Camelia, the Perl 6 bug

IRC log for #cdk, 2007-08-21

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All times shown according to UTC.

Time Nick Message
05:47 rojasm joined #cdk
06:32 jbrefort joined #cdk
06:54 egonw joined #cdk
07:10 jpansanel moin
07:31 jonalv joined #cdk
07:36 CIA-1 blueobelisk: neksa * r86 /ctfr/trunk/cml/cml2/valid/ (butane.cml index.xml linolein.cml oxidane.cml oxolane.cml):
07:36 CIA-1 blueobelisk: updated CML2 test files from Jerome's repository
07:36 CIA-1 blueobelisk: except for linolein.cml, which seems to have problems
07:36 carsten joined #cdk
07:39 CIA-1 blueobelisk: neksa * r87 /ctfr/trunk/ (11 files in 6 dirs): added SD file tests and updated Molfile samples
08:07 CIA-1 blueobelisk: pansanel * r88 /structures/trunk/src/ (amino_acids/2-aminoacetic_acid.cml esters/linolein.cml):
08:07 CIA-1 blueobelisk: Fix identifier tag for linolein
08:07 CIA-1 blueobelisk: Fix errorValue tag for 2-aminoacetic_acid
08:12 laszlof joined #cdk
08:16 CIA-1 cdk: fichte01 * r498 /trunk/protonprediction/Data/o​utput2/Models/Classification/ (37 files):
08:18 CIA-1 blueobelisk: pansanel * r89 /structures/trunk/src/ (524 files in 30 dirs): Fix units namespace
08:44 rojasm left #cdk
08:59 CIA-1 blueobelisk: egonw * r90 /cb/trunk/parse_wp_links.pl: Changed output, to allow sorting
09:05 CIA-1 qsar: egonw * r183 /trunk/CVSROOT/: Removed CVS leftover
09:25 CIA-1 qsar: egonw * r184 /trunk/qsar-dicts/descriptor-algorithms.owl: Added missing labels
09:26 CIA-1 qsar: egonw * r185 /trunk/qsar-dicts/descriptor-algorithms.owl: Use UTF-8: HTML entities are not defined.
09:28 CIA-1 qsar: egonw * r186 /trunk/qsar-dicts/descriptor-algorithms.owl: Literal parse types, to allow mixed content for bibtex cite elements.
09:30 CIA-1 qsar: egonw * r187 /trunk/qsar-dicts/descriptor-algorithms.owl: Literal parse types, to allow mixed content for MathML elements.
09:33 CIA-1 qsar: egonw * r188 /trunk/qsar-dicts/descriptor-algorithms.owl: Fixed some syntax errors: HTML elements are not allows, or should be namespaced otherwise; add missing MathML NS declaration
09:39 CIA-1 qsar: egonw * r189 /trunk/qsar-dicts/descriptor-algorithms.owl: Fixed ID
09:41 CIA-1 qsar: egonw * r190 /trunk/qsar-dicts/descriptor-algorithms.owl: Removed empty comment
09:44 CIA-1 qsar: egonw * r191 /trunk/qsar-dicts/descriptor-algorithms.owl: Fixed namespace prefix: domain and range are in http://www.w3.org/2000/01/rdf-schema#
09:53 CIA-1 qsar: egonw * r192 /trunk/qsar-dicts/descriptor-algorithms.owl: NS according to RDF customs
09:55 CIA-1 qsar: egonw * r193 /trunk/qsar-dicts/descriptor-algorithms.owl: Fixed MathML entities messed up in r192
10:00 CIA-1 qsar: egonw * r194 /trunk/qsar-dicts/descriptor-algorithms.owl: Mmmm... still the resources pointers are not correct
10:02 CIA-1 qsar: egonw * r195 /trunk/qsar-dicts/descriptor-algorithms.owl: Fixed a rdfs:domain: does this make the previous rdf:parseType commits obsolete?
10:05 CIA-1 qsar: egonw * r196 /trunk/qsar-dicts/descriptor-algorithms.owl: Maybe if I define it as Literal?
10:16 neksa_ changed the nick to neksa
10:31 carsten_ joined #cdk
10:39 CIA-1 qsar: egonw * r197 /trunk/qsar-dicts/descriptor-algorithms.owl: OK, maybe a bit consistent... TODO: look up difference between dataType and parseType
10:43 CIA-1 qsar: egonw * r198 /trunk/qsar-dicts/descriptor-algorithms.owl: Dietz and Graph Representations are not classes, so can't have equivalentClass... should be complementOf or ...
