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May 2010 model changes

by Rasmus Fogh last modified 2010-05-17 11:05

Proposed model changes, May 2010

We have accumulated several model change requests. It would be good to get them in now. We would need to decide which can be added to the next release (long term stable) without too much risk, and which would have to wait till the first leading edge release. Comments are welcome.


Proposed changes

  • Consider adding derived link AnnealProtocol->Software.
  • Add NmrCalc Data subclass holding SymmTracelessMatrix, for order tensors etc. (NB check name)
  • Check adding Volume/Height attributes to Peak, and how to fit work practices.
  • Check NmrCalc changes.Check NmrScreen changes, and add documentation

  • Put in draft NmrScreen package. DONE
  • Analysis.AnalysisProject.printWinFileName - change type to PathString DONE
  • Fix PeakDim.realValue (currently broken). Desired behavior is that PeakDim.realValue should be derived from PeakDim.value and PeakDim.peakDimComponents, except where it is explicitly set. Actual behaviour means it is set automatically upon saving and reloading. The fix would involve making realValue fully derived, and using an extra attribute PeakDim.realValueImpl to store the actual value.
    DONE
  • Add  LabeledMolecule.LabeledMixture.name    Line    0..1 DONE
  • Add LabeledMolceule.SingleAtomLabel.chemAtom derived link DONE
  • Change type of MultiTypeValue.textValue from Text to String DONE
  • Add Nmr.ExpTransfer.isDirect (Boolean) attribtue to distinguish e.g. direct and indirect NOESY transfer.
    DONE
  • Remove MultiTypesValue DataObjTypes (list-of- version of MultiTypeValue. Not in use, can always be added back). DONE
  • Introduce nD floatMatrix DataObjType. DONE
  • Add MultiTypeValue.floatMatrixValue attribute.
    Should behave as nested tuple matrix representation, and be settable wither with list,shape, or with nested list matrix as input. A draft versions can be seen here. DONE
  • Changes to NmrCalc package
    • Describe how to put in lists of values in documentation - for Floats the MultiTypeVaue.floatMatrix will be one way. DONE
    • Add ioRole and weight attributes to RunParameter class DONE
    • Add code and groupId attribtues to Data class DONE
    • Add a copy of NmrSim.NmrCalcEnergyTerm, complete with attributes and llniks, modified to fit with the rest. This will allow using NmrCalc instead of NmrSim. DONE
    • Change all hard links out-of-package to derived one-way links. This lets NmrCalc be used as a generic standalone data descriptor package in the new LIMS application. DONE
    • Add link to AnnealProtocol at top DONE
  • Remove NmrSim package and use NmrCalc in the future (See above) DONE
  • Add SymmTracelessMatrix DataObjType to use for orientation tensors etc. WAS THERE ALREADY
  • Completely redo WMS package DONE first draft
  • Add 2D shift distribution in NmrReference package. New class ChemAtomNmrDistrib with serial key, FloatMatrix distribution attribute, child of ChemCompNmrRef, ordered link to ChemAtomNmrRef to describe atoms. DONE

Changes to be done later

  • Move molsim.Symmetry to molecule package. This requires modifying the HADDOCK code to fit.







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