Translate two molecules dependent upon specific atoms

[mw00847]

Hi, I want to create a vector between two atoms below (O1, H4) so they are on the same plane and the distance between the molecules can edited.

O 0.000000 0.000000 0.000000
H 0.758602 0.000000 0.504284
H 0.260455 0.000000 -0.872893

O 3.000000 0.500000 0.000000
H 3.758602 0.500000 0.504284
H 3.260455 0.500000 -0.872893

Then with the new coordinates z can be extended by an array of r.

Thanks

[t-young31]

Hi @mw00847

I'm not sure what you mean by

a vector between two atoms [...] so they are on the same plane

hopefully the following is a useful start

import autode as ade

dimer = ade.Molecule(atoms=[
    ade.Atom("O", 0.000000, 0.0, 0.000000),
    ade.Atom("H", 0.758602, 0.0, 0.504284),
    ade.Atom("H", 0.260455, 0.0, -0.872893),
    ade.Atom("O", 3.000000, 0.5, 0.000000),
    ade.Atom("H", 3.758602, 0.5, 0.504284),
    ade.Atom("H", 3.260455, 0.5, -0.872893),
])

idxs = (3, 4, 5)  # NOTE: atoms are 0 indexed
vec = dimer.atoms.nvector(0, 3) 
r0 = dimer.atoms.distance(0, 3)
r = 1.0

for i in idxs:
    atom = dimer.atoms[i]
    atom.translate(vec * (r - r0))

dimer.print_xyz_file(filename="dimer_translated.xyz")