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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 os
import tempfile
import unittest
import warnings
from StringIO import StringIO

try:
    import numpy
except ImportError:
    from Bio import MissingPythonDependencyError
    raise MissingPythonDependencyError(
        "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, PDBIO
from Bio.PDB import HSExposureCA, HSExposureCB, ExposureCN
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning


# NB: the 'A_' prefix ensures this test case is run first
00033 class A_ExceptionTest(unittest.TestCase):
    """Errors and warnings while parsing of flawed PDB files.

    These tests must be executed because of the way Python's warnings module
    works -- a warning is only logged the first time it is encountered.
    """
00039     def test_1_warnings(self):
        """Check warnings: Parse a flawed PDB file in permissive mode.

        NB: The try/finally block is adapted from the warnings.catch_warnings
        context manager in the Python 2.6 standard library.
        """
        warnings.simplefilter('always', PDBConstructionWarning)
        try:
            # Equivalent to warnings.catch_warnings -- hackmagic
            orig_showwarning = warnings.showwarning
            all_warns = []
            def showwarning(*args, **kwargs):
                all_warns.append(args[0])
            warnings.showwarning = showwarning
            # Trigger warnings
            p = PDBParser(PERMISSIVE=True)
            p.get_structure("example", "PDB/a_structure.pdb")
            self.assertEqual(len(all_warns), 14)
            for wrn, msg in zip(all_warns, [
                # Expected warning messages:
                "Used element 'N' for Atom (name=N) with given element ''",
                "Used element 'C' for Atom (name=CA) with given element ''",
                "Atom names ' CA ' and 'CA  ' differ only in spaces at line 17.",
                "Used element 'CA' for Atom (name=CA  ) with given element ''",
                'Atom N defined twice in residue <Residue ARG het=  resseq=2 icode= > at line 21.',
                'disordered atom found with blank altloc before line 33.',
                "Residue (' ', 4, ' ') redefined at line 43.",
                "Blank altlocs in duplicate residue SER (' ', 4, ' ') at line 43.",
                "Residue (' ', 10, ' ') redefined at line 75.",
                "Residue (' ', 14, ' ') redefined at line 106.",
                "Residue (' ', 16, ' ') redefined at line 135.",
                "Residue (' ', 80, ' ') redefined at line 633.",
                "Residue (' ', 81, ' ') redefined at line 646.",
                'Atom O defined twice in residue <Residue HOH het=W resseq=67 icode= > at line 822.'
                ]):
                self.assertTrue(msg in str(wrn), str(wrn))
        finally:
            warnings.showwarning = orig_showwarning

00078     def test_2_strict(self):
        """Check error: Parse a flawed PDB file in strict mode."""
        warnings.simplefilter('ignore', PDBConstructionWarning)
        try:
            parser = PDBParser(PERMISSIVE=False)
            self.assertRaises(PDBConstructionException,
                   parser.get_structure, "example", "PDB/a_structure.pdb")
        finally:
            warnings.filters.pop()
     
00088     def test_3_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))       


00098 class HeaderTests(unittest.TestCase):
    """Tests for parse_pdb_header."""

