Merge pull request #406 from swails/master

Add support for native CHARMM files

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

@@ -377,5 +377,5 @@ def _format_83(f):
         return '%8.3f' % f
     if -9999999 < f < 99999999:
         return ('%8.3f' % f)[:8]
-    raise ValueError('coordinate "%s" could not be represnted '
+    raise ValueError('coordinate "%s" could not be represented '
                      'in a width-8 field' % f)

wrappers/python/tests/TestCharmmFiles.py

+import unittest
+from validateConstraints import *
+from simtk.openmm.app import *
+from simtk.openmm import *
+from simtk.unit import *
+import simtk.openmm.app.element as elem
+
+class TestCharmmFiles(unittest.TestCase):
+
+    """Test the GromacsTopFile.createSystem() method."""
+ 
+    def setUp(self):
+        """Set up the tests by loading the input files."""
+
+        # alanine tripeptide; no waters
+        self.psf_c = CharmmPsfFile('systems/ala_ala_ala.psf')
+        self.psf_x = CharmmPsfFile('systems/ala_ala_ala.xpsf')
+        self.psf_v = CharmmPsfFile('systems/ala_ala_ala.vpsf')
+        self.params = CharmmParameterSet(
+                            'systems/charmm22.rtf', 'systems/charmm22.par')
+        self.pdb = PDBFile('systems/ala_ala_ala.pdb')
+
+    def test_NonbondedMethod(self):
+        """Test both non-periodic methods for the systems"""
+
+        methodMap = {NoCutoff:NonbondedForce.NoCutoff, 
+                     CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic}
+        for top in (self.psf_c, self.psf_x, self.psf_v):
+            for method in methodMap:
+                system = top.createSystem(self.params, 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 top in (self.psf_c, self.psf_x, self.psf_v):
+            for method in [CutoffNonPeriodic]:
+                system = top.createSystem(self.params, nonbondedMethod=method,
+                                          nonbondedCutoff=2*nanometer, 
+                                          constraints=HBonds)
+                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_RemoveCMMotion(self):
+        """Test both options (True and False) for the removeCMMotion parameter."""
+
+        for b in [True, False]:
+            system = self.psf_c.createSystem(self.params, removeCMMotion=b)
+            self.assertEqual(any(isinstance(f, CMMotionRemover) for f in system.getForces()), b)
+
+    def test_ImplicitSolvent(self):
+        """Test implicit solvent using the implicitSolvent parameter.
+
+        """
+        system = self.psf_v.createSystem(self.params, implicitSolvent=OBC2)
+        self.assertTrue(any(isinstance(f, CustomGBForce) for f in system.getForces()))
+
+    def test_ImplicitSolventParameters(self):
+        """Test that solventDielectric and soluteDielectric are passed correctly.
+
+        """
+        system = self.psf_x.createSystem(self.params, implicitSolvent=GBn,
+                                         solventDielectric=50.0, 
+                                         soluteDielectric = 0.9)
+        found_matching_solvent_dielectric=False
+        found_matching_solute_dielectric=False
+        for force in system.getForces():
+            if isinstance(force, CustomGBForce):
+                for i in range(force.getNumGlobalParameters()):
+                    if force.getGlobalParameterName(i) == 'solventDielectric':
+                        if force.getGlobalParameterDefaultValue(i) == 50.0:
+                            found_matching_solvent_dielectric = True
+                    elif force.getGlobalParameterName(i) == 'soluteDielectric':
+                        if force.getGlobalParameterDefaultValue(i) == 0.9:
+                            found_matching_solute_dielectric = True
+            if isinstance(force, NonbondedForce):
+                self.assertEqual(force.getReactionFieldDielectric(), 1.0)
+        self.assertTrue(found_matching_solvent_dielectric and 
+                        found_matching_solute_dielectric)
+
+    def test_HydrogenMass(self):
+        """Test that altering the mass of hydrogens works correctly."""
+        
+        topology = self.psf_v.topology
+        hydrogenMass = 4*amu
+        system1 = self.psf_v.createSystem(self.params)
+        system2 = self.psf_v.createSystem(self.params, 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)
+
+if __name__ == '__main__':
+    unittest.main()
+

