def tearDown(self):
for dcd in [pathDatafile('multi_model_truncated'),
pathDatafile('dcd')]:
prefix = splitext(split(dcd)[1])[0]
for suffix in self.suffixes:
fn = join(TEMPDIR, prefix + suffix)
if isfile(fn): remove(fn)
def tearDown(self):
for dcd in [
pathDatafile('multi_model_truncated'),
pathDatafile('dcd')
]:
prefix = splitext(split(dcd)[1])[0]
for suffix in self.suffixes:
fn = join(TEMPDIR, prefix + suffix)
if isfile(fn): remove(fn)
def setUp(self):
self.output = join(TEMPDIR, 'test_prody_catdcd.dcd')
self.dcdpath = pathDatafile('dcd')
self.pdbpath = pathDatafile('multi_model_truncated')
self.dcd = DCDFile(self.dcdpath)
self.ag = parsePDB(self.pdbpath, model=1)
self.command = 'catdcd -o ' + self.output
self.tearDown()
def setUp(self):
self.output = join(TEMPDIR, 'test_prody_catdcd.dcd')
self.dcdpath = pathDatafile('dcd')
self.pdbpath = pathDatafile('multi_model_truncated')
self.dcd = DCDFile(self.dcdpath)
self.ag = parsePDB(self.pdbpath, model=1)
self.command = 'catdcd -o ' + self.output
self.tearDown()
def testPCACommandPDB(self):
dcd = pathDatafile('multi_model_truncated')
command = self.command + dcd
prefix = splitext(split(dcd)[1])[0]
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
for suffix in self.suffixes:
fn = join(TEMPDIR, prefix + suffix)
self.assertTrue(isfile(fn), msg=fn + ' not found')
def testPCACommandPDB(self):
dcd = pathDatafile('multi_model_truncated')
command = self.command + dcd
prefix = splitext(split(dcd)[1])[0]
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
for suffix in self.suffixes:
fn = join(TEMPDIR, prefix + suffix)
self.assertTrue(isfile(fn), msg=fn+' not found')
def setUp(self):
self.command = ('pca --pdb {pdb} '
'-e -r -o {outdir} -v -z -t all -j '
'-f %8g -d , -x .dat '
'-R -Q -J 1,2 '
'-F png -D 120 -W 5 -H 4 ').format(outdir=TEMPDIR,
pdb=pathDatafile('multi_model_truncated'))
self.suffixes = [
'_pca_cc.png',
'_pca.pca.npz',
'_pca_covariance.dat',
'_pca_cross-correlations.dat',
'_pca_proj_1_2.png',
'_pca_evalues.dat',
'_pca_proj.dat',
'_pca_evectors.dat',
'_pca_sf.png',
'_pca_extended_all.nmd',
'_pca.nmd',
]
self.tearDown()
def setUp(self):
self.command = ('pca --pdb {pdb} '
'-e -r -o {outdir} -v -z -t all -j '
'-f %8g -d , -x .dat '
'-R -Q -J 1,2 '
'-F png -D 120 -W 5 -H 4 ').format(
outdir=TEMPDIR,
pdb=pathDatafile('multi_model_truncated'))
self.suffixes = [
'_pca_cc.png',
'_pca.pca.npz',
'_pca_covariance.dat',
'_pca_cross-correlations.dat',
'_pca_proj_1_2.png',
'_pca_evalues.dat',
'_pca_proj.dat',
'_pca_evectors.dat',
'_pca_sf.png',
'_pca_extended_all.nmd',
'_pca.nmd',
]
self.tearDown()
def testMSF(self):
dcd = DCDFile(pathDatafile('dcd'))
ens = parseDatafile('dcd')
ens.superpose()
assert_array_almost_equal(calcMSF(dcd), calcMSF(ens), 4)
def testMSFfloat(self):
dcd = DCDFile(pathDatafile('dcd'), astype=float)
ens = parseDatafile('dcd', astype=float)
ens.superpose()
assert_array_almost_equal(calcMSF(dcd), calcMSF(ens), 10)
def testMSF(self):
dcd = DCDFile(pathDatafile('dcd'))
ens = parseDatafile('dcd')
ens.superpose()
assert_array_almost_equal(calcMSF(dcd), calcMSF(ens), 4)
# 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/>
"""This module contains unit tests for fragmenting function and methods."""