00101     def test_capsid(self):
        """Parse the header of a known PDB file (1A8O)."""
        parser = PDBParser()
        struct = parser.get_structure('1A8O', 'PDB/1A8O.pdb')
        self.assertAlmostEqual(struct.header['resolution'], 1.7)
        # Case-insensitive string comparisons
        known_strings = {
                'author': 'T.R.Gamble,S.Yoo,F.F.Vajdos,U.K.Von Schwedler,D.K.Worthylake,H.Wang,J.P.Mccutcheon,W.I.Sundquist,C.P.Hill',
                'deposition_date': '1998-03-27',
                'head': 'viral protein',
                'journal': 'AUTH   T.R.GAMBLE,S.YOO,F.F.VAJDOS,U.K.VON SCHWEDLER,AUTH 2 D.K.WORTHYLAKE,H.WANG,J.P.MCCUTCHEON,W.I.SUNDQUIST,AUTH 3 C.P.HILLTITL   STRUCTURE OF THE CARBOXYL-TERMINAL DIMERIZATIONTITL 2 DOMAIN OF THE HIV-1 CAPSID PROTEIN.REF    SCIENCE                       V. 278   849 1997REFN                   ISSN 0036-8075PMID   9346481DOI    10.1126/SCIENCE.278.5339.849',
                'journal_reference': 't.r.gamble,s.yoo,f.f.vajdos,u.k.von schwedler, d.k.worthylake,h.wang,j.p.mccutcheon,w.i.sundquist, c.p.hill structure of the carboxyl-terminal dimerization domain of the hiv-1 capsid protein. science v. 278 849 1997 issn 0036-8075 9346481 10.1126/science.278.5339.849 ',
                'keywords': 'capsid, core protein, hiv, c-terminal domain, viral protein',
                'name': ' hiv capsid c-terminal domain',
                'release_date': '1998-10-14',
                'structure_method': 'x-ray diffraction',
                }
        for key, expect in known_strings.iteritems():
            self.assertEqual(struct.header[key].lower(), expect.lower())

00121     def test_fibril(self):
        """Parse the header of another PDB file (2BEG)."""
        parser = PDBParser()
        struct = parser.get_structure('2BEG', 'PDB/2BEG.pdb')
        known_strings = {
                'author': 'T.Luhrs,C.Ritter,M.Adrian,D.Riek-Loher,B.Bohrmann,H.Dobeli,D.Schubert,R.Riek',
                'deposition_date': '2005-10-24',
                'head': 'protein fibril',
                'journal': "AUTH   T.LUHRS,C.RITTER,M.ADRIAN,D.RIEK-LOHER,B.BOHRMANN,AUTH 2 H.DOBELI,D.SCHUBERT,R.RIEKTITL   3D STRUCTURE OF ALZHEIMER'S AMYLOID-{BETA}(1-42)TITL 2 FIBRILS.REF    PROC.NATL.ACAD.SCI.USA        V. 102 17342 2005REFN                   ISSN 0027-8424PMID   16293696DOI    10.1073/PNAS.0506723102",
                'journal_reference': "t.luhrs,c.ritter,m.adrian,d.riek-loher,b.bohrmann, h.dobeli,d.schubert,r.riek 3d structure of alzheimer's amyloid-{beta}(1-42) fibrils. proc.natl.acad.sci.usa v. 102 17342 2005 issn 0027-8424 16293696 10.1073/pnas.0506723102 ",
                'keywords': "alzheimer's, fibril, protofilament, beta-sandwich, quenched hydrogen/deuterium exchange, pairwise mutagenesis, protein fibril",
                'name': " 3d structure of alzheimer's abeta(1-42) fibrils",
                'release_date': '2005-11-22',
                'structure_method': 'solution nmr',
                }
        for key, expect in known_strings.iteritems():
            self.assertEqual(struct.header[key].lower(), expect.lower())


00140 class ParseTest(unittest.TestCase):
    def setUp(self):
        warnings.simplefilter('ignore', PDBConstructionWarning)
        p = PDBParser(PERMISSIVE=1)
        self.structure = p.get_structure("example", "PDB/a_structure.pdb")
        warnings.filters.pop()

00147     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.assertTrue(isinstance(s, Seq))
        self.assertEqual(s.alphabet, generic_protein)
        self.assertEqual("RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGER"
                         "SDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYRC",
                         str(s))

00164     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.assertTrue(isinstance(s, Seq))
        self.assertEqual(s.alphabet, generic_protein)
        self.assertEqual("RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGER"
                         "SDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYRC",
                         str(s))

