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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
from MDAnalysisTests.datafiles import PDBQT_input, PDBQT_querypdb
from MDAnalysis.lib.NeighborSearch import AtomNeighborSearch
from numpy.testing import (
assert_equal,
)
import pytest
from MDAnalysisTests import make_Universe
class TestPDBQT(object):
@pytest.fixture()
def universe(self):
"""Set up the standard AdK system in implicit solvent."""
return mda.Universe(PDBQT_input)
def test_segid(self, universe):
sel = universe.select_atoms("segid A")
assert_equal(sel.n_atoms, 909, "failed to select segment A")
sel = universe.select_atoms("segid B")
assert_equal(sel.n_atoms, 896, "failed to select segment B")
def test_chainID(self, universe):
sel = universe.select_atoms("chainID A")
assert_equal(sel.n_atoms, 909, "failed to chainID segment A")
sel = universe.select_atoms("chainID B")
assert_equal(sel.n_atoms, 896, "failed to chainID segment B")
def test_protein(self, universe):
sel = universe.select_atoms("protein")
assert_equal(sel.n_atoms, 1805, "failed to select protein")
assert_equal(
sel.atoms.ix,
universe.atoms.ix,
"selected protein is not the same as auto-generated protein segment A+B",
)
def test_backbone(self, universe):
sel = universe.select_atoms("backbone")
assert_equal(sel.n_atoms, 796)
def test_neighborhood(self, universe):
"""test KDTree-based distance search around query atoms
Creates a KDTree of the protein and uses the coordinates of
the atoms in the query pdb to create a list of protein
residues within 4.0A of the query atoms.
"""
query_universe = mda.Universe(PDBQT_querypdb) # PDB file
protein = universe.select_atoms("protein")
ns_protein = AtomNeighborSearch(protein)
query_atoms = query_universe.atoms
residue_neighbors = ns_protein.search(query_atoms, 4.0)
assert_equal(len(residue_neighbors), 80)
def test_n_frames(self, universe):
assert_equal(
universe.trajectory.n_frames, 1, "wrong number of frames in pdb"
)
def test_time(self, universe):
assert_equal(universe.trajectory.time, 0.0, "wrong time of the frame")
def test_frame(self, universe):
assert_equal(
universe.trajectory.frame,
0,
"wrong frame number (0-based, should be 0 for single frame readers)",
)
class TestPDBQTWriter(object):
reqd_attributes = [
"names",
"types",
"resids",
"resnames",
"radii",
"charges",
]
@pytest.fixture()
def outfile(self, tmpdir):
return str(tmpdir) + "out.pdbqt"
@pytest.mark.parametrize(
"filename", ["test.pdbqt", "test.pdbqt.bz2", "test.pdbqt.gz"]
)
def test_roundtrip_writing_coords(self, filename, tmpdir):
with tmpdir.as_cwd():
u = mda.Universe(PDBQT_input)
u.atoms.write(filename)
u2 = mda.Universe(filename)
assert_equal(
u2.atoms.positions,
u.atoms.positions,
"Round trip does not preserve coordinates",
)
def test_roundtrip_formatting(self, outfile):
# Compare formatting of first line
u = mda.Universe(PDBQT_input)
u.atoms.write(outfile)
with open(PDBQT_input, "r") as inf:
l_ref = inf.readline().strip()
with open(outfile, "r") as inf:
inf.readline() # header
inf.readline() # cryst
l_new = inf.readline().strip()
assert l_ref == l_new
@staticmethod
def assert_writing_warns(u, outfile):
with pytest.warns(UserWarning):
u.atoms.write(outfile)
def test_write_no_charges(self, outfile):
attrs = self.reqd_attributes
attrs.remove("charges")
u = make_Universe(attrs, trajectory=True)
self.assert_writing_warns(u, outfile)
u2 = mda.Universe(outfile)
assert all(u2.atoms.charges == 0.0)
def test_write_no_chainids_with_segids(self, outfile):
attrs = self.reqd_attributes
attrs.append("segids")
u = make_Universe(attrs, trajectory=True)
u.atoms.write(outfile)
u2 = mda.Universe(outfile)
# Should have used last letter of segid as chainid
assert all(u2.atoms[:25].segids == "A")
assert all(u2.atoms[25:50].segids == "B")
def test_get_writer(self, outfile):
u = mda.Universe(PDBQT_input)
w = u.trajectory.Writer(outfile)
assert isinstance(w, mda.coordinates.PDBQT.PDBQTWriter)
w.close()
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