def saved_db():
"""Create and return a SystemDB object with the database file."""
db = SystemDB(filename="seamm.db")
yield db
db.close()
def test_system():
"""Test that we can get a System object"""
db = SystemDB(filename="file:seamm_db?mode=memory&cache=shared")
system = db.create_system(name="default")
assert str(type(system)) == "<class 'molsystem.system._System'>"
assert system.n_configurations == 0
db.close()
def disk_db(db_file):
"""Create and return a SystemDB object with the database file."""
db = SystemDB(filename=db_file)
yield db
db.close()
def test_bonds():
"""Test that we can get an Bonds object"""
db = SystemDB(filename="file:seamm_db?mode=memory&cache=shared")
system = db.create_system(name="default")
configuration = system.create_configuration()
bonds = configuration.bonds
assert str(type(bonds)) == "<class 'molsystem.bonds._Bonds'>"
db.close()
def test_atoms():
"""Test that we can get an Atoms object"""
db = SystemDB(filename="file:seamm_db?mode=memory&cache=shared")
system = db.create_system(name="default")
configuration = system.create_configuration()
atoms = configuration.atoms
assert str(type(atoms)) == "<class 'molsystem.atoms._Atoms'>"
db.close()
def test_configuration():
"""Test that we can get a Configuration object"""
db = SystemDB(filename="file:seamm_db?mode=memory&cache=shared")
system = db.create_system(name="default")
configuration = system.create_configuration()
_type = str(type(configuration))
assert _type == "<class 'molsystem.configuration._Configuration'>"
db.close()
def empty_db():
"""Create a system db with no systems."""
db = SystemDB(filename="file:seamm_db?mode=memory&cache=shared")
yield db
db.close()
try:
del db
except: # noqa: E722
print("Caught error deleting the database")
def full_db():
"""Create a system database with several systems."""
db = SystemDB(filename="file:seamm_db?mode=memory&cache=shared")
for filename in ["acy.mmcif"]:
with open(data_path / filename, "r") as fd:
text = fd.read()
system = db.add_system(name=Path(filename).stem)
configuration = system.create_configuration(name="default")
configuration.from_mmcif_text(text)
yield db
db.close()
def db_file(tmp_path_factory):
"""Create and temporary directory, and clean it up at the end."""
dirpath = tmp_path_factory.mktemp("data")
path = dirpath / "seamm.db"
db = SystemDB(filename=str(path))
db.close()
print(f"temp file: {path}")
yield str(path)
path.unlink()
dirpath.rmdir()
def two_dbs():
"""Create two different dbs."""
db1 = SystemDB(filename="file:seamm_db1?mode=memory&cache=shared")
system1 = db1.create_system(name="default")
system1.create_configuration(name="default")
db2 = SystemDB(filename="file:seamm_db2?mode=memory&cache=shared")
system2 = db2.create_system(name="default")
system2.create_configuration(name="default")
yield db1, db2
db1.close()
db2.close()
def test_adding_atoms():
"""Test that we can add atoms"""
db = SystemDB(filename="file:seamm_db?mode=memory&cache=shared")
system = db.create_system(name="default")
configuration = system.create_configuration()
atoms = configuration.atoms
symbol = ["Ar"] * 4
X = [2.0, 0.0, -2.0, 0.0]
Y = [0.0, 2.0, 0.0, -2.0]
Z = [0.0] * 4
ids = atoms.append(symbol=symbol, x=X, y=Y, z=Z)
assert atoms.n_atoms == 4
assert ids == [1, 2, 3, 4]
db.close()
def amino_acids():
"""Create a system database with 20 amino acids, each as a system."""
db = SystemDB(filename="file:amino_acids_db?mode=memory&cache=shared")
db.read_cif_file(data_path / "aminoacids.mmcif")
yield db
db.close()
def test_adding_bonds():
"""Test that we can add bonds"""
db = SystemDB(filename="file:seamm_db?mode=memory&cache=shared")
system = db.create_system(name="default")
configuration = system.create_configuration()
# TIP3P
r0 = 0.9572
theta0 = 104.52
# H locations are ±x, 0, z
x = r0 * math.sin(math.radians(theta0 / 2))
z = r0 * math.cos(math.radians(theta0 / 2))
X = [0.0, x, -x]
Y = [0.0, 0.0, 0.0]
Z = [0.0, z, z]
atno = [8, 1, 1]
name = ["O", "H1", "H2"]
i_atom = [0, 0]
j_atom = [1, 2]
atoms = configuration.atoms
atoms.add_attribute("name", "str", default="")
atom_ids = atoms.append(atno=atno, x=X, y=Y, z=Z, name=name)
i = [atom_ids[x] for x in i_atom]
j = [atom_ids[x] for x in j_atom]
bonds = configuration.bonds
bond_ids = bonds.append(i=j, j=i) # flipped on purpose so code orders.
assert bonds.n_bonds == 2
assert bond_ids == [1, 2]
db.close()
def aa_templates():
"""Create a system database with 20 amino acids, each as a template."""
db = SystemDB(filename="file:aa_templates_db?mode=memory&cache=shared")
db.read_cif_file(data_path / "aminoacids.mmcif")
templates = db.templates
for system in db.systems:
templates.create(
name=system.name,
category="amino acid",
configuration=system.configuration.id,
)
yield templates
db.close()
def testdb():
"""Create a database with amino acids and templates for each."""
db = SystemDB(filename="file:aa_templates_db?mode=memory&cache=shared")
db.read_cif_file(data_path / "aa-variants-v1.cif")
# Make the templates
templates = db.templates
for system in db.systems:
tmp = system.name.split("_")
if len(tmp) == 1:
category = "amino acid"
else:
if tmp[1] == "LL":
category = "residue"
elif tmp[1] == "LEO2":
category = "C-terminal residue"
elif tmp[1] == "LEO2H":
category = "protonated C-terminal residue"
elif tmp[1] == "LFOH":
category = "amino acid free neutral"
elif tmp[1] == "LFZW":
category = "amino acid free zwitterion"
elif tmp[1] == "LSN3":
category = "protonated N-terminal residue"
else:
raise ValueError(f"Don't recognize {tmp[1]} in {system.name}")
templates.create(name=system.name,
category=category,
configuration=system.configuration.id)
# Angiotensin II from SMILES
system = db.create_system("angiotensin")
configuration = system.create_configuration("SMILES")
configuration.from_smiles(SMILES)
# And read in
system.read_cif_file(data_path / "1n9v.cif")
yield db
db.close()
def test_construction():
"""Simplest test that we can make a SystemDB object"""
db = SystemDB(filename="file:seamm_db?mode=memory&cache=shared")
assert str(type(db)) == "<class 'molsystem.system_db.SystemDB'>"
assert db.n_systems == 0
db.close()