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tbgl
tools
mrdna
Commits
4a48abc6
Commit
4a48abc6
authored
Nov 24, 2020
by
cmaffeo2
Browse files
Exposed seq_dep_file option for oxDNA
parent
55af01d1
Changes
1
Hide whitespace changes
Inline
Side-by-side
mrdna/segmentmodel.py
View file @
4a48abc6
...
...
@@ -9,6 +9,8 @@ from .arbdmodel.nonbonded import *
from
copy
import
copy
,
deepcopy
from
.model.nbPot
import
nbDnaScheme
from
.
import
get_resource_path
import
re
from
scipy.special
import
erf
...
...
@@ -3803,7 +3805,8 @@ E = 0 0 0
delta_rotation
=
0.22
,
verlet_skin
=
0.5
,
max_backbone_force
=
100
,
external_forces_file
=
None
external_forces_file
=
None
,
seq_dep_file
=
None
):
if
seed
is
None
:
...
...
@@ -3858,6 +3861,16 @@ E = 0 0 0
else
:
external_forces
=
"external_forces = 1
\n
external_forces_file = {}"
.
format
(
external_forces_file
)
if
seq_dep_file
is
None
:
sequence_dependence
=
""
else
:
if
seq_dep_file
==
"oxDNA2"
:
seq_dep_file
=
get_resource_path
(
"oxDNA2_sequence_dependent_parameters.txt"
)
elif
seq_dep_file
==
"oxDNA1"
:
seq_dep_file
=
get_resource_path
(
"oxDNA1_sequence_dependent_parameters.txt"
)
sequence_dependence
=
"use_average_seq = 1
\n
seq_dep_file = {}"
.
format
(
seq_dep_file
)
with
open
(
filename
,
'w'
)
as
fh
:
fh
.
write
(
"""##############################
#### PROGRAM PARAMETERS ####
...
...
@@ -3889,6 +3902,7 @@ verlet_skin = {verlet_skin}
{max_backbone_force}
{external_forces}
{sequence_dependence}
##############################
#### INPUT / OUTPUT ####
...
...
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