renamed binding_site_idxs to receptor_idxs in UnbindingBC

Binding site indices was a misleading name. Receptor is better. This
drove an error in the examples where the whole protein idxs should
have been used but the binding site idxs were being used

Author: salotz

examples/Lennard_Jones_Pair/we.py

@@ -192,7 +192,7 @@ def image_distance(self, image_a, image_b):
                   initial_state=init_state,
                   topology=mdtraj_topology,
                   ligand_idxs=np.array(test_sys.ligand_indices),
-                  binding_site_idxs=np.array(test_sys.receptor_indices))
+                  receptor_idxs=np.array(test_sys.receptor_indices))
 
 ## Reporters
 

examples/seh_tppu_unbinding/we.py

@@ -330,7 +330,7 @@ def main(n_runs, n_cycles, steps, n_walkers, n_workers=1, debug_prints=False, se
                       initial_state=omm_state,
                       topology=crystal_traj.topology,
                       ligand_idxs=lig_idxs,
-                      binding_site_idxs=bs_idxs)
+                      receptor_idxs=prot_idxs)
 
 
     ## make the reporters

examples/seh_tppu_unbinding/we_timed.py

@@ -330,7 +330,7 @@ def main(runtime, steps, n_walkers, n_workers=1, debug_prints=False, seed=None):
                       initial_state=omm_state,
                       topology=crystal_traj.topology,
                       ligand_idxs=lig_idxs,
-                      binding_site_idxs=bs_idxs)
+                      receptor_idxs=prot_idxs)
 
 
     ## make the reporters

wepy/boundary_conditions/unbinding.py

@@ -37,23 +37,23 @@ def __init__(self, initial_state=None,
                  cutoff_distance=1.0,
                  topology=None,
                  ligand_idxs=None,
-                 binding_site_idxs=None):
+                 receptor_idxs=None):
 
         super().__init__()
 
         # test input
         assert initial_state is not None, "Must give an initial state"
         assert topology is not None, "Must give a reference topology"
         assert ligand_idxs is not None
-        assert binding_site_idxs is not None
+        assert receptor_idxs is not None
         assert type(cutoff_distance) is float
 
         self.initial_state = initial_state
         self.cutoff_distance = cutoff_distance
         self.topology = topology
 
         self.ligand_idxs = ligand_idxs
-        self.binding_site_idxs = binding_site_idxs
+        self.receptor_idxs = receptor_idxs
 
     def _calc_angle(self, v1, v2):
         return np.degrees(np.arccos(np.dot(v1, v2)/(la.norm(v1) * la.norm(v2))))
@@ -83,7 +83,7 @@ def _calc_min_distance(self, walker):
         # and get hte minimum distance
         min_distance = np.min(mdj.compute_distances(walker_traj,
                                                     it.product(self.ligand_idxs,
-                                                               self.binding_site_idxs)))
+                                                               self.receptor_idxs)))
         return min_distance
 
     def check_boundaries(self, walker):