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# Copyright 2012 Lenna X. Peterson (arklenna@gmail.com).
# All rights reserved.
#
# Tests adapted from test_PDB.py
#
# 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 MMCIF portion of the Bio.PDB module."""
import unittest
import warnings
try:
import numpy
from numpy import dot # Missing on old PyPy's micronumpy
del dot
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 Bio.PDB.")
from Bio.Seq import Seq
from Bio.Alphabet import generic_protein
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning
from Bio.PDB import PPBuilder, CaPPBuilder
from Bio.PDB.MMCIFParser import MMCIFParser, FastMMCIFParser
class ParseReal(unittest.TestCase):
"""Testing with real CIF file(s)."""
def test_parsers(self):
"""Extract polypeptides from 1A80."""
parser = MMCIFParser()
fast_parser = FastMMCIFParser()
structure = parser.get_structure("example", "PDB/1A8O.cif")
f_structure = fast_parser.get_structure("example", "PDB/1A8O.cif")
self.assertEqual(len(structure), 1)
self.assertEqual(len(f_structure), 1)
for ppbuild in [PPBuilder(), CaPPBuilder()]:
# ==========================================================
# Check that serial_num (model column) is stored properly
self.assertEqual(structure[0].serial_num, 1)
self.assertEqual(f_structure[0].serial_num, structure[0].serial_num)
# First try allowing non-standard amino acids,
polypeptides = ppbuild.build_peptides(structure[0], False)
f_polypeptides = ppbuild.build_peptides(f_structure[0], False)
self.assertEqual(len(polypeptides), 1)
self.assertEqual(len(f_polypeptides), 1)
pp = polypeptides[0]
f_pp = f_polypeptides[0]
# Check the start and end positions
self.assertEqual(pp[0].get_id()[1], 151)
self.assertEqual(pp[-1].get_id()[1], 220)
self.assertEqual(f_pp[0].get_id()[1], 151)
self.assertEqual(f_pp[-1].get_id()[1], 220)
# Check the sequence
s = pp.get_sequence()
f_s = f_pp.get_sequence()
self.assertEqual(s, f_s) # enough to test this
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))
def testModels(self):
"""Test file with multiple models"""
parser = MMCIFParser(QUIET=1)
f_parser = FastMMCIFParser(QUIET=1)
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
structure = parser.get_structure("example", "PDB/1LCD.cif")
f_structure = f_parser.get_structure("example", "PDB/1LCD.cif")
self.assertEqual(len(structure), 3)
self.assertEqual(len(f_structure), 3)
for ppbuild in [PPBuilder(), CaPPBuilder()]:
# ==========================================================
# Check that serial_num (model column) is stored properly
self.assertEqual(structure[0].serial_num, 1)
self.assertEqual(structure[1].serial_num, 2)
self.assertEqual(structure[2].serial_num, 3)
# 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], 1)
self.assertEqual(pp[-1].get_id()[1], 51)
# 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("MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR",
str(s))
# ==========================================================
# Now try strict version with only standard amino acids
polypeptides = ppbuild.build_peptides(structure[0], True)
self.assertEqual(len(polypeptides), 1)
pp = polypeptides[0]
# Check the start and end positions
self.assertEqual(pp[0].get_id()[1], 1)
self.assertEqual(pp[-1].get_id()[1], 51)
# Check the sequence
s = pp.get_sequence()
self.assertTrue(isinstance(s, Seq))
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual("MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR",
str(s))
# This structure contains several models with multiple lengths.
# The tests were failing.
structure = parser.get_structure("example", "PDB/2OFG.cif")
self.assertEqual(len(structure), 3)
def test_insertions(self):
"""Test file with residue insertion codes"""
parser = MMCIFParser(QUIET=1)
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
structure = parser.get_structure("example", "PDB/4ZHL.cif")
for ppbuild in [PPBuilder(), CaPPBuilder()]:
# First try allowing non-standard amino acids,
polypeptides = ppbuild.build_peptides(structure[0], False)
self.assertEqual(len(polypeptides), 2)
pp = polypeptides[0]
# Check the start and end positions (first segment only)
self.assertEqual(pp[0].get_id()[1], 16)
self.assertEqual(pp[-1].get_id()[1], 244)
# Check the sequence
refseq = "IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGR" \
"SRLNSNTQGEMKFEVENLILHKDYSADTLAYHNDIALLKIRSKEGRCAQPSRTIQTIALPSMY" \
"NDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQW" \
"KTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKE"
s = pp.get_sequence()
self.assertTrue(isinstance(s, Seq))
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual(refseq, str(s))
def test_filehandle(self):
"""Test if the parser can handle file handle as well as filename"""
parser = MMCIFParser()
structure = parser.get_structure("example", "PDB/1A8O.cif")
self.assertEqual(len(structure), 1)
structure = parser.get_structure("example", open("PDB/1A8O.cif"))
self.assertEqual(len(structure), 1)
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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