Changed name of SegmentModel command for updating splines

mrdna/segmentmodel.py

@@ -1416,7 +1416,11 @@ class SegmentModel(ArbdModel):
         assert( len(locParticles) == 0 )
         assert( len([b for s in self.segments for b in s.beads]) == 0 )
 
-    def _update_segment_positions(self, bead_coordinates): # TODO: rename to update_splines
+    def _update_segment_positions(self, bead_coordinates):
+        print("WARNING: called deprecated command '_update_segment_positions; use 'update_splines' instead")
+        return self.update_splines(bead_coordinates)
+
+    def update_splines(self, bead_coordinates):
         """ Set new function for each segments functions
         contour_to_position and contour_to_orientation """
 

mrdna/simulate.py

@@ -51,7 +51,7 @@ def multiresolution_simulation( model, output_name,
             except:
                 coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
             output_prefix = "%s-1" % output_name
-            model._update_segment_positions(coordinates)
+            model.update_splines(coordinates)
             model.simulate( outputPrefix = output_prefix, numSteps=0.95*coarse_steps, **simargs )
         else:
             output_prefix = "%s-1" % output_name
@@ -68,7 +68,7 @@ def multiresolution_simulation( model, output_name,
         full_output_prefix = "%s/%s" % (output_directory,output_prefix)
         simargs['timestep'] = 50e-6
         simargs['outputPeriod'] = fine_output_period
-        model._update_segment_positions(coordinates)
+        model.update_splines(coordinates)
         model._clear_beads()
         model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=True )
         model.simulate( outputPrefix = output_prefix, numSteps=fine_steps, **simargs )
@@ -81,7 +81,7 @@ def multiresolution_simulation( model, output_name,
         """ Freeze twist """
         output_prefix = "%s-3" % output_name
         full_output_prefix = "%s/%s" % (output_directory,output_prefix)
-        model._update_segment_positions(coordinates)
+        model.update_splines(coordinates)
         model._clear_beads()
         model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=False )
         model.simulate( outputPrefix = output_prefix, numSteps=fine_steps, **simargs )
@@ -94,7 +94,7 @@ def multiresolution_simulation( model, output_name,
         """ Atomic simulation """
         output_prefix = "%s-4" % output_name
         full_output_prefix = "%s/%s" % (output_directory,output_prefix)
-        model._update_segment_positions(coordinates)
+        model.update_splines(coordinates)
         model._clear_beads()
         model._generate_atomic_model(scale=backbone_scale)
         model.atomic_simulate( outputPrefix = output_prefix )