Commit 8cd55d13 authored by cmaffeo2's avatar cmaffeo2
Browse files

Fixed SegmentModel arguments

parent 2161b99c
......@@ -880,8 +880,6 @@ class StrandInSegment(Group):
def get_contour_points(self):
c0,c1 = [self.segment.nt_pos_to_contour(p) for p in (self.start,self.end)]
return np.linspace(c0,c1,self.num_nts)
class Strand(Group):
""" Class that holds atomic model, maps to segments """
......@@ -982,7 +980,7 @@ class Strand(Group):
nt.orientation = orientation.dot(default_orientation) # this one should be correct
class SegmentModel(ArbdModel):
def __init__(self, segments=[], local_twist=True,
def __init__(self, segments=[], local_twist=True, escapable_twist=True,
max_basepairs_per_bead=7,
max_nucleotides_per_bead=4,
dimensions=(1000,1000,1000), temperature=291,
......@@ -1002,7 +1000,7 @@ class SegmentModel(ArbdModel):
self._bonded_potential = dict() # cache bonded potentials
self._generate_bead_model( max_basepairs_per_bead, max_nucleotides_per_bead, local_twist)
self._generate_bead_model( max_basepairs_per_bead, max_nucleotides_per_bead, local_twist, escapable_twist)
self.useNonbondedScheme( nbDnaScheme )
......
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