def setUpClass(cls):
"""
Create an empty temporary database, load and write a template.
"""
cls.file_root = Path(tempfile.mkdtemp("-templatedb", "phyreengine-"))
cls.database = cls.file_root / "test.db"
TemplateDatabase.create(str(cls.database))
(cls.file_root / "2a" / "12as").mkdir(parents=True)
mmcif_buf = io.StringIO(minimal.MINIMAL_MMCIF)
mmcif_struc = Bio.PDB.MMCIFParser().get_structure("", mmcif_buf)
cls.sample_template = Template.build("12as", "A", mmcif_struc[0]["A"])
with (cls.file_root / "2a" / "12as" / "12as_A.pdb").open("w") as tout:
cls.sample_template.write(tout)
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 run(self, data, config=None, pipeline=None):
"""Create an empty fold library database."""
TemplateDatabase.create(self.template_db)
return data