97 lines
3.1 KiB
Python
97 lines
3.1 KiB
Python
"""Deals with testing the io system.
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Copyright (C) 2013, Joshua More and Michele Ceriotti
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http.//www.gnu.org/licenses/>.
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Note that this will only run if you have Python version 2.5 or later.
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Otherwise, replace all the with statements with f = filestream.
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"""
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import sys
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sys.path.append("../")
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sys.path.append("../../")
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import filecmp
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import os, sys
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import numpy as np
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from numpy.testing import assert_equal
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from common import local
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from ipi.engine.cell import Cell
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from ipi.utils.io import io_xyz
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from ipi.utils.io import io_pdb
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pos = np.array([i for i in range(3*3)])
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def test_read_xyz():
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"""Tests that xyz files are read correctly."""
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with open(local("test.pos_0.xyz"), "r") as f:
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atoms = io_xyz.read_xyz(f)
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assert(len(atoms) == 3)
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assert_equal(pos, atoms.q)
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def test_iter_xyz():
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"""Tests that xyz files with multiple frames are read correctly."""
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with open(local("test.pos_0.xyz"), "r") as f:
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for num, atoms in enumerate(io_xyz.iter_xyz(f)):
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assert(len(atoms) == 3)
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assert_equal(pos*(num+1), atoms.q)
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def test_read_pdb():
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"""Tests that pdb files are read correctly."""
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with open(local("test.pos_0.pdb"), "r") as f:
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atoms, cell = io_pdb.read_pdb(f)
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assert(len(atoms) == 3)
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assert_equal(pos, atoms.q)
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# TODO: test cell
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def test_iter_pdb():
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"""Tests that pdb files with multiple frames are read correctly."""
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with open(local("test.pos_0.pdb"), "r") as f:
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for num, (atoms, cell) in enumerate(io_pdb.iter_pdb(f)):
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assert(len(atoms) == 3)
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assert_equal(pos*(num+1), atoms.q)
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def test_print_pdb():
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"""Tests that pdb files are printed correctly."""
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with open(local("test.pos_0.pdb"), "r") as f:
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with open(local("test.pos_1.xyz"), "w") as out:
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for num, (atoms, cell) in enumerate(io_pdb.iter_pdb(f)):
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assert(len(atoms) == 3)
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assert_equal(pos*(num+1), atoms.q)
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io_xyz.print_xyz(atoms, Cell(h=np.identity(3, float)), filedesc=out)
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assert(filecmp.cmp(local("test.pos_0.xyz"), local("test.pos_1.xyz")))
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os.unlink(local("test.pos_1.xyz"))
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def test_print_xyz():
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"""Tests that xyz files are printed correctly."""
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with open(local("test.pos_0.pdb"), "r") as f:
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with open(local("test.pos_1.pdb"), "w") as out:
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for num, (atoms, cell) in enumerate(io_pdb.iter_pdb(f)):
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assert(len(atoms) == 3)
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assert_equal(pos*(num+1), atoms.q)
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io_pdb.print_pdb(atoms, Cell(h=np.identity(3, float)), filedesc=out)
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assert(filecmp.cmp(local("test.pos_0.pdb"), local("test.pos_1.pdb")))
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os.unlink(local("test.pos_1.pdb"))
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