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tbgl
tools
mrdna
Commits
b88b6f96
Commit
b88b6f96
authored
Mar 22, 2018
by
cmaffeo2
Browse files
Crossovers are now representated
parent
bd20f326
Changes
1
Hide whitespace changes
Inline
Side-by-side
segmentmodel.py
View file @
b88b6f96
...
...
@@ -47,12 +47,12 @@ class ConnectableElement():
def
__init__
(
self
,
connections
=
[]):
self
.
connections
=
connections
def
get_connections_and_locations
(
self
,
type_
=
None
):
def
get_connections_and_locations
(
self
,
type_
=
None
,
exclude
=
[]
):
""" Returns a list with each entry of the form:
connection, location_in_self, location_in_other """
ret
=
[]
for
c
in
self
.
connections
:
if
type_
is
None
or
c
.
type_
==
type_
:
if
type_
is
None
or
c
.
type_
==
type_
and
type_
not
in
exclude
:
if
c
.
A
.
container
is
self
:
ret
.
append
(
[
c
,
c
.
A
,
c
.
B
]
)
elif
c
.
B
.
container
is
self
:
...
...
@@ -367,6 +367,44 @@ class DoubleStrandedSegment(Segment):
end3
=
end3
.
end3
self
.
_connect_ends
(
self
.
end5
,
end3
,
type_
,
force_connection
=
force_connection
)
def
crossover
(
self
,
nt
,
other
,
other_nt
,
strands
=
None
,
other_strands
=
None
):
""" Add a crossover between two helices """
## Validate other, nt, other_nt
## TODO
## Fix input
if
strands
is
None
and
other_strands
is
None
:
## Regular double crossover
strands
=
[
'fwd'
,
'rev'
]
other_strands
=
list
(
strands
[::
-
1
])
elif
strands
is
None
:
strands
=
[]
for
d
in
other_strands
:
if
d
==
'fwd'
:
strands
.
append
(
'rev'
)
elif
d
==
'rev'
:
strands
.
append
(
'fwd'
)
elif
other_strands
==
None
:
other_strands
=
[]
for
d
in
strands
:
if
d
==
'fwd'
:
other_strands
.
append
(
'rev'
)
elif
d
==
'rev'
:
other_strands
.
append
(
'fwd'
)
if
isinstance
(
strands
,
str
):
strands
=
[
strands
]
if
isinstance
(
other_strands
,
str
):
other_strands
=
[
other_strands
]
## Create locations, connections and add to segments
c
=
nt
/
self
.
num_nts
print
(
self
.
name
,
nt
,
c
)
assert
(
c
>=
0
and
c
<=
1
)
loc
=
Location
(
self
,
address
=
c
,
type_
=
strands
)
c
=
other_nt
/
other
.
num_nts
print
(
other
.
name
,
other_nt
,
c
)
assert
(
c
>=
0
and
c
<=
1
)
other_loc
=
Location
(
other
,
address
=
c
,
type_
=
other_strands
)
self
.
_connect
(
other
,
Connection
(
loc
,
other_loc
,
type_
=
"crossover"
))
# TODO: use multiple crossover types
## Real work
def
_connect_ends
(
self
,
end1
,
end2
,
type_
,
force_connection
):
## TODO remove self?
...
...
@@ -520,12 +558,12 @@ class SegmentModel(ArbdModel):
self
.
useNonbondedScheme
(
nbDnaScheme
)
def
get_connections
(
self
,
type_
=
None
):
def
get_connections
(
self
,
type_
=
None
,
exclude
=
[]
):
""" Find all connections in model, without double-counting """
added
=
set
()
ret
=
[]
for
s
in
self
.
segments
:
items
=
[
e
for
e
in
s
.
get_connections_and_locations
(
type_
)
if
e
[
0
]
not
in
added
]
items
=
[
e
for
e
in
s
.
get_connections_and_locations
(
type_
,
exclude
=
exclude
)
if
e
[
0
]
not
in
added
]
added
.
update
([
e
[
0
]
for
e
in
items
])
ret
.
extend
(
items
)
return
ret
...
...
@@ -732,6 +770,19 @@ class SegmentModel(ArbdModel):
A
.
particle
=
B
.
particle
=
b
...
for
c
,
A
,
B
in
self
.
get_connections
(
exclude
=
"intrahelical"
):
s1
,
s2
=
[
l
.
container
for
l
in
(
A
,
B
)]
if
A
.
particle
is
not
None
and
B
.
particle
is
not
None
:
continue
assert
(
A
.
particle
is
None
)
assert
(
B
.
particle
is
None
)
## TODO: offload the work here to s1
a1
,
a2
=
[
l
.
address
for
l
in
(
A
,
B
)]
## TODO: if existing particle of same type is very nearby, use that instead
A
.
particle
=
s1
.
_generate_one_bead
(
a1
,
0
)
B
.
particle
=
s2
.
_generate_one_bead
(
a2
,
0
)
""" Some tests """
for
c
,
A
,
B
in
self
.
get_connections
(
"intrahelical"
):
for
l
in
(
A
,
B
):
...