wrappers/python/tests/systems/ala_ala_ala.pdb

+REMARK original generated coordinate pdb file
+ATOM      1  N   ALA X   1       0.024  -0.103  -0.101  1.00  0.00      P1   N
+ATOM      2  HT1 ALA X   1       0.027  -1.132  -0.239  1.00  0.00      P1   H
+ATOM      3  HT2 ALA X   1      -0.805   0.163   0.471  1.00  0.00      P1   H
+ATOM      4  HT3 ALA X   1      -0.059   0.384  -1.019  1.00  0.00      P1   H
+ATOM      5  CA  ALA X   1       1.247   0.375   0.636  1.00  0.00      P1   C
+ATOM      6  HA  ALA X   1       0.814   0.861   1.495  1.00  0.00      P1   H
+ATOM      7  CB  ALA X   1       2.057  -0.772   1.289  1.00  0.00      P1   C
+ATOM      8  HB1 ALA X   1       3.136  -0.752   1.032  1.00  0.00      P1   H
+ATOM      9  HB2 ALA X   1       1.990  -0.641   2.395  1.00  0.00      P1   H
+ATOM     10  HB3 ALA X   1       1.656  -1.782   1.063  1.00  0.00      P1   H
+ATOM     11  C   ALA X   1       1.956   1.579   0.036  1.00  0.00      P1   C
+ATOM     12  O   ALA X   1       1.219   2.525  -0.201  1.00  0.00      P1   O
+ATOM     13  N   ALA X   2       3.289   1.631  -0.202  1.00  0.00      P1   N
+ATOM     14  HN  ALA X   2       3.939   0.868  -0.174  1.00  0.00      P1   H
+ATOM     15  CA  ALA X   2       3.990   2.909  -0.215  1.00  0.00      P1   C
+ATOM     16  HA  ALA X   2       3.742   3.440   0.695  1.00  0.00      P1   H
+ATOM     17  CB  ALA X   2       3.662   3.802  -1.434  1.00  0.00      P1   C
+ATOM     18  HB1 ALA X   2       4.192   4.778  -1.358  1.00  0.00      P1   H
+ATOM     19  HB2 ALA X   2       3.956   3.311  -2.382  1.00  0.00      P1   H
+ATOM     20  HB3 ALA X   2       2.577   4.027  -1.467  1.00  0.00      P1   H
+ATOM     21  C   ALA X   2       5.487   2.654  -0.128  1.00  0.00      P1   C
+ATOM     22  O   ALA X   2       5.889   1.489  -0.137  1.00  0.00      P1   O
+ATOM     23  C   ALA X   3       8.018   5.323   0.136  1.00  0.00      P1   C
+ATOM     24  OT1 ALA X   3       7.032   6.119   0.127  1.00  0.00      P1   O
+ATOM     25  OT2 ALA X   3       9.219   5.692   0.188  1.00  0.00      P1   O
+ATOM     26  N   ALA X   3       6.275   3.733  -0.037  1.00  0.00      P1   N
+ATOM     27  HN  ALA X   3       5.963   4.691  -0.028  1.00  0.00      P1   H
+ATOM     28  CA  ALA X   3       7.707   3.802   0.068  1.00  0.00      P1   C
+ATOM     29  HA  ALA X   3       8.160   3.418  -0.833  1.00  0.00      P1   H
+ATOM     30  CB  ALA X   3       8.233   3.093   1.333  1.00  0.00      P1   C
+ATOM     31  HB1 ALA X   3       9.342   3.149   1.356  1.00  0.00      P1   H
+ATOM     32  HB2 ALA X   3       7.835   3.593   2.240  1.00  0.00      P1   H
+ATOM     33  HB3 ALA X   3       7.923   2.030   1.332  1.00  0.00      P1   H
+END