def conf2xyz(conf: Chem.Conformer,
outputname,
atom_list: list,
comment_line=''):
natoms = conf.GetNumAtoms()
s = "{}\n{}\n".format(natoms, comment_line)
for i in range(natoms):
position = conf.GetAtomPosition(i)
symbol = atom_list[i]
s += "{}\t{:.6} {:.6} {:.6}\n".format(symbol, position.x,
position.y, position.z)
with open(outputname, 'w') as f:
f.write(s)
def atom_coords(atom: Chem.Atom, conf: Chem.Conformer) -> List[float]:
"""Returns the x, y, and z coordinates of an atom in a molecule conformer.
"""
p = conf.GetAtomPosition(atom.GetIdx())
fts = [p.x, p.y, p.z]
return fts