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# Copyright 2016 by Jacek Smietanski. 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.
"""Testing access to the PDB over the internet."""
import contextlib
import os
import shutil
import tempfile
import unittest
import requires_internet
# We want to test this module:
from Bio.PDB.PDBList import PDBList
requires_internet.check()
class TestPBDListGetList(unittest.TestCase):
"""Test methods responsible for getting lists of entries."""
def test_get_recent_changes(self):
"""Tests the Bio.PDB.PDBList.get_recent_changes method."""
# obsolete_pdb declared to prevent from creating the "obsolete" directory
pdblist = PDBList(obsolete_pdb="unimportant")
url = pdblist.pdb_server + "/pub/pdb/data/status/latest/added.pdb"
entries = pdblist.get_status_list(url)
self.assertIsNotNone(entries)
def test_get_all_entries(self):
"""Tests the Bio.PDB.PDBList.get_all_entries method."""
# obsolete_pdb declared to prevent from creating the "obsolete" directory
pdblist = PDBList(obsolete_pdb="unimportant")
entries = pdblist.get_all_entries()
# As number of entries constantly grow, test checks if a certain number was
# exceeded
self.assertGreater(len(entries), 100000)
def test_get_all_obsolete(self):
"""Tests the Bio.PDB.PDBList.get_all_obsolete method."""
# obsolete_pdb declared to prevent from creating the "obsolete" directory
pdblist = PDBList(obsolete_pdb="unimportant")
entries = pdblist.get_all_obsolete()
# As number of obsolete entries constantly grow, test checks if a certain number
# was exceeded
self.assertGreater(len(entries), 3000)
def test_get_all_assemblies(self):
"""Tests the Bio.PDB.PDBList.get_all_assemblies method."""
# obsolete_pdb declared to prevent from creating the "obsolete" directory
pdblist = PDBList(obsolete_pdb="unimportant")
entries = pdblist.get_all_assemblies()
# As number of obsolete entries constantly grow, test checks if a certain number
# was exceeded
self.assertGreater(len(entries), 100000)
class TestPDBListGetStructure(unittest.TestCase):
"""Test methods responsible for getting structures."""
@contextlib.contextmanager
def make_temp_directory(self, directory):
temp_dir = tempfile.mkdtemp(dir=directory)
try:
yield temp_dir
finally:
shutil.rmtree(temp_dir)
def check(self, structure, filename, file_format, obsolete=False, pdir=None):
with self.make_temp_directory(os.getcwd()) as tmp:
pdblist = PDBList(pdb=tmp)
path = os.path.join(tmp, filename)
if pdir:
pdir = os.path.join(tmp, pdir)
pdblist.retrieve_pdb_file(
structure, obsolete=obsolete, pdir=pdir, file_format=file_format
)
self.assertTrue(os.path.isfile(path))
def test_retrieve_pdb_file_small_pdb(self):
"""Tests retrieving the small molecule in pdb format."""
structure = "127d"
self.check(
structure, os.path.join(structure[1:3], f"pdb{structure}.ent"), "pdb"
)
def test_retrieve_pdb_file_large_pdb(self):
"""Tests retrieving the bundle for large molecule in pdb-like format."""
structure = "3k1q"
self.check(
structure,
os.path.join(structure[1:3], f"{structure}-pdb-bundle.tar"),
"bundle",
)
def test_retrieve_pdb_file_obsolete_pdb(self):
"""Tests retrieving the obsolete molecule in pdb format."""
structure = "347d"
self.check(
structure,
os.path.join("obsolete", structure[1:3], f"pdb{structure}.ent"),
"pdb",
obsolete=True,
)
def test_retrieve_pdb_file_obsolete_mmcif(self):
"""Tests retrieving the obsolete molecule in mmcif format."""
structure = "347d"
self.check(
structure,
os.path.join("obsolete", structure[1:3], f"{structure}.cif"),
"mmCif",
obsolete=True,
)
def test_retrieve_pdb_file_mmcif(self):
"""Tests retrieving the (non-obsolete) molecule in mmcif format."""
structure = "127d"
self.check(structure, os.path.join(structure[1:3], f"{structure}.cif"), "mmCif")
def test_retrieve_pdb_file_obsolete_xml(self):
"""Tests retrieving the obsolete molecule in mmcif format."""
structure = "347d"
self.check(
structure,
os.path.join("obsolete", structure[1:3], f"{structure}.xml"),
"xml",
obsolete=True,
)
def test_retrieve_pdb_file_xml(self):
"""Tests retrieving the (non obsolete) molecule in xml format."""
structure = "127d"
self.check(structure, os.path.join(structure[1:3], f"{structure}.xml"), "xml")
def test_retrieve_pdb_file_mmtf(self):
"""Tests retrieving the molecule in mmtf format."""
structure = "127d"
self.check(structure, os.path.join(structure[1:3], f"{structure}.mmtf"), "mmtf")
def test_double_retrieve_structure(self):
"""Tests retrieving the same file to different directories."""
structure = "127d"
self.check(structure, os.path.join("a", f"{structure}.cif"), "mmCif", pdir="a")
self.check(structure, os.path.join("b", f"{structure}.cif"), "mmCif", pdir="b")
def test_invalid_file_format(self):
pdb_list = PDBList()
with self.assertRaises(ValueError) as context:
pdb_list.retrieve_pdb_file("127d", file_format="invalid")
self.assertEqual(
"Specified file_format invalid does not exist or is not supported. Please use one of the "
"following: pdb, mmCif, xml, mmtf, bundle.",
str(context.exception),
)
class TestPDBListGetAssembly(unittest.TestCase):
"""Test methods responsible for getting assemblies."""
@contextlib.contextmanager
def make_temp_directory(self, directory):
temp_dir = tempfile.mkdtemp(dir=directory)
try:
yield temp_dir
finally:
shutil.rmtree(temp_dir)
def check(self, structure, assembly_num, filename, file_format, pdir=None):
with self.make_temp_directory(os.getcwd()) as tmp:
pdblist = PDBList(pdb=tmp)
path = os.path.join(tmp, filename)
if pdir:
pdir = os.path.join(tmp, pdir)
pdblist.retrieve_assembly_file(
structure, assembly_num, pdir=pdir, file_format=file_format
)
self.assertTrue(os.path.isfile(path))
def test_retrieve_assembly_file_mmcif(self):
"""Tests retrieving a small assembly in mmCif format."""
structure = "127d"
assembly_num = "1"
self.check(
structure,
assembly_num,
os.path.join(structure[1:3], f"{structure}-assembly{assembly_num}.cif"),
"mmCif",
)
def test_retrieve_assembly_file_pdb(self):
"""Tests retrieving a small assembly in pdb format."""
structure = "127d"
assembly_num = "1"
self.check(
structure,
assembly_num,
os.path.join(structure[1:3], f"{structure}.pdb{assembly_num}"),
"pdb",
)
def test_double_retrieve_assembly(self):
"""Tests retrieving the same file to different directories."""
structure = "127d"
assembly_num = "1"
self.check(
structure,
assembly_num,
os.path.join("a", f"{structure}-assembly{assembly_num}.cif"),
"mmCif",
pdir="a",
)
self.check(
structure,
assembly_num,
os.path.join("b", f"{structure}-assembly{assembly_num}.cif"),
"mmCif",
pdir="b",
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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