10:43 egonw hi neksa
10:44 neksa hi egonw
10:45 neksa i was drafting the blogs with some screenshots, but got too tired last night. I'm now on #xesam. once I'm done there I'll hurry up with the posts
10:45 egonw OK
10:46 CIA-1 qsar: egonw * r199 /trunk/qsar-dicts/descriptor-algorithms.owl: complementOf should use rdf:resource, not rdfs:
10:47 neksa egonw: could you join #xesam to correct me if I'm wrong in discussion with kamstrup
10:58 dleidert joined #cdk
10:59 CIA-1 qsar: egonw * r200 /trunk/qsar-dicts/descriptor-algorithms.owl: Removed elements annotation and documentation that originated from the STTML version, which had not been removed yet.
11:03 jpansanel hi neksa
11:03 neksa hi Jerome, thanks for updates
11:04 neksa what was the prob with inchis in linolein and glycine?
11:13 carsten_ changed the nick to carsten
11:19 jpansanel glycine was another pb
11:20 jpansanel I don't for linolein
11:20 jpansanel I didn't have time to explore further the pb
11:20 jpansanel I've an important talk tomorrow
11:22 CIA-1 qsar: egonw * r201 /trunk/qsar-dicts/ (descriptor-algorithms.owl swrc_v0.3.owl): Moving to something RDF as replacement for BibTex.
11:26 CIA-1 jmol: hansonr * r8118 /trunk/Jmol/src/org/jmol/adapter/readers/more/ (GaussianReader.java JaguarReader.java): 11.3.11 Jaguar MO and charge reader
11:30 CIA-1 qsar: egonw * r202 /trunk/qsar-dicts/descriptor-algorithms.owl: Moving to something RDF as replacement for BibTex (not entirely happy about using this ontology from this ontoweb organisation).
11:42 CIA-1 cdk: mario_baseda * r8696 /trunk/cdk-taverna/src/main/ (4 files in 3 dirs): Classes modified/added
11:46 begert joined #cdk
11:47 begert hallo
11:47 egonw hi begert
11:47 begert suche den stafan
11:47 egonw er ist nicht hier
11:47 egonw und wir sprechen meistens English
11:48 begert ok
11:48 egonw a question
11:48 begert please
11:48 egonw is your 'clustering of metabolites' R code available as package?
11:48 egonw I'm heading in that direction myself... I'm at Plant Research International...
11:49 egonw in Wageningen, The Netherlands...
11:51 egonw you're in the group of Neumann, nicht?
11:51 begert sorry, i had a phone call
11:51 egonw :)
11:51 begert first: yes group of steffen neumann in halle
11:51 egonw (btw, shk3 was online yesterday evening... he still drops by)
11:52 begert second: who are you ?
11:52 egonw Egon Willighagen
11:52 egonw started a postdoc at PRI 1.5 months ago...
11:52 egonw on metabolomics
11:52 egonw and core developer of the CDK
11:52 begert ok
11:53 begert just a moment please
11:53 egonw sure :)
11:57 begert could you send me the link of what you mean, and btw: nice to meet you
11:57 egonw same here
11:57 egonw link about what? PRI?
11:57 begert no, the clustering code
11:58 egonw don't have code myself... just started... but see e.g. this article...
11:58 egonw (mom look up DOI)
11:59 thomas_ku joined #cdk
11:59 egonw 10.1104/pp.105.068130
11:59 thomas_ku moin
11:59 egonw "A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles."
11:59 egonw hi thomas_ku
12:00 egonw thomas_ku: Rajarshi released the SMILES 2 3D structure tool
12:00 egonw like Christian's code, but then different :)
12:00 egonw begert: we have a lot of GC/MS and LC/MS data
12:01 egonw begert: and clustering of peaks in that data, to match single metabolites, and grouping of metabolites based on profiles over a set of samples is something I am going to do
12:02 egonw begert: and I don't feel much for reproducing existing open source code...
12:02 egonw the section "Clustering von Metaboliten on http://www.ipb-halle.de/index.php?​id=151&type=98&no_cache=1 looked rather interesting
12:02 lambdabot2 Title: Leibniz Institut für Pflanzenbiochemie: Diplomarbeiten und Hiwi-Stellen
12:02 thomas_ku egonw: greate within the cdk? or where?
12:03 egonw it's C code I think...
12:03 thomas_ku A ok
12:03 egonw I asked him if it is also available as SOAP
12:03 thomas_ku that would be great
12:03 egonw thomas_ku: http://www.chembiogrid.org/cheminfo/smi23d/
12:03 lambdabot2 Title: 3D Coordinate Generation
12:08 begert egonw: article: I had a look at htis artice, there is no special package for this, these all are normal R functions
12:09 begert There is one in our group who does nothing but peak picking and alignment
12:09 egonw :)
12:09 egonw right... same here
12:09 begert as for me, I am rather in the data mining stuff
12:10 egonw my job is to automate these tasks as far as possible
12:10 begert that is raw data processing ?
