From 1e2394ef3d20c2dbee5b7737fd6f4daecc60f811 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 4 Sep 2018 14:14:58 -0500
Subject: [PATCH] Added support for having multiple intrahelical connections
from a single "location" in a segment; allows two ssDNA strands to emerge
from the ends of a dsDNA segment
---
dnarbd/segmentmodel.py | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/dnarbd/segmentmodel.py b/dnarbd/segmentmodel.py
index 6dbe417..fa05356 100644
--- a/dnarbd/segmentmodel.py
+++ b/dnarbd/segmentmodel.py
@@ -206,19 +206,22 @@ class SegmentParticle(PointParticle):
def get_intrahelical_above(self):
""" Returns bead directly above self """
- assert( len(self.intrahelical_neighbors) <= 2 )
+ # assert( len(self.intrahelical_neighbors) <= 2 )
for b in self.intrahelical_neighbors:
if b.get_contour_position(self.parent) > self.contour_position:
return b
def get_intrahelical_below(self):
""" Returns bead directly below self """
- assert( len(self.intrahelical_neighbors) <= 2 )
+ # assert( len(self.intrahelical_neighbors) <= 2 )
for b in self.intrahelical_neighbors:
if b.get_contour_position(self.parent) < self.contour_position:
return b
def _neighbor_should_be_added(self,b):
+ if type(self.parent) != type(b.parent):
+ return True
+
c1 = self.contour_position
c2 = b.get_contour_position(self.parent)
if c2 < c1:
@@ -241,8 +244,8 @@ class SegmentParticle(PointParticle):
add1 = self._neighbor_should_be_added(b)
add2 = b._neighbor_should_be_added(self)
if add1 and add2:
- assert(len(b.intrahelical_neighbors) <= 1)
- assert(len(self.intrahelical_neighbors) <= 1)
+ # assert(len(b.intrahelical_neighbors) <= 1)
+ # assert(len(self.intrahelical_neighbors) <= 1)
self.intrahelical_neighbors.append(b)
b.intrahelical_neighbors.append(self)
--
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