relax SVN archive

Created a script and log file to demonstrate differences between alignment tensor basis sets.

This shows that the inter-tensor angles and condition numbers are dependent on the basis set used.

Created 6 unit tests for the lib.geometry.vectors.vector_angle_atan2() function.

Added 6 unit tests for the lib.geometry.vectors.vector_angle_acos() function.

These are similar to those of the vector_angle_normal() function but unsigned angles are checked
for.

Renamed vector_angle() to vector_angle_normal() in the lib.geometry.vectors module.

This is to standardise the naming as there are now the standard vector angle formula implemented as
the vector_angle_acos() and vector_angle_atan2() functions.

Missing import.

Implemented the lib.geometry.vectors.vector_angle_acos() function.

This is used to calculate the inter-vector angle using the arccos of the dot product formula. The
function has been introduced into the relax library as the calculation is repeated throughout relax.

Implemented the lib.geometry.vectors.vector_angle_atan2() function.

This is for calculating the inter-vector angle using the more numerically stable atan2() formula.

Merged revisions 26595-26598 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26595 | bugman | 2014-11-17 11:56:50 +0100 (Mon, 17 Nov 2014) | 7 lines

Set more reasonable default values for the lib.structure.pdb_write functions atom() and hetatm().

The occupancy now defaults to 1.0 instead of '', and the temperature factor to 0.0 instead of ''.
This avoid painful errors when using these functions, as these arguments must be floating point
numbers at all times, hence the default value of '' causes a TypeError.
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r26596 | bugman | 2014-11-17 11:57:19 +0100 (Mon, 17 Nov 2014) | 3 lines

Removed an accidentally committed debugging printout.
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r26597 | bugman | 2014-11-17 12:04:25 +0100 (Mon, 17 Nov 2014) | 6 lines

Updated the PDB file in the test_suite/shared_data/model_free/sphere/ directory.

The relax library is now being used to create the PDB file. Additional TER and CONECT records are
now being created so the result is a more correct PDB file.
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r26598 | bugman | 2014-11-17 12:17:22 +0100 (Mon, 17 Nov 2014) | 3 lines

Converted all ATOM records to HETATM in the sphere.pdb file.
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Merged revisions 26595-26598 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26595 | bugman | 2014-11-17 11:56:50 +0100 (Mon, 17 Nov 2014) | 7 lines

Set more reasonable default values for the lib.structure.pdb_write functions atom() and hetatm().

The occupancy now defaults to 1.0 instead of '', and the temperature factor to 0.0 instead of ''.
This avoid painful errors when using these functions, as these arguments must be floating point
numbers at all times, hence the default value of '' causes a TypeError.
........
r26596 | bugman | 2014-11-17 11:57:19 +0100 (Mon, 17 Nov 2014) | 3 lines

Removed an accidentally committed debugging printout.
........
r26597 | bugman | 2014-11-17 12:04:25 +0100 (Mon, 17 Nov 2014) | 6 lines

Updated the PDB file in the test_suite/shared_data/model_free/sphere/ directory.

The relax library is now being used to create the PDB file. Additional TER and CONECT records are
now being created so the result is a more correct PDB file.
........
r26598 | bugman | 2014-11-17 12:17:22 +0100 (Mon, 17 Nov 2014) | 3 lines

Converted all ATOM records to HETATM in the sphere.pdb file.
........

Converted all ATOM records to HETATM in the sphere.pdb file.