1# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- 2# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 3# 4# MDAnalysis --- https://www.mdanalysis.org 5# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors 6# (see the file AUTHORS for the full list of names) 7# 8# Released under the GNU Public Licence, v2 or any higher version 9# 10# Please cite your use of MDAnalysis in published work: 11# 12# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, 13# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. 14# MDAnalysis: A Python package for the rapid analysis of molecular dynamics 15# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th 16# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. 17# 18# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. 19# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. 20# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 21# 22from __future__ import division, absolute_import 23 24 25from six import string_types 26import MDAnalysis 27import pytest 28 29from MDAnalysis.tests.datafiles import ( 30 CRD, 31 LAMMPSdata, 32 DLP_CONFIG_minimal, 33 GRO, 34 TPR, 35 DMS, 36 GMS_SYMOPT, 37 MMTF, 38 mol2_molecule, 39 PRM7, 40 PDB_small, 41 PDBQT_input, 42 PQR, 43 PRM, 44 PSF, 45 PRM12, 46 HoomdXMLdata, 47 XPDB_small, 48 XYZ_mini, 49 DLP_HISTORY_minimal, ) 50 51 52@pytest.mark.parametrize('prop', [ 53 'name', 54 'resname', 55 'type', 56 'segid', 57 'moltype', 58]) 59# topology formats curated from values available in 60# MDAnalysis._PARSERS 61@pytest.mark.parametrize( 'top_format, top', [ 62 ('CONFIG', DLP_CONFIG_minimal), 63 ('CRD', CRD), 64 ('DATA', LAMMPSdata), 65 ('DMS', DMS), 66 ('GMS', GMS_SYMOPT), 67 ('GRO', GRO), 68 ('HISTORY', DLP_HISTORY_minimal), 69 ('MMTF', MMTF), 70 ('MOL2', mol2_molecule), 71 ('PARM7', PRM7), 72 ('PDB', PDB_small), 73 ('PDBQT', PDBQT_input), 74 ('PQR', PQR), 75 ('PRMTOP', PRM), 76 ('PSF', PSF), 77 ('TOP', PRM12), 78 ('TPR', TPR), 79 ('XML', HoomdXMLdata), 80 ('XPDB', XPDB_small), 81 ('XYZ', XYZ_mini) 82]) 83def test_str_types(top_format, top, prop): 84 # Python 2/3 topology string type checking 85 # Related to Issue #1336 86 u = MDAnalysis.Universe(top, format=top_format) 87 if hasattr(u.atoms[0], prop): 88 assert isinstance(getattr(u.atoms[0], prop), string_types) 89