relax SVN archive

Improvements and expansion of the frame order test data generation base script.

More of the class variables are now defined in this base class and dummy methods are provided to
allow certain operations to be skipped (print_axis_system(), axes_to_pdb() and build_axes()).
Importantly, the script can now handle multiple modes of motion with the introduction of the key
_multi_system() and _state_loop() methods.

Created a simple double rotor geometric system to used for this frame order test data generation.

The system_create.py script creates the geometric system based on the CoMs of both domains in the
parent directory and two perpendicular rotation axes passing through both CoMs. A PDB file of the
representation is created by the script.

Merged revisions 22041-22045 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r22041 | bugman | 2014-01-23 14:27:58 +0100 (Thu, 23 Jan 2014) | 5 lines

Created the lib.geometry.vectors.unit_vector_from_2point() function.

This is used to quickly calculate the unit vector between two points.
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r22042 | bugman | 2014-01-23 15:35:52 +0100 (Thu, 23 Jan 2014) | 5 lines

The lib.structure.represent.rotor.rotor_pdb() function can now handle multiple rotors.

Previously this function would fail if called twice with the same structural object.
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r22043 | bugman | 2014-01-23 15:37:00 +0100 (Thu, 23 Jan 2014) | 5 lines

Added the has_molecule() method to the relax internal structural object.

This is used to quickly check if a molecule name already exists in the structural object.
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r22044 | bugman | 2014-01-24 11:50:00 +0100 (Fri, 24 Jan 2014) | 5 lines

More improvements for handling multiple rotors in the lib.structure.represent.rotor.rotor_pdb() function.

The atom numbering is now better handled.
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r22045 | bugman | 2014-01-24 14:33:51 +0100 (Fri, 24 Jan 2014) | 11 lines

Better support for the writing out of multiple molecules by the structure.write_pdb user function.

This is for the internal structural object write_pdb() method. Now each molecule is assigned a
different chain ID in the PDB file, and the chain IDs loaded into the structural object are ignored.
The chain IDs should however be preserved when using structure.read_pdb followed by
structure.write_pdb, without storing the ID.

A number of the Structure system tests had to be updated, as now the relax generated PDB files will
always write out a chain ID.
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Better support for the writing out of multiple molecules by the structure.write_pdb user function.

This is for the internal structural object write_pdb() method. Now each molecule is assigned a
different chain ID in the PDB file, and the chain IDs loaded into the structural object are ignored.
The chain IDs should however be preserved when using structure.read_pdb followed by
structure.write_pdb, without storing the ID.

A number of the Structure system tests had to be updated, as now the relax generated PDB files will
always write out a chain ID.

More improvements for handling multiple rotors in the lib.structure.represent.rotor.rotor_pdb() function.

The atom numbering is now better handled.

Added the has_molecule() method to the relax internal structural object.

This is used to quickly check if a molecule name already exists in the structural object.

The lib.structure.represent.rotor.rotor_pdb() function can now handle multiple rotors.

Previously this function would fail if called twice with the same structural object.

Created the lib.geometry.vectors.unit_vector_from_2point() function.

This is used to quickly calculate the unit vector between two points.

The Frame Order test data generation base script now loads all structures before rotating them.

This allows the progress printout to function correctly by not having any user function printouts
as the rotations are occurring.

Reintroduced the distribution PDB file creation to the frame order test data generation script.

This is the generate_base.py script in the test_suite/shared_data/frame_order/cam directory. The
ability to create the distribution.pdb file was long lost in this script, and can now be activated
using the DIST_PDB class variable.