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mrdna
Commits
c16fbbed
Commit
c16fbbed
authored
7 years ago
by
cmaffeo2
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Made beadModelTwist omit beadModel-style crossover bonds and angles
parent
2366e578
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1 changed file
beadModelTwist.py
+43
-40
43 additions, 40 deletions
beadModelTwist.py
with
43 additions
and
40 deletions
beadModelTwist.py
+
43
−
40
View file @
c16fbbed
...
...
@@ -257,7 +257,7 @@ class beadModelTwist():
# self._dihedralParamFiles = set()
self
.
twistPersistenceLength
=
twistPersistenceLength
self
.
apply_extra_crossover_potentials
=
False
self
.
_buildModel
(
part
,
maxBpsPerDNode
,
maxNtsPerSNode
)
...
...
@@ -1255,12 +1255,13 @@ component "data" value 3
self
.
addAngle
(
*
args
)
self
.
addAngle
(
n1
,
n2
,
n3
,
Angle
(
k
,
180
)
)
a
,
d
=
self
.
_getCrossoverAnglesAndDihedrals
()
for
nodes
,
sep
in
a
:
n1
,
n2
,
n3
=
nodes
k
=
(
1.0
/
2
)
*
1.5
*
kT
*
(
1.0
/
(
1
-
exp
(
-
float
(
sep
)
/
147
)))
*
0.00030461742
;
# kcal_mol/degree^2
self
.
addAngle
(
n1
,
n2
,
n3
,
Angle
(
k
,
90
)
)
if
self
.
apply_extra_crossover_potentials
:
a
,
d
=
self
.
_getCrossoverAnglesAndDihedrals
()
for
nodes
,
sep
in
a
:
n1
,
n2
,
n3
=
nodes
k
=
(
1.0
/
2
)
*
1.5
*
kT
*
(
1.0
/
(
1
-
exp
(
-
float
(
sep
)
/
147
)))
*
0.00030461742
;
# kcal_mol/degree^2
self
.
addAngle
(
n1
,
n2
,
n3
,
Angle
(
k
,
90
)
)
## Intrahelical 90 deg orientation angles
for
nodes
,
seps
in
self
.
_getOrientationAngles
():
...
...
@@ -1289,40 +1290,42 @@ component "data" value 3
def
_buildDihedrals
(
self
,
prefix
,
directory
=
"
potentials
"
):
kT
=
0.58622522
# kcal/mol
a
,
d
=
self
.
_getCrossoverAnglesAndDihedrals
()
for
nodes
,
sep
,
isFwd1
,
isFwd2
in
d
:
n1
,
n2
,
n3
,
n4
=
nodes
## <cos(q)> = exp(-s/Lp) = integrate( cos[x] exp(-A x^2), {x, 0, pi} ) / integrate( exp(-A x^2), {x, 0, pi} )
## Assume A is small
## int[B_] := Normal[Integrate[ Series[Cos[x] Exp[-B x^2], {B, 0, 1}], {x, 0, \[Pi]}]/
## Integrate[Series[Exp[-B x^2], {B, 0, 1}], {x, 0, \[Pi]}]]
## Actually, without assumptions I get fitFun below
## From http://www.annualreviews.org/doi/pdf/10.1146/annurev.bb.17.060188.001405
## units "3e-19 erg cm/ 295 k K" "nm" =~ 73
Lp
=
self
.
twistPersistenceLength
/
0.34
# set semi-arbitrarily as there is a large spread in literature
fitFun
=
lambda
x
:
np
.
real
(
erf
(
(
4
*
np
.
pi
*
x
+
1j
)
/
(
2
*
np
.
sqrt
(
x
))
))
*
np
.
exp
(
-
1
/
(
4
*
x
))
/
erf
(
2
*
np
.
sqrt
(
x
)
*
np
.
pi
)
-
exp
(
-
sep
/
Lp
)
k
=
opt
.
