import _pysssr
_sssr = _pysssr.sssr
from frowns.Cycle import Cycle
from frowns.perception import figueras
class PySSSRError(Exception): pass
def toposort(initialAtoms):
"""topologically sort the atoms and return the bonds as well.
Assumes that the atoms are the smallest set of rings"""
indices = {}
for atom in initialAtoms:
indices[atom.index] = 1
next = initialAtoms[0]
atoms = [next]
bonds = []
del indices[next.index]
while len(atoms) < len(initialAtoms):
for neighbor in next.oatoms:
if neighbor.index in indices:
del indices[neighbor.index]
bond = next.findbond(neighbor)
bonds.append(bond)
atoms.append(neighbor)
next = neighbor
break
else:
raise PySSSRError("Toposort Error: bad atoms for ring")
bonds.append(atoms[-1].findbond(atoms[0]))
return atoms, bonds
def sssr(molecule):
connections = []
for bond in molecule.bonds:
a1, a2 = bond.atoms
connections.append((a1.index, a2.index))
try:
indices = _sssr(len(molecule.atoms), connections)
except:
return figueras.sssr(molecule)
rings = []
cycles = []
for r in indices:
atoms = [molecule.atoms[x] for x in r]
atoms, bonds = toposort(atoms)
rings.append((atoms, bonds))
cycles.append(Cycle(atoms, bonds))
molecule.rings = rings
molecule.cycles = cycles
return molecule
if __name__ == "__main__":
from frowns import Smiles
import time
data = open("../Working/frowns/test/data/NCI_small").read()
count = 0
i = 0
for line in data.split("\n"):
i += 1
smiles = line.split()[0]
m = Smiles.smilin(smiles)
t1 = time.time()
m = sssr(m)
t2 = time.time()
count += (t2-t1)
assert len(m.cycles) == len(m.rings), "failed %s in %f average"%(float(count)/i)
print "average sssr", float(count)/i
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