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test_io.py
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Sat, Sep 14, 04:25

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

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