From 3a73f3a5ce9c1ac7a74af95e8a435733e68794e2 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 21 Dec 2018 12:10:10 -0600
Subject: [PATCH] Updated set_spline routine to include more detail
---
mrdna/segmentmodel.py | 19 +++++++++----------
1 file changed, 9 insertions(+), 10 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index d4333ed..5a9f4c5 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -503,11 +503,11 @@ class Segment(ConnectableElement, Group):
if about is None:
## TODO: do this more efficiently
- r[ids,:] = np.array([rotation_matrix.dot(r[i,:]) for i in range(r.shape[0])])
+ r[ids,:] = np.array([rotation_matrix.dot(r[i,:]) for i in ids])
else:
dr = np.array(about)
## TODO: do this more efficiently
- r[ids,:] = np.array([rotation_matrix.dot(r[i,:]-dr) + dr for i in range(r.shape[0])])
+ r[ids,:] = np.array([rotation_matrix.dot(r[i,:]-dr) + dr for i in ids])
self.set_splines(u,r)
@@ -520,10 +520,14 @@ class Segment(ConnectableElement, Group):
quats = [quaternion_from_matrix(o) for o in orientations]
self.set_orientation_splines(u, quats)
- def _set_splines_from_ends(self):
+ def _set_splines_from_ends(self, resolution=4):
self.quaternion_spline_params = None
- coords = np.array([self.start_position, self.end_position])
- self.set_splines([0,1], coords)
+ r0 = np.array(self.start_position)[np.newaxis,:]
+ r1 = np.array(self.end_position)[np.newaxis,:]
+ u = np.linspace(0,1, max(3,self.num_nt//int(resolution)))
+ s = u[:,np.newaxis]
+ coords = (1-s)*r0 + s*r1
+ self.set_splines(u, coords)
def clear_all(self):
Group.clear_all(self) # TODO: use super?
@@ -1002,11 +1006,6 @@ class DoubleStrandedSegment(Segment):
# for l in (self.start5,self.start3,self.end3,self.end5):
# self.locations.append(l)
- ## Set up interpolation for azimuthal angles
- a = np.array([self.start_position,self.end_position]).T
- tck, u = interpolate.splprep( a, u=[0,1], s=0, k=1)
- self.position_spline_params = (tck,u)
-
## TODO: initialize sensible spline for orientation
## Convenience methods
--
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