def make_new_h(atom, x, y, z):
"""Add a new hydrogen to an atom at the specified position.
Args:
atom: atom to protonate
x: x position of hydrogen
y: y position of hydrogen
z: z position of hydrogen
Returns:
new hydrogen atom
"""
new_h = Atom()
new_h.set_property(numb=None,
name='H{0:s}'.format(atom.name[1:]),
res_name=atom.res_name,
chain_id=atom.chain_id,
res_num=atom.res_num,
x=x,
y=y,
z=z,
occ=None,
beta=None)
new_h.element = 'H'
new_h.bonded_atoms = [atom]
new_h.charge = 0
new_h.steric_number = 0
new_h.number_of_lone_pairs = 0
new_h.number_of_protons_to_add = 0
new_h.num_pi_elec_2_3_bonds = 0
atom.bonded_atoms.append(new_h)
atom.conformation_container.add_atom(new_h)
return new_h
