From dc3feb95bdcbfbcb169aa43153b881ba3f21801f Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Thu, 13 Sep 2018 11:55:32 -0500
Subject: [PATCH] Improved support for short ssDNA segments
Previous commit fixed an issue for from_pdb reader, which used "sscrossover" connections, but broke models from the vHelix reader which used "intrahelical" connections. Now we convert "sscrossover" connections at the ends of segments into "intrahelical" connections.
---
mrdna/segmentmodel.py | 28 ++++++++++++++++++++++------
1 file changed, 22 insertions(+), 6 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index f642d6e..d7eb84d 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -34,7 +34,7 @@ TODO:
- rework Location class
- remove recursive calls
- document
- - add unit test of helices connected to themselves
+ - develop unit test suite
"""
class CircularDnaError(Exception):
pass
@@ -747,8 +747,9 @@ class Segment(ConnectableElement, Group):
existing_beads0 = {l.particle for l in self.locations if l.particle is not None}
existing_beads = sorted( list(existing_beads0), key=lambda b: b.get_contour_position(self) )
- if self.num_nt == 1 and all([l.particle is not None for l in self.locations]):
- return
+ # if self.num_nt == 1 and all([l.particle is not None for l in self.locations]):
+ # pdb.set_trace()
+ # return
for b in existing_beads:
assert(b.parent is not None)
@@ -995,9 +996,13 @@ class SingleStrandedSegment(Segment):
def connect_end3(self, end5, force_connection=False):
self._connect_end( end5, _5_to_3 = True, force_connection = force_connection )
- def connect_5end(self, end3, force_connection=False): # TODO: change name or possibly deprecate
+ def connect_start5(self, end3, force_connection=False):
self._connect_end( end3, _5_to_3 = False, force_connection = force_connection )
+ def connect_5end(self, end3, force_connection=False): # TODO: change name or possibly deprecate
+ print("WARNING: 'connect_5end' will be deprecated")
+ return self.connect_start5( end3, force_connection=False)
+
def _connect_end(self, other, _5_to_3, force_connection):
assert( isinstance(other, Location) )
if _5_to_3 == True:
@@ -1012,7 +1017,7 @@ class SingleStrandedSegment(Segment):
seg1 = other.container
seg2 = self
end1 = other
- end2 = self.end5
+ end2 = self.start
# assert( other.type_ == "end3" )
if (other.type_ is not "end3"):
print("WARNING: code does not prevent connecting 3prime to 3prime, etc")
@@ -1035,13 +1040,21 @@ class SingleStrandedSegment(Segment):
## TODO
## TODO: fix direction
+ if nt in (0,1,self.num_nt) and other_nt in (0,1,other.num_nt):
+ if nt_on_5prime == True:
+ other_end = other.start5 if strands_fwd[1] else other.end5
+ self.connect_end3( other_end )
+ else:
+ other_end = other.end3 if strands_fwd[1] else other.start3
+ self.connect_start5( other_end )
+ return
# c1 = self.nt_pos_to_contour(nt)
# # TODOTODO
# ## Ensure connections occur at ends, otherwise the structure doesn't make sense
# # assert(np.isclose(c1,0) or np.isclose(c1,1))
# assert(np.isclose(nt,0) or np.isclose(nt,self.num_nt-1))
- if nt == 0:
+ if nt == 0 and (nt_on_5prime or self.num_nt > 1):
c1 = 0
elif nt == self.num_nt-1:
c1 = 1
@@ -1825,6 +1838,7 @@ class SegmentModel(ArbdModel):
# assert( not np.isclose( np.linalg.norm(b1.collapsedPosition() - b2.collapsedPosition()), 0 ) )
if np.linalg.norm(b1.collapsedPosition() - b2.collapsedPosition()) < 1:
print("WARNING: some beads are very close")
+
parent = self._getParent(b1,b2)
## TODO: could be sligtly smarter about sep
@@ -1851,6 +1865,8 @@ class SegmentModel(ArbdModel):
dists[b1][b2] = sep
dists[b2][b1] = sep
+ if b1 is b2: continue
+
# dists[[b1,b2]] = dists[[b2,b1]] = sep
bond = self.get_bond_potential(k,d)
parent.add_bond( b1, b2, bond, exclude=True )
--
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