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tbgl
tools
mrdna
Commits
87fc5b22
Commit
87fc5b22
authored
Jul 05, 2018
by
cmaffeo2
Browse files
Fixed crossover angle potentials
parent
9f096897
Changes
2
Hide whitespace changes
Inline
Side-by-side
CanonicalNucleotideAtoms.py
View file @
87fc5b22
...
...
@@ -18,7 +18,7 @@ def stringToIntTuples(string, tupleLen, offset):
return
ret
class
CanonicalNucleotideFactory
(
Group
):
DefaultOrientation
=
rotationAboutAxis
([
0
,
0
,
1
],
80
)
DefaultOrientation
=
rotationAboutAxis
([
0
,
0
,
1
],
1
80
)
def
__init__
(
self
,
prefix
,
seq
):
self
.
sequence
=
seq
# TODO: used?
self
.
resname
=
resnames
[
seq
]
...
...
segmentmodel.py
View file @
87fc5b22
...
...
@@ -1783,23 +1783,18 @@ class SegmentModel(ArbdModel):
if
local_twist
:
k
=
(
1.0
/
2
)
*
1.5
*
kT
*
(
1.0
/
(
1
-
np
.
exp
(
-
float
(
1
)
/
147
)))
*
0.00030461742
;
# kcal_mol/degree^2
pot
=
self
.
get_angle_potential
(
k
,
120
)
if
'orientation_bead'
in
b1
.
__dict__
:
# t0 = 90 + 60
t0
=
150
if
A
.
on_fwd_strand
:
t0
=
30
# TODO handle antiparallel segments
o
=
b1
.
orientation_bead
pot
=
self
.
get_angle_potential
(
k
,
t0
)
self
.
add_angle
(
o
,
b1
,
b2
,
pot
)
if
'orientation_bead'
in
b2
.
__dict__
:
t0
=
150
if
B
.
on_fwd_strand
:
t0
=
30
o
=
b2
.
orientation_bead
pot
=
self
.
get_angle_potential
(
k
,
t0
)
self
.
add_angle
(
b1
,
b2
,
o
,
pot
)
t0
=
90
if
'orientation_bead'
in
b1
.
__dict__
:
t0
=
90
if
A
.
on_fwd_strand
:
t0
=
-
90
o1
=
b1
.
orientation_bead
if
u2
is
not
None
:
k
=
k_fn
(
dists
[
b2
][
u2
]
)
...
...
@@ -1807,9 +1802,11 @@ class SegmentModel(ArbdModel):
self
.
add_dihedral
(
o1
,
b1
,
b2
,
u2
,
pot
)
elif
d2
is
not
None
:
k
=
k_fn
(
dists
[
b2
][
d2
]
)
pot
=
self
.
get_dihedral_potential
(
k
,
t0
)
pot
=
self
.
get_dihedral_potential
(
k
,
-
t0
)
self
.
add_dihedral
(
o1
,
b1
,
b2
,
d2
,
pot
)
if
'orientation_bead'
in
b2
.
__dict__
:
t0
=
90
if
B
.
on_fwd_strand
:
t0
=
-
90
o2
=
b2
.
orientation_bead
if
u1
is
not
None
:
k
=
k_fn
(
dists
[
b1
][
u1
]
)
...
...
@@ -1817,7 +1814,7 @@ class SegmentModel(ArbdModel):
self
.
add_dihedral
(
o2
,
b2
,
b1
,
u1
,
pot
)
elif
d1
is
not
None
:
k
=
k_fn
(
dists
[
b1
][
d1
]
)
pot
=
self
.
get_dihedral_potential
(
k
,
t0
)
pot
=
self
.
get_dihedral_potential
(
k
,
-
t0
)
self
.
add_dihedral
(
o2
,
b2
,
b1
,
d1
,
pot
)
...
...
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