relax SVN archive

Added tests for the Dasha, Molmol, Grace, and OpenDX executables.

This is an extension of the ideas introduced to fix bug #7225 (https://gna.org/bugs/?7225). This
change was discussed at https://mail.gna.org/public/relax-devel/2006-09/msg00034.html (Message-id:
<7f080ed10609280917s139d2c2cm9f0edcbd5a9fc04c@...>).

Fix to bug #7225.

This bug was reported by Alex Hansen at https://gna.org/bugs/index.php?7225.

To enable comprehensible error messages when attempting to execute Modelfree4, the function
'self.test_binary()' was added to the file 'io.py'. This was described in the post located at
https://mail.gna.org/public/relax-devel/2006-09/msg00034.html (Message-id:
<7f080ed10609280917s139d2c2cm9f0edcbd5a9fc04c@...>). The implementation is slightly
different to the post though. Firstly the supplied string corresponding to the binary is tested to
see if the full path has been supplied. If so then the string is tested to see if the file exists
and if the file is executable. Otherwise the file is searched for in the PATH environmental
variable. Point 5 of the post at https://mail.gna.org/public/relax-devel/2006-09/msg00034.html,
testing that the binary is in the current directory was not implemented. The reason is because I
was unable to successfully modify the PATH variable.

Three new RelaxErrors have been created to print out comprehensible messages:
RelaxMissingBinaryError, RelaxNonExecError, and RelaxNoInPathError.

Modified the Modelfree4 execution code to test the return status when a PDB file is used.

Fix for bug #7224 (https://gna.org/bugs/?7224).

The problem was simply that the run name was being replaced by None.

Implemented a test for the test suite which catches bug #7224 (https://gna.org/bugs/?7224).

Partial fix for bug #7224 (https://gna.org/bugs/?7224).

The 'param_types' argument of the 'diffusion_tensor.init()' user function was changed to the value
of 3. The rational for this fix is given in the post at
https://mail.gna.org/public/relax-devel/2006-09/msg00042.html (Message-id:
<7f080ed10609300034j2e2487f2p2e252eb941a38e33@...>).

Changed the CSA values in the sample scripts from -160 ppm to -170 ppm.

This idea was suggested at https://mail.gna.org/public/relax-users/2006-09/msg00045.html
(Message-id: <7f080ed10609290808u3d30d31cp8ca6040a239a806d@...>). The parent thread by
Sébastien Morin of the subject of the CSA & bond length is located at
https://mail.gna.org/public/relax-users/2006-09/msg00042.html (Message-id:
<451C1910.6060108@...>).

Changes to Chapter 2 of the manual (sample scripts and the test suite).

These changes complete task #3781 (https://gna.org/task/?3781).

The sample script section has been modified and a section for the relax test suite has been added.

Merged r2579 to r2581 of the 1.2 line into the 1.3 line.

The command used was:
svn merge -r2578:2581 svn+ssh://bugman@.../svn/relax/1.2

This includes a fix for bug #7192 and a few other superficial changes.

Fix for bug #7192 (https://gna.org/bugs/index.php?7192).

This bug was reported by Alex Hansen (viochemist_at_gmail_dot_com) and was
originally described at:
https://mail.gna.org/public/relax-users/2006-09/msg00026.html
(Message-id: <481156b20609251426r4a74f9f1p8fcf564354e61892@...>).

In addition to the fix of not skipping unselected residues described at
https://mail.gna.org/public/relax-devel/2006-09/msg00018.html
(Message-id: <7f080ed10609261109p2c7229e4ie02a894ac110dc3a@...>), I
have also added code to the 'self.num_instances()' model-free function to catch
the situation of 'self.determine_param_set_type()' returning None. If this
occurs, RelaxFault is raised!