__author__ = 'Ahmet Bakan'
__copyright__ = 'Copyright (C) 2010-2012 Ahmet Bakan'
from prody.tests import TestCase
from prody import *
from prody.tests.test_datafiles import pathDatafile
WHOLE = fetchPDBLigand(pathDatafile('sti'))['ideal']
WHOLE_ALL = WHOLE.all
WHOLE_COPY = WHOLE.copy()
WHOLE_NOH = WHOLE.noh
WHOLE_NOH_COPY = WHOLE_NOH.copy()
SPLIT = WHOLE.select('not name N13 N21 C46 C22')
SPLIT_COPY = SPLIT.copy()
SPLIT_NOH = WHOLE.select('noh and not name N13 N21 C46 C22')
SPLIT_NOH_COPY = SPLIT_NOH.copy()
class TestFragment(TestCase):
def testWhole(self):
self.assertEqual(WHOLE.numFragments(), 1)
# 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/>
"""This module contains unit tests for fragmenting function and methods."""
__author__ = 'Ahmet Bakan'
__copyright__ = 'Copyright (C) 2010-2012 Ahmet Bakan'
from unittest import TestCase
from prody import *
from prody.tests.test_datafiles import pathDatafile
WHOLE = fetchPDBLigand(pathDatafile('sti'))['ideal']
WHOLE_ALL = WHOLE.all
WHOLE_COPY = WHOLE.copy()
WHOLE_NOH = WHOLE.noh
WHOLE_NOH_COPY = WHOLE_NOH.copy()
SPLIT = WHOLE.select('not name N13 N21 C46 C22')
SPLIT_COPY = SPLIT.copy()
SPLIT_NOH = WHOLE.select('noh and not name N13 N21 C46 C22')
SPLIT_NOH_COPY = SPLIT_NOH.copy()
class TestFragment(TestCase):
def testWhole(self):
self.assertEqual(WHOLE.numFragments(), 1)
"""This module contains unit tests for :mod:`.frame` module."""
__author__ = 'Ahmet Bakan'
__copyright__ = 'Copyright (C) 2010-2012 Ahmet Bakan'
from code import interact
from prody.tests import TestCase
from numpy import array
from numpy.testing import assert_allclose
from prody.trajectory import Trajectory
from prody.tests.test_datafiles import parseDatafile, pathDatafile
DCD = Trajectory(pathDatafile('dcd'))
PDB = parseDatafile('multi_model_truncated', model=1)
RMSD_ALL = array([0.0, 1.380, 1.745])
RMSD_CARBON = array([0.0, 0.964, 1.148])
class TestSuperpose(TestCase):
def setUp(self):
DCD.setCoords(PDB.getCoords())
DCD.reset()
def testAll(self):
rmsd = []
def testMSFfloat(self):
dcd = DCDFile(pathDatafile('dcd'), astype=float)
ens = parseDatafile('dcd', astype=float)
ens.superpose()
assert_array_almost_equal(calcMSF(dcd), calcMSF(ens), 10)
# along with this program. If not, see <http://www.gnu.org/licenses/>
"""This module contains unit tests for :mod:`.frame` module."""
__author__ = 'Ahmet Bakan'
__copyright__ = 'Copyright (C) 2010-2012 Ahmet Bakan'
from code import interact
from prody.tests import TestCase
from numpy import array
from numpy.testing import assert_allclose
from prody.trajectory import Trajectory
from prody.tests.test_datafiles import parseDatafile, pathDatafile
DCD = Trajectory(pathDatafile('dcd'))
PDB = parseDatafile('multi_model_truncated', model=1)
RMSD_ALL = array([0.0, 1.380, 1.745])
RMSD_CARBON = array([0.0, 0.964, 1.148])
class TestSuperpose(TestCase):
def setUp(self):
DCD.setCoords(PDB.getCoords())
DCD.reset()
def testAll(self):
rmsd = []
for frame in DCD:
# along with this program. If not, see <http://www.gnu.org/licenses/>
"""This module contains unit tests for fragmenting function and methods."""
__author__ = 'Ahmet Bakan'
__copyright__ = 'Copyright (C) 2010-2012 Ahmet Bakan'
from prody.tests import TestCase
from numpy import arange
from numpy.random import shuffle
from prody import *
from prody.tests.test_datafiles import pathDatafile
AG = prody.parsePDB(pathDatafile('pdb3mht.pdb'))
SHUFFLED = arange(len(AG))
SHUFFLED = AtomMap(AG, SHUFFLED)
class TestShuffled(TestCase):
def testCA(self):
self.assertEqual(AG.ca.numAtoms(), SHUFFLED.ca.numAtoms())
def testProtein(self):
self.assertEqual(AG.protein.numAtoms(), SHUFFLED.protein.numAtoms())