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test_PDB_unit.py

# Copyright 2009 by Eric Talevich.  All rights reserved.
# Revisions copyright 2009 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

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.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

00027 class PDBNeighborTest(unittest.TestCase):
    def setUp(self):
        warnings.resetwarnings()

00031     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)
 
 
00048 class PDBExceptionTest(unittest.TestCase):
00049     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

00059 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")
 
00066     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)
 
00076     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)
 
00086     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])

00298 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

00320     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))

00341     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"])

00363     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"])

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

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

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