Merge pull request #26 from choderalab/bugfix-fractional-ion

Bugfix for Swapper.update_fractional_ion

saltswap/swapper.py

@@ -808,9 +808,9 @@ def update_fractional_ion(self, residue_index, initial_force, final_force, fract
         molecule = [atom for atom in self.mutable_residues[residue_index].atoms()]
         atm_index = 0
         for atom in molecule:
-            charge = (1 - fraction) * initial_force[atm_index]["charge"] + fraction * final_force["charge"]
-            sigma = (1 - fraction) * initial_force[atm_index]["sigma"] + fraction * final_force["sigma"]
-            epsilon = (1 - fraction) * initial_force[atm_index]["epsilon"] + fraction * final_force["epsilon"]
+            charge = (1 - fraction) * initial_force[atm_index]["charge"] + fraction * final_force[atm_index]["charge"]
+            sigma = (1 - fraction) * initial_force[atm_index]["sigma"] + fraction * final_force[atm_index]["sigma"]
+            epsilon = (1 - fraction) * initial_force[atm_index]["epsilon"] + fraction * final_force[atm_index]["epsilon"]
             self.forces_to_update.setParticleParameters(atom.index, charge=charge, sigma=sigma, epsilon=epsilon)
             atm_index += 1
 

saltswap/tests/test_simulation.py

@@ -372,3 +372,21 @@ def test_ghmc_mcmc_sampler(self):
                                             delta_chem=0, nprop=1, npert=5)
         sampler.multimove(nmoves=2, mdsteps=1, saltsteps=1)
 
+    def test_update_fractional_ion(self):
+        """
+        Test the functionality of the Swapper.update_fractional_ion method.
+        """
+        integrator,context,swapper = self._create_langevin_system()
+        #Randomly select a water molecule:
+        water_index = np.random.choice(a=np.where(swapper.stateVector == 0)[0], size=1)[0]
+
+        #Completely change this molecule's non-bonded parameters to an anion:
+        swapper.update_fractional_ion(water_index, swapper.water_parameters, swapper.anion_parameters, fraction=1.0)
+
+        #Push change to context:
+        swapper.forces_to_update.updateParametersInContext(context)
+
+        # Update the state vector to keep track of this change: 0 is for water, 1 is for cations, and 2 is for anions.
+        swapper.stateVector[water_index] = 2
+
+

setup.py

@@ -4,7 +4,7 @@
     name='saltswap',
     author='Gregory A. Ross',
     author_email='gregory.ross@choderalab.org',
-    version='0.1dev',
+    version='0.5.2',
     url='https://github.com/choderalab/saltswap',
     packages=['saltswap', 'saltswap.tests'],
     license='MIT',