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]))