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mrdna
Commits
99709ad5
Commit
99709ad5
authored
Mar 02, 2021
by
cmaffeo2
Browse files
Decreased length of T-junction bond from crossover distance of 18.5 to more reasonable 12.5
parent
ab28bc85
Changes
1
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Inline
Side-by-side
mrdna/segmentmodel.py
View file @
99709ad5
...
...
@@ -2994,11 +2994,6 @@ class SegmentModel(ArbdModel):
intrahelical junctions between ds and ssDNA """
return
""" Add bond potential """
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 """
## Add potential to provide a particular orinetation
nt1
,
nt2
=
[
l
.
get_nt_pos
()
for
l
in
(
A
,
B
)]
...
...
@@ -3016,6 +3011,11 @@ class SegmentModel(ArbdModel):
if
local_twist
:
if
is_T_junction
:
""" Special case: one helix extends away from another in T-shaped junction """
""" Add bond potential """
k
=
1.0
*
count_crossovers
((
b1
,
b2
))
pot
=
self
.
get_bond_potential
(
k
,
12.5
)
self
.
add_bond
(
b1
,
b2
,
pot
)
if
is_end1
:
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
)
...
...
@@ -3029,10 +3029,20 @@ class SegmentModel(ArbdModel):
add_local_crossover_strand_orientation_potential
(
b2
,
b1
,
B
.
on_fwd_strand
)
else
:
""" Add bond potential """
k
=
1.0
*
count_crossovers
((
b1
,
b2
))
pot
=
self
.
get_bond_potential
(
k
,
18.5
)
self
.
add_bond
(
b1
,
b2
,
pot
)
""" Normal case: add orientation potential """
add_local_crossover_strand_orientation_potential
(
b1
,
b2
,
A
.
on_fwd_strand
)
add_local_crossover_strand_orientation_potential
(
b2
,
b1
,
B
.
on_fwd_strand
)
else
:
""" Add bond potential """
k
=
1.0
*
count_crossovers
((
b1
,
b2
))
pot
=
self
.
get_bond_potential
(
k
,
18.5
)
self
.
add_bond
(
b1
,
b2
,
pot
)
""" Add connection potentials """
processed_crossovers
=
set
()
...
...
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