From 63c45e3f6fb4cbc1e0e7d195e22822448dd6f91a Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Mon, 10 Sep 2018 15:17:10 -0500
Subject: [PATCH] Changed name of SegmentModel command for updating splines
---
mrdna/segmentmodel.py | 6 +++++-
mrdna/simulate.py | 8 ++++----
2 files changed, 9 insertions(+), 5 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index b2b4ef8..5324706 100644
--- a/mrdna/segmentmodel.py
+++ b/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 """
diff --git a/mrdna/simulate.py b/mrdna/simulate.py
index fef95d0..a735fc2 100644
--- a/mrdna/simulate.py
+++ b/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 )
--
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