00181     def test_structure(self):
        """Verify the structure of the parsed example PDB file."""
        # Structure contains 2 models
        self.assertEqual(len(self.structure), 2)
        # --- Checking model 0 ---
        m0 = self.structure[0]
        # Model 0 contains 1 chain
        self.assertEqual(len(m0), 1)
        # Chain 'A' contains 1 residue
        self.assertEqual(len(m0['A']), 1)
        # Residue ('H_PCA', 1, ' ') contains 8 atoms.
        residue = m0['A'].get_list()[0]
        self.assertEqual(residue.get_id(), ('H_PCA', 1, ' '))
        self.assertEqual(len(residue), 9)
        # --- Checking model 1 ---
        m1 = self.structure[1]
        # Model 1 contains 3 chains
        self.assertEqual(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.assertEqual(chain.get_id(), chn[0])
            self.assertEqual(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.assertEqual(residue.get_id(), res[0])
                self.assertEqual(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.assertEqual(disordered_count, res[2])
                elif disorder_lvl == 2:
                    # Point mutation -- check residue names
                    self.assertEqual(residue.disordered_get_id_list(), res[2])

00393     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 CA  ")
        self.assertEqual(" ".join(atom.element for atom in chain.get_atoms()),
                         "N C C C C O C O CA")
        #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")


00492 class ParseReal(unittest.TestCase):
    """Testing with real PDB files."""

00495     def test_empty(self):
        """Parse an empty file."""
        parser = PDBParser()
        filenumber, filename = tempfile.mkstemp()
        os.close(filenumber)
        try:
            struct = parser.get_structure('MT', filename)
            # Structure has no children (models)
            self.assertFalse(len(struct))
        finally:
            os.remove(filename)

00507     def test_c_n(self):
        """Extract polypeptides from 1A80."""
        parser = PDBParser(PERMISSIVE=False)
        structure = parser.get_structure("example", "PDB/1A8O.pdb")
        self.assertEqual(len(structure), 1)
        for ppbuild in [PPBuilder(), CaPPBuilder()]:
            #==========================================================
            #First try allowing non-standard amino acids,
            polypeptides = ppbuild.build_peptides(structure[0], False)
            self.assertEqual(len(polypeptides), 1)
            pp = polypeptides[0]
            # Check the start and end positions
            self.assertEqual(pp[0].get_id()[1], 151)
            self.assertEqual(pp[-1].get_id()[1], 220)
            # Check the sequence
            s = pp.get_sequence()
            self.assertTrue(isinstance(s, Seq))
            self.assertEqual(s.alphabet, generic_protein)
            #Here non-standard MSE are shown as M
            self.assertEqual("MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQ"
                             "NANPDCKTILKALGPGATLEEMMTACQG", str(s))
            #==========================================================
            #Now try strict version with only standard amino acids
            #Should ignore MSE 151 at start, and then break the chain
            #at MSE 185, and MSE 214,215
            polypeptides = ppbuild.build_peptides(structure[0], True)
            self.assertEqual(len(polypeptides), 3)
            #First fragment
            pp = polypeptides[0]
            self.assertEqual(pp[0].get_id()[1], 152)
            self.assertEqual(pp[-1].get_id()[1], 184)
            s = pp.get_sequence()
            self.assertTrue(isinstance(s, Seq))
            self.assertEqual(s.alphabet, generic_protein)
            self.assertEqual("DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW", str(s))
            #Second fragment
            pp = polypeptides[1]
            self.assertEqual(pp[0].get_id()[1], 186)
            self.assertEqual(pp[-1].get_id()[1], 213)
            s = pp.get_sequence()
            self.assertTrue(isinstance(s, Seq))
            self.assertEqual(s.alphabet, generic_protein)
            self.assertEqual("TETLLVQNANPDCKTILKALGPGATLEE", str(s))
            #Third fragment
            pp = polypeptides[2]
            self.assertEqual(pp[0].get_id()[1], 216)
            self.assertEqual(pp[-1].get_id()[1], 220)
            s = pp.get_sequence()
            self.assertTrue(isinstance(s, Seq))
            self.assertEqual(s.alphabet, generic_protein)
            self.assertEqual("TACQG", str(s))

