egonw or for anyone?
15:54 thomas_ku egonw:
15:54 thomas_ku no it doesn't work for me
15:55 thomas_ku I will go offline now
15:55 thomas_ku cu
15:55 egonw ack, thanx for checking
15:55 thomas_ku no prob
15:56 thomas_ku left #cdk
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19:55 CIA-1 cdk: fichte01 * r481 /trunk/protonprediction/Data/input/ (dataX_backup.txt dataY_backup.txt):
22:52 CIA-1 bioclipse: shk3 * r3702 /trunk/plugins/net.bioclipse.spectru​m/src/spok/utils/SpectrumUtils.java: probably a bug - string instead of constant

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