...
@@ -787,7 +838,7 @@ class SegmentModel(ArbdModel):
""" Add intrahelical bond potentials """
if
self
.
DEBUG
:
print
(
"Adding intrahelical bond potentials"
)
dists
=
dict
()
# built for later use
dists
=
dict
()
#
intrahelical distances
built for later use
intra_beads
=
self
.
_get_intrahelical_beads
()
if
self
.
DEBUG
:
print
(
" Adding %d bonds"
%
len
(
intra_beads
))
for
b1
,
b2
in
intra_beads
:
...
...
@@ -836,7 +887,7 @@ class SegmentModel(ArbdModel):
k
*=
0.5
# halve because orientation beads have similar springs
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
=
1.5
*
kT
*
(
1.0
/
(
1
-
np
.
exp
(
-
float
(
sep
)
/
3
)))
*
0.00030461742
;
# kcal_mol/degree^2
angle
=
self
.
get_angle_potential
(
k
,
180
)
parent
.
add_angle
(
b1
,
b2
,
b3
,
angle
)
...
...
@@ -908,6 +959,69 @@ class SegmentModel(ArbdModel):
pot
=
self
.
get_bond_potential
(
4
,
18.5
)
self
.
add_bond
(
b1
,
b2
,
pot
)
for
c
,
A
,
B
in
self
.
get_connections
(
"crossover"
):
b1
,
b2
=
[
loc
.
particle
for
loc
in
(
c
.
A
,
c
.
B
)]
pot
=
self
.
get_bond_potential
(
4
,
18.5
)
self
.
add_bond
(
b1
,
b2
,
pot
)
if
not
local_twist
:
## TODO
...
else
:
## TODO: fwd/rev
k
=
(
1.0
/
2
)
*
1.5
*
kT
*
(
1.0
/
(
1
-
np
.
exp
(
-
float
(
1
)
/
147
)))
*
0.00030461742
;
# kcal_mol/degree^2
if
'orientation_bead'
in
b1
.
__dict__
:
t0
=
90
+
60
# if f1: t0 -= 120
o
=
b1
.
orientation_bead
pot
=
self
.
get_angle_potential
(
k
,
t0
)
self
.
add_angle
(
o
,
b1
,
b2
,
pot
)
else
:
t0
=
90
+
60
# if f2: t0 -= 120
o
=
b2
.
orientation_bead
pot
=
self
.
get_angle_potential
(
k
,
t0
)
self
.
add_angle
(
b1
,
b2
,
o
,
pot
)
u1
,
u2
=
[
b
.
intrahelical_neighbors
[
-
1
]
for
b
in
(
b1
,
b2
)]
# TODO: fix this
d1
,
d2
=
[
b
.
intrahelical_neighbors
[
0
]
for
b
in
(
b1
,
b2
)]
# TODO: fix this
## TODO make k depend on sep
k
=
(
1.0
/
2
)
*
1.5
*
kT
*
(
1.0
/
(
1
-
np
.
exp
(
-
float
(
1
)
/
147
)))
*
0.00030461742
;
# kcal_mol/degree^2
t0
=
90
pot
=
self
.
get_dihedral_potential
(
k
,
t0
)
if
'orientation_bead'
in
b1
.
__dict__
:
o1
=
b1
.
orientation_bead
if
u2
is
not
None
:
self
.
add_dihedral
(
o1
,
b1
,
b2
,
u2
,
pot
)
elif
d2
is
not
None
:
self
.
add_dihedral
(
o2
,
b2
,
b1
,
d2
,
pot
)
if
'orientation_bead'
in
b2
.
__dict__
:
o2
=
b2
.
orientation_bead
if
u1
is
not
None
:
self
.
add_dihedral
(
o2
,
b2
,
b1
,
u1
,
pot
)
elif
d1
is
not
None
:
self
.
add_dihedral
(
o2
,
b2
,
b1
,
d1
,
pot
)
if
'orientation_bead'
in
b1
.
__dict__
and
'orientation_bead'
in
b2
.
__dict__
:
if
u1
is
not
None
and
u2
is
not
None
:
t0
=
0
pot
=
self
.
get_dihedral_potential
(
k
,
t0
)
self
.
add_dihedral
(
u1
,
b1
,
b2
,
u2
,
pot
)
elif
d1
is
not
None
and
d2
is
not
None
:
t0
=
0
pot
=
self
.
get_dihedral_potential
(
k
,
t0
)
self
.
add_dihedral
(
d1
,
b1
,
b2
,
d2
,
pot
)
elif
d1
is
not
None
and
u2
is
not
None
:
t0
=
180
pot
=
self
.
get_dihedral_potential
(
k
,
t0
)
self
.
add_dihedral
(
d1
,
b1
,
b2
,
u2
,
pot
)
elif
u1
is
not
None
and
d2
is
not
None
:
t0
=
180
pot
=
self
.
get_dihedral_potential
(
k
,
t0
)
self
.
add_dihedral
(
u1
,
b1
,
b2
,
d2
,
pot
)
# def get_bead(self, location):
# if type(location.container) is not list:
...
...
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