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FormatExchange meeting 7 Nov 2011

Summary of FormatExchange meeting, status and plans.


  • FormatExchange has been successfully ported to the new Qt GUI, and has a nice, smooth interface.
  • We are aiming for a release of FormatExchange in the trunk (beta) release of CcpNmr by end December / start January, which covers the goals of our contract with Doroteya. The program will contain reading of NmrView and Sparky projects, as well as reading of coordinates. The latter may be a bit unpolished.
  • Doroteya will have a version ready for commenting by Nov 15. Some short term improvements are needed: Complete integration of coordinate reading; Add missing GUI components and ReDo; Get CCPN project output up to date; Allow for Assignmetn-Atom matches that are not 1:1; Fix known issues. Marc will check in some speed improvements. We at CCPN will then test and comment. Doroteya will finish adding new features by the end of November, and spend December adding documentation, fixing bugs, and getting ready for release. The CCPN crew will test during December.
  • Marc's coordinate is a robust parser without an attached interface. It will be used it to read coordinate files for FormatExchange, but the interface on top must be done by Doroteya.
  • Pieter has added restraints to the FormatExchange XML model, and is well advanced in being able to read all the most important restraint formats. Next point is restraint validation code. The EBI has no need for a user interface to fix data - at deposition data are either accepted as is or refused. The EBI is using the same system as Doroteya / Marc and there are no potential compatibility issues.
  • There are some longer term improvements still outstanding. Some might fit in before release if ther eis time.
    • Consider changing XML reader to speed up processing (sometimes painfully slow at present). Marc has the issue in hand.
    • Add processing of resonance groups / spin systems. Might be relatively easy once the rest is done.
    • Increase the number of formats covered
    • Add restraint list coverage to the user interface.
    • Automatic file type recognition.
    • Improved experiment type detection.
    • Grouping and classification of Warnings.
    • Handling of unknown ChemComps.
    • Optimise and improve user interface.
    • Use of FormatConverter parsers versus new stand-alone parsers (by Tim). In principle avoiding the FormatConverter code would be an advantage, but it would depend on the quality and convenience of the alternative.
    • Add CCPN project merging. Should be done by CCPN team.