Renamed abstract_polymer to polymer

arbdmodel/fjc_polymer_model.py

@@ -7,7 +7,7 @@ import sys
 
 ## Local imports
 from . import ArbdModel, ParticleType, PointParticle, Group, get_resource_path    
-from .abstract_polymer import PolymerSection, AbstractPolymerGroup
+from .polymer import PolymerSection, PolymerGroup
 from .interactions import NonbondedScheme, HarmonicBond, HarmonicPotential
 from .coords import quaternion_to_matrix
 
@@ -115,7 +115,7 @@ class FjcModel(ArbdModel):
             # raise NotImplementedError("HpsModel must be provided a sequences argument")
             sequences = [None for i in range(len(polymers))]
 
-        self.polymer_group = AbstractPolymerGroup(polymers)
+        self.polymer_group = PolymerGroup(polymers)
         self.sequences = sequences
         self.rest_length = rest_length
         self.spring_constant = spring_constant

arbdmodel/hps_polymer_model.py

@@ -7,7 +7,7 @@ import sys
 
 ## Local imports
 from . import ArbdModel, ParticleType, PointParticle, Group, get_resource_path    
-from .abstract_polymer import PolymerSection, AbstractPolymerGroup
+from .polymer import PolymerSection, PolymerGroup
 from .interactions import NonbondedScheme, HarmonicBond, HarmonicAngle, HarmonicDihedral
 from .coords import quaternion_to_matrix
 
@@ -263,7 +263,7 @@ class HpsModel(ArbdModel):
         if sequences is None:
             raise NotImplementedError("HpsModel must be provided a sequences argument")
 
-        self.polymer_group = AbstractPolymerGroup(polymers)
+        self.polymer_group = PolymerGroup(polymers)
         self.sequences = sequences
         ArbdModel.__init__(self, [], **kwargs)
 

arbdmodel/kh_polymer_model.py

@@ -6,7 +6,7 @@ import sys
 
 ## Local imports
 from . import ArbdModel, ParticleType, PointParticle, Group, get_resource_path    
-from .abstract_polymer import PolymerSection, AbstractPolymerGroup
+from .polymer import PolymerSection, PolymerGroup
 from .interactions import NonbondedScheme, HarmonicBond, HarmonicAngle, HarmonicDihedral
 from .coords import quaternion_to_matrix
 from .kh_polymer_model_pair_epsilon import epsilon_mj
@@ -279,7 +279,7 @@ class KhModel(ArbdModel):
         if sequences is None:
             raise NotImplementedError("KhModel must be provided a sequences argument")
 
-        self.polymer_group = AbstractPolymerGroup(polymers)
+        self.polymer_group = PolymerGroup(polymers)
         self.sequences = sequences
         ArbdModel.__init__(self, [], **kwargs)
 

arbdmodel/onck_polymer_model.py

@@ -7,7 +7,7 @@ import sys
 
 ## Local imports
 from . import ArbdModel, ParticleType, PointParticle, Group, get_resource_path    
-from .abstract_polymer import PolymerSection, AbstractPolymerGroup
+from .polymer import PolymerSection, PolymerGroup
 from .interactions import NonbondedScheme, HarmonicBond, HarmonicAngle, HarmonicDihedral
 from .coords import quaternion_to_matrix
 
@@ -277,7 +277,7 @@ class OnckModel(ArbdModel):
         if sequences is None:
             raise NotImplementedError("OnckModel must be provided a sequences argument")
 
-        self.polymer_group = AbstractPolymerGroup(polymers)
+        self.polymer_group = PolymerGroup(polymers)
         self.sequences = sequences
         ArbdModel.__init__(self, [], **kwargs)
 

arbdmodel/abstract_polymer.py → arbdmodel/polymer.py

@@ -402,7 +402,7 @@ class PolymerSection(ConnectableElement):
         for c in cl:
             yield c
             
-class AbstractPolymerGroup():
+class PolymerGroup():
     def __init__(self, polymers=[],
                  **kwargs):
 

arbdmodel/sali_polymer_model.py

@@ -7,7 +7,7 @@ import sys
 
 ## Local imports
 from . import ArbdModel, ParticleType, PointParticle, Group, get_resource_path    
-from .abstract_polymer import PolymerSection, AbstractPolymerGroup
+from .polymer import PolymerSection, PolymerGroup
 from .interactions import NonbondedScheme, HarmonicBond, HarmonicPotential
 from .coords import quaternion_to_matrix
 
@@ -125,7 +125,7 @@ class SaliModel(ArbdModel):
         if sequences is None:
             raise NotImplementedError("HpsModel must be provided a sequences argument")
 
-        self.polymer_group = AbstractPolymerGroup(polymers)
+        self.polymer_group = PolymerGroup(polymers)
         self.sequences = sequences
         ArbdModel.__init__(self, [], **kwargs)
 

arbdmodel/ssdna_two_bead.py

@@ -4,7 +4,7 @@ import sys
 
 ## Local imports
 from . import ArbdModel, ParticleType, PointParticle, Group, get_resource_path
-from .abstract_polymer import PolymerSection, AbstractPolymerGroup
+from .polymer import PolymerSection, PolymerGroup
 from .interactions import TabulatedPotential, HarmonicBond, HarmonicAngle, HarmonicDihedral
 from .coords import quaternion_to_matrix
 
@@ -163,7 +163,7 @@ class DnaModel(ArbdModel):
         kwargs['timestep'] = 20e-6
         kwargs['cutoff'] = 35
         
-        self.polymer_group = AbstractPolymerGroup(polymers)
+        self.polymer_group = PolymerGroup(polymers)
         self.strands = [DnaStrandFromPolymer(p) for p in self.polymer_group.polymers]
 
         ArbdModel.__init__(self, self.strands, **kwargs)