Enable group site restraints

mrdna/arbdmodel/__init__.py

@@ -74,7 +74,8 @@ class Parent():
         self.exclusions = []
         self.bond_angles = []
         self.product_potentials = []
-
+        self.group_sites = []
+        
         self.rigid = False
 
         ## TODO: self.cacheInvalid = True # What will be in the cache?
@@ -172,7 +173,7 @@ class Parent():
 
     def get_restraints(self):
         ret = []
-        for c in self.children:
+        for c in self.children +  self.group_sites:
             ret.extend( c.get_restraints() )
         return ret
 
@@ -761,7 +762,8 @@ class ArbdModel(PdbModel):
                 raise NotImplementedError
             self.particles = particles
             self.idx = None
-
+            self.restraints = []
+            
         def get_center(self):
             c = np.array((0,0,0))
             for p in self.particles:
@@ -769,6 +771,12 @@ class ArbdModel(PdbModel):
             c = c / len(self.particles)
             return c
 
+        def add_restraint(self, restraint):
+            self.restraints.append( restraint )
+        def get_restraints(self):
+            return [(self,r) for r in self.restraints]
+
+
     def __init__(self, children, origin=None, dimensions=(1000,1000,1000), temperature=291, timestep=50e-6,
                  particle_integrator = 'Brown',
                  cutoff=50, decomp_period=1000, pairlist_distance=None, nonbonded_resolution=0.1,