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# -*- coding: utf-8 -*-
#
# Copyright (c) 2023, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
import os
import unittest
import numpy
from cclib.bridge import cclib2openbabel
class OpenbabelTest(unittest.TestCase):
"""Tests for the cclib2openbabel bridge in cclib."""
def setUp(self) -> None:
self.path = os.path.abspath(os.path.dirname(__file__))
def test_makeopenbabel(self) -> None:
try:
from openbabel import openbabel
except:
import openbabel
atomnos = numpy.array([1, 8, 1], "i")
atomcoords = numpy.array([[[-1., 1., 0.], [0., 0., 0.], [1., 1., 0.]]])
obmol = cclib2openbabel.makeopenbabel(atomcoords=atomcoords, atomnos=atomnos)
obconversion = openbabel.OBConversion()
formatok = obconversion.SetOutFormat("inchi")
assert obconversion.WriteString(obmol).strip() == "InChI=1S/H2O/h1H2"
def test_makeopenbabel_and_makecclib(self) -> None:
"""Ensure that makeopenbabel and makecclib are inverse of each other"""
atomnos = numpy.array([1, 8, 1], "i")
atomcoords = numpy.array([[[-1., 1., 0.], [0., 0., 0.], [1., 1., 0.]]])
# makecclib(makeopenbabel(...))
obmol = cclib2openbabel.makeopenbabel(atomcoords=atomcoords, atomnos=atomnos)
data = cclib2openbabel.makecclib(obmol)
numpy.testing.assert_allclose(data.atomcoords, atomcoords)
numpy.testing.assert_allclose(data.atomnos, atomnos)
# makeopenbabel(makecclib(...))
obmol = cclib2openbabel.makeopenbabel(atomcoords=data.atomcoords, atomnos=data.atomnos)
data = cclib2openbabel.makecclib(obmol) # this line is just to make the test easier
numpy.testing.assert_allclose(data.atomcoords, atomcoords)
numpy.testing.assert_allclose(data.atomnos, atomnos)
def test_readfile(self) -> None:
"""Try to load an XYZ file with uracyl through Openbabel"""
data = cclib2openbabel.readfile(f"{self.path}/uracil.xyz", "XYZ")
assert data.natom == 12
if __name__ == "__main__":
unittest.main()
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