Package prompt :: Module eliminate :: Class Eliminate
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Class Eliminate

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Instance Methods [hide private]
 
__init__(self, relax)
Class containing the function for model elimination.
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eliminate(self, run=None, function=None, args=None)
Function for model elimination.
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Method Details [hide private]

eliminate(self, run=None, function=None, args=None)

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Function for model elimination.

Keyword arguments
~~~~~~~~~~~~~~~~~

run:  The name of the run(s).  By supplying a single string, array of strings, or None, a
single run, multiple runs, or all runs will be selected respectively.

function:  A user supplied function for model elimination.

args:  A tuple of arguments for model elimination.


Description
~~~~~~~~~~~

This function is used for model validation to eliminate or reject models prior to model
selection.  Model validation is a part of mathematical modelling whereby models are either
accepted or rejected.

Empirical rules are used for model rejection and are listed below.  However these can be
overridden by supplying a function.  The function should accept five arguments, a string
defining a certain parameter, the value of the parameter, the run name, the minimisation
instance (ie the residue index if the model is residue specific), and the function
arguments.  If the model is rejected, the function should return 1, otherwise it should
return 0.  The function will be executed multiple times, once for each parameter of the
model.

The 'args' keyword argument should be a tuple, a list enclosed in round brackets, and will
be passed to the user supplied function or the inbuilt function.  For a description of the
arguments accepted by the inbuilt functions, see below.

Once a model is rejected, the select flag corresponding to that model will be set to 0 so
that model selection, or any other function, will then skip the model.



Local tm model elimination rule
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The local tm, in some cases, may exceed the value expected for a global correlation time.
Generally the tm value will be stuck at the upper limit defined for the parameter.  These
models are eliminated using the rule:

    tm >= c

The default value of c is 50 ns, although this can be overridden by supplying the value (in
seconds) as the first element of the args tuple.


Internal correlation times {te, tf, ts} model elimination rules
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

These parameters may experience the same problem as the local tm in that the model fails and
the parameter value is stuck at the upper limit.  These parameters are constrained using the
formula (te, tf, ts <= 2tm).  These failed models are eliminated using the rule:

    te, tf, ts >= c . tm

The default value of c is 1.5.  Because of round-off errors and the constraint algorithm,
setting c to 2 will result in no models being eliminated as the minimised parameters will
always be less than 2tm.  The value can be changed by supplying the value as the second
element of the tuple.


Arguments
~~~~~~~~~

The 'args' argument must be a tuple of length 2, the elements of which must be numbers.  For
example, to eliminate models which have a local tm value greater than 25 ns and models with
internal correlation times greater than 1.5 times tm, set 'args' to (25 * 1e-9, 1.5).