relax SVN archive

Completion of task #3146, mapping parameters onto structure through Molmol macros.

The task is located as https://gna.org/task/?func=detailitem&item_id=3146.

Arbitrary colour gradients are supported. To allow this, the 'colour_start' and 'colour_end'
keyword arguments have been added to the 'molmol.write()' user function. These can either be colour
names like 'red' or an RGB (red, green, blue) array such as [1.0, 1.0, 1.0] which is white. The
file colour.py has been added to the base directory for colour support. It contains two functions,
the first being 'self.linear_gradient()' which takes a value between zero and one and determines the
RGB vector of that value when zero is the start colour and one is the end colour. The second
function, 'self.rgb()' takes a string representing a colour and translates it to an RGB array.

For the 'classic' style, only the mapping of model-free parameters is currently supported. The
function 'self.molmol_macro_classic()' has been added to the model-free specific code. A number of
auxiliary functions 'self.molmol_macro_classic_*()' are called by this main function to generate the
Molmol commands for colouring, setting the width, and setting the style of backbone bonds, for
creating the Molmol macro header, and for translating order parameters, correlation times, and
chemical exchange into values between zero and one for the colour gradients.

A number of new RelaxError objects have been created for the colours, etc.

Reorganisation of code introduced at r2450 for consistency

Following the suggestion of Edward dAuvergne on relax-devel
https://mail.gna.org/public/relax-devel/2006-04/msg00005.html
the code introduced at r2450 has been reorganised into specific
functions for the various run types

Fix for bug #5698 and related issues.

Adds several missing functions to specific_fns/jw_mapping.py, and some
missing pointers to jw_mapping functions in specific_fns/specific_setup.py

Also adds jw_mapping tests to the test suite

fix for missing files from maths_fns in r2455

edward at nmr-relax.com

https://gna.org/bugs/index.php?func=detailitem&item_id=5602

removed memory leak in fitting functions c module

edward at nmr-relax.com

https://gna.org/bugs/index.php?func=detailitem&item_id=5602
https://gna.org/bugs/index.php?func=detailitem&item_id=5473

The creation of a framework for the generation of Molmol macros.

A large number of changes and additions have been made including:

The user function 'molmol.write()' has been created.

A number of functions in the generic molmol code have been renamed. These are 'open_pipe' to
'pipe_open', 'pipe_open' to 'pipe_open_test', and 'write' to 'pipe_write'.

The functions 'self.write()' and 'self.create_macro()' have been added to 'generic_fns/molmol.py'.
The first function calls the second which returns an array of Molmol commands. The point of
splitting the functions is so in the future 'self.exec_macro()' can be added to pipe the command
directly into Molmol.

The two functions 'self.molmol_macro()' and 'self.molmol_macro_classic()' have been added to the
model-free specific code. The second function currently returns a dummy array so that the resultant
macro is useless. The first function is returned by the specific_setup.py code.

A new error class called 'RelaxStyleError' has been created. This error is to be called anytime an
argument called 'style' is unrecognised.

Added Gary Thompson to the list of full access committers.

The run type 'hybrid' model-statistic returning function now handles numerous instances.

Fix for bug introduced in r2450. overfit_deselect() evaluated
self.relax.data.diff[run], and this raised a KeyError in the event the
run was of the local_tm modelfree type.

Fix for bug #5501. Removes all residue selection on read operations, and
impliments protection from underfitting in minimise(), grid_search() and
calc()