Merge pull request #4 from swails/bond

namedtuple and singleton

wrappers/python/setup.py

@@ -229,8 +229,8 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
 
 
 def main():
-    if sys.version_info < (2, 6):
-        reportError("OpenMM requires Python 2.6 or better.")
+    if sys.version_info < (2, 7):
+        reportError("OpenMM requires Python 2.7 or better.")
     if platform.system() == 'Darwin':
         macVersion = [int(x) for x in platform.mac_ver()[0].split('.')]
         if tuple(macVersion) < (10, 5):

wrappers/python/simtk/openmm/app/forcefield.py

@@ -45,6 +45,7 @@ import simtk.openmm as mm
 import simtk.unit as unit
 from . import element as elem
 from simtk.openmm.app import Topology
+from simtk.openmm.app.internal.singleton import Singleton
 
 def _convertParameterToNumber(param):
     if unit.is_quantity(param):
@@ -89,44 +90,44 @@ def _createFunctions(force, functions):
 
 # Enumerated values for nonbonded method
 
-class NoCutoff(object):
+class NoCutoff(Singleton):
     def __repr__(self):
         return 'NoCutoff'
 NoCutoff = NoCutoff()
 
-class CutoffNonPeriodic(object):
+class CutoffNonPeriodic(Singleton):
     def __repr__(self):
         return 'CutoffNonPeriodic'
 CutoffNonPeriodic = CutoffNonPeriodic()
 
-class CutoffPeriodic(object):
+class CutoffPeriodic(Singleton):
     def __repr__(self):
         return 'CutoffPeriodic'
 CutoffPeriodic = CutoffPeriodic()
 
-class Ewald(object):
+class Ewald(Singleton):
     def __repr__(self):
         return 'Ewald'
 Ewald = Ewald()
 
-class PME(object):
+class PME(Singleton):
     def __repr__(self):
         return 'PME'
 PME = PME()
 
 # Enumerated values for constraint type
 
-class HBonds(object):
+class HBonds(Singleton):
     def __repr__(self):
         return 'HBonds'
 HBonds = HBonds()
 
-class AllBonds(object):
+class AllBonds(Singleton):
     def __repr__(self):
         return 'AllBonds'
 AllBonds = AllBonds()
 
-class HAngles(object):
+class HAngles(Singleton):
     def __repr__(self):
         return 'HAngles'
 HAngles = HAngles()

wrappers/python/simtk/openmm/app/internal/singleton.py

+"""
+Creates a subclass for all classes intended to be a singleton. This
+maintains the correctness of instance is instance even following
+pickling/unpickling
+"""
+class Singleton(object):
+    _inst = None
+    def __new__(cls):
+        if cls._inst is None:
+            cls._inst = super(Singleton, cls).__new__(cls)
+        return cls._inst
+
+    def __reduce__(self):
+        return repr(self)
+

wrappers/python/simtk/openmm/app/topology.py

@@ -32,35 +32,37 @@ from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
+from collections import namedtuple
 import os
 import xml.etree.ElementTree as etree
 from simtk.openmm.vec3 import Vec3
+from simtk.openmm.app.internal.singleton import Singleton
 from simtk.unit import nanometers, sqrt, is_quantity
 from copy import deepcopy
 
 # Enumerated values for bond type
 
-class Single(object):
+class Single(Singleton):
     def __repr__(self):
         return 'Single'
 Single = Single()
 
-class Double(object):
+class Double(Singleton):
     def __repr__(self):
         return 'Double'
 Double = Double()
 
-class Triple(object):
+class Triple(Singleton):
     def __repr__(self):
         return 'Triple'
 Triple = Triple()
 
-class Aromatic(object):
+class Aromatic(Singleton):
     def __repr__(self):
         return 'Aromatic'
 Aromatic = Aromatic()
 
-class Amide(object):
+class Amide(Singleton):
     def __repr__(self):
         return 'Amide'
 Amide = Amide()
@@ -437,7 +439,7 @@ class Atom(object):
     def __repr__(self):
         return "<Atom %d (%s) of chain %d residue %d (%s)>" % (self.index, self.name, self.residue.chain.index, self.residue.index, self.residue.name)
 
-class Bond(tuple):
+class Bond(namedtuple('Bond', ['atom1', 'atom2'])):
     """A Bond object represents a bond between two Atoms within a Topology.
 
     This class extends tuple, and may be interpreted as a 2 element tuple of Atom objects.
@@ -445,7 +447,7 @@ class Bond(tuple):
 
     def __new__(cls, atom1, atom2, type=None, order=None):
         """Create a new Bond.  You should call addBond() on the Topology instead of calling this directly."""
-        bond = tuple.__new__(cls, (atom1, atom2))
+        bond = super(Bond, cls).__new__(cls, atom1, atom2)
         bond.type = type
         bond.order = order
         return bond

wrappers/python/tests/TestTopology.py

+import pickle
 import sys
 import unittest
 from simtk.openmm.app import *
@@ -26,6 +27,14 @@ class TestTopology(unittest.TestCase):
         """Test getters for number of atoms, residues, chains."""
         self.check_pdbfile('systems/1T2Y.pdb', 271, 25, 1)
 
+    def test_bondtype_singleton(self):
+        """ Tests that the bond types are really singletons """
+        self.assertIs(Single, pickle.loads(pickle.dumps(Single)))
+        self.assertIs(Double, pickle.loads(pickle.dumps(Double)))
+        self.assertIs(Triple, pickle.loads(pickle.dumps(Triple)))
+        self.assertIs(Aromatic, pickle.loads(pickle.dumps(Aromatic)))
+        self.assertIs(Amide, pickle.loads(pickle.dumps(Amide)))
+
     def test_residue_bonds(self):
         """Test retrieving bonds for a residue produces expected results."""
         # Create a test topology