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test_PDB.py

# Copyright 2009 by Eric Talevich.  All rights reserved.
# Revisions copyright 2009-2010 by Peter Cock.  All rights reserved.
#
# Converted by Eric Talevich from an older unit test copyright 2002
# by Thomas Hamelryck.
# 
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.

"""Unit tests for the Bio.PDB module."""
import unittest
import warnings
from StringIO import StringIO

try:
    from numpy.random import random
except ImportError:
    from Bio import MissingExternalDependencyError
    raise MissingExternalDependencyError(\
        "Install NumPy if you want to use Bio.PDB.")

from Bio.Seq import Seq
from Bio.Alphabet import generic_protein
from Bio.PDB import PDBParser, PPBuilder, CaPPBuilder
from Bio.PDB import HSExposureCA, HSExposureCB, ExposureCN
from Bio.PDB.NeighborSearch import NeighborSearch
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning

00030 class PDBNeighborTest(unittest.TestCase):
    def setUp(self):
        warnings.resetwarnings()

00034     def test_neighbor_search(self):
        """NeighborSearch: Find nearby randomly generated coordinates.
         
        Based on the self test in Bio.PDB.NeighborSearch.
        """
        class RandomAtom:
            def __init__(self):
                self.coord = 100 * random(3)
            def get_coord(self):
                return self.coord
        for i in range(0, 20):
            atoms = [RandomAtom() for j in range(100)]
            ns = NeighborSearch(atoms)
            hits = ns.search_all(5.0)
            self.assert_(hits >= 0)
 
 
00051 class PDBExceptionTest(unittest.TestCase):
00052     def test_strict(self):
        """Check error: Parse a flawed PDB file in strict mode."""
        warnings.resetwarnings()
        parser = PDBParser(PERMISSIVE=False)
        self.assertRaises(PDBConstructionException,
                parser.get_structure, "example", "PDB/a_structure.pdb")

    #TODO - check get expected warnings, may require Python 2.6+
    #See Bug 2820

00062     def test_bad_xyz(self):
        """Check error: Parse an entry with bad x,y,z value."""
        data = "ATOM      9  N   ASP A 152      21.554  34.953  27.691  1.00 19.26           N\n"
        parser = PDBParser(PERMISSIVE=False)
        s = parser.get_structure("example", StringIO(data))
        data = "ATOM      9  N   ASP A 152      21.ish  34.953  27.691  1.00 19.26           N\n"
        self.assertRaises(PDBConstructionException,
                parser.get_structure, "example", StringIO(data))       


00072 class PDBParseTest(unittest.TestCase):
    def setUp(self):
        warnings.resetwarnings()
        warnings.simplefilter('ignore', PDBConstructionWarning)
        p = PDBParser(PERMISSIVE=1)
        self.structure = p.get_structure("example", "PDB/a_structure.pdb")
 
00079     def test_c_n(self):
        """Extract polypeptides using C-N."""
        ppbuild = PPBuilder()
        polypeptides = ppbuild.build_peptides(self.structure[1])
        self.assertEqual(len(polypeptides), 1)
        pp = polypeptides[0]
        # Check the start and end positions
        self.assertEqual(pp[0].get_id()[1], 2)
        self.assertEqual(pp[-1].get_id()[1], 86)
        # Check the sequence
        s = pp.get_sequence()
        self.assert_(isinstance(s, Seq))
        self.assertEqual(s.alphabet, generic_protein)
        self.assertEqual("RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGER"
                         "SDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYRC",
                         str(s))
 
00096     def test_ca_ca(self):
        """Extract polypeptides using CA-CA."""
        ppbuild = CaPPBuilder()
        polypeptides = ppbuild.build_peptides(self.structure[1])
        self.assertEqual(len(polypeptides), 1)
        pp = polypeptides[0]
        # Check the start and end positions
        self.assertEqual(pp[0].get_id()[1], 2)
        self.assertEqual(pp[-1].get_id()[1], 86)
        # Check the sequence
        s = pp.get_sequence()
        self.assert_(isinstance(s, Seq))
        self.assertEqual(s.alphabet, generic_protein)
        self.assertEqual("RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGER"
                         "SDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYRC",
                         str(s))
 
