From 07ed55e0d0f37d0ffecb4eb74b3b4ebe8cb10431 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Sat, 22 Sep 2018 15:43:50 -0500
Subject: [PATCH] Fixed issue with quaternion orientations in
segmentmodel_from_lists
---
mrdna/readers/segmentmodel_from_lists.py | 10 +++++++---
mrdna/readers/segmentmodel_from_pdb.py | 2 --
2 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/mrdna/readers/segmentmodel_from_lists.py b/mrdna/readers/segmentmodel_from_lists.py
index 8d53e24..fbf8da2 100644
--- a/mrdna/readers/segmentmodel_from_lists.py
+++ b/mrdna/readers/segmentmodel_from_lists.py
@@ -88,11 +88,15 @@ def set_splines(seg, coordinates, hid, hmap, hrank, fwd, orientation=None):
for rank in range(int(maxrank)+1):
ids = np.where((hmap == hid) * (hrank == rank))[0]
coords.append(np.mean( [coordinates[r,:] for r in ids ], axis=0 ))
- contours.append( float(rank)/maxrank )
+ contours.append( float(rank+0.5)/(maxrank+1) )
+ last_q = None
if orientation is not None:
ids = np.where((hmap == hid) * (hrank == rank) * fwd)[0]
assert(len(ids) == 1)
- quats.append( quaternion_from_matrix( orientation[ids[0]] ) )
+ q = quaternion_from_matrix( orientation[ids[0]] )
+ if last_q is not None and last_q[1:].dot(q[1:]) < 0:
+ q = -1*q
+ quats.append(q)
## TODO: average quaterion with reverse direction
coords = np.array(coords)
@@ -153,7 +157,7 @@ def model_from_basepair_stack_3prime(coordinates, basepair, stack, three_prime,
hmap,hrank,fwd = basepairs_and_stacks_to_helixmap(bps,stack)
double_stranded_helices = np.unique(hmap[hmap >= 0])
strands = _three_prime_list_to_strands(three_prime)
-
+
""" Add ssDNA to hmap """
hid = double_stranded_helices[-1]+1
ss_residues = hmap < 0
diff --git a/mrdna/readers/segmentmodel_from_pdb.py b/mrdna/readers/segmentmodel_from_pdb.py
index e42e87d..3cbb683 100644
--- a/mrdna/readers/segmentmodel_from_pdb.py
+++ b/mrdna/readers/segmentmodel_from_pdb.py
@@ -258,8 +258,6 @@ def SegmentModelFromPdb(*args,**kwargs):
bps = find_basepairs(u, centers, transforms)
stacks = find_stacks(u, centers, transforms)
- # pdb.set_trace()
-
## Find three-prime ends
three_prime = -np.ones(bps.shape, dtype=np.int)
for s in u.segments:
--
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