Camelia, the Perl 6 bug

IRC log for #cdk, 2009-04-06

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All times shown according to UTC.

Time Nick Message
06:03 jbrefort joined #cdk
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08:33 shk3 joined #cdk
08:42 egonw joined #cdk
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10:22 sneumann Hi there, a while ago the question was whether our code
10:23 sneumann for writing mzAnnotate (CMLcor + CMLSpect)
10:23 sneumann could recycle stuff from NMRshiftDB
10:24 sneumann So, shk3: how specific are the NMRshiftDB objects to NMR data
10:24 sneumann and how is the CMLSpect-writing implemented ?
10:26 shk3 the objects hold peaks
10:26 sneumann FQDN of the object or the path ?
10:27 shk3 whats fqdn?
10:27 shk3 CML writing is done via building jumbo objects
10:28 sneumann Fully-Qualified-Domain-Name, i.e. package path.
10:28 sneumann Jumbo is one of the CDK - CML dependencies for CML stuff ?
10:29 shk3 yes
10:29 sneumann So we have that already "on board" if we use CDK.
10:29 sneumann Do the objects have to be derived from some jumbo stuff,
10:29 sneumann Do the objects have to be derived from some jumbo stuff,?
10:30 shk3 cdk has a jar called cmlxom-2.5...
10:31 shk3 nmrshiftdb has an older version of that
10:31 sneumann Are they (in)compatible ?
10:31 egonw cmlxom is the java object side of CML
10:32 egonw yes, there tend to be a few inconsistencies
10:32 egonw but not much
10:32 shk3 which thing incompatible to what?
10:32 egonw there has been some shuffling of metadata
10:32 egonw and what elements are allowed here and there
10:33 egonw though 2.5 is pretty flexible nowadays...
10:33 egonw and leaves much to 'conventions'
10:33 egonw as explained in the CMLSpect paper
10:33 sneumann Which sample code whould be best starting point ?
10:34 shk3 for writing cml?
10:34 egonw or for mzAnnotate?
10:34 sneumann for writing CMLSpect with cmlxom25
10:35 sneumann i.e. a few molecules,
10:35 egonw I would suggest CDK's cdk.libio.cml.Convertor
10:35 shk3 that's molecules
10:35 sneumann a few spectra and metadata between the two
10:35 shk3 for spectra
10:35 shk3 have a look at method getCMLSpect()
10:35 egonw the API is similar for spectra
10:35 egonw shk3: of which class?
10:36 shk3 in org.openscience.nmrshiftdb.om.DBSpectrum
10:36 shk3 don't hurry
10:36 shk3 it's all coming
10:36 shk3 :-)
10:36 egonw :)
10:50 shk3 did that help?
11:28 zarah joined #cdk
17:21 CIA-62 cdk: shk3 * r14539 /jchempaint/trunk/src/main/org/openscience/jchempa‚Äčint/resources/userhelp_jcp/contain/molecules.html: minor change in help

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