00113     def test_structure(self):
        """Verify the structure of the parsed example PDB file."""
        # Structure contains 2 models
        self.assertEquals(len(self.structure), 2)
        # --- Checking model 0 ---
        m0 = self.structure[0]
        # Model 0 contains 1 chain
        self.assertEquals(len(m0), 1)
        # Chain 'A' contains 1 residue
        self.assertEquals(len(m0['A']), 1)
        # Residue ('H_PCA', 1, ' ') contains 8 atoms.
        residue = m0['A'].get_list()[0]
        self.assertEquals(residue.get_id(), ('H_PCA', 1, ' '))
        self.assertEquals(len(residue), 8)
        # --- Checking model 1 ---
        m1 = self.structure[1]
        # Model 1 contains 3 chains
        self.assertEquals(len(m1), 3)
        # Deconstruct this data structure to check each chain
        chain_data = [ # chain_id, chain_len, [(residue_id, residue_len), ...]
            ('A', 86, [ ((' ', 0, ' '), 1 ),
                        ((' ', 2, ' '), 11),
                        ((' ', 3, ' '), 6, 1), # disordered
                        ((' ', 4, ' '), 4 ),
                        ((' ', 5, ' '), 6 ),
                        ((' ', 6, ' '), 9 ),
                        ((' ', 7, ' '), 4 ),
                        ((' ', 8, ' '), 4 ),
                        ((' ', 9, ' '), 4 ),
                        ((' ', 10, ' '), 6, ['GLY', 'SER']), # point mut
                        ((' ', 11, ' '), 7 ),
                        ((' ', 12, ' '), 6 ),
                        ((' ', 13, ' '), 7 ),
                        ((' ', 14, ' '), 4, ['ALA', 'GLY']), # point mut
                        ((' ', 15, ' '), 8, 3), # disordered
                        ((' ', 16, ' '), 11, ['ARG', 'TRP']), # point mut
                        ((' ', 17, ' '), 6 ),
                        ((' ', 18, ' '), 6 ),
                        ((' ', 19, ' '), 6 ),
                        ((' ', 20, ' '), 8 ),
                        ((' ', 21, ' '), 14),
                        ((' ', 22, ' '), 4 ),
                        ((' ', 23, ' '), 14),
                        ((' ', 24, ' '), 6 ),
                        ((' ', 25, ' '), 4 ),
                        ((' ', 26, ' '), 8 ),
                        ((' ', 27, ' '), 6 ),
                        ((' ', 28, ' '), 9, 5), # disordered
                        ((' ', 29, ' '), 7 ),
                        ((' ', 30, ' '), 12),
                        ((' ', 31, ' '), 6 ),
                        ((' ', 32, ' '), 4 ),
                        ((' ', 33, ' '), 11),
                        ((' ', 34, ' '), 7 ),
                        ((' ', 35, ' '), 6 ),
                        ((' ', 36, ' '), 9 ),
                        ((' ', 37, ' '), 8 ),
                        ((' ', 38, ' '), 9 ),
                        ((' ', 39, ' '), 6 ),
                        ((' ', 40, ' '), 14),
                        ((' ', 41, ' '), 6 ),
                        ((' ', 42, ' '), 4 ),
                        ((' ', 43, ' '), 9 ),
                        ((' ', 44, ' '), 11),
                        ((' ', 45, ' '), 6, 1), # disordered
                        ((' ', 46, ' '), 8 ),
                        ((' ', 47, ' '), 10),
                        ((' ', 48, ' '), 11),
                        ((' ', 49, ' '), 6 ),
                        ((' ', 50, ' '), 4 ),
                        ((' ', 51, ' '), 5 ),
                        ((' ', 52, ' '), 5 ),
                        ((' ', 53, ' '), 7 ),
                        ((' ', 54, ' '), 4 ),
                        ((' ', 55, ' '), 8 ),
                        ((' ', 56, ' '), 7 ),
                        ((' ', 57, ' '), 7 ),
                        ((' ', 58, ' '), 6 ),
                        ((' ', 59, ' '), 4 ),
                        ((' ', 60, ' '), 9 ),
                        ((' ', 61, ' '), 8 ),
                        ((' ', 62, ' '), 11),
                        ((' ', 63, ' '), 6 ),
                        ((' ', 64, ' '), 6 ),
                        ((' ', 65, ' '), 6 ),
                        ((' ', 66, ' '), 7 ),
                        ((' ', 67, ' '), 10),
                        ((' ', 68, ' '), 4 ),
                        ((' ', 69, ' '), 14),
                        ((' ', 70, ' '), 6 ),
                        ((' ', 71, ' '), 4 ),
                        ((' ', 72, ' '), 4 ),
                        ((' ', 73, ' '), 4 ),
