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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
import pytest
import MDAnalysis as mda
from MDAnalysisTests.util import import_not_available
requires_rdkit = pytest.mark.skipif(
import_not_available("rdkit"), reason="requires RDKit"
)
@requires_rdkit
class TestConvertTo:
@pytest.fixture(scope="class")
def u(self):
return mda.Universe.from_smiles("CCO")
def test_convert_to_case_insensitive(self, u):
mol = u.atoms.convert_to("rdkit")
def test_convert_to_lib_as_method(self, u):
mol = u.atoms.convert_to.rdkit()
def test_convert_to_kwargs(self, u):
mol = u.atoms.convert_to("RDKIT", NoImplicit=False)
assert mol.GetAtomWithIdx(0).GetNoImplicit() is False
def test_convert_to_lib_method_kwargs(self, u):
mol = u.atoms.convert_to.rdkit(NoImplicit=False)
assert mol.GetAtomWithIdx(0).GetNoImplicit() is False
class TestAccessor:
def test_access_from_class(self):
assert (
mda.core.AtomGroup.convert_to
is mda.core.accessors.ConverterWrapper
)
class TestConverterWrapper:
def test_raises_valueerror(self):
u = mda.Universe.empty(1)
with pytest.raises(
ValueError, match="No 'mdanalysis' converter found"
):
u.atoms.convert_to("mdanalysis")
@requires_rdkit
def test_single_instance(self):
u1 = mda.Universe.from_smiles("C")
u2 = mda.Universe.from_smiles("CC")
assert (
u1.atoms.convert_to.rdkit.__wrapped__
is u2.atoms.convert_to.rdkit.__wrapped__
)
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