Python parseDatafileの例

コード例 #1

    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)

コード例 #2

ファイル: test_editing.py プロジェクト: anindita85/ProDy

from numpy.testing import assert_array_equal

from numpy import concatenate

from prody.dynamics import calcGNM, calcANM
from prody.dynamics import extendModel, extendMode, extendVector

from prody.tests.test_datafiles import parseDatafile

from prody import _PY3K

if not _PY3K:
    range = xrange

ATOMS = parseDatafile('1ubi').protein.copy()
ANM, NODES = calcANM(ATOMS)
GNM = calcGNM(ATOMS)[0]

EXT1D = concatenate([[i] * len(res)
                     for i, res in enumerate(ATOMS.iterResidues())])

EXT3D = concatenate([list(range(i*3, (i+1)*3)) * len(res) 
                     for i, res in enumerate(ATOMS.iterResidues())])


class TestExtending(unittest.TestCase):
    
    def testModel3d(self):

        ext = extendModel(ANM, NODES, ATOMS)[0]

コード例 #3

from prody.tests import unittest
from prody.tests.test_datafiles import parseDatafile, pathDatafile

from prody.trajectory import DCDFile
from prody.measure import calcDistance, buildDistMatrix
from prody.measure import calcAngle, calcPsi, calcPhi
from prody.measure import calcCenter
from prody.measure import calcMSF
from prody import LOGGER
LOGGER.verbosity = None

ATOL = 1e-5
RTOL = 0

UBI = parseDatafile('1ubi')
UBI_NTER = UBI['A', 1]
UBI_GLY10 = UBI['A', 10]
UBI_CTER = UBI['A', 76]


class TestDihedrals(unittest.TestCase):
    """Test functions that calculate dihedral angles."""
    def testCalcPsi(self):

        assert_approx_equal(14.386, calcPsi(UBI_GLY10), 2)

    def testCalcPhi(self):

        assert_approx_equal(87.723, calcPhi(UBI_GLY10), 2)

コード例 #4

    def testMSF(self):

        dcd = DCDFile(pathDatafile('dcd'))
        ens = parseDatafile('dcd')
        ens.superpose()
        assert_array_almost_equal(calcMSF(dcd), calcMSF(ens), 4)

コード例 #5

ファイル: __init__.py プロジェクト: npabon/ProDy

# along with this program.  If not, see <http://www.gnu.org/licenses/>

__author__ = 'Ahmet Bakan'
__copyright__ = 'Copyright (C) 2010-2012 Ahmet Bakan'

from numpy import array, invert, ones, tile

from prody import Ensemble, PDBEnsemble, LOGGER
from prody.tests.test_datafiles import parseDatafile, DATA_FILES

LOGGER.verbosity = 'none'

ATOL = 1e-5
RTOL = 0

ATOMS = parseDatafile('multi_model_truncated', subset='ca')
ALLATOMS = parseDatafile('multi_model_truncated')
DCD = parseDatafile('dcd')
COORDS = ATOMS.getCoords()
COORDSETS = ATOMS.getCoordsets()
ENSEMBLE = Ensemble(ATOMS)
CONF = ENSEMBLE[0]
DATA = DATA_FILES['multi_model_truncated']
ENSEMBLE_RMSD = DATA['rmsd_ca']
ENSEMBLE_SUPERPOSE = DATA['rmsd_ca_aligned']

ENSEMBLEW = Ensemble(ATOMS)
ENSEMBLEW.setWeights(ones(len(ATOMS), dtype=float))
CONFW = ENSEMBLEW[0]

PDBENSEMBLE = PDBEnsemble('PDBEnsemble')

コード例 #6

ファイル: test_editing.py プロジェクト: npabon/ProDy

from numpy.testing import assert_array_equal

from numpy import concatenate

from prody.dynamics import calcGNM, calcANM
from prody.dynamics import extendModel, extendMode, extendVector

from prody.tests import unittest
from prody.tests.test_datafiles import parseDatafile

from prody import _PY3K

if not _PY3K:
    range = xrange

ATOMS = parseDatafile('1ubi').protein.copy()
ANM, NODES = calcANM(ATOMS)
GNM = calcGNM(ATOMS)[0]

EXT1D = concatenate([[i] * len(res)
                     for i, res in enumerate(ATOMS.iterResidues())])

EXT3D = concatenate([
    list(range(i * 3, (i + 1) * 3)) * len(res)
    for i, res in enumerate(ATOMS.iterResidues())
])


class TestExtending(unittest.TestCase):
    def testModel3d(self):

コード例 #7

ファイル: test_measure.py プロジェクト: njekin/ProDy

    def testMSF(self):

        dcd = DCDFile(pathDatafile('dcd'))
        ens = parseDatafile('dcd')
        ens.superpose()
        assert_array_almost_equal(calcMSF(dcd), calcMSF(ens), 4)

コード例 #8

ファイル: test_measure.py プロジェクト: njekin/ProDy

    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)

コード例 #9

ファイル: test_transform.py プロジェクト: njekin/ProDy

"""This module contains unit tests for :mod:`prody.measure.transform` module.
"""

__author__ = 'Ahmet Bakan'
__copyright__ = 'Copyright (C) 2010-2012 Ahmet Bakan'

from numpy import zeros, ones, eye, all
from numpy.testing import assert_equal

from prody.tests import unittest
from prody.tests.test_datafiles import parseDatafile

from prody.measure import moveAtoms, wrapAtoms

UBI = parseDatafile('1ubi')


class TestMoveAtoms(unittest.TestCase):

    def testToArgument(self):

        atoms = UBI.ca

        coords = UBI.getCoords()
        center = atoms._getCoords().mean(0)
        moveAtoms(atoms, to=zeros(3), ag=True)
        assert_equal(UBI._getCoords(), coords - center)

    def testByArgument(self):

