def _connect_and_reconnect(chf, bond_vector):
first = mb.clone(chf)
second = mb.clone(chf)
first.add(mb.Port(anchor=first[0], orientation=bond_vector,
separation=0.075), label='up')
second.add(mb.Port(anchor=second[0], orientation=-bond_vector,
separation=0.075), label='down')
c2h2f2 = mb.Compound(subcompounds=(first, second))
mb.force_overlap(first, first['up'], second['down'])
fccf_dihedral_init = calc_dihedral(first[2].pos, first[0].pos,
second[0].pos, second[2].pos)
c2h2f2.remove_bond((first[0], second[0]))
mb.force_overlap(first, first['port[0]'], second['port[0]'])
fccf_dihedral_final = calc_dihedral(first[2].pos, first[0].pos,
second[0].pos, second[2].pos)
return fccf_dihedral_init, fccf_dihedral_final
def _connect_and_reconnect(chf, bond_vector):
first = mb.clone(chf)
second = mb.clone(chf)
first.add(mb.Port(anchor=first[0], orientation=bond_vector,
separation=0.075), label='up')
second.add(mb.Port(anchor=second[0], orientation=-bond_vector,
separation=0.075), label='down')
c2h2f2 = mb.Compound(subcompounds=(first, second))
mb.force_overlap(first, first['up'], second['down'])
fccf_dihedral_init = calc_dihedral(first[2].pos, first[0].pos,
second[0].pos, second[2].pos)
c2h2f2.remove_bond((first[0], second[0]))
mb.force_overlap(first, first['port[0]'], second['port[0]'])
fccf_dihedral_final = calc_dihedral(first[2].pos, first[0].pos,
second[0].pos, second[2].pos)
return fccf_dihedral_init, fccf_dihedral_final
