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import utils
import os
import unittest
import sys
import subprocess
import pickle
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
utils.set_search_paths(TOPDIR)
import ihm.reader
def get_example_dir():
return os.path.join(TOPDIR, "examples")
def get_example_path(fname):
return os.path.join(get_example_dir(), fname)
class Tests(unittest.TestCase):
@unittest.skipIf('APPVEYOR' in os.environ,
"AppVeyor environments have old SSL certs")
@unittest.skipIf('GITHUB_ACTIONS' in os.environ,
"Example is slow and fails when PDB-IHM is down")
def test_validator_example(self):
"""Test validator example"""
subprocess.check_call([sys.executable,
get_example_path("validate_pdb_ihm.py")])
def test_simple_docking_example(self):
"""Test simple-docking example"""
with utils.temporary_directory() as tmpdir:
subprocess.check_call([sys.executable,
get_example_path("simple-docking.py")],
cwd=tmpdir)
# Make sure that a complete output file was produced and that we
# can read it
with open(os.path.join(tmpdir, 'output.cif')) as fh:
contents = fh.readlines()
self.assertEqual(len(contents), 321)
with open(os.path.join(tmpdir, 'output.cif')) as fh:
s, = ihm.reader.read(fh)
def test_locations_example(self):
"""Test locations example"""
subprocess.check_call([sys.executable, "locations.py"],
cwd=get_example_dir())
out = get_example_path("output.cif")
# Make sure that a complete output file was produced and that we
# can read it
with open(out) as fh:
contents = fh.readlines()
self.assertEqual(len(contents), 71)
with open(out) as fh:
s, = ihm.reader.read(fh)
os.unlink(out)
def test_ligands_water_example(self):
"""Test ligands_water example"""
subprocess.check_call([sys.executable, "ligands_water.py"],
cwd=get_example_dir())
out = get_example_path("output.cif")
# Make sure that a complete output file was produced and that we
# can read it
with open(out) as fh:
contents = fh.readlines()
self.assertEqual(len(contents), 255)
with open(out) as fh:
s, = ihm.reader.read(fh)
# Make sure that resulting Python objects are picklable
testpck = 'test-lig-wat.pck'
with open(testpck, 'wb') as fh:
pickle.dump(s, fh, protocol=-1)
with open(testpck, 'rb') as fh:
_ = pickle.load(fh)
os.unlink(out)
os.unlink(testpck)
def test_non_standard_residues_example(self):
"""Test non_standard_residues example"""
subprocess.check_call([sys.executable, "non_standard_residues.py"],
cwd=get_example_dir())
out = get_example_path("output.cif")
# Make sure that a complete output file was produced and that we
# can read it
with open(out) as fh:
contents = fh.readlines()
self.assertEqual(len(contents), 66)
with open(out) as fh:
s, = ihm.reader.read(fh)
os.unlink(out)
def test_stream_parser_example(self):
"""Test stream_parser example"""
subprocess.check_call([sys.executable, "stream_parser.py"],
cwd=get_example_dir())
def test_token_reader_example(self):
"""Test token_reader example"""
subprocess.check_call([sys.executable, "token_reader.py"],
cwd=get_example_dir())
if __name__ == '__main__':
unittest.main()
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