fixed renaming in examples

mbuild/examples/pmpc/brush.py

@@ -10,10 +10,10 @@
 from initiator import Initiator
 
 
-class PMPC(Compound):
+class Brush(Compound):
     """ """
     def __init__(self, chain_length=4, alpha=pi/4):
-        super(PMPC, self).__init__(self)
+        super(Brush, self).__init__(self)
 
         # Add parts
         self.add(Silane(), 'silane')
@@ -30,5 +30,5 @@ def __init__(self, chain_length=4, alpha=pi/4):
         self.add(self.silane.down, label='down', containment=False)
 
 if __name__ == "__main__":
-    pmpc = PMPC(chain_length=1, alpha=pi/4)
+    pmpc = Brush(chain_length=1, alpha=pi/4)
     pmpc.visualize(show_ports=True)

mbuild/examples/pmpc/initiator.py

@@ -10,7 +10,7 @@ def __init__(self):
         super(Initiator, self).__init__(self)
 
         # Look for data file in same directory as this python module.
-        self.append_from_file('initiator.pdb')
+        self.append_from_file('initiator.pdb', relative_to_module=self.__module__)
 
         # Transform the coordinate system such that the two carbon atoms
         # that are part of the backbone are on the y axis, C_1 at the origin.

mbuild/examples/pmpc/mpc.py

@@ -9,7 +9,7 @@ def __init__(self, alpha=0):
         super(MPC, self).__init__(self)
 
         # Look for data file in same directory as this python module.
-        self.append_from_file('mpc.pdb')
+        self.append_from_file('mpc.pdb', relative_to_module=self.__module__)
 
         # Transform the coordinate system of mpc such that the two carbon atoms
         # that are part of the backbone are on the y axis, c_backbone at the origin.

mbuild/examples/pmpc/pmpc_brush_layer.py

@@ -7,9 +7,10 @@
 from mbuild.tools.parameterize.atomtyper import find_atomtypes
 from mbuild.tools.tiled_compound import TiledCompound
 
-from mbuild.components.surfaces.betacristobalite import Betacristobalite
+from brush import Brush
 from mbuild.components.atoms.H import H
-from pmpc import PMPC
+from mbuild.components.surfaces.betacristobalite import Betacristobalite
+from mpc import MPC
 
 
 class PMPCLayer(Compound):
@@ -21,19 +22,20 @@ def __init__(self, mask, tile_x=1, tile_y=1, chain_length=4, alpha=pi/4):
         tc = TiledCompound(surface, tile_x, tile_y, 1, kind="tiled_surface")
         self.add(tc, 'tiled_surface')
 
-        pmpc = PMPC(chain_length=chain_length, alpha=alpha)
+        brush = Brush(chain_length=chain_length, alpha=alpha)
         hydrogen = H()
 
-        apply_mask(self.tiled_surface, pmpc, mask, backfill=hydrogen)
+        apply_mask(self.tiled_surface, brush, mask, backfill=hydrogen)
 
+def main():
+    mask = random_mask_2d(1)
+    return PMPCLayer(mask=mask, chain_length=3, alpha=pi/4, tile_x=1, tile_y=1)
 
 if __name__ == "__main__":
-    mask = random_mask_2d(1)
-    pmpc_layer = PMPCLayer(mask=mask, chain_length=3, alpha=pi/4, tile_x=1, tile_y=1)
+    pmpc_layer = main()
     pmpc_layer.visualize(show_ports=True)
-    # find_atomtypes(pmpc_layer)
-    #
-    # pmpc_layer = pmpc_layer.to_trajectory(chain_types=[Betacristobalite, PMPC],
-    #                                       residue_types=[MPC])
-    # pmpc_layer.topology.find_forcefield_terms()
-    # pmpc_layer.save(filename='brush_layer.top')
+    find_atomtypes(pmpc_layer)
+    pmpc_layer = pmpc_layer.to_trajectory(chain_types=[Betacristobalite, Brush],
+                                          residue_types=[MPC])
+    pmpc_layer.topology.find_forcefield_terms()
+    pmpc_layer.save(filename='brush_layer.top')

mbuild/examples/reload/reload.py

@@ -2,7 +2,7 @@
 
 from numpy import pi
 
-from mbuild.examples.pmpc_brush_layer.brush import Brush
+from mbuild.examples.pmpc.brush import Brush
 from mbuild.coordinate_transform import rotate_around_z
 
 

mbuild/tests/test_examples.py

@@ -38,8 +38,8 @@ def test_methane(self):
         import mbuild.examples.methane.methane as example
         example.main()
 
-    def test_pmpc_brush_layer(self):
-        import mbuild.examples.pmpc_brush_layer.pmpc_brush_layer as example
+    def test_pmpc(self):
+        import mbuild.examples.pmpc.pmpc_brush_layer as example
         example.main()
 
     def test_reload(self):