12:10 egonw that too... base line correction
12:10 begert ok
12:10 egonw correction for differences in RT between samples
12:10 egonw XCMS like stuff
12:10 begert ok
12:10 begert yes
12:11 egonw OK, so I have only just started...
12:11 egonw so no code yet, still looking around, and writing up my TODO list for this postdoc
12:11 egonw which is within a new Dutch metabolomics center
12:11 begert yes
12:12 egonw http://www.metabolomicscentre.nl/
12:12 lambdabot2 Title: Netherlands Metabolomics Centre
12:12 begert thy
12:12 begert thx
12:12 egonw in terms of 'full disclosure' :)
12:13 begert you should contact ralf tautenhahn
12:14 egonw he's the author of XCMS, right?
12:14 egonw I've seen his name, at least
12:14 begert no something like coauthor
12:14 begert author is smith
12:14 begert c.smith
12:15 egonw ack, found it on bioconductor
12:15 egonw yes, might do so when it is decided what my priorities will be
12:17 begert my issue is currently the nmr shift prediction based on the cdk descriptors
12:17 egonw ah, excellent
12:17 begert do you know these ?
12:18 egonw yes, you need shk3 (stefan) or steinbeck for the details...
12:18 begert in more detail I mean
12:18 egonw yes, a bit...
12:18 begert ok
12:18 egonw I guess you refer to the HOSE code based one, right?
12:18 begert yes
12:18 * egonw worked on a NMR based structure elucidator within Bioclipse in the group of Steinbeck last year
12:18 begert about 450
12:18 egonw where Stefan was still too then
12:19 begert ok
12:20 egonw in the CDK are only default values, not the full HOSE/shift table from NMRShiftDB
12:20 begert ok
12:20 egonw and you really need the latter...
12:21 egonw I can point you to the code I used...
12:21 egonw mom
12:21 CIA-1 jmol: hansonr * r8119 /trunk/Jmol/src/org/jmol/adapter​/readers/more/JaguarReader.java: 11.3.11 Jaguar reader mo HOMO
12:21 egonw it's within this Bioclipse plugin: http://bioclipse.svn.sf.net/svnroot/bioclipse/​trunk/playground/plugins/net.bioclipse.seneca/
12:21 lambdabot2 Title: Revision 3707: /trunk/playground/plugins/net.bioclipse.seneca, http://tinyurl.com/yrquw2
12:22 egonw you would need the predictor jar in jars/
12:22 egonw and this bit of code: http://bioclipse.svn.sf.net/svnroot/bioclipse/tru​nk/playground/plugins/net.bioclipse.seneca/src/ne​t/bioclipse/seneca/judges/WCCNMRShiftDBJudge.java
12:22 lambdabot2 http://tinyurl.com/38mcjm
12:22 egonw somewhere down the middle is the prediction done:
12:23 egonw shifts[carbonCount] = predictor.predict(ac, ac.getAtom(f))[1];
12:23 egonw OK, this is 13C NMR...
12:23 egonw not sure if that's what you actually want... (which might actually be 1H NMR)
12:23 begert ah, thanks, I have to ask Stefan to understand this fully
12:23 CIA-1 jmol: hansonr * r8120 /trunk/Jmol/src/org/jmol/ (7 files in 4 dirs): 11.3.11 # bug fix: mo not showing titles
12:24 begert yes we focus on H, C seems not to be that problem
12:25 egonw OK
12:28 egonw do you happen to go to Ulm in September?
12:28 begert no
12:33 CIA-1 jmol: hansonr * r8121 /branches/v11_2/Jmol/src/org/jmol/ (12 files in 5 dirs): (log message trimmed)
12:33 CIA-1 jmol: 11.2.9 VERSION
12:33 CIA-1 jmol: # bug fix dots nn% not operational
12:34 CIA-1 jmol: # bug fix for state of multi-polymer protein cannot be restored
12:34 CIA-1 jmol: # bug fix for script window using swing thread start not from event queue
12:34 CIA-1 jmol: # bug fix for script window not showing undo/redo buttons
12:34 CIA-1 jmol: # bug fix: lcaoCartoon for sp center requires "sp2" not "sp"
12:50 begert egon ?
12:50 egonw yes
12:50 begert can you tell me how to plot a smiles string in R ?
