r27404 - /trunk/pipe_control/structure/main.py -- January 30, 2015 - 18:54

Author: bugman
Date: Fri Jan 30 18:54:08 2015
New Revision: 27404

URL: http://svn.gna.org/viewcvs/relax?rev=27404&view=rev
Log:
Updates for the structure.sequence_alignment user function.

This is for the changes to the 
lib.structure.internal.coordinates.assemble_atomic_coordinates()
function return values.  The new object ID, model, and molecule flat lists 
are used directly for
storing the alignment results in the relax data store.


Modified:
    trunk/pipe_control/structure/main.py

Modified: trunk/pipe_control/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27404&r1=27403&r2=27404&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py        (original)
+++ trunk/pipe_control/structure/main.py        Fri Jan 30 18:54:08 2015
@@ -1299,8 +1299,8 @@
     # Assemble the structural objects.
     objects, object_names, pipes = assemble_structural_objects(pipes=pipes, 
models=models, molecules=molecules)
 
-    # Assemble the atomic coordinates of all structures.
-    ids, atom_pos, mol_names, res_names, res_nums, atom_names, elements, 
one_letter_codes, num_mols = assemble_atomic_coordinates(objects=objects, 
object_names=object_names, molecules=molecules, models=models)
+    # Assemble the atomic coordinates of all molecules.
+    ids, object_id_list, model_list, molecule_list, atom_pos, mol_names, 
res_names, res_nums, atom_names, elements, one_letter_codes, num_mols = 
assemble_atomic_coordinates(objects=objects, object_names=object_names, 
molecules=molecules, models=models)
 
     # MSA.
     if msa_algorithm == 'Central Star':
@@ -1311,15 +1311,8 @@
     if not hasattr(ds, 'sequence_alignment'):
         ds.sequence_alignment = Sequence_alignments()
 
-    # Flatten the lists.
-    flat_models = []
-    flat_molecules = []
-    for i in range(len(pipes)):
-        flat_models += models[i]
-        flat_molecules += molecules[i]
-
     # Store the alignment.
-    ds.sequence_alignment.add(object_ids=ids, models=flat_models, 
molecules=flat_molecules, sequences=one_letter_codes, strings=strings, 
gaps=gaps, msa_algorithm=msa_algorithm, 
pairwise_algorithm=pairwise_algorithm, matrix=matrix, 
gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, 
end_gap_open_penalty=end_gap_open_penalty, 
end_gap_extend_penalty=end_gap_extend_penalty)
+    ds.sequence_alignment.add(object_ids=object_id_list, models=model_list, 
molecules=molecule_list, sequences=one_letter_codes, strings=strings, 
gaps=gaps, msa_algorithm=msa_algorithm, 
pairwise_algorithm=pairwise_algorithm, matrix=matrix, 
gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, 
end_gap_open_penalty=end_gap_open_penalty, 
end_gap_extend_penalty=end_gap_extend_penalty)
 
 
 def set_vector(spin=None, xh_vect=None):