leastsq
(
fitFun
,
x0
=
exp
(
-
sep
/
Lp
)
)
k
=
k
[
0
][
0
]
*
2
*
kT
*
0.00030461742
# intrinsicDegrees=30
# fitFun = lambda x: (1.0/(2*x) - 2*np.sqrt(np.pi)*np.exp(-4*np.pi**2*x) / (np.sqrt(x)*erf(2*np.pi*np.sqrt(x))) ) - \
# ( (intrinsicDegrees*np.pi/180)**2 + 2*(1-exp(-sep/Lp)) )
# k = opt.leastsq( fitFun, x0=1/(1-exp(-sep/Lp)) )
# k = k[0][0] * 2*kT*0.00030461742
t0
=
sep
*
(
360.0
/
10.5
)
# pdb.set_trace()
if
isFwd1
[
0
]:
t0
-=
120
if
isFwd2
[
0
]:
t0
+=
120
t0
=
t0
%
360
# if n2.idx == 0:
# print( n1.idx,n2.idx,n3.idx,n4.idx,k,t0,sep )
self
.
addDihedral
(
n1
,
n2
,
n3
,
n4
,
Dihedral
(
k
,
t0
)
)
if
self
.
apply_extra_crossover_potentials
:
a
,
d
=
self
.
_getCrossoverAnglesAndDihedrals
()
for
nodes
,
sep
,
isFwd1
,
isFwd2
in
d
:
n1
,
n2
,
n3
,
n4
=
nodes
## <cos(q)> = exp(-s/Lp) = integrate( cos[x] exp(-A x^2), {x, 0, pi} ) / integrate( exp(-A x^2), {x, 0, pi} )
## Assume A is small
## int[B_] := Normal[Integrate[ Series[Cos[x] Exp[-B x^2], {B, 0, 1}], {x, 0, \[Pi]}]/
## Integrate[Series[Exp[-B x^2], {B, 0, 1}], {x, 0, \[Pi]}]]
## Actually, without assumptions I get fitFun below
## From http://www.annualreviews.org/doi/pdf/10.1146/annurev.bb.17.060188.001405
## units "3e-19 erg cm/ 295 k K" "nm" =~ 73
Lp
=
self
.
twistPersistenceLength
/
0.34
# set semi-arbitrarily as there is a large spread in literature
fitFun
=
lambda
x
:
np
.
real
(
erf
(
(
4
*
np
.
pi
*
x
+
1j
)
/
(
2
*
np
.
sqrt
(
x
))
))
*
np
.
exp
(
-
1
/
(
4
*
x
))
/
erf
(
2
*
np
.
sqrt
(
x
)
*
np
.
pi
)
-
exp
(
-
sep
/
Lp
)
k
=
opt
.
leastsq
(
fitFun
,
x0
=
exp
(
-
sep
/
Lp
)
)
k
=
k
[
0
][
0
]
*
2
*
kT
*
0.00030461742
# intrinsicDegrees=30
# fitFun = lambda x: (1.0/(2*x) - 2*np.sqrt(np.pi)*np.exp(-4*np.pi**2*x) / (np.sqrt(x)*erf(2*np.pi*np.sqrt(x))) ) - \
# ( (intrinsicDegrees*np.pi/180)**2 + 2*(1-exp(-sep/Lp)) )
# k = opt.leastsq( fitFun, x0=1/(1-exp(-sep/Lp)) )
# k = k[0][0] * 2*kT*0.00030461742
t0
=
sep
*
(
360.0
/
10.5
)
# pdb.set_trace()
if
isFwd1
[
0
]:
t0
-=
120
if
isFwd2
[
0
]:
t0
+=
120
t0
=
t0
%
360
# if n2.idx == 0:
# print( n1.idx,n2.idx,n3.idx,n4.idx,k,t0,sep )
self
.
addDihedral
(
n1
,
n2
,
n3
,
n4
,
Dihedral
(
k
,
t0
)
)
for
nodes
,
seps
in
self
.
_getOrientationDihedrals
():
n1
,
n2
,
n3
,
n4
=
nodes
...
...
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