def main():
"""A quick test for updating a Compound and traversing its hierarchy. """
# Create a compound and write it to file.
brush1 = Brush()
brush1.save("brush1.pdb")
# Create another compound, rotate it and write it to file.
brush2 = Brush()
mb.rotate_around_z(brush2, pi/2)
brush2.save("brush2.pdb")
# Load brush2.pdb into brush1, modifying the atom positions of brush1.
brush1.update_coordinates("brush2.pdb")
brush1.save("modified_brush1.pdb")
# Access the internals of the updated brush1.
print(brush1['pmpc'])
for mpc in brush1['pmpc']['monomer']:
print(mpc)
def test_reload(self):
from mbuild.examples.pmpc.brush import Brush
from numpy import pi
# Create a compound and write it to file.
brush1 = Brush()
brush1.save("brush1.pdb")
# Create another compound, rotate it and write it to file.
brush2 = Brush()
mb.rotate_around_z(brush2, pi/2)
brush2.save("brush2.pdb")
# Load brush2.pdb into brush1, modifying the atom positions of brush1.
brush1.update_coordinates("brush2.pdb")
brush1.save("modified_brush1.pdb")
assert brush1['pmpc'].n_particles == 164
assert brush1['pmpc'].n_bonds == 163
assert len(brush1['pmpc']['monomer']) == 4
assert brush1['pmpc']['monomer'][0].n_particles == 41
assert brush1['pmpc']['monomer'][0].n_bonds == 40
def __init__(self,
pattern,
tile_x=1,
tile_y=1,
chain_length=4,
alpha=pi / 4):
surface = Betacristobalite()
brush = Brush(chain_length=chain_length, alpha=alpha)
hydrogen = H()
super(PMPCLayer, self).__init__(surface,
brush,
backfill=hydrogen,
pattern=pattern,
tile_x=tile_x,
tile_y=tile_y)
def test_reload(self):
from mbuild.examples.pmpc.brush import Brush
from numpy import pi
# Create a compound and write it to file.
brush1 = Brush()
brush1.save("brush1.pdb")
# Create another compound, rotate it and write it to file.
brush2 = Brush()
mb.rotate(brush2, pi / 2, [0, 0, 1])
brush2.save("brush2.pdb")
# Load brush2.pdb into brush1, modifying the atom positions of brush1.
brush1.update_coordinates("brush2.pdb")
brush1.save("modified_brush1.pdb")
assert brush1['pmpc'].n_particles == 164
assert brush1['pmpc'].n_bonds == 163
assert len(brush1['pmpc']['monomer']) == 4
assert brush1['pmpc']['monomer'][0].n_particles == 41
assert brush1['pmpc']['monomer'][0].n_bonds == 40