Merge branch 'new_plugin' of https://github.com/justinGilmer/mbuild into new_plugin

Author: mattwthompson

mbuild/__init__.py

@@ -7,5 +7,5 @@
 from mbuild.port import Port
 from mbuild.recipes import *
 from mbuild.lattice import Lattice
-
+from mbuild.recipes import recipes
 from mbuild.version import version

mbuild/examples/alkane/alkane.py

@@ -25,7 +25,7 @@ def __init__(self, n=3, cap_front=True, cap_end=True):
             n += 1
         if not cap_end:
             n += 1
-        chain = Polymer(CH2(), n=n-2, port_labels=('up', 'down'))
+        chain = mb.recipes.Polymer(CH2(), n=n-2, port_labels=('up', 'down'))
         self.add(chain, 'chain')
 
         if cap_front:
@@ -44,4 +44,4 @@ def __init__(self, n=3, cap_front=True, cap_end=True):
             # Hoist port label to Alkane level.
             self.add(chain['down'], 'down', containment=False)
 
-# -- ==alkane== --
+# -- ==alkane== --

mbuild/examples/alkane_monolayer/alkane_monolayer.py

@@ -10,7 +10,7 @@
 from mbuild.examples.alkane_monolayer.alkylsilane import AlkylSilane
 
 
-class AlkaneMonolayer(Monolayer):
+class AlkaneMonolayer(mb.recipes.Monolayer):
     """An akylsilane monolayer on beta-cristobalite. """
 
     def __init__(self, pattern, tile_x=1, tile_y=1, chain_length=10):
@@ -35,4 +35,4 @@ def __init__(self, pattern, tile_x=1, tile_y=1, chain_length=10):
                                               pattern=pattern, tile_x=tile_x,
                                               tile_y=tile_y)
 
-# -- ==alkane_monolayer== --
+# -- ==alkane_monolayer== --

mbuild/examples/pmpc/brush.py

@@ -17,7 +17,7 @@ def __init__(self, chain_length=4, alpha=pi/4):
         # Add parts
         self.add(Silane(), label='silane')
         self.add(Initiator(), label='initiator')
-        self.add(Polymer(MPC(alpha=alpha), n=chain_length,
+        self.add(mb.recipes.Polymer(MPC(alpha=alpha), n=chain_length,
                             port_labels=('up', 'down')), label='pmpc')
         self.add(CH3(), label='methyl')
 

mbuild/examples/pmpc/pmpc_brush_layer.py

@@ -6,13 +6,14 @@
 
 from numpy import pi
 
+import mbuild as mb
 from mbuild.lib.atoms import H
 from mbuild.lib.surfaces import Betacristobalite
 from mbuild.lib.recipes import Monolayer
 from mbuild.examples.pmpc.brush import Brush
 
 
-class PMPCLayer(Monolayer):
+class PMPCLayer(mb.recipes.Monolayer):
     """Create a layer of grafted pMPC brushes on a beta-cristobalite surface."""
     def __init__(self, pattern, tile_x=1, tile_y=1, chain_length=4, alpha=pi / 4):
         surface = Betacristobalite()
@@ -22,4 +23,4 @@ def __init__(self, pattern, tile_x=1, tile_y=1, chain_length=4, alpha=pi / 4):
                                         pattern=pattern, tile_x=tile_x,
                                         tile_y=tile_y)
 
-# -- ==pmpc_brush_layer== --
+# -- ==pmpc_brush_layer== --

mbuild/lib/recipes/monolayer.py

@@ -38,15 +38,15 @@ def __init__(self, surface, chains, fractions=None, backfill=None, pattern=None,
         super(Monolayer, self).__init__()
 
         # Replicate the surface.
-        tiled_compound = TiledCompound(surface, n_tiles=(tile_x, tile_y, 1))
+        tiled_compound = mb.recipes.TiledCompound(surface, n_tiles=(tile_x, tile_y, 1))
         self.add(tiled_compound, label='tiled_surface')
 
         if pattern is None:  # Fill the surface.
             pattern = mb.Random2DPattern(len(tiled_compound.referenced_ports()))
 
         if isinstance(chains, mb.Compound):
             chains = [chains]
-        
+
         if fractions:
             fractions = list(fractions)
             if len(chains) != len(fractions):

mbuild/lib/recipes/silica_interface.py

@@ -61,13 +61,13 @@ def _cleave_interface(self, bulk_silica, tile_x, tile_y, thickness):
         """
         O_buffer = self._O_buffer
         tile_z = int(math.ceil((thickness + 2*O_buffer) / bulk_silica.periodicity[2]))
-        bulk = TiledCompound(bulk_silica, n_tiles=(tile_x, tile_y, tile_z))
+        bulk = mb.recipes.TiledCompound(bulk_silica, n_tiles=(tile_x, tile_y, tile_z))
 
