Merge remote-tracking branch 'upstream/master' into vagrant

wrappers/python/simtk/openmm/app/internal/charmm/_charmmfile.py

@@ -47,7 +47,6 @@ class CharmmFile(object):
     """
 
     def __init__(self, fname, mode='r'):
-        self.closed = False
         if mode not in ('r', 'w'):
             raise ValueError('Cannot open CharmmFile with mode "%s"' % mode)
         if mode == 'r':
@@ -58,6 +57,7 @@ class CharmmFile(object):
             self._handle = open(fname, mode)
         except IOError, e:
             raise CharmmFileError(str(e))
+        self.closed = False
         self.line_number = 0
 
     def write(self, *args, **kwargs):

wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py

@@ -42,6 +42,32 @@ TINY = 1e-8
 
 # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
+def _tracking(fcn):
+    """ Decorator to indicate the list has changed """
+    def new_fcn(self, *args):
+        self.changed = True
+        return fcn(self, *args)
+    return new_fcn
+
+class TrackedList(list):
+    """
+    This creates a list type that allows you to see if anything has changed
+    """
+    def __init__(self, arg=[]):
+        self.changed = False
+        list.__init__(self, arg)
+
+    __delitem__ = _tracking(list.__delitem__)
+    append = _tracking(list.append)
+    extend = _tracking(list.extend)
+    __setitem__ = _tracking(list.__setitem__)
+
+# Python 3 does not have __delslice__, but make sure we override it for Python 2
+if hasattr(TrackedList, '__delslice__'):
+    TrackedList.__delslice__ = _tracking(TrackedList.__delslice__)
+
+# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
 class AtomType(object):
     """
     Atom types can either be compared by indexes or names. Can be assigned with
@@ -61,6 +87,9 @@ class AtomType(object):
         - _member_number (int, private) : The order in which this atom type
                 was 'added' this is used to make sure that atom types added
                 last have priority in assignment in the generated hash tables
+        - nbfix (dict) : Dictionary that maps nbfix terms with other atom types.
+                         Dict entries are (rmin, epsilon) -- precombined values
+                         for that particular atom pair
     Example:
     >>> at = AtomType('HA', 1, 1.008, 1)
     >>> at.name, at.number
@@ -93,6 +122,9 @@ class AtomType(object):
         self.atomic_number = atomic_number
         # We have no LJ parameters as of yet
         self.epsilon = self.rmin = self.epsilon_14 = self.rmin_14 = None
+        # Store each NBFIX term as a dict with the atom type string matching to
+        # a 2-element tuple that is rmin, epsilon
+        self.nbfix = dict()
 
     def __eq__(self, other):
         """
@@ -123,6 +155,12 @@ class AtomType(object):
         """ The integer representation of an AtomType is its index """
         return self.number
 
+    def add_nbfix(self, typename, rmin, epsilon, rmin14, epsilon14):
+        """ Adds a new NBFIX exclusion for this atom """
+        if rmin14 is None: rmin14 = rmin
+        if epsilon14 is None: epsilon14 = epsilon
+        self.nbfix[typename] = (rmin, epsilon, rmin14, epsilon14)
+
     def __str__(self):
         return self.name
 
@@ -311,7 +349,7 @@ class Atom(object):
 
 # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
-class AtomList(list):
+class AtomList(TrackedList):
     """ A list of Atom instances.  """
 
     def unmark(self):
@@ -424,7 +462,7 @@ class ResidueList(list):
         elif (self._last_residue != (resname, resnum) or
               system != self._last_residue.system):
             if (self._last_residue.idx == resnum and
-                system == self._last_residue.system):
+                self._last_residue.system == system):
                 lresname = self._last_residue.resname
                 warnings.warn('Residue %d split into separate residues %s '
                               'and %s' % (resnum, lresname, resname),
@@ -1047,28 +1085,6 @@ class _CmapGrid(object):
 
 # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
-def _tracking(fcn):
-    """ Decorator to indicate the list has changed """
-    def new_fcn(self, *args):
-        self.changed = True
-        return fcn(self, *args)
-    return new_fcn
-
-class TrackedList(list):
-    """
-    This creates a list type that allows you to see if anything has changed
-    """
-    def __init__(self, arg=[]):
-        self.changed = False
-        list.__init__(self, arg)
-
-    __delitem__ = _tracking(list.__delitem__)
-    append = _tracking(list.append)
-    extend = _tracking(list.extend)
-    __setitem__ = _tracking(list.__setitem__)
-
-# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-
 if __name__ == '__main__':
     import doctest
     doctest.testmod()

wrappers/python/tests/TestCharmmFiles.py

@@ -100,6 +100,33 @@ class TestCharmmFiles(unittest.TestCase):
         totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
         self.assertAlmostEqual(totalMass1, totalMass2)
 
+    def test_NBFIX(self):
+        """Tests CHARMM systems with NBFIX Lennard-Jones modifications"""
+        import warnings
+        warnings.filterwarnings('ignore', category=CharmmPSFWarning)
+        psf = CharmmPsfFile('systems/ala3_solv.psf')
+        crd = CharmmCrdFile('systems/ala3_solv.crd')
+        params = CharmmParameterSet('systems/par_all36_prot.prm',
+                                    'systems/toppar_water_ions.str')
+        # Box dimensions (found from bounding box)
+        psf.setBox(32.7119500*angstroms, 32.9959600*angstroms, 33.0071500*angstroms)
+
+        # Turn off charges so we only test the Lennard-Jones energies
+        for a in psf.atom_list:
+            a.charge = 0.0
+
+        # Now compute the full energy
+        plat = Platform.getPlatformByName('Reference')
+        system = psf.createSystem(params, nonbondedMethod=PME,
+                                  nonbondedCutoff=8*angstroms)
+
+        con = Context(system, VerletIntegrator(2*femtoseconds), plat)
+        con.setPositions(crd.positions)
+
+        state = con.getState(getEnergy=True, enforcePeriodicBox=True)
+        ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
+        self.assertAlmostEqual(ene, 15490.0033559, delta=0.05)
+
 if __name__ == '__main__':
     unittest.main()