Hello,
This indeed seems to be sort-of and ECI bug. The reason I say sort-f is
that it seems a bit daft to me that the LabeledMolecule constructor allows
the name not to be that of a Molecule. (The constructor checks validity
but not with "complete=True".)
The problem with fixing LabeledMolecule.name is that it is frozen. So the
two options would be to either edit the ccp/molecule/LabeledMolecule xml
file by hand or to do something like the following at the prompt:
>>> labeledMolecule = top.project.findFirstLabeledMolecule(name='p7:methanol_CN')
>>> labeledMolecule.__dict__['name'] = 'p7'
The GUI would not update (we are bypassing the normal API code) but it
ought to save with that name and then reload ok.
LabeledMolecule was in v1.
If you go to http://www2.ccpn.ac.uk/download/ccpnmr/ you will find older
releases. The data model version is indeed out of sync with Analysis
versions.
Wayne
On Fri, 16 Nov 2012, Gary Thompson wrote:
> Hi Rasmus
>
> Sorry more detail, I seem to be somethat confused how this came about and
> what to do...
>
> I seem to have a molecule and two labelled molecules:
>
>
> print top.nmrProject.parent.labeledMolecules
>
> frozenset([<ccp.molecule.LabeledMolecule.LabeledMolecule
> ['p7:methanol_CN']>,<ccp.molecule.LabeledMolecule.LabeledMolecule
> ['p7:methanol_N']>])
>
> print top.nmrProject.parent.molecules
>
> frozenset([<ccp.molecule.Molecule.Molecule ['p7']>])
>
> The labelled molecules were (I believe) added as I set up samples in the eci
> interface (one is labelle dmehtanol_ N and the other methanol_CN) surely they
> should all refer to the same molecule (in actual fact they refer to None)
>
>
> print list(top.nmrProject.parent.labeledMolecules)[0].molecule
>
> None
>
> print list(top.nmrProject.parent.labeledMolecules)[1].molecule
>
> None
>
>
> with names
>
>
> print list(top.nmrProject.parent.labeledMolecules)[0].name
>
> p7:methanol_CN
>
> print list(top.nmrProject.parent.labeledMolecules)[1].name
>
> p7:methanol_N
>
> am I right in seeming to find that this is an eci problem? NB the original
> data model was imported from a version 1.0 model via the update server, did
> version 1.0 have a labelledMolecule?
>
> Finally how do a I correct the names of the labelled molecules? surely they
> now both have to be p7, but at the same time they are keyed by just their
> name and so you can's have two called p7... with different labelling...
>
>
> Sorry, further questions: where do I find older versions of the datamodel on
> the ccpn web site? secondly the version of the model on the website is 2.05,
> I take it the data model version is out of sync with the analysis software
> versions?
>
> once again thanks for any help
>
> regards
> gary
>
> --
> -------------------------------------------------------------------
> Dr Gary Thompson [Homans Lab Research Coordinator]
>
> Astbury Centre for Structural Molecular Biology,
> University of Leeds,
> Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
> email: [log in to unmask] Fax +44-113-3431935
> -------------------------------------------------------------------
>
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