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tools
mrdna
Commits
3cfec3ce
Commit
3cfec3ce
authored
Sep 20, 2018
by
cmaffeo2
Browse files
Updated method for spring constant
parent
dbcd2764
Changes
1
Hide whitespace changes
Inline
Side-by-side
mrdna/segmentmodel.py
View file @
3cfec3ce
...
...
@@ -15,6 +15,8 @@ from scipy import interpolate
from
.model.CanonicalNucleotideAtoms
import
canonicalNtFwd
,
canonicalNtRev
,
seqComplement
from
.model.CanonicalNucleotideAtoms
import
enmTemplateHC
,
enmTemplateSQ
,
enmCorrectionsHC
from
.model.spring_from_lp
import
k_angle
as
angle_spring_from_lp
# import pdb
"""
TODO:
...
...
@@ -2069,10 +2071,7 @@ class SegmentModel(ArbdModel):
kT
=
0.58622522
# kcal/mol
if
b1
.
type_
.
name
[
0
]
==
"D"
and
b2
.
type_
.
name
[
0
]
==
"D"
and
b3
.
type_
.
name
[
0
]
==
"D"
:
## <cos(q)> = exp(-s/Lp) = integrate( x^4 exp(-A x^2) / 2, {x, 0, pi} ) / integrate( x^2 exp(-A x^2), {x, 0, pi} )
## <cos(q)> ~ 1 - 3/4A
## where A = k_spring / (2 kT)
k
=
1.5
*
kT
*
(
1.0
/
(
1
-
np
.
exp
(
-
float
(
sep
)
/
147
)))
*
0.00030461742
;
# kcal_mol/degree^2
k
=
angle_spring_from_lp
(
sep
,
147
)
if
local_twist
:
## TODO optimize this paramter
k
*=
0.5
# halve because orientation beads have similar springs
...
...
@@ -2082,7 +2081,7 @@ class SegmentModel(ArbdModel):
else
:
## TODO: get correct number from ssDNA model
k
=
1.5
*
kT
*
(
1.0
/
(
1
-
np
.
exp
(
-
float
(
sep
)
/
3
)))
*
0.00030461742
;
# kcal_mol/degree^2
k
=
angle_spring_from_lp
(
sep
,
2
)
angle
=
self
.
get_angle_potential
(
k
,
180
)
parent
.
add_angle
(
b1
,
b2
,
b3
,
angle
)
...
...
@@ -2126,7 +2125,7 @@ class SegmentModel(ArbdModel):
parent
=
self
.
_getParent
(
b1
,
b2
)
""" Add heuristic 90 degree potential to keep orientation bead orthogonal """
k
=
(
1.0
/
2
)
*
1.5
*
kT
*
(
1.0
/
(
1
-
np
.
exp
(
-
float
(
sep
)
/
147
)
))
*
0.00030461742
;
# kcal_mol/degree^2
k
=
0.5
*
angle_spring_from_lp
(
sep
,
147
)
pot
=
self
.
get_angle_potential
(
k
,
90
)
parent
.
add_angle
(
o1
,
b1
,
b2
,
pot
)
parent
.
add_angle
(
b1
,
b2
,
o2
,
pot
)
...
...
@@ -2146,7 +2145,8 @@ class SegmentModel(ArbdModel):
parent
.
add_dihedral
(
o1
,
b1
,
b2
,
o2
,
pot
)
def
k_angle
(
sep
):
return
1.5
*
kT
*
(
1.0
/
(
1
-
np
.
exp
(
-
float
(
sep
)
/
147
)))
*
0.00030461742
;
# kcal_mol/degree^2
return
0.5
*
angle_spring_from_lp
(
sep
,
147
)
def
k_xover_angle
(
sep
):
return
0.5
*
k_angle
(
sep
)
...
...
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