========================
Other : NMR Calculations
========================


.. |pulldown| image:: ../images/pulldown.png
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.. |check| image:: ../images/check.png
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.. |radio| image:: ../images/radio.png
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.. |float| image:: ../images/float.png
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.. |int| image:: ../images/int.png
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.. |entry| image:: ../images/entry.png
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.. |button| image:: ../images/button.png
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.. |ramp| image:: ../images/ramp.png
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.. |selector| image:: ../images/selector.png
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**View and Edit External NMR Calculations**

This popup window is used to view the various calculations, performed by
programs external to CCPN (like CING or ARIA), that have nonetheless been
setup inside CCPN software to use CCPN data.

*This popup is somewhat of a prototype, so its functionality is neither
complete nor throughly tested, but it is the only way to get an overview of
certain types of data.*

The popup window is divided into two tabs. The first "Calculation Groups" tabs
shows the various types of software that calculations have been setup for. It
should be noted that this system is general and where possible the user should
consider using the dedicated graphical interfaces to run particular pieces of
software (like those in the main Structure menu).

The "Calculation Runs" tab shows the various jobs that have been setup, and
possibly run, for the different kinds of software. The user can change the
software calculation group via the top most pulldown menu, then change the
"Run Number" to look though the jobs ("runs") that have been setup. New, blank
or duplicated, "run" specifications can be made at any time. A specification
may also be deleted, but a run may only be edited if it has not been used by
the calculation; a run is a record or what was done. A completed run may
effectively be edited by making a copy first.

The data that relates to a job/run is divided into three sub-tabs to indicate
what the input data from the CCPN project is, what settings are used during
the calculation, and what the output CCPN data is. The input data is further
sub-divided into various categories of data, and the user can (if the job is
editable) use the [Add ...] and [Remove ...] buttons to dictate which CCPN
entities will be selected for the calculation. Not all types of data will be
appropriate for all calculations; further incentive to use the specialised
program interfaces when they are available, rather than this general one.

The "Run Settings" tab is filled with a table of all of the parameters that
have been associated with the currently selected run. A parameter will
have an identifying code and perhaps a group to collect certain parameters
together. Some parameters may just represent a simple value, but others
may associate a value with a "Data Object"; a CCPN data model entity
containing NMR information or a reference to external data held on disk.

The "Output Data" table lists all of the CCPN entities that were generated or
modified by the selected calculation job (if it were run).

It is notable that a "run" specification will persist even if some or all of
the CCPN data entities (e.g. restraint lists) it was originally linked to have
been deleted. In this way the user still has a record that something was run,
and there is no restriction on the normal manipulation of CCPN data. If a CCPN
data item has disappeared then the run will list it as "*DATA MISSING*".


Main Panel
==========

|button| **Clone**: Clone popup window

|button| **Help**: Show popup help document

|button| **Close**: Close popup

Calculation Groups
==================

*Documentation missing*

===========  ==============================================================================
**Table 1**
-------------------------------------------------------------------------------------------
        *#*  Row number 
     *Name*  name of calculation group (often a program name) 
*Num. Runs*  The number of calculation run specifications stored for the group  *(Editable)*
===========  ==============================================================================



|button| **Add New Calculation Group**: Add a new grouping (e.g. by program name) to contain calculation specifications

|button| **Delete Calculation Group**: Delete the selected calculation group (program settings) and all calculation run settings it contains

Calculation Runs
================

*Documentation missing*

|pulldown| **Calculation Group**: Selects which program (or other calculation grouping) a set of calculations relate to


|pulldown| **Run Number**: Selects which calculation job or "run" is currently being viewed or edited

|button| **New Run**: Make a setup for a new calculation run

|button| **Copy Run**: Make a new calculation run by copying the current one

|button| **Delete Run**: Delete the current calculation run settings

Input Data
==========

*Documentation missing*

|pulldown| **Molecular System**: Selects which molecular system the calculation will be run on

|entry| **Run Details**: User-editable textual comment for the current calculation

Structures
==========

*Documentation missing*

============  ================================================================================
**Table 2**
----------------------------------------------------------------------------------------------
         *#*  Row number 
*Mol System*  Code for the molecular system to which the structure relates 
  *Ensemble*  The id number of the structure ensemble within its molecular system 
    *Models*  The numbers of the conformational models considered 
============  ================================================================================



|button| **Remove Selected Models**: Remove the selected structural models from consideration (does not delete the coordinates)

|button| **Add Ensemble**: Add the selected structure ensemble as calculation input

|pulldown| ***None***: Selects a structure ensemble which may be added as calculation input

|button| **Add Model**: Add the selected conformational model to the calculation input

|pulldown| ***None***: Selects a conformational model which may be added as calculation input

Shifts & Measurements
=====================

*Documentation missing*

===========  =============================================================================
**Table 3**
------------------------------------------------------------------------------------------
        *#*  Row number 
*Data Type*  The kind of measurement data used and calculation input 
   *Serial*  The serial number used to uniquely identify the measurement list 
*List Name*  The textual name of the measurement list 
     *Size*  The number of individual measurements in the list 
  *Details*  User-specified textual comment 
===========  =============================================================================



|button| **Remove Selected**: Remove the selected measurement list from consideration (does not delete the data)

|button| **Add Measurement List**: Add the selected measurement list as calculation input

|pulldown| ***None***: Selects a measurement list which may be added as calculation input

Peak Lists
==========

*Documentation missing*

============  =========================================================================
**Table 4**
---------------------------------------------------------------------------------------
         *#*  Row number 
*Experiment*  The name of the experiment that contains the input peak list 
  *Spectrum*  The name of the spectrum that contains the input peak list 
    *Serial*  The serial number of the input peak list within its spectrum 
     *Peaks*  The number of peaks in the peak list 
============  =========================================================================



|button| **Remove Selected**: Remove the selected peak list from consideration (does not delete the data)

|button| **Add Peak List**: Add the selected peak list as calculation input

|pulldown| ***None***: Selects a peak list which may be added as calculation input

Restraint Lists
===============

*Documentation missing*

================  ==================================================================================
**Table 5**
----------------------------------------------------------------------------------------------------
             *#*  Row number 
*Restraint Type*  The type of restraints in the input restraint list 
 *Restraint Set*  The restraint set that contains the input restraint list 
        *Serial*  The serial number of the input restraintlist within its restraint set 
     *List Name*  The textual name of the input restraint list 
    *Restraints*  The number of restraints in the input restraint list 
================  ==================================================================================



|button| **Remove Selected**: Remove the selected restraint list from consideration (does not delete the data)

|button| **Add Restraint List**: Add the selected restraint list as calculation input

|pulldown| ***None***: Selects a restraint list which may be added as calculation input

Run Settings
============

*Documentation missing*

=============  ===========================================================================
**Table 6**
------------------------------------------------------------------------------------------
          *#*  The serial number of the parameter; an internal CCPN numbering 
       *Code*  The identifying code (one word name) of the parameter 
      *Group*  The group to which the parameter belongs 
       *Name*  Human reasable name or decription of the parameter 
   *Value(s)*  The current value associated with the parameter 
*Data Object*  *Documentation missing* 
=============  ===========================================================================



Output Data
===========

*Documentation missing*

============  =============================================================================
**Table 7**
-------------------------------------------------------------------------------------------
 *Data Type*  The kind of data output by the calculation 
         *#*  the serial number of the output data, within the calculation run 
      *Name*  The name of the output data 
 *CCPN Data*  The identity of any CPN objects that are lined to/as output data 
*Parameters*  Any parameters which relate to the output data 
    *Weight*  Any fractional weighting that was applied to the output data 
============  =============================================================================



