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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 MDAnalysis as mda
import pytest
from pytest import approx
from MDAnalysis.analysis.nucleicacids import (
NucPairDist,
WatsonCrickDist,
MajorPairDist,
MinorPairDist,
)
from MDAnalysisTests.datafiles import RNA_PSF, RNA_PDB
from MDAnalysis.core.groups import ResidueGroup
@pytest.fixture(scope="module")
def u():
return mda.Universe(RNA_PSF, RNA_PDB)
@pytest.fixture(scope="module")
def strand(unv=u):
unv = mda.Universe(RNA_PSF, RNA_PDB)
return unv.select_atoms("segid RNAA")
def test_empty_ag_error(strand):
strand1 = ResidueGroup([strand.residues[0]])
strand2 = ResidueGroup([strand.residues[1]])
with pytest.raises(ValueError, match="returns an empty AtomGroup"):
NucPairDist.select_strand_atoms(strand1, strand2, "UNK1", "O2")
@pytest.fixture(scope="module")
def wc_rna(strand, client_NucPairDist):
strand1 = ResidueGroup([strand.residues[0], strand.residues[21]])
strand2 = ResidueGroup([strand.residues[1], strand.residues[22]])
WC = WatsonCrickDist(strand1, strand2)
WC.run(**client_NucPairDist)
return WC
def test_wc_dist_shape(wc_rna):
assert wc_rna.results.distances.shape == (1, 2)
def test_wc_dist_results_keys(wc_rna):
assert "distances" in wc_rna.results
def test_wc_dist(wc_rna):
assert wc_rna.results.distances[0, 0] == approx(4.3874702, rel=1e-3)
assert wc_rna.results.distances[0, 1] == approx(4.1716404, rel=1e-3)
def test_wc_dist_invalid_residue_types(u):
strand = u.select_atoms("resid 1-10")
strand1 = ResidueGroup([strand.residues[0], strand.residues[21]])
strand2 = ResidueGroup([strand.residues[2], strand.residues[22]])
with pytest.raises(ValueError, match="is not a valid nucleic acid"):
WatsonCrickDist(strand1, strand2)
def test_selection_length_mismatch(strand):
sel1 = strand.residues[1:10]
sel2 = strand.residues[1:9]
with pytest.raises(ValueError, match="Selections must be same length"):
NucPairDist(sel1, sel2)
def test_wc_dist_deprecation_warning(strand):
strand1 = [strand.residues[0], strand.residues[21]]
strand2 = [strand.residues[1], strand.residues[22]]
with pytest.deprecated_call():
WatsonCrickDist(strand1, strand2)
def test_wc_dist_strand_verification(strand):
strand1 = [strand.residues[0], strand[0]]
strand2 = [strand.residues[1], strand.residues[22]]
with pytest.raises(TypeError, match="contains non-Residue elements"):
WatsonCrickDist(strand1, strand2)
@pytest.mark.parametrize("key", [0, 1, 2, "parsnips", "time", -1])
def test_wc_dis_results_keyerrs(wc_rna, key):
with pytest.raises(KeyError, match=f"{key}"):
wc_rna.results[key]
def test_minor_dist(strand, client_NucPairDist):
strand1 = ResidueGroup([strand.residues[2], strand.residues[19]])
strand2 = ResidueGroup([strand.residues[16], strand.residues[4]])
MI = MinorPairDist(strand1, strand2)
MI.run(**client_NucPairDist)
assert MI.results.distances[0, 0] == approx(15.06506, rel=1e-3)
assert MI.results.distances[0, 1] == approx(3.219116, rel=1e-3)
def test_major_dist(strand, client_NucPairDist):
strand1 = ResidueGroup([strand.residues[1], strand.residues[4]])
strand2 = ResidueGroup([strand.residues[11], strand.residues[8]])
MA = MajorPairDist(strand1, strand2)
MA.run(**client_NucPairDist)
assert MA.results.distances[0, 0] == approx(26.884272, rel=1e-3)
assert MA.results.distances[0, 1] == approx(13.578535, rel=1e-3)
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