Merge pull request #177 from JoaoRodrigues/reproducible_addatoms

Added a seed parameter to addMissingAtoms to allow reproducible results

pdbfixer/pdbfixer.py

@@ -855,9 +855,15 @@ class PDBFixer(object):
         self.missingAtoms = missingAtoms
         self.missingAtoms = missingAtoms
         self.missingTerminals = missingTerminals
         self.missingTerminals = missingTerminals
 
 
-    def addMissingAtoms(self):
+    def addMissingAtoms(self, seed=None):
         """Add all missing heavy atoms, as specified by the missingAtoms, missingTerminals, and missingResidues fields.
         """Add all missing heavy atoms, as specified by the missingAtoms, missingTerminals, and missingResidues fields.
 
 
+        Parameters
+        ----------
+        seed : int
+            Integer to set the random seed number of the integrator used in the minimization of the
+            coordinates of the newly-added atoms.
+
         Notes
         Notes
         -----
         -----
         You must already have called findMissingAtoms() to have identified atoms to be added.
         You must already have called findMissingAtoms() to have identified atoms to be added.
@@ -924,6 +930,8 @@ class PDBFixer(object):
             # Do an energy minimization.
             # Do an energy minimization.
 
 
             integrator = mm.LangevinIntegrator(300*unit.kelvin, 10/unit.picosecond, 5*unit.femtosecond)
             integrator = mm.LangevinIntegrator(300*unit.kelvin, 10/unit.picosecond, 5*unit.femtosecond)
+            if seed is not None:
+                integrator.setRandomNumberSeed(seed)
             context = mm.Context(system, integrator)
             context = mm.Context(system, integrator)
             context.setPositions(newPositions)
             context.setPositions(newPositions)
             mm.LocalEnergyMinimizer.minimize(context)
             mm.LocalEnergyMinimizer.minimize(context)