Added ability to add custom extra lines to BD file using extra_bd_file_lines attribute in arbdmodel

mrdna/model/arbdmodel.py

@@ -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

@@ -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