def __init__(self):
super(Silane, self).__init__()
mb.load('silane.pdb',
compound=self,
relative_to_module=self.__module__)
mb.x_axis_transform(self, new_origin=self[0], point_on_x_axis=self[1])
self.add(mb.Port(anchor=self[0], orientation=[0, 0, -1], shift=0.07),
name='down')
def __init__(self, ):
super(Silane, self).__init__()
mb.load('silane.pdb', compound=self, relative_to_module=self.__module__)
# Transform the coordinate system such that the silicon atom is at the
# origin and the oxygen atoms are on the x axis.
mb.x_axis_transform(self, new_origin=self[0], point_on_x_axis=self[1])
# Add bottom port.
self.add(mb.Port(anchor=self[0]), 'down')
self['down'].translate(np.array([0, -.07, 0]))
# Add top port.
self.add(mb.Port(anchor=self[0]), 'up')
self['up'].translate(np.array([0, .07, 0]))
def __init__(self, ):
super(Silane, self).__init__()
mb.load('silane.pdb', compound=self, relative_to_module=self.__module__)
# Transform the coordinate system such that the silicon atom is at the
# origin and the oxygen atoms are on the x axis.
mb.x_axis_transform(self, new_origin=self[0], point_on_x_axis=self[1])
# Add bottom port.
self.add(mb.Port(anchor=self[0]), 'down')
mb.translate(self['down'], np.array([0, -.07, 0]))
# Add top port.
self.add(mb.Port(anchor=self[0]), 'up')
mb.translate(self['up'], np.array([0, .07, 0]))
def __init__(self, ):
super(Silane, self).__init__()
mb.load(
"silane.pdb",
compound=self,
relative_to_module=self.__module__,
infer_hierarchy=False,
backend="parmed",
skip_bonds=True,
)
# Transform the coordinate system such that the silicon atom is at the
# origin and the oxygen atoms are on the x axis.
mb.x_axis_transform(self, new_origin=self[0], point_on_x_axis=self[1])
# Add bottom port.
self.add(mb.Port(anchor=self[0]), "down")
self["down"].translate(np.array([0, -0.07, 0]))
# Add top port.
self.add(mb.Port(anchor=self[0]), "up")
self["up"].translate(np.array([0, 0.07, 0]))