00559     def test_strict(self):
        """Parse 1A8O.pdb file in strict mode."""
        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")

00653     def test_model_numbering(self):
        """Preserve model serial numbers during I/O."""
        def confirm_numbering(struct):
            self.assertEqual(len(struct), 20)
            for idx, model in enumerate(struct):
                self.assertTrue(model.serial_num, idx + 1)
                self.assertTrue(model.serial_num, model.id + 1)
        parser = PDBParser()
        struct1 = parser.get_structure("1mot", "PDB/1MOT.pdb")
        confirm_numbering(struct1)
        # Round trip: serialize and parse again
        io = PDBIO()
        io.set_structure(struct1)
        filenumber, filename = tempfile.mkstemp()
        os.close(filenumber)
        try:
            io.save(filename)
            struct2 = parser.get_structure("1mot", filename)
            confirm_numbering(struct2)
        finally:
            os.remove(filename)


00676 class Exposure(unittest.TestCase):
    "Testing Bio.PDB.HSExposure."
    def setUp(self):
        warnings.simplefilter('ignore', PDBConstructionWarning)
        pdb_filename = "PDB/a_structure.pdb"
        structure=PDBParser(PERMISSIVE=True).get_structure('X', pdb_filename)
        warnings.filters.pop()
        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

00698     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))

00719     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"])

00741     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"])

00758 class Atom_Element(unittest.TestCase):
    """induces Atom Element from Atom Name"""

    def setUp(self):
        warnings.simplefilter('ignore', PDBConstructionWarning)
        pdb_filename = "PDB/a_structure.pdb"
        structure=PDBParser(PERMISSIVE=True).get_structure('X', pdb_filename)
        warnings.filters.pop()
        self.residue = structure[0]['A'][('H_PCA', 1, ' ')]

00768     def test_AtomElement(self):
        """ Atom Element """
        atoms = self.residue.child_list
        self.assertEqual('N', atoms[0].element) # N
        self.assertEqual('C', atoms[1].element) # Alpha Carbon
        self.assertEqual('CA', atoms[8].element) # Calcium

00775     def test_ions(self):
        """Element for magnesium is assigned correctly."""
        pdb_filename = "PDB/ions.pdb"
        structure=PDBParser(PERMISSIVE=True).get_structure('X', pdb_filename)
        warnings.filters.pop()
        # check magnesium atom
        atoms = structure[0]['A'][('H_ MG', 1, ' ')].child_list
        self.assertEqual('MG', atoms[0].element)

00784 class IterationTests(unittest.TestCase):        

    def setUp(self):
        self.struc = PDBParser(PERMISSIVE=True).get_structure('X', "PDB/a_structure.pdb")

00789     def test_get_chains(self):
        """Yields chains from different models separately."""
        chains = [chain.id for chain in self.struc.get_chains()]
        self.assertEqual(chains, ['A','A', 'B', ' '])

00794     def test_get_residues(self):
        """Yields all residues from all models."""
        residues = [resi.id for resi in self.struc.get_residues()]
        self.assertEqual(len(residues), 167)

00799     def test_get_atoms(self):
        """Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed."""
        atoms = ["%12s"%str((atom.id, atom.altloc)) for atom in self.struc.get_atoms()]
        self.assertEqual(len(atoms), 756)


#class RenumberTests(unittest.TestCase):
#    """Tests renumbering of structures."""
#    
#    def setUp(self):
#        warnings.simplefilter('ignore', PDBConstructionWarning)
#        pdb_filename = "PDB/1A8O.pdb"
#        self.structure=PDBParser(PERMISSIVE=True).get_structure('X', pdb_filename)
#        warnings.filters.pop()
#        
#    def test_renumber_residues(self):
#        """Residues in a structure are renumbered."""
#        self.structure.renumber_residues()
#        nums = [resi.id[1] for resi in self.structure[0]['A'].child_list]
#        print nums
# 
# -------------------------------------------------------------

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

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