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tbgl
tools
mrdna
Commits
1eb40b0b
Commit
1eb40b0b
authored
Apr 01, 2018
by
cmaffeo2
Browse files
Fixed some small bugs
parent
8cd55d13
Changes
3
Hide whitespace changes
Inline
Side-by-side
arbdmodel.py
View file @
1eb40b0b
...
...
@@ -411,7 +411,7 @@ class PdbModel(Transformable, Parent):
fh
.
write
(
"CRYST1 {:>5f} {:>5f} {:>5f} 90.00 90.00 90.00 P 1 1
\n
"
.
format
(
*
self
.
dimensions
))
## Write coordinates
formatString
=
"ATOM {:>5d} {:^4s}{:1s}{:3s} {:1s}{:>5s} {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}{:2s}{:2f}
\n
"
formatString
=
"ATOM {:>5d} {:^
4.
4s}{:
1.
1s}{:
3.
3s} {:
1.
1s}{:>
5.
5s} {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}{:
2.
2s}{:2f}
\n
"
for
p
in
self
.
particles
:
## http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
idx
=
p
.
idx
+
1
...
...
@@ -453,8 +453,8 @@ class PdbModel(Transformable, Parent):
## From vmd/plugins/molfile_plugin/src/psfplugin.c
## "%d %7s %10s %7s %7s %7s %f %f"
formatString
=
"{idx:>8d} {segname:7s} {resid:<10s} {resname:7s}"
+
\
" {name:7s} {type:7s} {charge:f} {mass:f}
\n
"
formatString
=
"{idx:>8d} {segname:
7.
7s} {resid:<
10.
10s} {resname:
7.
7s}"
+
\
" {name:
7.
7s} {type:
7.
7s} {charge:f} {mass:f}
\n
"
for
p
in
self
.
particles
:
idx
=
p
.
idx
+
1
try
:
...
...
@@ -714,6 +714,8 @@ class ArbdModel(PdbModel):
for
k
,
v
in
zip
(
'XYZ'
,
self
.
dimensions
):
params
[
'origin'
+
k
]
=
-
v
*
0.5
params
[
'dim'
+
k
]
=
v
params
[
'pairlistDistance'
]
-=
params
[
'cutoff'
]
## Actually write the file
with
open
(
filename
,
'w'
)
as
fh
:
...
...
@@ -742,6 +744,7 @@ systemSize {dimX} {dimY} {dimZ}
## Write entries for each type of particle
for
pt
,
num
in
self
.
getParticleTypesAndCounts
():
## TODO create new particle types if existing has grid
particleParams
=
pt
.
__dict__
.
copy
()
particleParams
[
'num'
]
=
num
fh
.
write
(
"""
...
...
@@ -750,8 +753,14 @@ num {num}
diffusion {diffusivity}
"""
.
format
(
**
particleParams
))
if
'grid'
in
particleParams
:
for
g
in
pt
[
'grid'
]:
if
not
isinstance
(
pt
.
grid
,
list
):
pt
.
grid
=
[
pt
.
grid
]
for
g
in
pt
.
grid
:
fh
.
write
(
"gridFile {}
\n
"
.
format
(
g
))
## TODO: make this prettier? multiple scaling factors?
gridFileScale
=
1.0
if
'gridFileScale'
in
pt
.
__dict__
:
gridFileScale
=
pt
.
gridFileScale
fh
.
write
(
"gridFileScale {}
\n
"
.
format
(
gridFileScale
))
else
:
fh
.
write
(
"gridFile null.dx
\n
"
)
...
...
nbPot.py
View file @
1eb40b0b
...
...
@@ -18,6 +18,7 @@ def maxForce(x,u,maxForce=40):
f
[
ids
]
=
-
maxForce
u
=
np
.
hstack
(
((
0
),
np
.
cumsum
(
-
f
*
dx
))
)
assert
(
np
.
any
(
x
>
40
)
)
ids
=
np
.
where
(
x
>
40
)[
0
]
u
=
u
-
np
.
mean
(
u
[
ids
])
...
...
segmentmodel.py
View file @
1eb40b0b
...
...
@@ -191,14 +191,14 @@ class SegmentParticle(PointParticle):
if
seg
==
self
.
parent
:
return
seg
.
contour_to_nt_pos
(
self
.
contour_position
)
else
:
cl
=
[
e
for
e
in
self
.
parent
.
get_connections_and_locations
()
i
n
B
.
container
is
seg
]
dc
=
[(
self
.
contour_position
-
A
.
address
)
**
2
for
c
,
A
,
B
in
e
]
cl
=
[
e
for
e
in
self
.
parent
.
get_connections_and_locations
()
i
f
e
[
2
]
.
container
is
seg
]
dc
=
[(
self
.
contour_position
-
A
.
address
)
**
2
for
c
,
A
,
B
in
cl
]
if
len
(
dc
)
==
0
:
pdb
.
set_trace
()
i
=
np
.
argmin
(
dc
)
c
,
A
,
B
=
cl
[
i
]
## TODO: generalize, removing np.abs and conditional
delta_nt
=
np
.
abs
(
A
.
container
.
contour_to_nt_pos
(
self
.
contour_position
-
A
.
address
)
)
B_nt_pos
=
seg
.
contour_to_nt_pos
(
B
.
address
)
...