         interface = mb.Compound(periodicity=(bulk.periodicity[0],
                                              bulk.periodicity[1],
                                              0.0))
         for i, particle in enumerate(bulk.particles()):
-            if ((particle.name == 'Si' and O_buffer < particle.pos[2] < (thickness + O_buffer)) or 
+            if ((particle.name == 'Si' and O_buffer < particle.pos[2] < (thickness + O_buffer)) or
                     (particle.name == 'O' and particle.pos[2] < (thickness + 2*O_buffer))):
                 interface_particle = mb.Compound(name=particle.name, pos=particle.pos)
                 interface.add(interface_particle, particle.name + "_{}".format(i))
@@ -154,5 +154,5 @@ def _adjust_stoichiometry(self):
 
 if __name__ == "__main__":
     from mbuild.lib.bulk_materials import AmorphousSilica
-    silica_interface = SilicaInterface(bulk_silica=AmorphousSilica(), thickness=1.2)
+    silica_interface = mb.recipes.SilicaInterface(bulk_silica=AmorphousSilica(), thickness=1.2)
     silica_interface.save('silica_interface.mol2', show_ports=True)

mbuild/lib/surfaces/betacristobalite.py

@@ -32,7 +32,7 @@ def __init__(self):
         for particle in self.particles():
             if particle.name.startswith('O') and particle.pos[2] > 1.0:
                 count += 1
-                port = mb.Port(anchor=particle, orientation=[0, 0, 1], 
+                port = mb.Port(anchor=particle, orientation=[0, 0, 1],
                                separation=0.1)
                 self.add(port, 'port_{}'.format(count))
                 particle.name = 'O'  # Strip numbers required in .mol2 files.
@@ -41,5 +41,5 @@ def __init__(self):
 
 if __name__ == "__main__":
     single = Betacristobalite()
-    multiple = TiledCompound(single, n_tiles=(2, 1, 1), name="tiled")
+    multiple = mb.recipes.TiledCompound(single, n_tiles=(2, 1, 1), name="tiled")
     multiple.save('betacristobalite.mol2')

mbuild/tests/test_monolayer.py

@@ -12,12 +12,12 @@ def test_monolayer(self, ch2):
         m = 8
         pattern = mb.Grid2DPattern(n, m)
 
-        chain = Polymer(ch2, n=10)
-        monolayer = Monolayer(
-                              surface=Betacristobalite(),
-                              chains=chain,
-                              backfill=H(),
-                              pattern=pattern)
+        chain = mb.recipes.Polymer(ch2, n=10)
+        monolayer = mb.recipes.Monolayer(
+                                            surface=Betacristobalite(),
+                                            chains=chain,
+                                            backfill=H(),
+                                            pattern=pattern)
 
         assert monolayer.n_particles == 1900 + n * m * (10*3) + (100 - n*m)
         assert monolayer.n_bonds == 2400 + n * m * (10 * 2 + 9 + 1) + (100 - n * m)
@@ -27,13 +27,13 @@ def test_pattern_kwargs(self, ch2):
         m = 8
         pattern = mb.Grid2DPattern(n, m)
 
-        chain = Polymer(ch2, n=10)
-        monolayer = Monolayer(surface=Betacristobalite(),
-                              chains=H(),
-                              guest_port_name='up',
-                              backfill=chain,
-                              backfill_port_name='down',
-                              pattern=pattern)
+        chain = mb.recipes.Polymer(ch2, n=10)
+        monolayer = mb.recipes.Monolayer(surface=Betacristobalite(),
+                                            chains=H(),
+                                            guest_port_name='up',
+                                            backfill=chain,
+                                            backfill_port_name='down',
+                                            pattern=pattern)
 
         chains = 100 - (n*m)
 
@@ -46,10 +46,10 @@ def test_mixed_monolayer(self, ch2):
         pattern = mb.Grid2DPattern(n, m)
         fractions = [0.75,0.25]
 
-        chain_a = Polymer(ch2, n=5)
-        chain_b = Polymer(ch2, n=15)
-        monolayer = Monolayer(surface=Betacristobalite(),
-                              chains=[chain_a, chain_b],
+        chain_a = mb.recipes.Polymer(ch2, n=5)
+        chain_b = mb.recipes.Polymer(ch2, n=15)
+        monolayer = mb.recipes.Monolayer(surface=Betacristobalite(),
+                                 chains=[chain_a, chain_b],
                                  fractions=fractions,
                                  backfill=H(),
                                  pattern=pattern)

mbuild/tests/test_plugins.py

@@ -0,0 +1,16 @@
+import pytest
+
+from mbuild.tests.base_test import BaseTest
+
+
+class TestPlugins(BaseTest):
+    def test_basic_import(self):
+        import mbuild.recipes
+
+    @pytest.mark.parametrize(
+        'recipe_name',
+        ['Monolayer', 'Polymer', 'SilicaInterface', 'TiledCompound'],
+    )
+    def test_recipes_contents(self, recipe_name):
+        import mbuild.recipes
+        recipe_name in dir(mbuild.recipes)