# Read a molecule written as XYZ text into atoms: symbol, atomic number,
# position (the parser is lib/xyz.viv).
from xyz import parse_xyz

text = "3\nwater\nO  0.000000  0.000000  0.117300\nH  0.000000  0.757200 -0.469200\nH  0.000000 -0.757200 -0.469200\n"
m = parse_xyz(text)
for i, sym in enumerate(m.symbols) {
    print(f"{sym:<2} Z = {m.z[i]:2d}   {m.xyz[i, 0]:9.6f} {m.xyz[i, 1]:9.6f} {m.xyz[i, 2]:9.6f}")
}
# the O-H distance, in angstroms
d = m.xyz[1, 0:3] - m.xyz[0, 0:3]
print("r(OH) =", fmt(sqrt(sum(d * d)), ".4f"), "A")

# SPDX-License-Identifier: MIT OR Apache-2.0
# SPDX-FileCopyrightText: 2026 The Viv authors