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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 os
import tempfile
import unittest
import warnings
try:
import numpy
from numpy import dot #Missing on PyPy's micronumpy
del dot
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.PDB.")
try:
import Bio.PDB.mmCIF.MMCIFlex
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError("C extension MMCIFlex not installed.")
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
class ParseReal(unittest.TestCase):
"""Testing with real CIF file(s)."""
def test_parser(self):
"""Extract polypeptides from 1A80."""
parser = MMCIFParser()
structure = parser.get_structure("example", "PDB/1A8O.cif")
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))
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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