def test_find_most_similair_conformation(self):
molref = """
OpenBabel12071321472D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END"""
mol = """
OpenBabel12071321472D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END
"""
can = mol_2_can(mol)
dbi = DBInterface(self.ses)
db_ethane = Molecule(SMILES='CC')
dbi.add_molecule(db_ethane)
db_mol = dbi.get_molecule(can)
db_mol.add_conformation(Conformation(Mol=molref))
self.ses.add(db_mol)
db_conf = db_mol.find_most_similair_conf(mol)[0]
assert str(db_conf.Mol) == molref
def test_add_0_rmsd_conf_existing_mol(self):
coord = """
OpenBabel12071320143D
5 4 0 0 0 0 0 0 0 0999 V2000
1.0663 0.0688 -0.0295 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1585 0.0688 -0.0295 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7023 0.7365 0.7544 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7023 -0.9440 0.1568 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7023 0.4138 -0.9997 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
M END
"""
conf = Conformation(Mol=coord, Molecule_SMILES='C')
can = mol_2_can(coord)
dbi = DBInterface(self.ses)
db_methane = Molecule(SMILES='C')
dbi.add_molecule(db_methane)
db_mol = dbi.get_molecule(can)
db_mol.add_conformation(conf)
self.ses.add(db_mol)
db_conf = db_mol.get_conformation(coord, 0.0000001)
assert db_conf == conf
def test_add_molecule(self):
smiles = 'CCCCCCC'
mol = Molecule(SMILES=smiles, IUPACName='Heptane')
dbi = DBInterface(self.ses)
dbi.add_molecule(mol)
data_mol = dbi.get_molecule(smiles)
assert str(data_mol.SMILES) == str(mol.SMILES)