biopython/Tests/test_SeqIO_PdbIO.py

# 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.
"""Tests for SeqIO PdbIO module."""
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 None

from Bio import SeqIO
from Bio import BiopythonParserWarning
from Bio.PDB.PDBExceptions import PDBConstructionWarning


def SeqresTestGenerator(extension, parser):
    """Test factory for tests reading SEQRES (or similar) records.

    This is a factory returning a parameterised superclass for tests reading
    sequences from the sequence records of structure files.

    Arguments:
        extension:
            The extension of the files to read from the ``PDB`` directory (e.g.
            ``pdb`` or ``cif``).
        parser:
            The name of the SeqIO parser to use (e.g. ``pdb-atom``).

    """

    class SeqresTests(unittest.TestCase):
        """Use "parser" to parse sequence records from a structure file.

        Args:
            parser (str): Name of the parser used by SeqIO.
            extension (str): Extension of the files to parse.

        """

        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." + extension, parser))
            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(chain.seq, actual_seq)

        def test_seqres_read(self):
            """Read a single-chain structure by sequence entries.

            Reference:
            http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=1A8O
            """
            chain = SeqIO.read("PDB/1A8O." + extension, parser)
            self.assertEqual(chain.id, "1A8O:A")
            self.assertEqual(chain.annotations["chain"], "A")
            self.assertEqual(
                chain.seq,
                "MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPD"
                "CKTILKALGPGATLEEMMTACQG",
            )

        def test_seqres_missing(self):
            """Parse a PDB with no SEQRES entries."""
            chains = list(SeqIO.parse("PDB/a_structure." + extension, parser))
            self.assertEqual(len(chains), 0)

    return SeqresTests


class TestPdbSeqres(SeqresTestGenerator("pdb", "pdb-seqres")):
    """Test pdb-seqres SeqIO driver."""


class TestCifSeqres(SeqresTestGenerator("cif", "cif-seqres")):
    """Test cif-seqres SeqIO driver."""


def AtomTestGenerator(extension, parser):
    """Test factory for tests reading ATOM (or similar) records.

    See SeqresTestGenerator for more information.
    """

    class AtomTests(unittest.TestCase):
        def test_atom_parse(self):
            """Parse a multi-chain structure by ATOM entries.

            Reference:
            http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=2BEG
            """
            chains = list(SeqIO.parse("PDB/2BEG." + extension, parser))
            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(chain.annotations["model"], 0)
                self.assertEqual(chain.seq, actual_seq)

            with warnings.catch_warnings():
                warnings.simplefilter("ignore", PDBConstructionWarning)
                chains = list(SeqIO.parse("PDB/2XHE." + extension, parser))
            actual_seq = (
                "DRLSRLRQMAAENQXXXXXXXXXXXXXXXXXXXXXXXPEPFMADFFNRVK"
                "RIRDNIEDIEQAIEQVAQLHTESLVAVSKEDRDRLNEKLQDTMARISALG"
                "NKIRADLKQIEKENKRAQQEGTFEDGTVSTDLRIRQSQHSSLSRKFVKVM"
                "TRYNDVQAENKRRYGENVARQCRVVEPSLSDDAIQKVIEHGXXXXXXXXX"
                "XXXXXXXXNEIRDRHKDIQQLERSLLELHEMFTDMSTLVASQGEMIDRIE"
                "FSVEQSHNYV"
            )
            self.assertEqual(chains[1].seq, actual_seq)

        def test_atom_read(self):
            """Read a single-chain structure by ATOM entries.

            Reference:
            http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=1A8O
            """
            chain = SeqIO.read("PDB/1A8O." + extension, parser)
            self.assertEqual(chain.id, "1A8O:A")
            self.assertEqual(chain.annotations["chain"], "A")
            self.assertEqual(chain.annotations["model"], 0)
            self.assertEqual(
                chain.seq,
                "MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTIL"
                "KALGPGATLEEMMTACQG",
            )

    return AtomTests


class TestPdbAtom(AtomTestGenerator("pdb", "pdb-atom")):
    """Test pdb-atom SeqIO driver."""

    def test_atom_noheader(self):
        """Parse a PDB with no HEADER line."""
        with warnings.catch_warnings():
            warnings.simplefilter("ignore", PDBConstructionWarning)
            warnings.simplefilter("ignore", BiopythonParserWarning)
            chains = list(SeqIO.parse("PDB/1LCD.pdb", "pdb-atom"))

        self.assertEqual(len(chains), 1)
        self.assertEqual(
            chains[0].seq, "MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR"
        )

    def test_atom_read_noheader(self):
        """Read a single-chain PDB without a header by ATOM entries."""
        with warnings.catch_warnings():
            warnings.simplefilter("ignore", PDBConstructionWarning)
            warnings.simplefilter("ignore", BiopythonParserWarning)
            chain = SeqIO.read("PDB/a_structure.pdb", "pdb-atom")
        self.assertEqual(chain.id, "????:A")
        self.assertEqual(chain.annotations["chain"], "A")
        self.assertEqual(chain.seq, "Q")

    def test_atom_with_insertion(self):
        """Read a PDB with residue insertion code."""
        chain = SeqIO.read("PDB/2n0n_M1.pdb", "pdb-atom")
        self.assertEqual(chain.seq, "HAEGKFTSEF")


class TestCifAtom(AtomTestGenerator("cif", "cif-atom")):
    """Test cif-atom SeqIO driver."""

    def test_atom_read_noheader(self):
        """Read a single-chain CIF without a header by ATOM entries."""
        with warnings.catch_warnings():
            warnings.simplefilter("ignore", PDBConstructionWarning)
            warnings.simplefilter("ignore", BiopythonParserWarning)
            chain = SeqIO.read("PDB/a_structure.cif", "cif-atom")
        self.assertEqual(chain.id, "????:A")
        self.assertEqual(chain.annotations["chain"], "A")
        self.assertEqual(
            chain.seq,
            "MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG",
        )


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)