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# Copyright 2012 Lenna X. Peterson (arklenna@gmail.com).
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# Tests adapted from test_PDB.py
"""Unit tests for the MMCIF portion of the Bio.PDB module."""
import tempfile
import unittest
import warnings
try:
import numpy as np
from numpy import dot # Missing on old PyPy's micronumpy
del dot
from numpy.linalg import det # Missing in PyPy 2.0 numpypy
from numpy.linalg import svd # Missing in PyPy 2.0 numpypy
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.PDB."
) from None
from Bio.PDB import CaPPBuilder
from Bio.PDB import PDBIO
from Bio.PDB import PDBParser
from Bio.PDB import PPBuilder
from Bio.PDB.MMCIFParser import FastMMCIFParser
from Bio.PDB.MMCIFParser import MMCIFParser
from Bio.PDB.PDBExceptions import PDBConstructionWarning
from Bio.PDB.PDBExceptions import PDBIOException
from Bio.Seq import Seq
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)
parser_lab_res = MMCIFParser(auth_residues=False, QUIET=True)
fast_parser_lab_res = FastMMCIFParser(auth_residues=False, QUIET=True)
parser_lab_chain = MMCIFParser(auth_chains=False, QUIET=True)
fast_parser_lab_chain = FastMMCIFParser(auth_chains=False, QUIET=True)
structure_lr = parser_lab_res.get_structure("example", "PDB/1A8O.cif")
f_structure_lr = fast_parser_lab_res.get_structure("example", "PDB/1A8O.cif")
structure_lc = parser_lab_chain.get_structure("example", "PDB/1A8O.cif")
f_structure_lc = fast_parser_lab_chain.get_structure("example", "PDB/1A8O.cif")
self.assertEqual(len(list(structure_lr.get_atoms())), 556)
self.assertEqual(len(list(f_structure_lr.get_atoms())), 556)
self.assertEqual(len(list(structure_lc.get_atoms())), 644)
self.assertEqual(len(list(f_structure_lc.get_atoms())), 644)
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.assertIsInstance(s, Seq)
# Here non-standard MSE are shown as M
self.assertEqual(
"MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQ"
"NANPDCKTILKALGPGATLEEMMTACQG",
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.assertIsInstance(s, Seq)
self.assertEqual("DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW", 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.assertIsInstance(s, Seq)
self.assertEqual("TETLLVQNANPDCKTILKALGPGATLEE", 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.assertIsInstance(s, Seq)
self.assertEqual("TACQG", s)
s_atoms = list(structure.get_atoms())
f_atoms = list(f_structure.get_atoms())
for atoms in [s_atoms, f_atoms]:
self.assertEqual(len(atoms), 644)
atom_names = ["N", "CA", "C", "O", "CB"]
self.assertEqual([a.get_name() for a in atoms[:5]], atom_names)
self.assertEqual([a.get_id() for a in atoms[:5]], atom_names)
self.assertEqual([a.get_fullname() for a in atoms[:5]], atom_names)
self.assertEqual(
[a.get_occupancy() for a in atoms[:5]], [1.0, 1.0, 1.0, 1.0, 1.0]
)
self.assertIsInstance(atoms[0].get_coord(), np.ndarray)
coord = np.array([19.594, 32.367, 28.012], dtype=np.float32)
np.testing.assert_array_equal(atoms[0].get_coord(), coord)
self.assertEqual(atoms[0].get_bfactor(), 18.03)
for atom in atoms:
self.assertIsNone(atom.get_anisou())
def test_with_anisotrop(self):
parser = MMCIFParser()
fast_parser = FastMMCIFParser()
structure = parser.get_structure("example", "PDB/4CUP.cif")
f_structure = fast_parser.get_structure("example", "PDB/4CUP.cif")
self.assertEqual(len(structure), 1)
self.assertEqual(len(f_structure), 1)
s_atoms = list(structure.get_atoms())
f_atoms = list(f_structure.get_atoms())
self.assertEqual(len(s_atoms), len(f_atoms))
for atoms in [s_atoms, f_atoms]:
atom_names = ["N", "CA", "C", "O", "CB"]
self.assertEqual([a.get_name() for a in atoms[:5]], atom_names)
self.assertEqual([a.get_id() for a in atoms[:5]], atom_names)
self.assertEqual([a.get_fullname() for a in atoms[:5]], atom_names)
self.assertEqual(
[a.get_occupancy() for a in atoms[:5]], [1.0, 1.0, 1.0, 1.0, 1.0]
)
self.assertIsInstance(atoms[0].get_coord(), np.ndarray)
coord = np.array([50.346, 19.287, 17.288], dtype=np.float32)
np.testing.assert_array_equal(atoms[0].get_coord(), coord)
self.assertEqual(atoms[0].get_bfactor(), 32.02)
ansiou = np.array(
[0.4738, -0.0309, -0.0231, 0.4524, 0.0036, 0.2904], dtype=np.float32
)
np.testing.assert_array_equal(atoms[0].get_anisou(), ansiou)
ansiou = np.array(
[1.1242, 0.2942, -0.0995, 1.1240, -0.1088, 0.8221], dtype=np.float32
)
atom_937 = list(f_structure[0]["A"])[114]["CB"]
np.testing.assert_array_equal(atom_937.get_anisou(), ansiou)
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.assertIsInstance(s, Seq)
# Here non-standard MSE are shown as M
self.assertEqual("MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR", 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.assertIsInstance(s, Seq)
self.assertEqual("MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR", 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.assertIsInstance(s, Seq)
self.assertEqual(refseq, 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)
with open("PDB/1A8O.cif") as handle:
structure = parser.get_structure("example", handle)
self.assertEqual(len(structure), 1)
def test_point_mutations_main(self):
"""Test if MMCIFParser parse point mutations correctly."""
