updated opls145B; fixed unneccessary rebuilding of compound.atoms in …

…traj.update_compound

mosdef_gomc/tools/parameterize/oplsaa.py

@@ -121,17 +121,12 @@ def opls_145(atom):
 @Element('C')
 @NeighborCount(3)
 @NeighborsExactly('C', 3)
+@NeighborsExactly('145', 3)
 @Whitelist('145B')
 @Blacklist([145])
 def opls_145B(atom):
     """Biphenyl C1 """
-    # Store for checking neighbors outside the first ring.
-    ring_one = benzene(atom)
-    if ring_one:
-        for neighbor in atom.neighbors:
-            if neighbor not in ring_one:
-                if benzene(neighbor):
-                    return True
+    return True
 
 
 @Element('H')

mosdef_gomc/trajectory.py

@@ -84,12 +84,11 @@ def from_compound(cls, compound, show_ports=False, **kwargs):
         return traj
 
     def update_compound(self, compound, frame=0):
-        assert(isinstance(compound, Compound))
+        assert isinstance(compound, Compound)
 
-        for chain in self.topology.chains:
-            for res in chain.residues:
-                for atom in res.atoms:
-                    compound.atoms[atom.index].pos = self.xyz[frame, atom.index]
+        atoms = compound.atoms
+        for atom in self.topology.atoms:
+            atoms[atom.index].pos = self.xyz[frame, atom.index]
 
     def to_compound(self, part=None, frame=0):
         if part is None: