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# Copyright (c) 2024, 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.
from cclib.bridge import cclib2biopython
from cclib.parser.utils import find_package
import numpy
class BiopythonTest:
"""Tests for the cclib2biopython bridge in cclib."""
def setup_method(self):
if not find_package("Bio"):
raise ImportError("Must install biopython to run this test")
def test_makebiopython(self):
from Bio.PDB.Superimposer import Superimposer
atomnos = numpy.array([1, 8, 1], "i")
a = numpy.array([[-1, 1, 0], [0, 0, 0], [1, 1, 0]], "f")
b = numpy.array([[1.1, 2, 0], [1, 1, 0], [2, 1, 0]], "f")
si = Superimposer()
si.set_atoms(
cclib2biopython.makebiopython(a, atomnos), cclib2biopython.makebiopython(b, atomnos)
)
ref = 0.29337859596
assert abs(si.rms - ref) < 1.0e-6
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