                        ((' ', 74, ' '), 8, 3), # disordered
                        ((' ', 75, ' '), 8 ),
                        ((' ', 76, ' '), 12),
                        ((' ', 77, ' '), 6 ),
                        ((' ', 78, ' '), 6 ),
                        ((' ', 79, ' '), 4, 4), # disordered
                        ((' ', 80, ' '), 4, ['GLY', 'SER']), # point mut
                        ((' ', 81, ' '), 8, ['ASN', 'LYS']), # point mut
                        ((' ', 82, ' '), 6 ),
                        ((' ', 83, ' '), 9 ),
                        ((' ', 84, ' '), 12),
                        ((' ', 85, ' '), 11),
                        ((' ', 86, ' '), 6 ),
                        ]),
            ('B', 4, [ (('H_NAG', 1, ' '), 14),
                        (('H_NAG', 2, ' '), 14),
                        (('H_NAG', 3, ' '), 14),
                        (('H_NAG', 4, ' '), 14),
                        ]),
            (' ', 76, [ (('W', 1, ' '), 1),
                        (('W', 2, ' '), 1),
                        (('W', 3, ' '), 1),
                        (('W', 4, ' '), 1),
                        (('W', 5, ' '), 1),
                        (('W', 6, ' '), 1),
                        (('W', 7, ' '), 1),
                        (('W', 8, ' '), 1),
                        (('W', 9, ' '), 1),
                        (('W', 10, ' '), 1),
                        (('W', 11, ' '), 1),
                        (('W', 12, ' '), 1),
                        (('W', 13, ' '), 1),
                        (('W', 14, ' '), 1),
                        (('W', 15, ' '), 1),
                        (('W', 16, ' '), 1),
                        (('W', 17, ' '), 1),
                        (('W', 18, ' '), 1),
                        (('W', 19, ' '), 1),
                        (('W', 20, ' '), 1),
                        (('W', 21, ' '), 1),
                        (('W', 22, ' '), 1),
                        (('W', 23, ' '), 1),
                        (('W', 24, ' '), 1),
                        (('W', 25, ' '), 1),
                        (('W', 26, ' '), 1),
                        (('W', 27, ' '), 1),
                        (('W', 28, ' '), 1),
                        (('W', 29, ' '), 1),
                        (('W', 30, ' '), 1),
                        (('W', 31, ' '), 1),
                        (('W', 32, ' '), 1),
                        (('W', 33, ' '), 1),
                        (('W', 34, ' '), 1),
                        (('W', 35, ' '), 1),
                        (('W', 36, ' '), 1),
                        (('W', 37, ' '), 1),
                        (('W', 38, ' '), 1),
                        (('W', 39, ' '), 1),
                        (('W', 40, ' '), 1),
                        (('W', 41, ' '), 1),
                        (('W', 42, ' '), 1),
                        (('W', 43, ' '), 1),
                        (('W', 44, ' '), 1),
                        (('W', 45, ' '), 1),
                        (('W', 46, ' '), 1),
                        (('W', 47, ' '), 1),
                        (('W', 48, ' '), 1),
                        (('W', 49, ' '), 1),
                        (('W', 50, ' '), 1),
                        (('W', 51, ' '), 1),
                        (('W', 52, ' '), 1),
                        (('W', 53, ' '), 1),
                        (('W', 54, ' '), 1),
                        (('W', 55, ' '), 1),
                        (('W', 56, ' '), 1),
                        (('W', 57, ' '), 1),
                        (('W', 58, ' '), 1),
                        (('W', 59, ' '), 1),
                        (('W', 60, ' '), 1),
                        (('W', 61, ' '), 1),
                        (('W', 62, ' '), 1),
                        (('W', 63, ' '), 1),
                        (('W', 64, ' '), 1),
                        (('W', 65, ' '), 1),
                        (('W', 66, ' '), 1),
                        (('W', 67, ' '), 1),
                        (('W', 68, ' '), 1),
                        (('W', 69, ' '), 1),
                        (('W', 70, ' '), 1),
                        (('W', 71, ' '), 1),
                        (('W', 72, ' '), 1),
                        (('W', 73, ' '), 1),
                        (('W', 74, ' '), 1),
                        (('W', 75, ' '), 1),
                        (('W', 77, ' '), 1),
                        ])
                        ]
 
