Commit 4a48abc6 authored by cmaffeo2's avatar cmaffeo2
Browse files

Exposed seq_dep_file option for oxDNA

parent 55af01d1
......@@ -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\nexternal_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\nseq_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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