From 466df3d28b0dc06b3fac88ff70fe028509a927ef Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 13 Aug 2019 16:58:26 -0500
Subject: [PATCH] Fixed minor issues with segentmodel_from_lists
---
mrdna/readers/segmentmodel_from_lists.py | 18 +++++++++++++++---
1 file changed, 15 insertions(+), 3 deletions(-)
diff --git a/mrdna/readers/segmentmodel_from_lists.py b/mrdna/readers/segmentmodel_from_lists.py
index aa12c75..d44825e 100644
--- a/mrdna/readers/segmentmodel_from_lists.py
+++ b/mrdna/readers/segmentmodel_from_lists.py
@@ -84,10 +84,11 @@ def basepairs_and_stacks_to_helixmap(basepairs,stacks_above):
assert(helixmap[nt] == -1)
assert(helixmap[bp] == -1)
- all_nts.append(nt)
if nt == nt0:
break
+ all_nts.append(nt)
+
if counter > 1e6:
raise Exception("DNA is apparently too long; probably there is something wrong with the structure")
counter += 1
@@ -98,7 +99,6 @@ def basepairs_and_stacks_to_helixmap(basepairs,stacks_above):
for nt in group:
bp = basepairs[nt]
is_fwd[bp] = 0
- rank +=1
helixmap[nt] = helixmap[bp] = hid
helixrank[nt] = helixrank[bp] = rank
processed.add(nt)
@@ -263,7 +263,19 @@ def model_from_basepair_stack_3prime(coordinates, basepair, stack, three_prime,
f1,f2 = [fwd[i] for i in (r1,r2)]
if nt1 in (0,seg1.num_nt-1) or nt2 in (0,seg2.num_nt-1):
- seg1.add_crossover(nt1,seg2,nt2,[f1,f2],type_="terminal_crossover")
+ if nt1 in (0,seg1.num_nt-1) and nt2 in (0,seg2.num_nt-1):
+ if nt1 == 0:
+ end1 = seg1.start5 if f1 else seg1.start3
+ else:
+ end1 = seg1.end3 if f1 else seg1.end5
+ if nt2 == 0:
+ end2 = seg2.start5 if f2 else seg2.start3
+ else:
+ end2 = seg2.end3 if f2 else seg2.end5
+ seg1._connect_ends( end1, end2, type_='intrahelical')
+
+ else:
+ seg1.add_crossover(nt1,seg2,nt2,[f1,f2],type_="terminal_crossover")
else:
seg1.add_crossover(nt1,seg2,nt2,[f1,f2])
--
GitLab