        for c_idx, chn in enumerate(chain_data):
            # Check chain ID and length
            chain = m1.get_list()[c_idx]
            self.assertEquals(chain.get_id(), chn[0])
            self.assertEquals(len(chain), chn[1])
            for r_idx, res in enumerate(chn[2]):
                residue = chain.get_list()[r_idx]
                # Check residue ID and atom count
                self.assertEquals(residue.get_id(), res[0])
                self.assertEquals(len(residue), res[1])
                disorder_lvl = residue.is_disordered()
                if disorder_lvl == 1:
                    # Check the number of disordered atoms
                    disordered_count = sum(1 for atom in residue
                                           if atom.is_disordered())
                    if disordered_count:
                        self.assertEquals(disordered_count, res[2])
                elif disorder_lvl == 2:
                    # Point mutation -- check residue names
                    self.assertEquals(residue.disordered_get_id_list(), res[2])

00325     def test_details(self):
        """Verify details of the parsed example PDB file."""
        structure = self.structure
        self.assertEqual(len(structure), 2)

        #First model
        model = structure[0]
        self.assertEqual(model.id, 0)
        self.assertEqual(model.level, "M")
        self.assertEqual(len(model), 1)
        chain = model["A"]
        self.assertEqual(chain.id, "A")
        self.assertEqual(chain.level, "C")
        self.assertEqual(len(chain), 1)
        self.assertEqual(" ".join(residue.resname for residue in chain), "PCA")
        self.assertEqual(" ".join(atom.name for atom in chain.get_atoms()),
                         "N CA CB CG CD OE C O")
        self.assertEqual(" ".join(atom.element for atom in chain.get_atoms()),
                         "N C C C C O C O")
        #Second model
        model = structure[1]
        self.assertEqual(model.id, 1)
        self.assertEqual(model.level, "M")
        self.assertEqual(len(model), 3)
        chain = model["A"]
        self.assertEqual(chain.id, "A")
        self.assertEqual(chain.level, "C")
        self.assertEqual(len(chain), 86)
        self.assertEqual(" ".join(residue.resname for residue in chain),
                         "CYS ARG CYS GLY SER GLN GLY GLY GLY SER THR CYS "
                         "PRO GLY LEU ARG CYS CYS SER ILE TRP GLY TRP CYS "
                         "GLY ASP SER GLU PRO TYR CYS GLY ARG THR CYS GLU "
                         "ASN LYS CYS TRP SER GLY GLU ARG SER ASP HIS ARG "
                         "CYS GLY ALA ALA VAL GLY ASN PRO PRO CYS GLY GLN "
                         "ASP ARG CYS CYS SER VAL HIS GLY TRP CYS GLY GLY "
                         "GLY ASN ASP TYR CYS SER GLY GLY ASN CYS GLN TYR "
                         "ARG CYS")
        self.assertEqual(" ".join(atom.name for atom in chain.get_atoms()),
                         "C N CA C O CB CG CD NE CZ NH1 NH2 N CA C O CB SG "
                         "N CA C O N CA C O CB OG N CA C O CB CG CD OE1 NE2 "
                         "N CA C O N CA C O N CA C O N CA C O CB OG N CA C "
                         "O CB OG1 CG2 N CA C O CB SG N CA C O CB CG CD N "
                         "CA C O N CA C O CB CG CD1 CD2 N CA C O CB CG CD NE "
                         "CZ NH1 NH2 N CA C O CB SG N CA C O CB SG N CA C O "
                         "CB OG N CA C O CB CG1 CG2 CD1 N CA C O CB CG CD1 "
                         "CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 N CA C O N CA C O CB "
                         "CG CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 N CA C O CB SG "
                         "N CA C O N CA C O CB CG OD1 OD2 N CA C O CB OG N "
                         "CA C O CB CG CD OE1 OE2 N CA C O CB CG CD N CA C O "
