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src/e/e/eebprogramming-HEAD/lec10review/6structure.py   eebprogramming(Download)
#!/usr/bin/env python
# taken from http://pycogent.sourceforge.net/
from cogent.parse.pdb import PDBParser
from cogent.format.pdb import PDBWriter
import tempfile, os
pdb_file = open('data/4TSV.pdb')
new_structure = PDBParser(pdb_file)

src/c/o/cogent-1.5.3/tests/test_parse/test_pdb.py   cogent(Download)
#!/usr/bin/env python
"""Unit tests for the pdb parser.
"""
from cogent.util.unit_test import TestCase, main
from cogent.parse.pdb import dict2pdb, dict2ter, pdb2dict, get_symmetry, \
    def test_PDBParser(self):
        """tests the UI parsing function.
        """
        fh = open('data/2E12.pdb')
        structure = PDBParser(fh, 'JUNK')

src/p/y/pycogent-HEAD/tests/test_parse/test_pdb.py   pycogent(Download)
#!/usr/bin/env python
"""Unit tests for the pdb parser.
"""
from cogent.util.unit_test import TestCase, main
from cogent.parse.pdb import dict2pdb, dict2ter, pdb2dict, get_symmetry, \
    def test_PDBParser(self):
        """tests the UI parsing function.
        """
        fh = open('data/2E12.pdb')
        structure = PDBParser(fh, 'JUNK')

src/c/o/cogent-1.5.3/tests/test_struct/test_asa.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.app.util import ApplicationNotFoundError
from cogent.parse.pdb import PDBParser
from cogent.struct.selection import einput
from cogent.maths.stats.test import correlation
    def test_asa_xtra(self):
        """test internal asa"""
        self.input_file = os.path.join('data', '2E12.pdb')
        self.input_structure = PDBParser(open(self.input_file))
        self.assertRaises(ValueError, asa.asa_xtra, self.input_structure, mode='a')
    def test_asa_xtra_stride(self):
        """test asa via stride"""
        self.input_file = os.path.join('data', '2E12.pdb')
        self.input_structure = PDBParser(open(self.input_file))
        try:
    def test_compare(self):
        """compares internal asa to stride."""
        self.input_file = os.path.join('data', '2E12.pdb')
        self.input_structure = PDBParser(open(self.input_file))
        try:
    def test_uc(self):
        """compares asa within unit cell."""
        self.input_file = os.path.join('data', '2E12.pdb')
        self.input_structure = PDBParser(open(self.input_file))
        asa.asa_xtra(self.input_structure, symmetry_mode='uc', xtra_key='ASA_UC')

src/p/y/pycogent-HEAD/tests/test_struct/test_asa.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.app.util import ApplicationNotFoundError
from cogent.parse.pdb import PDBParser
from cogent.struct.selection import einput
from cogent.maths.stats.test import correlation
    def test_asa_xtra(self):
        """test internal asa"""
        self.input_file = os.path.join('data', '2E12.pdb')
        self.input_structure = PDBParser(open(self.input_file))
        self.assertRaises(ValueError, asa.asa_xtra, self.input_structure, mode='a')
    def test_asa_xtra_stride(self):
        """test asa via stride"""
        self.input_file = os.path.join('data', '2E12.pdb')
        self.input_structure = PDBParser(open(self.input_file))
        try:
    def test_compare(self):
        """compares internal asa to stride."""
        self.input_file = os.path.join('data', '2E12.pdb')
        self.input_structure = PDBParser(open(self.input_file))
        try:
    def test_uc(self):
        """compares asa within unit cell."""
        self.input_file = os.path.join('data', '2E12.pdb')
        self.input_structure = PDBParser(open(self.input_file))
        asa.asa_xtra(self.input_structure, symmetry_mode='uc', xtra_key='ASA_UC')

src/p/y/pycogent-HEAD/tests/test_struct/test_selection.py   pycogent(Download)
try:
    from cogent.util.unit_test import TestCase, main
    from cogent.parse.pdb import PDBParser
    from cogent.struct.selection import einput, select
except ImportError:

src/p/y/pycogent-HEAD/tests/test_struct/test_manipulation.py   pycogent(Download)
try:
    from cogent.util.unit_test import TestCase, main
    from cogent.parse.pdb import PDBParser
    from cogent.format.pdb import PDBWriter
    from cogent.struct.selection import einput

src/p/y/pycogent-HEAD/tests/test_struct/test_contact.py   pycogent(Download)
try:
    from cogent.util.unit_test import TestCase, main
    from cogent.parse.pdb import PDBParser
    from cogent.struct.selection import einput
except ImportError:

src/p/y/pycogent-HEAD/tests/test_struct/test_annotation.py   pycogent(Download)
try:
    from cogent.util.unit_test import TestCase, main
    from cogent.parse.pdb import PDBParser
    from cogent.struct.annotation import xtradata
    from cogent.struct.selection import einput

src/p/y/pycogent-HEAD/tests/test_parse/test_stride.py   pycogent(Download)
    from cogent.util.unit_test import TestCase, main
    from cogent.struct.selection import einput
    from cogent.parse.pdb import PDBParser
    from cogent.parse.stride import stride_parser
    from cogent.app.stride import Stride, stride_xtra

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