cyclization modelling with SMILES

[astar]

Dear All;

We are a academic group working on a bioinformatics application written in Java, that involves certain chemistry solutions. That's the part we need some help solving. We are storing our molecules in SMILES format, and at the end our goal is to turn linear structures into cyclisized.

FIRST QUESTION: are SMILES the best choice for database entries and computation
of new structres???

SECOND QUESTION: if you model spontaneous cyclization from a linear compound, how can you determine which product out of all possible ones is most likely to be the real thing

THIRD QUESTION: is there a software that can help us solve "second question", and could you recomend us some(it should cooperate with SMILES "Daylight toolkit" if possible)

P.S. are there any Java libraries for this stuff???

Thanks for all suggestions!