                         "CB CG CD1 CD2 CE1 CE2 CZ OH N CA C O CB SG N CA C "
                         "O N CA C O CB CG CD NE CZ NH1 NH2 N CA C O CB OG1 "
                         "CG2 N CA C O CB SG N CA C O CB CG CD OE1 OE2 N CA "
                         "C O CB CG OD1 ND2 N CA C O CB CG CD CE NZ N CA C O "
                         "CB SG N CA C O CB CG CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 "
                         "CH2 N CA C O CB OG N CA C O N CA C O CB CG CD OE1 "
                         "OE2 N CA C O CB CG CD NE CZ NH1 NH2 N CA C O CB OG "
                         "N CA C O CB CG OD1 OD2 N CA C O CB CG ND1 CD2 CE1 "
                         "NE2 N CA C O CB CG CD NE CZ NH1 NH2 N CA C O CB SG "
                         "N CA C O N CA C O CB N CA C O CB N CA C O CB CG1 "
                         "CG2 N CA C O N CA C O CB CG OD1 ND2 N CA C O CB CG "
                         "CD N CA C O CB CG CD N CA C O CB SG N CA C O N CA "
                         "C O CB CG CD OE1 NE2 N CA C O CB CG OD1 OD2 N CA C "
                         "O CB CG CD NE CZ NH1 NH2 N CA C O CB SG N CA C O "
                         "CB SG N CA C O CB OG N CA C O CB CG1 CG2 N CA C O "
                         "CB CG ND1 CD2 CE1 NE2 N CA C O N CA C O CB CG CD1 "
                         "CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 N CA C O CB SG N CA C "
                         "O N CA C O N CA C O N CA C O CB CG OD1 ND2 N CA C O "
                         "CB CG OD1 OD2 N CA C O CB CG CD1 CD2 CE1 CE2 CZ OH "
                         "N CA C O CB SG N CA C O CB OG N CA C O N CA C O N "
                         "CA C O CB CG OD1 ND2 N CA C O CB SG N CA C O CB CG "
                         "CD OE1 NE2 N CA C O CB CG CD1 CD2 CE1 CE2 CZ OH N "
                         "CA C O CB CG CD NE CZ NH1 NH2 N CA C O CB SG")
        self.assertEqual(" ".join(atom.element for atom in chain.get_atoms()),
                         "C N C C O C C C N C N N N C C O C S N C C O N C C O "
                         "C O N C C O C C C O N N C C O N C C O N C C O N C C "
                         "O C O N C C O C O C N C C O C S N C C O C C C N C C "
                         "O N C C O C C C C N C C O C C C N C N N N C C O C S "
                         "N C C O C S N C C O C O N C C O C C C C N C C O C C "
                         "C C N C C C C C N C C O N C C O C C C C N C C C C C "
                         "N C C O C S N C C O N C C O C C O O N C C O C O N C "
                         "C O C C C O O N C C O C C C N C C O C C C C C C C O "
                         "N C C O C S N C C O N C C O C C C N C N N N C C O C "
                         "O C N C C O C S N C C O C C C O O N C C O C C O N N "
                         "C C O C C C C N N C C O C S N C C O C C C C N C C C "
                         "C C N C C O C O N C C O N C C O C C C O O N C C O C "
                         "C C N C N N N C C O C O N C C O C C O O N C C O C C "
                         "N C C N N C C O C C C N C N N N C C O C S N C C O N "
                         "C C O C N C C O C N C C O C C C N C C O N C C O C C "
                         "O N N C C O C C C N C C O C C C N C C O C S N C C O "
                         "N C C O C C C O N N C C O C C O O N C C O C C C N C "
                         "N N N C C O C S N C C O C S N C C O C O N C C O C C "
                         "C N C C O C C N C C N N C C O N C C O C C C C N C C "
                         "C C C N C C O C S N C C O N C C O N C C O N C C O C "
                         "C O N N C C O C C O O N C C O C C C C C C C O N C C "
                         "O C S N C C O C O N C C O N C C O N C C O C C O N N "
                         "C C O C S N C C O C C C O N N C C O C C C C C C C O "
                         "N C C O C C C N C N N N C C O C S")

