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# Copyright 2016 Joao P. Rodrigues (j.p.g.l.m.rodrigues@gmail.com).
# 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.
"""Unit tests to compare objects parsed by different structure parsers."""
import os
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.PDB.MMCIFParser import MMCIFParser
from Bio.PDB import PDBParser
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning
class CompareStructures(unittest.TestCase):
"""Tests for comparing the same structure parsed by PDB and MMCIF parsers"""
def setUp(self):
# Silence!
warnings.simplefilter('ignore', PDBConstructionWarning)
pdbparser = PDBParser(QUIET=1)
cifparser = MMCIFParser(QUIET=1)
modpath = os.path.abspath(os.path.dirname(__file__))
pdb_file = os.path.join(modpath, "PDB", "1LCD.pdb")
cif_file = os.path.join(modpath, "PDB", "1LCD.cif")
self.pdbo = pdbparser.get_structure('pdb', pdb_file)
self.cifo = cifparser.get_structure('pdb', cif_file)
def test_compare_models(self):
"""Compared parsed models"""
cif_models = [(m.id, len(m.child_list)) for m in self.cifo.get_models()]
pdb_models = [(m.id, len(m.child_list)) for m in self.pdbo.get_models()]
self.assertEqual(len(cif_models), len(pdb_models))
self.assertEqual([i[0] for i in cif_models], [i[0] for i in pdb_models])
self.assertEqual([i[1] for i in cif_models], [i[1] for i in pdb_models])
def test_compare_chains(self):
"""Compare parsed chains"""
cif_chains = [(c.id, len(c.child_list)) for c in self.cifo.get_chains()]
pdb_chains = [(c.id, len(c.child_list)) for c in self.pdbo.get_chains()]
self.assertEqual(len(cif_chains), len(pdb_chains))
self.assertEqual([i[0] for i in cif_chains], [i[0] for i in pdb_chains])
self.assertEqual([i[1] for i in cif_chains], [i[1] for i in pdb_chains])
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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