Camelia, the Perl 6 bug

IRC log for #cdk, 2007-08-19

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All times shown according to UTC.

Time Nick Message
07:13 egonw joined #cdk
08:00 jbrefort joined #cdk
08:22 carsten joined #cdk
08:23 jbrefort hey carsten
08:25 carsten Guten Morgen
08:29 jbrefort my laptop is dead :(
08:30 carsten outch
08:30 carsten Julias THinkPad died last year as well
08:31 jbrefort I have no more display
08:31 carsten ok, so you can access the hdd
08:31 jbrefort yes
08:32 carsten in julias case the hdd mainboard died
08:32 jbrefort much worse
08:34 egonw jbrefort: won't have time to pay a closer look at your crystal stuff... but it looked good
08:34 jbrefort thanks
08:44 egonw I second the comment by peter to make each allotrope a separate file...
09:04 jbrefort each structure in a separate file
09:04 egonw then we can easily link to each crystal structure, by pointing to SVN
09:04 egonw or to a file in a certain dir when installed as package
09:07 jbrefort that's the idea
09:10 neksa joined #cdk
12:31 CIA-1 cdk: mario_baseda * r8695 /trunk/cdk-taverna/src/ (20 files in 4 dirs): Classes modified/added
13:12 CIA-1 cdk: fichte01 * r483 /trunk/protonprediction/Data​/output2/Models/Regression/ (19 files):
13:18 CIA-1 cdk: fichte01 * r484 /trunk/protonprediction/Data/ou​tput2/Models/Regression/.RData:
13:19 egonw joined #cdk
13:24 CIA-1 cdk: fichte01 * r485 /trunk/protonprediction/Data​/output2/Models/Regression/ (39 files):
17:24 CIA-1 cdk: fichte01 * r486 /trunk/protonprediction/Data/output2/Models/ (4 files in 2 dirs):
17:27 shk3 joined #cdk
17:29 egonw hi shk3
17:29 shk3 hi
17:29 egonw did you get my mail?
17:30 shk3 yes
17:30 shk3 not sure what you mean
17:30 egonw the chemical structure does not have explicit hydrogens
17:30 egonw and the peaks are therefore assigned to heavy atoms...
17:30 egonw much like in the submit on the web server
17:31 egonw but the CMLSpect download for a 1H NMR does have explicit hydrogens...
17:31 shk3 which format/source are you talking about?
17:31 egonw JCAMP
17:32 egonw about those 5000 1H NMR spectra
17:32 shk3 sorry, which 5000?
17:32 egonw I asked you about a JCAMP data set, right?
17:32 shk3 you wrote: "is that something your CMLSpect reader
17:32 shk3 in NMRShiftDB can deal with?
17:32 shk3 "
17:32 shk3 did you?
17:32 egonw yes
17:33 shk3 sorry, I had too much trouble over the last few months
17:33 shk3 ...
17:33 shk3 do you mean jcamp reader?
17:33 egonw no worries...
17:33 egonw I think you told me you did not have a JCAMP reader...
17:33 egonw or at least, not one that read both the chemical structure (JCAMP-CS) and the spectrum (JCAMP-DX)
17:34 shk3 we have, the one from jcamp-dx project
17:34 shk3 that might be
17:34 shk3 not sure if it reads structures
17:34 egonw had a brief look at the code... and I think it does not read JCAMP-CS
17:34 egonw anyway...
17:34 egonw I have a convertor which creates CMLSpect from it...
17:35 shk3 great
17:35 shk3 so you have 5000 spectra for us?
17:35 egonw well... 1 at this moment...
17:35 shk3 shouldn't be a problem to read them
17:35 egonw but it comes from a set of 5000
17:35 egonw well...
17:35 egonw there is this one problem...
17:36 egonw which I tried to write down :)
17:36 egonw the file is a bit tricky...
17:36 egonw the JCAMP-CS part does not have H atoms...
17:36 egonw while it is a 1H spectrum
17:36 shk3 the explicit hs are not really a problem
17:36 shk3 might give wrong assignments only in bad cases
17:36 egonw right...
17:37 egonw where the two hydrogens attached to the same heavy atom actually have different shifts...
17:37 egonw ok, fair
17:37 shk3 yes
17:37 egonw so, say we have ethanol...
17:37 shk3 so send me the file and I have a look
17:37 egonw then it's fine to say peak at 3.5 angstrom is assigned to the second carbon?
17:37 shk3 shouldn't be a problem to make a parser based on cdk/jumbo
17:37 shk3 yes
17:38 egonw ok, then I know enough...
17:38 egonw it's the last bit missing from the convertor...
17:38 egonw it spit valid CMLSpect which nicely opens in Bioclipse...
17:38 egonw will send you the file in about 15 minutes or so...
17:38 shk3 then there shouldn't be a problem
17:38 egonw btw, files two bug reports about ethanol...
17:39 CIA-1 cdk: fichte01 * r487 /trunk/protonprediction/Data/output2/Models/ (3 files):
17:39 shk3 I try to get the nmrshiftdb bits in bioclipse right
17:40 shk3 submit, predict, spectrum search and general search seems to work
17:40 egonw did that get broken?
17:40 egonw I have used that a lot in the past...
17:41 shk3 well, there were minor problem
17:41 shk3 s
17:41 egonw ah, ic...
17:41 shk3 e. g. predicted and saved spectra could not open
17:41 shk3 not sure if it worked once
17:41 shk3 might have done so
18:01 egonw ok, email in 5 minutes...
18:06 egonw sent
18:06 egonw shk3: please reply with properties you like to see added...
18:16 egonw and any comments of course
18:17 egonw etc etc ...
18:32 shk3 will do that asap
18:32 shk3 have some other things in schedule for this evening
18:36 Nout joined #cdk
18:41 CIA-1 cdk: fichte01 * r488 /trunk/protonprediction/Data/output1/dataY.txt:
18:58 steinbeck joined #cdk
19:01 CIA-1 cdk: fichte01 * r489 /trunk/protonprediction/Da​ta/input/data_backup.txt:
21:03 CIA-1 jmol: hansonr * r8112 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (Molecules.java Orbitals.java WebExport.java WebPanel.java): 11.3.11 webexport fixes
21:05 CIA-1 jmol: hansonr * r8113 /trunk/Jmol/src/org/openscience/j​mol/app/webexport/WebExport.java: 11.3.11 -- cleanup
22:12 CIA-1 jmol: hansonr * r8114 /trunk/Jmol/src/org/jmol/ (6 files in 3 dirs): 11.3.11 bug fix : lcaoCartoon for sp center requires "sp2" not "sp"
23:09 CIA-1 jmol: hansonr * r8115 /trunk/Jmol/src/org/jmol/ (5 files in 2 dirs):
23:09 CIA-1 jmol: 11.3.11 new feature: lcaoCartoon rotate [x|y|z] degrees create "px"
23:09 CIA-1 jmol: for example:
23:09 CIA-1 jmol: lcaoCartoon rotate z 20 create "px"

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