00423 class Exposure(unittest.TestCase):
    "Testing Bio.PDB.HSExposure."
    def setUp(self):
        warnings.resetwarnings()
        warnings.simplefilter('ignore', PDBConstructionWarning)
        pdb_filename = "PDB/a_structure.pdb"
        structure=PDBParser(PERMISSIVE=True).get_structure('X', pdb_filename)
        self.model=structure[1]
        #Look at first chain only
        a_residues=list(self.model["A"].child_list)
        self.assertEqual(86, len(a_residues))
        self.assertEqual(a_residues[0].get_resname(), "CYS")
        self.assertEqual(a_residues[1].get_resname(), "ARG")
        self.assertEqual(a_residues[2].get_resname(), "CYS")
        self.assertEqual(a_residues[3].get_resname(), "GLY")
        #...
        self.assertEqual(a_residues[-3].get_resname(), "TYR")
        self.assertEqual(a_residues[-2].get_resname(), "ARG")
        self.assertEqual(a_residues[-1].get_resname(), "CYS")
        self.a_residues = a_residues
        self.radius = 13.0

00445     def test_HSExposureCA(self):
        """HSExposureCA."""
        hse = HSExposureCA(self.model, self.radius)
        residues = self.a_residues
        self.assertEqual(0, len(residues[0].xtra))
        self.assertEqual(0, len(residues[1].xtra))
        self.assertEqual(3, len(residues[2].xtra))
        self.assertAlmostEqual(0.81250973133184456, residues[2].xtra["EXP_CB_PCB_ANGLE"])
        self.assertEqual(14, residues[2].xtra["EXP_HSE_A_D"])
        self.assertEqual(14, residues[2].xtra["EXP_HSE_A_U"])
        self.assertEqual(3, len(residues[3].xtra))
        self.assertAlmostEqual(1.3383737, residues[3].xtra["EXP_CB_PCB_ANGLE"])
        self.assertEqual(13, residues[3].xtra["EXP_HSE_A_D"])
        self.assertEqual(16, residues[3].xtra["EXP_HSE_A_U"])
        #...
        self.assertEqual(3, len(residues[-2].xtra))
        self.assertAlmostEqual(0.77124014456278489, residues[-2].xtra["EXP_CB_PCB_ANGLE"])
        self.assertEqual(24, residues[-2].xtra["EXP_HSE_A_D"])
        self.assertEqual(24, residues[-2].xtra["EXP_HSE_A_U"])
        self.assertEqual(0, len(residues[-1].xtra))

00466     def test_HSExposureCB(self):
        """HSExposureCB."""
        hse = HSExposureCB(self.model, self.radius)
        residues = self.a_residues
        self.assertEqual(0, len(residues[0].xtra))
        self.assertEqual(2, len(residues[1].xtra))
        self.assertEqual(20, residues[1].xtra["EXP_HSE_B_D"])
        self.assertEqual(5, residues[1].xtra["EXP_HSE_B_U"])
        self.assertEqual(2, len(residues[2].xtra))
        self.assertEqual(10, residues[2].xtra["EXP_HSE_B_D"])
        self.assertEqual(18, residues[2].xtra["EXP_HSE_B_U"])
        self.assertEqual(2, len(residues[3].xtra))
        self.assertEqual(7, residues[3].xtra["EXP_HSE_B_D"])
        self.assertEqual(22, residues[3].xtra["EXP_HSE_B_U"])
        #...
        self.assertEqual(2, len(residues[-2].xtra))
        self.assertEqual(14, residues[-2].xtra["EXP_HSE_B_D"])
        self.assertEqual(34, residues[-2].xtra["EXP_HSE_B_U"])
        self.assertEqual(2, len(residues[-1].xtra))
        self.assertEqual(23, residues[-1].xtra["EXP_HSE_B_D"])
        self.assertEqual(15, residues[-1].xtra["EXP_HSE_B_U"])

