From f10ad0596874e2b94075da8a3219812cb2820260 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 11 Jul 2023 17:37:14 -0500
Subject: [PATCH] Renamed abstract_polymer to polymer
---
arbdmodel/fjc_polymer_model.py | 4 ++--
arbdmodel/hps_polymer_model.py | 4 ++--
arbdmodel/kh_polymer_model.py | 4 ++--
arbdmodel/onck_polymer_model.py | 4 ++--
arbdmodel/{abstract_polymer.py => polymer.py} | 2 +-
arbdmodel/sali_polymer_model.py | 4 ++--
arbdmodel/ssdna_two_bead.py | 4 ++--
7 files changed, 13 insertions(+), 13 deletions(-)
rename arbdmodel/{abstract_polymer.py => polymer.py} (99%)
diff --git a/arbdmodel/fjc_polymer_model.py b/arbdmodel/fjc_polymer_model.py
index cec6a93..ee63f7f 100644
--- a/arbdmodel/fjc_polymer_model.py
+++ b/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
diff --git a/arbdmodel/hps_polymer_model.py b/arbdmodel/hps_polymer_model.py
index 1d246b9..4d4dbfc 100644
--- a/arbdmodel/hps_polymer_model.py
+++ b/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)
diff --git a/arbdmodel/kh_polymer_model.py b/arbdmodel/kh_polymer_model.py
index 3d56f2b..63573de 100644
--- a/arbdmodel/kh_polymer_model.py
+++ b/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)
diff --git a/arbdmodel/onck_polymer_model.py b/arbdmodel/onck_polymer_model.py
index a63429d..9a59c1d 100644
--- a/arbdmodel/onck_polymer_model.py
+++ b/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)
diff --git a/arbdmodel/abstract_polymer.py b/arbdmodel/polymer.py
similarity index 99%
rename from arbdmodel/abstract_polymer.py
rename to arbdmodel/polymer.py
index 9c80f61..c121dd2 100644
--- a/arbdmodel/abstract_polymer.py
+++ b/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):
diff --git a/arbdmodel/sali_polymer_model.py b/arbdmodel/sali_polymer_model.py
index 3956a2e..595f90e 100644
--- a/arbdmodel/sali_polymer_model.py
+++ b/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)
diff --git a/arbdmodel/ssdna_two_bead.py b/arbdmodel/ssdna_two_bead.py
index 9fa861e..98ffb6e 100644
--- a/arbdmodel/ssdna_two_bead.py
+++ b/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)
--
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