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mrdna
Commits
f506105a
Commit
f506105a
authored
Aug 13, 2019
by
cmaffeo2
Browse files
Added ability to add custom extra lines to BD file using extra_bd_file_lines attribute in arbdmodel
parent
5bd0d211
Changes
2
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Inline
Side-by-side
mrdna/model/arbdmodel.py
View file @
f506105a
...
...
@@ -628,7 +628,7 @@ class PdbModel(Transformable, Parent):
class
ArbdModel
(
PdbModel
):
def
__init__
(
self
,
children
,
dimensions
=
(
1000
,
1000
,
1000
),
temperature
=
291
,
timestep
=
50e-6
,
cutoff
=
50
,
decompPeriod
=
10000
,
pairlistDistance
=
None
,
nonbondedResolution
=
0.1
,
remove_duplicate_bonded_terms
=
True
):
def
__init__
(
self
,
children
,
dimensions
=
(
1000
,
1000
,
1000
),
temperature
=
291
,
timestep
=
50e-6
,
cutoff
=
50
,
decompPeriod
=
10000
,
pairlistDistance
=
None
,
nonbondedResolution
=
0.1
,
remove_duplicate_bonded_terms
=
True
,
extra_bd_file_lines
=
""
):
PdbModel
.
__init__
(
self
,
children
,
dimensions
,
remove_duplicate_bonded_terms
)
self
.
temperature
=
temperature
...
...
@@ -641,6 +641,8 @@ class ArbdModel(PdbModel):
self
.
decompPeriod
=
decompPeriod
self
.
pairlistDistance
=
pairlistDistance
self
.
extra_bd_file_lines
=
extra_bd_file_lines
self
.
numParticles
=
0
self
.
particles
=
[]
self
.
type_counts
=
None
...
...
@@ -857,6 +859,8 @@ pairlistDistance {pairlistDistance}
origin {originX} {originY} {originZ}
systemSize {dimX} {dimY} {dimZ}
{extra_bd_file_lines}
\n
"""
.
format
(
**
params
))
## Write entries for each type of particle
...
...
mrdna/segmentmodel.py
View file @
f506105a
...
...
@@ -436,7 +436,7 @@ class Segment(ConnectableElement, Group):
self
.
sequence
=
None
def
__repr__
(
self
):
return
"<{} {}[{:d}]>"
.
format
(
type
(
self
),
self
.
name
,
self
.
num_nt
)
return
"<{} {}[{:d}]>"
.
format
(
str
(
type
(
self
)
).
split
(
'.'
)[
-
1
]
,
self
.
name
,
self
.
num_nt
)
def
set_splines
(
self
,
contours
,
coords
):
tck
,
u
=
interpolate
.
splprep
(
coords
.
T
,
u
=
contours
,
s
=
0
,
k
=
1
)
...
...
@@ -1540,15 +1540,18 @@ class SegmentModel(ArbdModel):
dimensions
=
(
5000
,
5000
,
5000
),
temperature
=
291
,
timestep
=
50e-6
,
cutoff
=
50
,
decompPeriod
=
10000
,
pairlistDistance
=
None
,
nonbondedResolution
=
0
,
DEBUG
=
0
,
debye_length
=
None
nonbondedResolution
=
0
,
DEBUG
=
0
,
debye_length
=
None
,
extra_bd_file_lines
=
""
,
):
self
.
DEBUG
=
DEBUG
if
DEBUG
>
0
:
print
(
"Building ARBD Model"
)
ArbdModel
.
__init__
(
self
,
segments
,
dimensions
,
temperature
,
timestep
,
cutoff
,
decompPeriod
,
pairlistDistance
=
None
,
nonbondedResolution
=
0
)
nonbondedResolution
=
0
,
extra_bd_file_lines
=
extra_bd_file_lines
)
# self.max_basepairs_per_bead = max_basepairs_per_bead # dsDNA
...
...
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