r27410 - in /trunk: lib/structure/internal/coordinates.py pipe_control/structure/main.py -- January 31, 2015 - 11:32

Author: bugman
Date: Sat Jan 31 11:32:07 2015
New Revision: 27410

URL: http://svn.gna.org/viewcvs/relax?rev=27410&view=rev
Log:
Added a function for assemble the common atomic coordinates taking sequence 
alignments into account.

This is the new pipe_control.structure.main.assemble_structural_coordinates() 
function.  It takes
the sequence alignment logic out of the 
lib.structure.internal.coordinates.assemble_coord_array()
function so that sequence alignments in the relax data store can be used.  
The logic has also been
redefined as:  1, use a sequence alignment from the relax data store if 
present;  2, use no sequence
alignment if coordinates only come from structural models;  3, fall back to a 
residue number based
alignment.  The residue number based alignment is yet to be implemented.

As a consequence, the 
lib.structure.internal.coordinates.assemble_coord_array() function has been
greatly simplified.  It no longer handles sequence alignments, but instead 
expects the residue
skipping data structure, built from the alignment, as an argument.  The 
seq_info_flag argument has
also been eliminated in this function as well as the 
pipe_control.structure.main module.


Modified:
    trunk/lib/structure/internal/coordinates.py
    trunk/pipe_control/structure/main.py

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: trunk/lib/structure/internal/coordinates.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/coordinates.py?rev=27410&r1=27409&r2=27410&view=diff

Modified: trunk/pipe_control/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27410&r1=27409&r2=27410&view=diff