Added unittest and 1 system tests. Includes 1 bugfix to resolving a circular...

Added unittest and 1 system tests. Includes 1 bugfix to resolving a circular import and 1 bugfix where dms wasn't creating the topology correctly when the water was specified in different chains

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

@@ -20,11 +20,11 @@ from amberinpcrdfile import AmberInpcrdFile
 from dcdfile import DCDFile
 from gromacsgrofile import GromacsGroFile
 from gromacstopfile import GromacsTopFile
-from desmonddmsfile import DesmondDMSFile
 from dcdreporter import DCDReporter
 from modeller import Modeller
 from statedatareporter import StateDataReporter
 from element import Element
+from desmonddmsfile import DesmondDMSFile
 
 # Enumerated values
 

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

@@ -122,10 +122,12 @@ class DesmondDMSFile(object):
         q = '''SELECT id, name, anum, resname, resid, chain, x, y, z
         FROM particle'''
         for (atomId, atomName, atomNumber, resName, resId, chain, x, y, z) in self._conn.execute(q):
+            newChain = False
             if chain != lastChain:
                 lastChain = chain
                 c = top.addChain()
-            if resId != lastResId:
+                newChain = True
+            if resId != lastResId or newChain:
                 lastResId = resId
                 if resName in PDBFile._residueNameReplacements:
                     resName = PDBFile._residueNameReplacements[resName]

wrappers/python/tests/TestDesmondDMSFile.py

+import os
+import unittest
+from simtk.openmm.app import *
+from simtk.openmm import *
+from simtk.unit import *
+import simtk.openmm.app.element as elem
+
+class TestDesmondDMSFile(unittest.TestCase):
+    def setUp(self):
+        """Set up the tests by loading the input files."""
+
+        # alanine dipeptide with explicit water
+        path = os.path.join(os.path.dirname(__file__), 'systems/alanine-dipeptide-explicit-amber99SBILDN-tip3p.dms')
+        self.dms = DesmondDMSFile(path)
+    
+    def test_NonbondedMethod(self):
+        """Test all five options for the nonbondedMethod parameter."""
+
+        methodMap = {NoCutoff:NonbondedForce.NoCutoff, 
+                     CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic, 
+                     CutoffPeriodic:NonbondedForce.CutoffPeriodic, 
+                     Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
+        for method in methodMap:
+            system = self.dms.createSystem(nonbondedMethod=method)
+            forces = system.getForces()
+            self.assertTrue(any(isinstance(f, NonbondedForce) and 
+                                f.getNonbondedMethod()==methodMap[method] 
+                                for f in forces))
+                                
+    def test_Cutoff(self):
+        """Test to make sure the nonbondedCutoff parameter is passed correctly."""
+
+        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
+            system = self.dms.createSystem(nonbondedMethod=method, 
+                                            nonbondedCutoff=2*nanometer)
+            cutoff_distance = 0.0*nanometer
+            cutoff_check = 2.0*nanometer
+            for force in system.getForces():
+                if isinstance(force, NonbondedForce):
+                    cutoff_distance = force.getCutoffDistance()
+            self.assertEqual(cutoff_distance, cutoff_check)
+
+    def test_EwaldErrorTolerance(self):
+        """Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
+
+        for method in [Ewald, PME]:
+            system = self.dms.createSystem(nonbondedMethod=method,
+                                            ewaldErrorTolerance=1e-6)
+            tolerance = 0
+            tolerance_check = 1e-6
+            for force in system.getForces():
+                if isinstance(force, NonbondedForce):
+                    tolerance = force.getEwaldErrorTolerance()
+            self.assertEqual(tolerance, tolerance_check)
+
+    def test_RemoveCMMotion(self):
+        """Test both options (True and False) for the removeCMMotion parameter."""
+
+        for b in [True, False]:
+            system = self.dms.createSystem(removeCMMotion=b)
+            self.assertEqual(any(isinstance(f, CMMotionRemover) for f in system.getForces()), b)
+
+    def test_HydrogenMass(self):
+        """Test that altering the mass of hydrogens works correctly."""
+        
+        topology = self.dms.topology
+        hydrogenMass = 4*amu
+        system1 = self.dms.createSystem()
+        system2 = self.dms.createSystem(hydrogenMass=hydrogenMass)
+        for atom in topology.atoms():
+            if atom.element == elem.hydrogen:
+                self.assertNotEqual(hydrogenMass, system1.getParticleMass(atom.index))
+                self.assertEqual(hydrogenMass, system2.getParticleMass(atom.index))
+        totalMass1 = sum([system1.getParticleMass(i) for i in range(system1.getNumParticles())]).value_in_unit(amu)
+        totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
+        self.assertAlmostEqual(totalMass1, totalMass2)