Commit 62826908 authored by cmaffeo2's avatar cmaffeo2
Browse files

Improved potentials around crossovers

1) Proper accounting for a single bond representing a double crossover
2) Parallel-helix dihedral angle spring constant is now computed from three "springs" placed in series that represent:
   a) the flexibility of the bond on one side of the crossover
   b) the intrinsic flexibility of the crossover
   c) the flexibility of the bond on the other side of the crossover
parent fa4b1dae
......@@ -2461,6 +2461,15 @@ class SegmentModel(ArbdModel):
parent.add_dihedral(o1,b1,b2,o2, pot)
def count_crossovers(beads):
count = 0
for b in beads:
for l in b.locations:
if l.connection is not None:
if l.connection.type_ == "crossover":
count += 1
return count
def add_local_crossover_strand_orientation_potential(b1,b2, b1_on_fwd_strand):
""" Adds a dihedral angle potential so bead b2 at opposite
......@@ -2559,7 +2568,13 @@ class SegmentModel(ArbdModel):
## TODO?: Check length-dependence of this potential
if a is not None:
k = k_xover_angle( dists[b][a]+dists[c][d] )
k_intrinsic = 0.00086
k = [1/k for k in (4*k_xover_angle( dists[b][a] ),
4*k_xover_angle( dists[c][d] ))]
k = sum(k)**-1
k = k * count_crossovers((b1,b2))/4
pot = self.get_dihedral_potential(k,t0)
self.add_dihedral( a,b,c,d, pot )
......@@ -2612,7 +2627,8 @@ class SegmentModel(ArbdModel):
""" Add bond potential """
pot = self.get_bond_potential(4,18.5)
k = 1.0 * count_crossovers((b1,b2))
pot = self.get_bond_potential(k,18.5)
self.add_bond(b1,b2, pot)
""" Add parallel helices potential, possibly """
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