self._run_point_mutation_tests(MMCIFParser(QUIET=True))
def test_point_mutations_fast(self):
"""Test if FastMMCIFParser can parse point mutations correctly."""
self._run_point_mutation_tests(FastMMCIFParser(QUIET=True))
def _run_point_mutation_tests(self, parser):
"""Shared test code for testing point mutations."""
structure = parser.get_structure("example", "PDB/3JQH.cif")
# Residue 1 and 15 should be disordered.
res_1 = structure[0]["A"][1]
res_15 = structure[0]["A"][15]
# Cursory check -- this would be true even if the residue just
# contained some disordered atoms.
self.assertTrue(res_1.is_disordered(), "Residue 1 is disordered")
self.assertTrue(res_15.is_disordered(), "Residue 15 is disordered")
# Check a non-mutated residue just to be sure we didn't break the
# parser and cause everything to be disordered.
self.assertFalse(
structure[0]["A"][13].is_disordered(), "Residue 13 is not disordered"
)
# Check that the residue types were parsed correctly.
self.assertEqual(
set(res_1.disordered_get_id_list()),
{"PRO", "SER"},
"Residue 1 is proline/serine",
)
self.assertEqual(
set(res_15.disordered_get_id_list()),
{"ARG", "GLN", "GLU"},
"Residue 15 is arginine/glutamine/glutamic acid",
)
# Quickly check that we can switch between residues and that the
# correct set of residues was parsed.
res_1.disordered_select("PRO")
self.assertAlmostEqual(
res_1["CA"].get_occupancy(), 0.83, 2, "Residue 1 proline occupancy correcy"
)
res_1.disordered_select("SER")
self.assertAlmostEqual(
res_1["CA"].get_occupancy(), 0.17, 2, "Residue 1 serine occupancy correcy"
)
def test_header(self):
"""Test if the parser populates header data."""
parser = MMCIFParser(QUIET=1)
# test default values
structure = parser.get_structure("example", "PDB/a_structure.cif")
self.assertEqual("", structure.header["idcode"])
self.assertEqual("", structure.header["head"])
self.assertEqual("", structure.header["deposition_date"])
self.assertEqual("", structure.header["structure_method"])
self.assertIsNone(structure.header["resolution"])
# test extracting fields
structure = parser.get_structure("example", "PDB/1A8O.cif")
self.assertEqual("1A8O", structure.header["idcode"])
self.assertEqual("Viral protein", structure.header["head"])
self.assertEqual("", structure.header["deposition_date"])
self.assertEqual("X-RAY DIFFRACTION", structure.header["structure_method"])
self.assertEqual(1.7, structure.header["resolution"])
# test not confused by '.' or '?'
structure = parser.get_structure("example", "PDB/1SSU_mod.cif")
# self.assertIsNone(structure.header["resolution"])
self.assertEqual(4.1, structure.header["resolution"])
class CIFtoPDB(unittest.TestCase):
"""Testing conversion between formats: CIF to PDB."""
def test_conversion(self):
"""Parse 1LCD.cif, write 1LCD.pdb, parse again and compare."""
cif_parser = MMCIFParser(QUIET=1)
cif_struct = cif_parser.get_structure("example", "PDB/1LCD.cif")
pdb_writer = PDBIO()
pdb_writer.set_structure(cif_struct)
filenumber, filename = tempfile.mkstemp()
pdb_writer.save(filename)
pdb_parser = PDBParser(QUIET=1)
pdb_struct = pdb_parser.get_structure("example_pdb", filename)
# comparisons
self.assertEqual(len(pdb_struct), len(cif_struct))
pdb_atom_names = [a.name for a in pdb_struct.get_atoms()]
cif_atom_names = [a.name for a in cif_struct.get_atoms()]
self.assertEqual(pdb_atom_names, cif_atom_names)
pdb_atom_elems = [a.element for a in pdb_struct.get_atoms()]
cif_atom_elems = [a.element for a in cif_struct.get_atoms()]
self.assertEqual(pdb_atom_elems, cif_atom_elems)
def test_conversion_not_preserve_numbering(self):
"""Convert mmCIF to PDB and renumber atom serials."""
cif_parser = MMCIFParser(QUIET=1)
cif_struct = cif_parser.get_structure("example", "PDB/a_structure.cif")
pdb_writer = PDBIO()
pdb_writer.set_structure(cif_struct)
filenumber, filename = tempfile.mkstemp()
pdb_writer.save(filename, preserve_atom_numbering=False)
def test_conversion_preserve_numbering(self):
"""Convert mmCIF to PDB and preserve original serial numbering."""
cif_parser = MMCIFParser(QUIET=1)
cif_struct = cif_parser.get_structure("example", "PDB/a_structure.cif")
pdb_writer = PDBIO()
pdb_writer.set_structure(cif_struct)
filenumber, filename = tempfile.mkstemp()
with self.assertRaises(PDBIOException):
pdb_writer.save(filename, preserve_atom_numbering=True)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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