def toInChIKey(mol, backend='rdkit-first', aug_level=0):
"""
Convert a molecular structure to an InChI Key string.
For aug_level=0, generates the canonical InChI.
For aug_level=1, appends the molecule multiplicity.
For aug_level=2, appends positions of unpaired and paired electrons.
Uses RDKit or OpenBabel for conversion.
Args:
backend choice of backend, 'try-all', 'rdkit', or 'openbabel'
aug_level level of augmentation, 0, 1, or 2
"""
cython.declare(key=str, ulayer=str, player=str, mlayer=str)
if aug_level == 0:
return _write(mol, 'inchikey', backend)
elif aug_level == 1:
key = toInChIKey(mol, backend=backend)
mlayer = '-mult{0}'.format(mol.multiplicity) if mol.multiplicity != 0 else ''
return key + mlayer
elif aug_level == 2:
key = toInChIKey(mol, backend=backend)
ulayer, player = inchiutil.create_augmented_layers(mol)
return inchiutil.compose_aug_inchi_key(key, ulayer, player)
else:
raise ValueError("Implemented values for aug_level are 0, 1, or 2.")
def toInChIKey(mol, backend='rdkit-first', aug_level=0):
"""
Convert a molecular structure to an InChI Key string.
For aug_level=0, generates the canonical InChI.
For aug_level=1, appends the molecule multiplicity.
For aug_level=2, appends positions of unpaired and paired electrons.
Uses RDKit or OpenBabel for conversion.
Args:
backend choice of backend, 'try-all', 'rdkit', or 'openbabel'
aug_level level of augmentation, 0, 1, or 2
"""
cython.declare(key=str, ulayer=str, player=str, mlayer=str)
if aug_level == 0:
return _write(mol, 'inchikey', backend)
elif aug_level == 1:
key = toInChIKey(mol, backend=backend)
mlayer = '-mult{0}'.format(mol.multiplicity) if mol.multiplicity != 0 else ''
return key + mlayer
elif aug_level == 2:
key = toInChIKey(mol, backend=backend)
ulayer, player = inchiutil.create_augmented_layers(mol)
return inchiutil.compose_aug_inchi_key(key, ulayer, player)
else:
raise ValueError("Implemented values for aug_level are 0, 1, or 2.")
def test_triplet_methylene(self):
adjlist = """
multiplicity 3
1 C u2 p0 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
"""
mol = Molecule().from_adjacency_list(adjlist)
ulayer, player = create_augmented_layers(mol)
self.assertEquals(U_LAYER_PREFIX + '1,1', ulayer)
self.assertTrue(not player)
def test_nitrate(self):
"""
Test that N atom in the p-layer has correct symbol.
"""
adjlist = """
1 O u0 p2 c0 {4,D}
2 O u0 p3 c-1 {4,S}
3 O u0 p3 c-1 {4,S}
4 N u0 p0 c+1 {1,D} {2,S} {3,S}
"""
mol = Molecule().from_adjacency_list(adjlist)
ulayer, player = create_augmented_layers(mol)
self.assertTrue(not ulayer)
self.assertTrue(player.contains(P_LAYER_PREFIX + '1(0)'))
def test_c4h6(self):
"""
Test that 3-butene-1,2-diyl biradical is always resulting in the
same u-layer, regardless of the original order.
"""
# radical positions 3 and 4
adjlist1 = """
1 C u0 p0 c0 {2,D} {5,S} {6,S}
2 C u0 p0 c0 {1,D} {3,S} {7,S}
3 C u1 p0 c0 {2,S} {4,S} {8,S}
4 C u1 p0 c0 {3,S} {9,S} {10,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}
9 H u0 p0 c0 {4,S}
10 H u0 p0 c0 {4,S}
"""
# radical positions 1 and 2
adjlist2 = """
1 C u1 p0 c0 {2,S} {5,S} {6,S}
2 C u1 p0 c0 {1,S} {3,S} {7,S}
3 C u0 p0 c0 {2,S} {4,D} {8,S}
4 C u0 p0 c0 {3,D} {9,S} {10,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}
9 H u0 p0 c0 {4,S}
10 H u0 p0 c0 {4,S}
"""
u_layers = []
for adjlist in [adjlist1, adjlist2]:
mol = Molecule().from_adjacency_list(adjlist)
u_layer = create_augmented_layers(mol)[0]
u_layers.append(u_layer)
self.assertEquals(u_layers[0], u_layers[1])
def test_methane(self):
smi = 'C'
mol = Molecule().from_smiles(smi)
ulayer, player = create_augmented_layers(mol)
self.assertTrue(not ulayer)
self.assertTrue(not player)