...
@@ -318,9 +318,9 @@ class Segment(ConnectableElement, Group):
axis
=
self
.
contour_to_tangent
(
s
)
orientation
=
rotationAboutAxis
(
axis
,
self
.
twist_per_nt
*
self
.
contour_to_nt_pos
(
s
),
normalizeAxis
=
True
)
def
get_contour_sorted_connections_and_locations
(
self
):
def
get_contour_sorted_connections_and_locations
(
self
,
type_
):
sort_fn
=
lambda
c
:
c
[
1
].
address
cl
=
self
.
get_connections_and_locations
()
cl
=
self
.
get_connections_and_locations
(
type_
)
return
sorted
(
cl
,
key
=
sort_fn
)
def
randomize_unset_sequence
(
self
):
...
...
@@ -778,6 +778,9 @@ class DoubleStrandedSegment(Segment):
pos
=
self
.
contour_to_position
(
contour_position
)
if
self
.
local_twist
:
orientation
=
self
.
contour_to_orientation
(
contour_position
)
if
orientation
is
None
:
print
(
"WARNING: local_twist is True, but orientation is None; using identity"
)
orientation
=
np
.
eye
(
3
)
opos
=
pos
+
orientation
.
dot
(
np
.
array
((
Segment
.
orientation_bond
.
r0
,
0
,
0
))
)
o
=
SegmentParticle
(
Segment
.
orientation_particle
,
opos
,
nts
,
num_nts
=
nts
,
parent
=
self
)
...
...
@@ -998,7 +1001,7 @@ class SegmentModel(ArbdModel):
# self.max_nucleotides_per_bead = max_nucleotides_per_bead # ssDNA
self
.
children
=
self
.
segments
=
segments
self
.
_bonded_potential
=
dict
()
# cache bonded potentials
self
.
_bonded_potential
=
dict
()
# cache
for
bonded potentials
self
.
_generate_bead_model
(
max_basepairs_per_bead
,
max_nucleotides_per_bead
,
local_twist
,
escapable_twist
)
...
...
@@ -1116,14 +1119,18 @@ class SegmentModel(ArbdModel):
for
s
in
self
.
segments
:
cabs
=
s
.
get_connections_and_locations
(
"intrahelical"
)
if
np
.
any
(
[
B
.
particle
is
None
for
c
,
A
,
B
in
cabs
]
):
print
(
"WARNING: none type found in connection, skipping"
)
cabs
=
[
e
for
e
in
cabs
if
e
[
2
].
particle
is
not
None
]
beads
=
list
(
set
(
s
.
beads
+
[
A
.
particle
for
c
,
A
,
B
in
cabs
]))
## Add nearby beads
for
c
,
A
,
B
in
cabs
:
## TODOTODO test?
bs
=
filter
(
B
.
particle
.
intrahelical_neighbors
,
lambda
x
:
x
is
not
None
and
x
not
in
beads
)
filter_fn
=
lambda
x
:
x
is
not
None
and
x
not
in
beads
bs
=
list
(
filter
(
filter_fn
,
B
.
particle
.
intrahelical_neighbors
)
)
beads
.
extend
(
bs
)
bs
=
filter
(
bs
.
intrahelical_neighbors
,
lambda
x
:
x
is
not
None
and
x
not
in
beads
)
bs
=
list
(
filter
(
filter_fn
,
[
n
for
b
in
bs
for
n
in
b
.
intrahelical_neighbors
]
)
)
beads
.
extend
(
bs
)
...
...
@@ -1438,7 +1445,8 @@ class SegmentModel(ArbdModel):
twist_per_nt
=
0.5
*
(
p1
.
twist_per_nt
+
p2
.
twist_per_nt
)
angle
=
sep
*
twist_per_nt
if
angle
>
360
or
angle
<
-
360
:
raise
Exception
(
"The twist between beads is too large"
)
print
(
"WARNING: twist angle out of normal range... proceeding anyway"
)
# raise Exception("The twist between beads is too large")
k
=
self
.
_get_twist_spring_constant
(
sep
)
if
escapable_twist
:
...
...
@@ -1543,9 +1551,7 @@ class SegmentModel(ArbdModel):
for
s
in
self
.
segments
:
for
cl
in
s
.
get_contour_sorted_connections_and_locations
(
"crossover"
):
...
def
_generate_strands
(
self
):
self
.
strands
=
strands
=
[]
...
...
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