00488     def test_ExposureCN(self):
        """HSExposureCN."""
        hse = ExposureCN(self.model, self.radius)
        residues = self.a_residues
        self.assertEqual(0, len(residues[0].xtra))
        self.assertEqual(1, len(residues[1].xtra))
        self.assertEqual(25, residues[1].xtra["EXP_CN"])
        self.assertEqual(1, len(residues[2].xtra))
        self.assertEqual(28, residues[2].xtra["EXP_CN"])
        self.assertEqual(1, len(residues[3].xtra))
        self.assertEqual(29, residues[3].xtra["EXP_CN"])
        #...
        self.assertEqual(1, len(residues[-2].xtra))
        self.assertEqual(48, residues[-2].xtra["EXP_CN"])
        self.assertEqual(1, len(residues[-1].xtra))
        self.assertEqual(38, residues[-1].xtra["EXP_CN"])

00505 class AssortedMisc(unittest.TestCase):
    "Testing with real PDB files."

00508     def test_strict(self):
        """Parse 1A8O.pdb file in strict mode."""
        warnings.resetwarnings()
        parser = PDBParser(PERMISSIVE=False)
        structure = parser.get_structure("example", "PDB/1A8O.pdb")
        self.assertEqual(len(structure), 1)
        model = structure[0]
        self.assertEqual(model.id, 0)
        self.assertEqual(model.level, "M")
        self.assertEqual(len(model), 1)
        chain = model["A"]
        self.assertEqual(chain.id, "A")
        self.assertEqual(chain.level, "C")
        self.assertEqual(len(chain), 158)
        self.assertEqual(" ".join(residue.resname for residue in chain),
                         "MSE ASP ILE ARG GLN GLY PRO LYS GLU PRO PHE ARG "
                         "ASP TYR VAL ASP ARG PHE TYR LYS THR LEU ARG ALA "
                         "GLU GLN ALA SER GLN GLU VAL LYS ASN TRP MSE THR "
                         "GLU THR LEU LEU VAL GLN ASN ALA ASN PRO ASP CYS "
                         "LYS THR ILE LEU LYS ALA LEU GLY PRO GLY ALA THR "
                         "LEU GLU GLU MSE MSE THR ALA CYS GLN GLY HOH HOH "
                         "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH "
                         "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH "
                         "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH "
                         "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH "
                         "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH "
                         "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH "
                         "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH "
                         "HOH HOH")
        self.assertEqual(" ".join(atom.name for atom in chain.get_atoms()),
                         "N CA C O CB CG SE CE N CA C O CB CG OD1 OD2 N CA "
                         "C O CB CG1 CG2 CD1 N CA C O CB CG CD NE CZ NH1 "
                         "NH2 N CA C O CB CG CD OE1 NE2 N CA C O N CA C O "
                         "CB CG CD N CA C O CB CG CD CE NZ N CA C O CB CG "
                         "CD OE1 OE2 N CA C O CB CG CD N CA C O CB CG CD1 "
                         "CD2 CE1 CE2 CZ N CA C O CB CG CD NE CZ NH1 NH2 N "
                         "CA C O CB CG OD1 OD2 N CA C O CB CG CD1 CD2 CE1 "
                         "CE2 CZ OH N CA C O CB CG1 CG2 N CA C O CB CG OD1 "
                         "OD2 N CA C O CB CG CD NE CZ NH1 NH2 N CA C O CB "
                         "CG CD1 CD2 CE1 CE2 CZ N CA C O CB CG CD1 CD2 CE1 "
                         "CE2 CZ OH N CA C O CB CG CD CE NZ N CA C O CB "
                         "OG1 CG2 N CA C O CB CG CD1 CD2 N CA C O CB CG CD "
                         "NE CZ NH1 NH2 N CA C O CB N CA C O CB CG CD OE1 "
                         "OE2 N CA C O CB CG CD OE1 NE2 N CA C O CB N CA C "
                         "O CB OG N CA C O CB CG CD OE1 NE2 N CA C O CB CG "
                         "CD OE1 OE2 N CA C O CB CG1 CG2 N CA C O CB CG CD "
