Commit 466df3d2 authored by cmaffeo2's avatar cmaffeo2
Browse files

Fixed minor issues with segentmodel_from_lists

parent 76463bb3
......@@ -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])
......
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