relax SVN archive

Increased max kex to value 1e18 for unit test of lin/ns_cpmg_2site_expanded.py.

Small fix in parameter calculation in unit test _dispersion/test_ns_cpmg_2site_expanded.

Modified unit test to have standard population of pA=0.95, and a correctly calculation of dw in ppm to rad/s.

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

Merged revisions 23474-23478,23480-23481 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

........
r23474 | bugman | 2014-05-27 17:06:23 +0200 (Tue, 27 May 2014) | 6 lines

Deletion of the pipe_control.structure.main.create_cone_pdb() function.

This is only used in the frame order analysis, but has been made redundant by the
lib.structure.represent.cone.cone() function.
........
r23475 | bugman | 2014-05-27 17:08:55 +0200 (Tue, 27 May 2014) | 6 lines

Fix for the heterogen section of the internal structural object write_pdb() method.

A number of checks were performed to see if the PDB heterogen records were the same for all
structures, but this is meaningless as the structures can of course be different.
........
r23476 | bugman | 2014-05-27 17:17:56 +0200 (Tue, 27 May 2014) | 13 lines

Completed the frame_order.pdb_model user function backend for the frame order PDB representation.

Most of this backend, including the axes and cone representations, had been broken for quite a while
and were being skipped with an early return statement. This has now been made functional and a few
fixes have been made.

For the 'rotor' and 'free rotor' model, the neg_cone argument is now ignored so that only one model
is produced in the final frame order PDB representation file. For all other models, the rotor
representation is no longer centred to the point on axis closest to the centre of mass, as the pivot
is unambiguously defined. The rotor representation has also been made larger in these models so
that it is outside of the cone, and the propeller blades are now staggered.
........
r23477 | bugman | 2014-05-27 17:19:16 +0200 (Tue, 27 May 2014) | 6 lines

Fixes for the lib.structure.represent.cone module.

The function arguments named 'cone' have been renamed to 'cone_obj' so that they do not clash with
the cone() function in the module namespace.
........
r23478 | bugman | 2014-05-27 17:21:53 +0200 (Tue, 27 May 2014) | 7 lines

Fix for the lib.structure.geometric.generate_vector_residues() function.

The atom numbers are no longer read from the internal structural object, as these are not reliable.
If another geometric representation exists in the object, then the atom numbers could be None. Or
loading structures from multiple PDB files can cause the numbering to be repeated or out of order.
........
r23480 | tlinnet | 2014-05-27 18:47:25 +0200 (Tue, 27 May 2014) | 3 lines

Modified py_type from "list" to "float_array" in uf_object type in user function dx.map.

Bug #22035: (https://gna.org/bugs/?22035) The dx.map user function is broken in the GUI.
........
r23481 | tlinnet | 2014-05-27 18:47:30 +0200 (Tue, 27 May 2014) | 3 lines

Added py_type "list_val_or_list_of_list_val" to be handled in GUI uf_objects.

Bug #22035: (https://gna.org/bugs/?22035) The dx.map user function is broken in the GUI.
........

Added py_type "list_val_or_list_of_list_val" to be handled in GUI uf_objects.

Bug #22035: (https://gna.org/bugs/?22035) The dx.map user function is broken in the GUI.

Modified py_type from "list" to "float_array" in uf_object type in user function dx.map.

Bug #22035: (https://gna.org/bugs/?22035) The dx.map user function is broken in the GUI.

Merged revisions 23474-23478 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23474 | bugman | 2014-05-27 17:06:23 +0200 (Tue, 27 May 2014) | 6 lines

Deletion of the pipe_control.structure.main.create_cone_pdb() function.

This is only used in the frame order analysis, but has been made redundant by the
lib.structure.represent.cone.cone() function.
........
r23475 | bugman | 2014-05-27 17:08:55 +0200 (Tue, 27 May 2014) | 6 lines

Fix for the heterogen section of the internal structural object write_pdb() method.

A number of checks were performed to see if the PDB heterogen records were the same for all
structures, but this is meaningless as the structures can of course be different.
........
r23476 | bugman | 2014-05-27 17:17:56 +0200 (Tue, 27 May 2014) | 13 lines

Completed the frame_order.pdb_model user function backend for the frame order PDB representation.

Most of this backend, including the axes and cone representations, had been broken for quite a while
and were being skipped with an early return statement. This has now been made functional and a few
fixes have been made.

For the 'rotor' and 'free rotor' model, the neg_cone argument is now ignored so that only one model
is produced in the final frame order PDB representation file. For all other models, the rotor
representation is no longer centred to the point on axis closest to the centre of mass, as the pivot
is unambiguously defined. The rotor representation has also been made larger in these models so
that it is outside of the cone, and the propeller blades are now staggered.
........
r23477 | bugman | 2014-05-27 17:19:16 +0200 (Tue, 27 May 2014) | 6 lines

Fixes for the lib.structure.represent.cone module.

The function arguments named 'cone' have been renamed to 'cone_obj' so that they do not clash with
the cone() function in the module namespace.
........
r23478 | bugman | 2014-05-27 17:21:53 +0200 (Tue, 27 May 2014) | 7 lines

Fix for the lib.structure.geometric.generate_vector_residues() function.

The atom numbers are no longer read from the internal structural object, as these are not reliable.
If another geometric representation exists in the object, then the atom numbers could be None. Or
loading structures from multiple PDB files can cause the numbering to be repeated or out of order.
........

Fix for the lib.structure.geometric.generate_vector_residues() function.

The atom numbers are no longer read from the internal structural object, as these are not reliable.
If another geometric representation exists in the object, then the atom numbers could be None. Or
loading structures from multiple PDB files can cause the numbering to be repeated or out of order.

Fixes for the lib.structure.represent.cone module.

The function arguments named 'cone' have been renamed to 'cone_obj' so that they do not clash with
the cone() function in the module namespace.

Completed the frame_order.pdb_model user function backend for the frame order PDB representation.

Most of this backend, including the axes and cone representations, had been broken for quite a while
and were being skipped with an early return statement. This has now been made functional and a few
fixes have been made.

For the 'rotor' and 'free rotor' model, the neg_cone argument is now ignored so that only one model
is produced in the final frame order PDB representation file. For all other models, the rotor
representation is no longer centred to the point on axis closest to the centre of mass, as the pivot
is unambiguously defined. The rotor representation has also been made larger in these models so
that it is outside of the cone, and the propeller blades are now staggered.