                         "CE NZ N CA C O CB CG OD1 ND2 N CA C O CB CG CD1 "
                         "CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 N CA C O CB CG SE CE "
                         "N CA C O CB OG1 CG2 N CA C O CB CG CD OE1 OE2 N "
                         "CA C O CB OG1 CG2 N CA C O CB CG CD1 CD2 N CA C "
                         "O CB CG CD1 CD2 N CA C O CB CG1 CG2 N CA C O CB "
                         "CG CD OE1 NE2 N CA C O CB CG OD1 ND2 N CA C O CB "
                         "N CA C O CB CG OD1 ND2 N CA C O CB CG CD N CA C "
                         "O CB CG OD1 OD2 N CA C O CB SG N CA C O CB CG CD "
                         "CE NZ N CA C O CB OG1 CG2 N CA C O CB CG1 CG2 "
                         "CD1 N CA C O CB CG CD1 CD2 N CA C O CB CG CD CE "
                         "NZ N CA C O CB N CA C O CB CG CD1 CD2 N CA C O N "
                         "CA C O CB CG CD N CA C O N CA C O CB N CA C O CB "
                         "OG1 CG2 N CA C O CB CG CD1 CD2 N CA C O CB CG CD "
                         "OE1 OE2 N CA C O CB CG CD OE1 OE2 N CA C O CB CG "
                         "SE CE N CA C O CB CG SE CE N CA C O CB OG1 CG2 N "
                         "CA C O CB N CA C O CB SG N CA C O CB CG CD OE1 "
                         "NE2 N CA C O OXT O O O O O O O O O O O O O O O O "
                         "O O O O O O O O O O O O O O O O O O O O O O O O "
                         "O O O O O O O O O O O O O O O O O O O O O O O O "
                         "O O O O O O O O O O O O O O O O O O O O O O O O")
        self.assertEqual(" ".join(atom.element for atom in chain.get_atoms()),
                         "N C C O C C SE C N C C O C C O O N C C O C C C C "
                         "N C C O C C C N C N N N C C O C C C O N N C C O "
                         "N C C O C C C N C C O C C C C N N C C O C C C O "
                         "O N C C O C C C N C C O C C C C C C C N C C O C "
                         "C C N C N N N C C O C C O O N C C O C C C C C C "
                         "C O N C C O C C C N C C O C C O O N C C O C C C "
                         "N C N N N C C O C C C C C C C N C C O C C C C C "
                         "C C O N C C O C C C C N N C C O C O C N C C O C "
                         "C C C N C C O C C C N C N N N C C O C N C C O C "
                         "C C O O N C C O C C C O N N C C O C N C C O C O "
                         "N C C O C C C O N N C C O C C C O O N C C O C C "
                         "C N C C O C C C C N N C C O C C O N N C C O C C "
                         "C C N C C C C C N C C O C C SE C N C C O C O C N "
                         "C C O C C C O O N C C O C O C N C C O C C C C N "
                         "C C O C C C C N C C O C C C N C C O C C C O N N "
                         "C C O C C O N N C C O C N C C O C C O N N C C O "
                         "C C C N C C O C C O O N C C O C S N C C O C C C "
                         "C N N C C O C O C N C C O C C C C N C C O C C C "
                         "C N C C O C C C C N N C C O C N C C O C C C C N "
                         "C C O N C C O C C C N C C O N C C O C N C C O C "
                         "O C N C C O C C C C N C C O C C C O O N C C O C "
                         "C C O O N C C O C C SE C N C C O C C SE C N C C "
                         "O C O C N C C O C N C C O C S N C C O C C C O N "
                         "N C C O O O O O O O O O O O O O O O O O O O O O "
                         "O O O O O O O O O O O O O O O O O O O O O O O O "
                         "O O O O O O O O O O O O O O O O O O O O O O O O "
                         "O O O O O O O O O O O O O O O O O O O O O")


# -------------------------------------------------------------

if __name__ == '__main__':
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)

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