TestPickle.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
import simtk.openmm.app.forcefield as forcefield
import copy
import pickle

class TestPickle(unittest.TestCase):
    """Pickling / deepcopy of OpenMM state and integrator objects."""

    def setUp(self):
        """Set up the tests by loading the input pdb files and force field
        xml files.

        """
        # alanine dipeptide with explicit water
        self.pdb1 = PDBFile('systems/alanine-dipeptide-explicit.pdb')
        self.forcefield1 = ForceField('amber99sb.xml', 'tip3p.xml')
        self.topology1 = self.pdb1.topology
        self.topology1.setUnitCellDimensions(Vec3(2, 2, 2))

        # alalnine dipeptide with implicit water
        self.pdb2 = PDBFile('systems/alanine-dipeptide-implicit.pdb')
        self.forcefield2 = ForceField('amber99sb.xml', 'amber99_obc.xml')


    def test_deepcopy(self):
        """Test that serialization/deserialization works (via deepcopy)."""

        system = self.forcefield1.createSystem(self.pdb1.topology)
        integrator = VerletIntegrator(2*femtosecond)
        context = Context(system, integrator)
        context.setPositions(self.pdb1.positions)
        state = context.getState(getPositions=True, getForces=True, getEnergy=True)

        system2 = copy.deepcopy(system)
        #integrator2 = copy.deepcopy(integrator)
        state2 = copy.deepcopy(state)
        
        str_state = pickle.dumps(state)
        #str_integrator = pickle.dumps(integrator)
        
        state3 = pickle.loads(str_state)
        context.setState(state3)


        del context, integrator

if __name__ == '__main__':
    unittest.main()