Author: bugman
Date: Tue Sep 30 18:08:57 2014
New Revision: 26103
URL: http://svn.gna.org/viewcvs/relax?rev=26103&view=rev
Log:
Implemented the backend of the structure.mean user function.
This primarily occurs within the internal structural object in the new mean()
method. The
pipe_control.structure.main.mean() function simply checks if the current data
pipe is correctly set
up and then calls the structural object mean() method.
Modified:
trunk/lib/structure/internal/object.py
trunk/pipe_control/structure/main.py
Modified: trunk/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=26103&r1=26102&r2=26103&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Tue Sep 30 18:08:57 2014
@@ -2100,6 +2100,41 @@
return True
+ def mean(self):
+ """Calculate the mean structure from all models in the structural data
object."""
+
+ # Create a new model for the mean structure.
+ num = self.num_models()
+ self.add_model()
+ mean_model = self.structural_data[-1]
+
+ # The selection object.
+ selection = self.selection()
+
+ # Loop over the molecules and atoms.
+ for mol_index, i in selection.loop():
+ # Set the mean structure coordinate to zero.
+ mean_model.mol[mol_index].x[i] = 0.0
+ mean_model.mol[mol_index].y[i] = 0.0
+ mean_model.mol[mol_index].z[i] = 0.0
+
+ # Loop over the models and sum the coordinates.
+ for model_index in range(num):
+ model_cont = self.structural_data[model_index]
+ mean_model.mol[mol_index].x[i] +=
model_cont.mol[mol_index].x[i]
+ mean_model.mol[mol_index].y[i] +=
model_cont.mol[mol_index].y[i]
+ mean_model.mol[mol_index].z[i] +=
model_cont.mol[mol_index].z[i]
+
+ # Averages.
+ mean_model.mol[mol_index].x[i] /= num
+ mean_model.mol[mol_index].y[i] /= num
+ mean_model.mol[mol_index].z[i] /= num
+
+ # Delete all models but the mean.
+ for model_index in reversed(range(num)):
+ self.delete(model=self.structural_data[model_index].num)
+
+
def model_loop(self, model=None):
"""Generator method for looping over the models in numerical order.
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=26103&r1=26102&r2=26103&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Tue Sep 30 18:08:57 2014
@@ -622,8 +622,12 @@
def mean():
"""Calculate the mean structure from all models in the structural data
object."""
- # Test if the current data pipe exists.
- check_pipe()
+ # Checks.
+ check_pipe()
+ check_structure()
+
+ # Call the specific code.
+ cdp.structure.mean()
def read_gaussian(file=None, dir=None, set_mol_name=None, set_model_num=None,
verbosity=1, fail=True):
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