relax SVN archive

Epydoc is now documenting everything!

The whitelist system of selected what to document was not working! Too many packages are changing,
especially in the branches. Therefore absolutely everything is now being documented, including the
test suite. This will allow all new packages to be automatically documented.

This patch fixed assignment of columns of parameter file.

This changed_parameterfile_settings_patch file was attached to https://gna.org/task/?6847 by Michael
Bieri (https://gna.org/users/michaelbieri), in the zip file calc_modelfree.py_patch.tar.gz
(https://gna.org/support/download.php?file_id=7750).

Note, this is only for testing the OMP data (https://gna.org/task/?6847#comment1). In future, this
can be set in a Settings Window (not included yet).

The patch was not fully applied, the RELAX_DATA variable was the only part changed. The SEQ_DATA
change was whitespace at the end, which should not be there anyway. The other changes are not of
use as the code was eliminated and replaced with a call to dAuvergne_protocol.

An additional function is added, that converts a string (such as 'xxx * e-1') into a float.

This convert_string_to_float_patch file was attached to https://gna.org/task/?6847 by Michael
Bieri (https://gna.org/users/michaelbieri), in the zip file calc_modelfree.py_patch.tar.gz
(https://gna.org/support/download.php?file_id=7750).

This function is used to read in bond length or csa values set in settings window as float values.

The following changes were made to the patch:
converttofloat was renamed to convert_to_float to match relax' standards,
''' was replaced with """ (again a relax standard),
The single space at the start of the docstring header line was removed and a full stop added
(both are needed to meet the standard),
The docstring expanded,
Comments were added and the lines with '######################' removed.

If no residues are selected to get excluded from analysis (modelfree), an empty file will be created.

This create_empty_unresolved_file_patch file was attached to https://gna.org/task/?6847 by Michael
Bieri (https://gna.org/users/michaelbieri), in the zip file calc_modelfree.py_patch.tar.gz
(https://gna.org/support/download.php?file_id=7750).

Successful relax calculation will be displayed in relaxGUI Log Window and not as a pop-up.

This feedback_after_calc_patch file was attached to https://gna.org/task/?6847 by Michael Bieri
(https://gna.org/users/michaelbieri), in the zip file calc_modelfree.py_patch.tar.gz
(https://gna.org/support/download.php?file_id=7750).

Replaced: relax_run_ok() to print ''.

Manually applied the import_global_relax_settings_patch file.

This was attached to https://gna.org/task/?6847 by Michael Bieri
(https://gna.org/users/michaelbieri), in the zip file calc_modelfree.py_patch.tar.gz
(https://gna.org/support/download.php?file_id=7750).

Values set in the Settings Window are now imported into model-free calculation.

Settings are: Bond length, CSA value, Proton (specify label of proton in PDB file), minimisation
algorithm, size of grid inc.

In addition, system output is redirected to the Log Window.

Note that much of this is will change when using the relax data store.

Manually applied the import_math_wx_patch file.

This was attached to https://gna.org/task/?6847 by Michael Bieri
(https://gna.org/users/michaelbieri), in the zip file calc_modelfree.py_patch.tar.gz
(https://gna.org/support/download.php?file_id=7750).

Python modules wx and math are imported inti calc_modelfree.py.

The wx module is required to update the Log Window and the math to make exponential calculations.

Manually applied the more_input_start_model_free_patch file.

This was attached to https://gna.org/task/?6847 by Michael Bieri
(https://gna.org/users/michaelbieri), in the zip file calc_modelfree.py_patch.tar.gz
(https://gna.org/support/download.php?file_id=7750).

Manually applied the redirect_patch file.

This was attached to https://gna.org/task/?6847 by Michael Bieri
(https://gna.org/users/michaelbieri), in the zip file calc_modelfree.py_patch.tar.gz
(https://gna.org/support/download.php?file_id=7750).

The new class has been copied and pasted to the bottom of the module, and the comment above the
class was converted into a class docstring.

Fixed the calls to filedialog.openfile() in the auto model-free protocol.

The cwd is now opened by default for each of the '+' buttons.