Exposed seq_dep_file option for oxDNA

mrdna/segmentmodel.py

@@ -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    ####