def __get_ring_candidates(self, mol, hints):
flags = dict([(atom, 1) for atom in mol.atoms])
if hints:
for atom in mol.atoms:
rank = hints.rank(atom)
if not rank or rank > self.max_ring_size:
flags[atom] = 0
while True:
no_change = True
for atom in mol.atoms:
if flags[atom]:
deg = mol.degree(atom)
if deg > 1:
v = 0
for i in xrange(deg):
v += flags[mol.neighbor_atom(atom, i)]
if v > 1:
break
if v < 2:
flags[atom] = 0
no_change = False
else:
flags[atom] = 0
no_change = False
if no_change:
break
atoms = [k for k, v in flags if v]
return split(Molecule(atoms, None, mol))
def __make_sssr(self, part, max_ring_size):
assert len(part.atoms) < len(part.bonds)
rings = []
visited_bonds = set()
for bond in part.bonds:
if bond not in visited_bonds:
ring = RingFinder.find_ring(part, bond, max_ring_size)
if ring:
rings.append(ring)
for i in ring.bond:
visited_bonds.add(i)
assert len(rings) == len(part.bonds) - len(part.atoms) + 1
self.rings += rings
if len(visited_bonds) == len(part.bonds):
self.blocks[part] = rings
else:
self.blocks[part] = split(Molecule(None, list(visited_bonds), part))
def save_mol_set(cursor, frame, data, vdw_radius=None, tor=0.2):
mol = parse_mol(data, vdw_radius, tor)
molset = split(mol)
for molI in molset:
f = formula(molI)
s = format_mol(molI, 'mol')
code, _, k = inchi(s)
moltype = save_mol_type(cursor, len(molI.atoms), len(molI.bonds), f, k, code)
atomid = [mol.atoms.index(i) for i in molI.atoms]
bondid = []
for bond in molI.bonds:
atom1 = mol.atoms.index(bond.atom1)
atom2 = mol.atoms.index(bond.atom2)
if atom1 > atom2:
atom1, atom2 = atom2, atom1
bondid.append((atom1, atom2))
molid = save_molecule(cursor, moltype, atomid, bondid)
cursor.execute(SQL_INSERT_MOL_IN_FRAME, (frame, molid))