From d17a1b56c71ac9cd0cdf08c08398f60dae90b2d7 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Mon, 8 Apr 2019 10:32:56 -0500
Subject: [PATCH] Bug fix for previous commit
---
mrdna/segmentmodel.py | 32 ++++++++++++++++----------------
1 file changed, 16 insertions(+), 16 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 6250250..9434d4b 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -2399,7 +2399,7 @@ class SegmentModel(ArbdModel):
sign = 1 if b1_on_fwd_strand else -1
- # if b1.parent.name == "D72" or b2.parent.name == "D72":
+ # if b1.parent.name == "8-1" or b2.parent.name == "8-1":
# print()
# print(b1.parent.name, b2.parent.name, b1_on_fwd_strand)
# import pdb
@@ -2494,7 +2494,7 @@ class SegmentModel(ArbdModel):
""" Functions for adding crossover potentials """
def add_ss_crossover_potentials(connection,A,B, add_bond=True):
- b1,b2 = [loc.particle for loc in (c.A,c.B)]
+ b1,b2 = [loc.particle for loc in (A,B)]
if (b1,b2,A.on_fwd_strand,B.on_fwd_strand) in processed_crossovers:
return
@@ -2524,7 +2524,7 @@ class SegmentModel(ArbdModel):
def add_crossover_potentials(connection,A,B):
## TODO: use a better description here
- b1,b2 = [loc.particle for loc in (c.A,c.B)]
+ b1,b2 = [loc.particle for loc in (A,B)]
if (b1,b2,A.on_fwd_strand,B.on_fwd_strand) in processed_crossovers:
return
@@ -2542,8 +2542,8 @@ class SegmentModel(ArbdModel):
""" Add parallel helices potential, possibly """
## Add potential to provide a particular orinetation
- nt1,nt2 = [l.get_nt_pos() for l in (c.A,c.B)]
- is_end1, is_end2 = [nt in (0,l.container.num_nt-1) for nt,l in zip((nt1,nt2),(c.A,c.B))]
+ nt1,nt2 = [l.get_nt_pos() for l in (A,B)]
+ is_end1, is_end2 = [nt in (0,l.container.num_nt-1) for nt,l in zip((nt1,nt2),(A,B))]
is_T_junction = (is_end1 and not is_end2) or (is_end2 and not is_end1)
if (not is_end1) and (not is_end2):
@@ -2558,41 +2558,41 @@ class SegmentModel(ArbdModel):
if is_T_junction:
""" Special case: one helix extends away from another in T-shaped junction """
if is_end1:
- b1_forward = c.A.on_fwd_strand if nt1 == 0 else not c.A.on_fwd_strand
- add_local_tee_orientation_potential(b1,b2, b1_forward, c.B.on_fwd_strand)
+ b1_forward = A.on_fwd_strand if nt1 == 0 else not A.on_fwd_strand
+ add_local_tee_orientation_potential(b1,b2, b1_forward, B.on_fwd_strand)
else:
- add_local_crossover_strand_orientation_potential(b1,b2, c.A.on_fwd_strand)
+ add_local_crossover_strand_orientation_potential(b1,b2, A.on_fwd_strand)
if is_end2:
- b2_forward = c.B.on_fwd_strand if nt2 == 0 else not c.B.on_fwd_strand
- add_local_tee_orientation_potential(b2,b1, b2_forward, c.A.on_fwd_strand)
+ b2_forward = B.on_fwd_strand if nt2 == 0 else not B.on_fwd_strand
+ add_local_tee_orientation_potential(b2,b1, b2_forward, A.on_fwd_strand)
else:
- add_local_crossover_strand_orientation_potential(b2,b1, c.B.on_fwd_strand)
+ add_local_crossover_strand_orientation_potential(b2,b1, B.on_fwd_strand)
else:
""" Normal case: add orientation potential """
- add_local_crossover_strand_orientation_potential(b1,b2, c.A.on_fwd_strand)
- add_local_crossover_strand_orientation_potential(b2,b1, c.B.on_fwd_strand)
+ add_local_crossover_strand_orientation_potential(b1,b2, A.on_fwd_strand)
+ add_local_crossover_strand_orientation_potential(b2,b1, B.on_fwd_strand)
""" Add connection potentials """
processed_crossovers = set()
# pdb.set_trace()
for c,A,B in self.get_connections("sscrossover"):
- p1,p2 = [loc.container for loc in (c.A,c.B)]
+ p1,p2 = [loc.container for loc in (A,B)]
assert(any([isinstance(p,SingleStrandedSegment) for p in (p1,p2)]))
add_ss_crossover_potentials(c,A,B)
for c,A,B in self.get_connections("intrahelical"):
- ps = [loc.container for loc in (c.A,c.B)]
+ ps = [loc.container for loc in (A,B)]
if any([isinstance(p,SingleStrandedSegment) for p in ps]) and \
any([isinstance(p,DoubleStrandedSegment) for p in ps]):
add_ss_crossover_potentials(c,A,B, add_bond=False)
for c,A,B in sum([self.get_connections(term) for term in ("crossover","terminal_crossover")],[]):
- p1,p2 = [loc.container for loc in (c.A,c.B)]
+ p1,p2 = [loc.container for loc in (A,B)]
if any([isinstance(p,SingleStrandedSegment) for p in (p1,p2)]):
add_ss_crossover_potentials(c,A,B)
--
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