コード例 #10

ファイル: test_measure.py プロジェクト: njekin/ProDy

from prody.tests import unittest
from prody.tests.test_datafiles import parseDatafile, pathDatafile

from prody.trajectory import DCDFile
from prody.measure import calcDistance, buildDistMatrix
from prody.measure import calcAngle, calcPsi, calcPhi
from prody.measure import calcCenter
from prody.measure import calcMSF
from prody import LOGGER
LOGGER.verbosity = None

ATOL = 1e-5
RTOL = 0


UBI = parseDatafile('1ubi')
UBI_NTER = UBI['A', 1]
UBI_GLY10 = UBI['A', 10]
UBI_CTER = UBI['A', 76]

class TestDihedrals(unittest.TestCase):

    """Test functions that calculate dihedral angles."""

    def testCalcPsi(self):

        assert_approx_equal(14.386, calcPsi(UBI_GLY10), 2)

    def testCalcPhi(self):

        assert_approx_equal(87.723, calcPhi(UBI_GLY10), 2)

コード例 #11

ファイル: test_contacts.py プロジェクト: npabon/ProDy

# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>

__author__ = 'Ahmet Bakan'
__copyright__ = 'Copyright (C) 2010-2012 Ahmet Bakan'

from numpy import array, concatenate, unique
from numpy.testing import assert_array_equal, assert_equal

from prody.tests import unittest
from prody.tests.test_datafiles import parseDatafile, pathDatafile

from prody.measure import Contacts, findNeighbors, iterNeighbors
from prody.measure import buildDistMatrix, calcDistance

UBI = parseDatafile('1ubi')
UBI_XYZ = UBI._getCoords()
UBI_MIN = UBI_XYZ.min(0)
UBI_MAX = UBI_XYZ.max(0)
UBI_UC = UBI_MAX - UBI_MIN
N0P = [-1, 0, 1]
UBI_EDGES = UBI_MIN + UBI_UC * array([(i, j, k) for i in N0P for j in N0P
                                      for k in N0P])
UBI_RADIUS = 20

UBI_CONTACTS = Contacts(UBI_XYZ)
UBI_CONTACTS_PBC = Contacts(UBI_XYZ, UBI_UC)


class TestContacts(unittest.TestCase):
    """Test functions that calculate dihedral angles."""

コード例 #12

"""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:
            frame.superpose()

コード例 #13

ファイル: test_frame.py プロジェクト: njekin/ProDy

"""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:

コード例 #14

ファイル: __init__.py プロジェクト: anindita85/ProDy

# along with this program.  If not, see <http://www.gnu.org/licenses/>

__author__ = 'Ahmet Bakan'
__copyright__ = 'Copyright (C) 2010-2012 Ahmet Bakan'

from numpy import array, invert, ones, tile 

from prody import Ensemble, PDBEnsemble, LOGGER
from prody.tests.test_datafiles import parseDatafile, DATA_FILES

LOGGER.verbosity = 'none'

ATOL = 1e-5
RTOL = 0

ATOMS = parseDatafile('multi_model_truncated', subset='ca')
ALLATOMS = parseDatafile('multi_model_truncated')
DCD = parseDatafile('dcd')
COORDS = ATOMS.getCoords()
COORDSETS = ATOMS.getCoordsets()
ENSEMBLE = Ensemble(ATOMS)
CONF = ENSEMBLE[0]
DATA = DATA_FILES['multi_model_truncated']
ENSEMBLE_RMSD = DATA['rmsd_ca']
ENSEMBLE_SUPERPOSE = DATA['rmsd_ca_aligned']

ENSEMBLEW = Ensemble(ATOMS)
ENSEMBLEW.setWeights(ones(len(ATOMS), dtype=float))
CONFW = ENSEMBLEW[0]
        
PDBENSEMBLE = PDBEnsemble('PDBEnsemble')

コード例 #15

ファイル: test_contacts.py プロジェクト: njekin/ProDy

# along with this program.  If not, see <http://www.gnu.org/licenses/>

__author__ = "Ahmet Bakan"
__copyright__ = "Copyright (C) 2010-2012 Ahmet Bakan"

from numpy import array, concatenate, unique
from numpy.testing import assert_array_equal, assert_equal

from prody.tests import unittest
from prody.tests.test_datafiles import parseDatafile, pathDatafile

from prody.measure import Contacts, findNeighbors, iterNeighbors
from prody.measure import buildDistMatrix, calcDistance


UBI = parseDatafile("1ubi")
UBI_XYZ = UBI._getCoords()
UBI_MIN = UBI_XYZ.min(0)
UBI_MAX = UBI_XYZ.max(0)
UBI_UC = UBI_MAX - UBI_MIN
N0P = [-1, 0, 1]
UBI_EDGES = UBI_MIN + UBI_UC * array([(i, j, k) for i in N0P for j in N0P for k in N0P])
UBI_RADIUS = 20

UBI_CONTACTS = Contacts(UBI_XYZ)
UBI_CONTACTS_PBC = Contacts(UBI_XYZ, UBI_UC)


class TestContacts(unittest.TestCase):

    """Test functions that calculate dihedral angles."""