Author: bugman
Date: Thu Dec 11 11:37:33 2014
New Revision: 27084
URL: http://svn.gna.org/viewcvs/relax?rev=27084&view=rev
Log:
Converted the structure.superimpose user function to the new
pipes/models/molecules/atom_id design.
The user function arguments have not changed, however the backend now uses the
new
pipe_control.structure.main.assemble_coordinates() function. This is to simply
decrease the number
of failure points possible in the structure user functions. The change has no
effect on the user
function use or results.
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=27084&r1=27083&r2=27084&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Thu Dec 11 11:37:33 2014
@@ -1103,33 +1103,12 @@
if centre_type not in allowed:
raise RelaxError("The superimposition centre type '%s' is unknown. It
must be one of %s." % (centre_type, allowed))
- # Test if the current data pipe exists.
- check_pipe()
-
- # Validate the models.
- cdp.structure.validate_models()
-
# Create a list of all models.
if models == None:
- models = []
- for model in cdp.structure.model_loop():
- models.append(model.num)
-
- # The selection object.
- selection = cdp.structure.selection(atom_id=atom_id)
-
- # Assemble the atomic coordinates of all models.
- coord = []
- for model in models:
- coord.append([])
- for pos in cdp.structure.atom_loop(selection=selection,
model_num=model, pos_flag=True):
- coord[-1].append(pos[0])
- coord[-1] = array(coord[-1])
-
- # Assemble the element types.
- elements = []
- for elem in cdp.structure.atom_loop(selection=selection, model_num=model,
element_flag=True):
- elements.append(elem)
+ models = cdp.structure.model_list()
+
+ # Assemble the atomic coordinates and obtain the corresponding element
information.
+ coord, ids, elements = assemble_coordinates(models=[models],
atom_id=atom_id, elements_flag=True)
# The different algorithms.
if method == 'fit to mean':
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