def __init__(self):
super(Initiator, self).__init__()
# Look for data file in same directory as this python module.
mb.load('initiator.pdb', compound=self, 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.
mb.y_axis_transform(self, new_origin=self[0], point_on_y_axis=self[21])
# Add bottom port
self.add(mb.Port(anchor=self[0]), 'down')
# Place the port.
mb.translate(self['down'], self[0].pos + np.array([0.0, -0.07, 0.0]))
# Add top port.
self.add(mb.Port(anchor=self[21]), 'up')
# Place the port.
mb.translate(self['up'], self[21].pos + np.array([0.0, 0.07, 0.0]))
def __init__(self):
super(Initiator, self).__init__()
# Look for data file in same directory as this python module.
mb.load('initiator.pdb', compound=self, 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.
mb.y_axis_transform(self, new_origin=self[0], point_on_y_axis=self[21])
# Add bottom port
self.add(mb.Port(anchor=self[0]), 'down')
# Place the port.
self['down'].translate(np.array([0.0, -0.07, 0.0]))
# Add top port.
self.add(mb.Port(anchor=self[21]), 'up')
# Place the port.
self['up'].translate(np.array([0.0, 0.07, 0.0]))
def __init__(self, alpha=0):
super(MPC, self).__init__()
# Look for data file in same directory as this python module.
mb.load('mpc.pdb', compound=self, 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.
C_top = self[37]
# this can be achieved with the following alternative syntax:
# C_top = self.labels["atom[37]"]
# C_top = self.labels["atom"][37]
C_bottom = self[1]
mb.y_axis_transform(self, new_origin=C_top, point_on_y_axis=C_bottom)
# Add top port.
self.add(mb.Port(anchor=C_top), label='up')
mb.translate(self['up'], C_top.pos - (C_top.pos - C_bottom.pos)*1.50)
# Add bottom port
self.add(mb.Port(anchor=C_bottom), 'down')
mb.rotate_around_y(self['down'], alpha)
mb.translate(self['down'], C_bottom.pos - (C_bottom.pos - C_top.pos)*1.50)
