Author: tlinnet
Date: Tue May 27 18:52:21 2014
New Revision: 23482
URL: http://svn.gna.org/viewcvs/relax?rev=23482&view=rev
Log:
Merged revisions 23474-23478,23480-23481 via svnmerge from
svn+ssh://tlinnet@xxxxxxxxxxx/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.
........
Modified:
branches/disp_speed/ (props changed)
branches/disp_speed/gui/uf_objects.py
branches/disp_speed/lib/structure/geometric.py
branches/disp_speed/lib/structure/internal/object.py
branches/disp_speed/lib/structure/represent/cone.py
branches/disp_speed/pipe_control/structure/main.py
branches/disp_speed/specific_analyses/frame_order/uf.py
branches/disp_speed/user_functions/dx.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/disp_speed/gui/uf_objects.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/gui/uf_objects.py?rev=23482&r1=23481&r2=23482&view=diff
Modified: branches/disp_speed/lib/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/structure/geometric.py?rev=23482&r1=23481&r2=23482&view=diff
Modified: branches/disp_speed/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/structure/internal/object.py?rev=23482&r1=23481&r2=23482&view=diff
Modified: branches/disp_speed/lib/structure/represent/cone.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/structure/represent/cone.py?rev=23482&r1=23481&r2=23482&view=diff
Modified: branches/disp_speed/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/pipe_control/structure/main.py?rev=23482&r1=23481&r2=23482&view=diff
Modified: branches/disp_speed/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/specific_analyses/frame_order/uf.py?rev=23482&r1=23481&r2=23482&view=diff
Modified: branches/disp_speed/user_functions/dx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/user_functions/dx.py?rev=23482&r1=23481&r2=23482&view=diff
r23482 - in /branches/disp_speed: ./ gui/ lib/structure/ lib/structure/internal/ lib/structure/represent/ pipe_control/struc...