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):
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