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# Copyright 2012 by Eric Talevich. All rights reserved.
# 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.
import unittest
import warnings
try:
import numpy
from numpy import dot # Missing on PyPy's micronumpy
del dot
# We don't need this (?) but Bio.PDB imports it automatically :(
from numpy.linalg import svd, det # Missing in PyPy 2.0 numpypy
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use PDB formats with SeqIO.")
from Bio import SeqIO
from Bio.PDB.PDBExceptions import PDBConstructionWarning
class TestPdbSeqres(unittest.TestCase):
def test_seqres_parse(self):
"""Parse a multi-chain PDB by SEQRES entries.
Reference:
http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=2BEG
"""
chains = list(SeqIO.parse('PDB/2BEG.pdb', 'pdb-seqres'))
self.assertEqual(len(chains), 5)
actual_seq = 'DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA'
for chain, chn_id in zip(chains, 'ABCDE'):
self.assertEqual(chain.id, '2BEG:' + chn_id)
self.assertEqual(chain.annotations['chain'], chn_id)
self.assertEqual(str(chain.seq), actual_seq)
def test_seqres_read(self):
"""Read a single-chain PDB by SEQRES entries.
Reference:
http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=1A8O
"""
chain = SeqIO.read('PDB/1A8O.pdb', 'pdb-seqres')
self.assertEqual(chain.id, '1A8O:A')
self.assertEqual(chain.annotations['chain'], 'A')
self.assertEqual(str(chain.seq),
'MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTIL'
'KALGPGATLEEMMTACQG')
def test_seqres_missing(self):
"""Parse a PDB with no SEQRES entries."""
chains = list(SeqIO.parse('PDB/a_structure.pdb', 'pdb-seqres'))
self.assertEqual(len(chains), 0)
class TestPdbAtom(unittest.TestCase):
def test_atom_parse(self):
"""Parse a multi-chain PDB by ATOM entries.
Reference:
http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=2BEG
"""
chains = list(SeqIO.parse('PDB/2BEG.pdb', 'pdb-atom'))
self.assertEqual(len(chains), 5)
actual_seq = 'LVFFAEDVGSNKGAIIGLMVGGVVIA'
for chain, chn_id in zip(chains, 'ABCDE'):
self.assertEqual(chain.id, '2BEG:' + chn_id)
self.assertEqual(chain.annotations['chain'], chn_id)
self.assertEqual(str(chain.seq), actual_seq)
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
chains = list(SeqIO.parse('PDB/2XHE.pdb', 'pdb-atom'))
actual_seq = 'DRLSRLRQMAAENQXXXXXXXXXXXXXXXXXXXXXXXPEPFMADFFNRVK'\
'RIRDNIEDIEQAIEQVAQLHTESLVAVSKEDRDRLNEKLQDTMARISALG'\
'NKIRADLKQIEKENKRAQQEGTFEDGTVSTDLRIRQSQHSSLSRKFVKVM'\
'TRYNDVQAENKRRYGENVARQCRVVEPSLSDDAIQKVIEHGXXXXXXXXX'\
'XXXXXXXXNEIRDRHKDIQQLERSLLELHEMFTDMSTLVASQGEMIDRIE'\
'FSVEQSHNYV'
self.assertEqual(str(chains[1].seq), actual_seq)
def test_atom_read(self):
"""Read a single-chain PDB by ATOM entries.
Reference:
http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=1A8O
"""
chain = SeqIO.read('PDB/1A8O.pdb', 'pdb-atom')
self.assertEqual(chain.id, '1A8O:A')
self.assertEqual(chain.annotations['chain'], 'A')
self.assertEqual(str(chain.seq),
'MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTIL'
'KALGPGATLEEMMTACQG')
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
chain = SeqIO.read('PDB/a_structure.pdb', 'pdb-atom')
self.assertEqual(chain.id, '????:A')
self.assertEqual(chain.annotations['chain'], 'A')
self.assertEqual(str(chain.seq), 'E')
def test_atom_noheader(self):
"""Parse a PDB with no HEADER line."""
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
warnings.simplefilter('ignore', UserWarning)
chains = list(SeqIO.parse('PDB/1LCD.pdb', 'pdb-atom'))
self.assertEqual(len(chains), 1)
self.assertEqual(str(chains[0].seq), 'MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR')
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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