# -*- 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 GNU Public Licence, v2 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. # # 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 # from __future__ import absolute_import 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_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' def test_roundtrip_writing_coords(self, outfile): u = mda.Universe(PDBQT_input) u.atoms.write(outfile) u2 = mda.Universe(outfile) 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()