From e09f423a939356c18bb719c55252d13c3743d65b Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 17 Aug 2018 17:59:08 -0500
Subject: [PATCH] fixup: Updated method of adding atomistic DNA nucleotides,
including orientation
---
CanonicalNucleotideAtoms.py | 5 +++--
segmentmodel.py | 9 +++++++--
2 files changed, 10 insertions(+), 4 deletions(-)
diff --git a/CanonicalNucleotideAtoms.py b/CanonicalNucleotideAtoms.py
index a608eb0..f2eb3ae 100644
--- a/CanonicalNucleotideAtoms.py
+++ b/CanonicalNucleotideAtoms.py
@@ -59,8 +59,9 @@ class Nucleotide(Group):
return seg._get_atomic_nucleotide(nt_idx, is_fwd)
class CanonicalNucleotideFactory(Group):
- # DefaultOrientation = rotationAboutAxis([0,0,1], 180)
- DefaultOrientation = rotationAboutAxis([1,0,0], 180)
+ DefaultOrientation = rotationAboutAxis([0,0,1], 180).dot(
+ rotationAboutAxis([1,0,0], 180))
+
def __init__(self, prefix, seq):
self.sequence = seq # TODO: used?
self.resname = resnames[seq]
diff --git a/segmentmodel.py b/segmentmodel.py
index 16906cd..c45801f 100644
--- a/segmentmodel.py
+++ b/segmentmodel.py
@@ -408,24 +408,29 @@ class Segment(ConnectableElement, Group):
def contour_to_orientation(self,s):
assert( isinstance(s,float) or isinstance(s,int) or len(s) == 1 ) # TODO make vectorized version
+
orientation = None
if self.quaternion_spline_params is None:
axis = self.contour_to_tangent(s)
axis = axis / np.linalg.norm(axis)
rotAxis = np.cross(axis,np.array((0,0,1)))
rotAxisL = np.linalg.norm(rotAxis)
- theta = np.arcsin(rotAxisL)
if rotAxisL > 0.001:
+ theta = np.arcsin(rotAxisL)
orientation0 = rotationAboutAxis( rotAxis/rotAxisL, theta*180/np.pi, normalizeAxis=False )
else:
- orientation0 = np.eye(3)
+ if axis.dot(np.array((0,0,1))) > 0:
+ orientation0 = np.eye(3)
+ else:
+ orientation0 = rotationAboutAxis( np.array((1,0,0)), 180, normalizeAxis=False )
orientation = rotationAboutAxis( axis, self.twist_per_nt*self.contour_to_nt_pos(s), normalizeAxis=False )
orientation = orientation.dot(orientation0)
else:
q = interpolate.splev( s, self.quaternion_spline_params )
if len(q) > 1: q = np.array(q).T # TODO: is this needed?
orientation = quaternion_to_matrix(q)
+
return orientation
def get_contour_sorted_connections_and_locations(self,type_):
--
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