From 225345862a42b5d6acb00c2092ac8022904cbc1b Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 3 Mar 2020 17:43:40 -0600
Subject: [PATCH] Slightly updated routine for circular DNA in case beads
overlap
---
mrdna/segmentmodel.py | 54 +++++++++++++++++++++++++++++++++++++++++--
1 file changed, 52 insertions(+), 2 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 03984be..0e52a44 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -359,6 +359,30 @@ given context, provide the position
# nt_pos = self.get_nt_position(seg)
# return seg.nt_pos_to_contour(nt_pos)
+ def combine(self, other):
+ assert(other in self.intrahelical_neighbors)
+ assert(self in other.intrahelical_neighbors)
+
+ self.intrahelical_neighbors.remove(other)
+ other.intrahelical_neighbors.remove(self)
+ for b in other.intrahelical_neighbors:
+ b.intrahelical_neighbors.remove(other)
+ b.intrahelical_neighbors.append(self)
+ self.intrahelical_neighbors.append(b)
+ for l in other.locations:
+ self.locations.append(l)
+ l.particle = self
+
+ ## Remove bead
+ other.parent.children.remove(other)
+ if other in other.parent.beads:
+ other.parent.beads.remove(other)
+ if 'orientation_bead' in other.__dict__:
+ other.parent.children.remove(other.orientation_bead)
+
+ for b in list(other.parent.bonds):
+ if other in b[:2]: other.parent.bonds.remove(b)
+
def update_position(self, contour_position):
self.contour_position = contour_position
self.position = self.parent.contour_to_position(contour_position)
@@ -2285,6 +2309,32 @@ class SegmentModel(ArbdModel):
for b in (b1,b2): assert( b is not None )
b1.make_intrahelical_neighbor(b2)
+ def _combine_zero_sep_beads():
+ skip_keys = []
+ for b1,b2 in [k for k,v in special_seps.items() if v == 0]:
+ if (b1,b2) in skip_keys: continue
+ del special_seps[(b1,b2)]
+ del special_seps[(b2,b1)]
+ skip_keys.append((b2,b1))
+
+ for b in b2.intrahelical_neighbors:
+ if b is b1: continue
+ if b is not b1 and b.parent is b2.parent:
+ sep = np.abs(b2.contour_position - b.contour_position) * b.parent.num_nt
+ special_seps[(b,b1)] = sep
+ special_seps[(b1,b)] = sep
+ b1.combine(b2)
+
+ for k in list(special_seps.keys()):
+ if b2 in k:
+ if b2 == k[0]:
+ newkey = (b1,k[1])
+ else:
+ newkey = (k[0],b2)
+ special_seps[newkey] = special_seps[k]
+ del special_seps[k]
+ _combine_zero_sep_beads()
+
""" Reassign bead types """
if self.DEBUG: print("Assigning bead types")
beadtype_s = dict()
@@ -3267,8 +3317,8 @@ class SegmentModel(ArbdModel):
ntsJ1,ntsJ2 = [segJ.contour_to_nt_pos(B.address) for B in (B1,B2)]
ntsI = ntsI2-ntsI1+1
ntsJ = ntsJ2-ntsJ1+1
- assert( np.isclose( ntsI, int(round(ntsI)) ) )
- assert( np.isclose( ntsJ, int(round(ntsJ)) ) )
+ # assert( np.isclose( ntsI, int(round(ntsI)) ) )
+ # assert( np.isclose( ntsJ, int(round(ntsJ)) ) )
ntsI,ntsJ = [int(round(i)) for i in (ntsI,ntsJ)]
## Find if dsDNA "segments" are pointing in same direction
--
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