relax SVN archive

Reverted the change of r2462. This was an attempt at fixing bug #5746.

The bug which was reported by Chris MacRaild is located at
https://gna.org/bugs/?func=detailitem&item_id=5746.

The command used to revert the change was:

$ svn merge -r2462:2461 .

Fix to bug #5753.

The bug is located at https://gna.org/bugs/?func=detailitem&item_id=5753.

The fix simply involved adding a test for the presence of the run name key in self.relax.data.pdb.

Fix to bug #5752.

The bug report is located at https://gna.org/bugs/index.php?func=detailitem&item_id=5752.

The problem was simply two calls to 'file.pipe_write()' which should have been 'file.write()' as
'file' is a real file object.

Fix to bug #5746.

The bug report submitted by Chris MacRaild "c.a.macraild at leeds.ac.uk" is located at
https://gna.org/bugs/?func=detailitem&item_id=5746.

The issue was simply an incorrect test in the 'self.model_statistics()' function of the model-free
specific code. An 'and' should have been an 'or'.

All the model-free Molmol functions have been moved into their own class Molmol.

Adds the test data missing from r2457

https://mail.gna.org/public/relax-devel/2006-04/msg00014.html

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