From 5fa683956a288e8a02076038fba76c16ecb62f40 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Mon, 10 Dec 2018 10:43:18 -0600
Subject: [PATCH] Removed temporary code for manually optimizing initial
azimuthal angle
---
mrdna/segmentmodel.py | 24 ------------------------
1 file changed, 24 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 5e698c4..e9fb792 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -2755,10 +2755,6 @@ class SegmentModel(ArbdModel):
nt1.basepair = nt2
nt2.basepair = nt1
- def _update_orientations(self,orientation):
- for s in self.strands:
- s.update_atomic_orientations(orientation)
-
def write_atomic_ENM(self, output_name, lattice_type=None):
## TODO: ensure atomic model was generated already
if lattice_type is None:
@@ -2997,26 +2993,6 @@ proc calcforces {} {
for s in self.strands:
first_atomic_index = s.generate_atomic_model(scale,first_atomic_index)
self._assign_basepairs()
- return
-
- ## Angle optimization
- angles = np.linspace(-180,180,180)
- score = []
- for a in angles:
- o = rotationAboutAxis([0,0,1], a)
- sum2 = count = 0
- for s in self.strands:
- s.update_atomic_orientations(o)
- for s1,s2 in zip(s.strand_segments[:-1],s.strand_segments[1:]):
- nt1 = s1.children[-1]
- nt2 = s2.children[0]
- o3 = nt1.atoms_by_name["O3'"]
- p = nt2.atoms_by_name["P"]
- sum2 += np.sum((p.collapsedPosition()-o3.collapsedPosition())**2)
- count += 1
- score.append(sum2/count)
- print(angles[np.argmin(score)])
- print(score)
def vmd_tube_tcl(self, file_name="drawTubes.tcl"):
with open(file_name, 'w') as tclFile:
--
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