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|
# 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
class PDBNeighborTest(unittest.TestCase):
def setUp(self):
warnings.resetwarnings()
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)
class PDBExceptionTest(unittest.TestCase):
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
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))
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")
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))
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))
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])
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")
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
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))
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"])
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"])
class AssortedMisc(unittest.TestCase):
"Testing with real PDB files."
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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