def test_add_del_pdb(self):
"""Add and delete a PDB entry."""
template_db = TemplateDatabase(str(self.database), str(self.file_root))
template_db.add_pdb("1del", self._METADATA)
template_db.commit()
self.assertEqual(template_db.get_pdb("1del"), self._METADATA)
template_db.del_pdb("1del")
template_db.commit()
with self.assertRaises(template_db.PdbNotFoundException):
template_db.get_pdb("1del")
def test_add_update_pdb(self):
"""Add and delete a PDB entry."""
template_db = TemplateDatabase(str(self.database), str(self.file_root))
template_db.add_pdb("1del", self._METADATA)
template_db.commit()
self.assertEqual(template_db.get_pdb("1del"), self._METADATA)
altered_meta = self._METADATA.copy()
altered_meta["resolution"] = 100
template_db.update_pdb("1del", altered_meta)
template_db.commit()
self.assertEqual(template_db.get_pdb("1del"), altered_meta)
def setUp(self):
"""Create a temporary pipeline state in `self.state`."""
# Save dummy template to library.
self.pdb_lib_dir = pathlib.Path(tempfile.mkdtemp())
template_file = (self.pdb_lib_dir / "xy" / "1xyz" / "1xyz_A.pdb")
template_file.parent.mkdir(parents=True)
template = self.template()
with template_file.open("w") as template_out:
template.write(template_out)
# Create a temporary template database and add dummy template
_, db_file = tempfile.mkstemp("-foldlib", "phyreengine-")
self.template_db = pathlib.Path(db_file)
TemplateDatabase.create(str(self.template_db))
template_db = TemplateDatabase(
str(self.template_db),
str(self.pdb_lib_dir))
template_db.add_pdb("1xyz", {
"deposition_date": datetime.date(2000, 1, 1),
"release_date": datetime.date(2000, 1, 1),
"last_update_date": datetime.date(2000, 1, 1),
"method": "X-RAY CRYSTALLOGRAPHY",
})
template_db.add_template(template)
template_db.commit()
# Create empty directory for storing models and chdir there.
self.model_dir = pathlib.Path(tempfile.mkdtemp())
self.orig_dir = os.getcwd()
os.chdir(str(self.model_dir))
# Create pipeline state that can be modified without consequence.
self.state = {
"query_sequence": copy.deepcopy(self._QUERY_SEQ),
"PDB": "1xyz",
"chain": "A",
"alignment": copy.deepcopy(self._ALIGNMENT),
"rank": 1
}
self.modeller = HomologyModeller(
str(self.template_db),
str(self.pdb_lib_dir))
self.results = self.modeller.run(self.state)
def test_add_retrieve_del_template(self):
"""Add PDB and template to database."""
template_db = TemplateDatabase(str(self.database), str(self.file_root))
template_db.add_pdb("12AS", self._METADATA)
template_db.add_template(self.sample_template)
template_db.commit()
template = template_db.get_template("12AS", "A")
self.assertEqual(template.canonical_seq,
self.sample_template.canonical_seq)
self.assertEqual(template.canonical_indices,
self.sample_template.canonical_indices)
self.assertEqual(template.mapping, self.sample_template.mapping)
template_db.del_template("12as", "A")
template_db.commit()
with self.assertRaises(template_db.TemplateNotFoundException):
template_db.get_template("12as", "A")