12:51 egonw the SMILES itself, or a corresponding diagram?
12:51 begert a smiles like O=C(O)CC(C)(C)C as a plotted molecule
12:52 begert like JChemPaint does
12:52 egonw right
12:52 * egonw is thinking...
12:52 egonw Rajarshi Guha worked on the CDK-R bridge, see CDK News
12:52 egonw and e.g. this PDF: http://cheminfo.informatics.indian​a.edu/~rguha/writing/pres/rcdk.pdf
12:52 lambdabot2 http://tinyurl.com/2cxhwn
12:52 begert rcdk I assume
12:53 begert yes
12:53 egonw yes
12:53 egonw but not sure about the 2D diagram
12:53 begert already worked with this ?
12:53 egonw should be possible, but not sure how that would be done
12:53 egonw not with the latest set up...
12:53 begert okay, thanks
12:53 egonw I had it installed at some point...
12:54 egonw ask on cdk-user
12:54 begert thy
12:54 begert thx
12:54 egonw this is of general interest
12:54 egonw US keyboard?
12:54 begert no, stupidity
12:54 egonw :)
12:54 begert ;-)
13:07 CIA-1 cdk: fichte01 * r499 /trunk/protonprediction/Data/ (131 files in 3 dirs):
13:09 egonw begert: fichte01 is building 1H NMR prediction models, together with Stefan and Steinbeck
13:10 thomas_ku left #cdk
13:11 begert ;-) yes thats me
13:12 egonw oh, really?
13:12 egonw sorry, did not know...
13:12 egonw I though fichte01 was from tuebingen :)
13:12 begert ;-) no ..
13:12 begert initially this nick was a misunderstanding
13:13 begert but thanks a lot, I would have welcomed co-workers
13:13 egonw I would love to helped with this project...
13:14 begert but no time ?
13:14 egonw I did my PhD work (not awarded yet) in chemometrics
13:14 egonw right, too busy
13:14 begert thats cool
13:14 egonw and since we do not do much NMR/MS here... :(
13:15 begert there is a package on mass decomposition to be published which  makes heavy use of chemometrics
13:15 begert is from böcker in jena
13:15 begert I would like to to stuff like that next
13:15 begert but time is a factor
13:16 egonw right
13:16 begert there will be an r frontend to that
13:16 egonw sounds interesting
13:17 begert especially usefull for annotation of peak signals, could be
13:17 begert but machines need good resolution I think,
13:20 laszlof joined #cdk
13:38 egonw begert: need to go, very nice talking to you, hope to see you online here more often, bye!
13:48 begert likewise, bye
13:54 CIA-1 bioclipse: jonalv * r3708 /trunk/playground/plugins/net.biocl​ipse.keyring/META-INF/MANIFEST.MF: Exports the dialogs package for use from other plugins
14:13 CIA-1 jmol: hansonr * r8122 /trunk/Jmol/src/org/jmol/ (2 files in 2 dirs):
14:13 CIA-1 jmol: 11.2.9 VERSION
14:13 CIA-1 jmol: # final settings for Jaguar reader for now
14:27 CIA-1 jmol: hansonr * r8123 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.11 VERSION
15:08 carsten joined #cdk
15:31 CIA-1 bioclipse: jonalv * r3709 /trunk/playground/plugins/net.bioclipse.keyr​ing/src/net/bioclipse/keyring/KeyRing.java: Statusbar information when logged in is now shown. It is also shown after someone logs out but not before anyone have logged in a first time (yet)
15:46 CIA-1 bioclipse: jonalv * r3710 /trunk/playground/plugins/net.bioclipse.keyr​ing/src/net/bioclipse/keyring/KeyRing.java: Listeners are not informed of happenings to sandbox instances
17:14 shk3 joined #cdk
17:49 CIA-1 jmol: nicove * r8124 /trunk/Jmol-FAH/projects/p3644.xyz.gz: Folding@Home
17:54 CIA-1 jmol: nicove * r8125 /branches/v11_2/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
17:55 CIA-1 jmol: nicove * r8126 /branches/v11_2/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
17:59 CIA-1 jmol: nicove * r8127 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
18:17 CIA-1 jmol: hansonr * r8128 /trunk/Jmol/src/org/jmol/adapter​/readers/more/JaguarReader.java: 11.3.11 ready -- JaguarReader gaussian fix
18:25 CIA-1 jmol: hansonr * r8129 /trunk/Jmol/src/org/jmol/adapter​/readers/more/JaguarReader.java: code cleaning
18:32 dleidert joined #cdk
18:46 jbrefort joined #cdk
19:15 egonw joined #cdk

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