From 0a7989b3a9bae2d0c5a46e7230e310ecfbcdbbbf Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 21 Sep 2018 19:14:47 -0500
Subject: [PATCH] Protect intrahelical beads from merging with crossovers
---
mrdna/segmentmodel.py | 15 +++++++++++----
1 file changed, 11 insertions(+), 4 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 1fa1be2..4101d4b 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -1875,6 +1875,7 @@ class SegmentModel(ArbdModel):
else:
b = s1._generate_one_bead(a1,0)
A.particle = B.particle = b
+ b.is_intrahelical = True
b.locations.extend([A,B])
# pdb.set_trace()
@@ -1892,20 +1893,26 @@ class SegmentModel(ArbdModel):
if A.particle is None:
b = s1.get_nearest_bead(a1)
- if b is not None and s1.contour_to_nt_pos(np.abs(b.contour_position-a1)) < min(max_basepairs_per_bead, max_nucleotides_per_bead)*0.5:
+ try:
+ bead_is_far = s1.contour_to_nt_pos(np.abs(b.contour_position-a1)) >= min(max_basepairs_per_bead, max_nucleotides_per_bead)*0.5
+ if bead_is_far or "is_intrahelical" in b.__dict__:
+ raise Exception("not close")
## combine beads
b.update_position( 0.5*(b.contour_position + a1) ) # avg position
- else:
+ except:
b = s1._generate_one_bead(a1,0)
A.particle = b
b.locations.append(A)
if B.particle is None:
b = s2.get_nearest_bead(a2)
- if b is not None and s2.contour_to_nt_pos(np.abs(b.contour_position-a2)) < min(max_basepairs_per_bead, max_nucleotides_per_bead)*0.5:
+ try:
+ bead_is_far = s2.contour_to_nt_pos(np.abs(b.contour_position-a2)) >= min(max_basepairs_per_bead, max_nucleotides_per_bead)*0.5
+ if bead_is_far or "is_intrahelical" in b.__dict__:
+ raise Exception("not close")
## combine beads
b.update_position( 0.5*(b.contour_position + a2) ) # avg position
- else:
+ except:
b = s2._generate_one_bead(a2,0)
B.particle = b
b.locations.append(B)
--
GitLab