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Im currently developing an organic conversion simulator which would help to generate in-between steps of the conversion when the starting compound and the ending compound is been provided. I'm in search of a searching mechanism to get the in-between compounds. I have come across Brute force as a solution to search through. But as I'm having like 200 reactions in my library to check for each compound i think it will result in a lot of time consumption. What other techniques or algorithms will be less time consuming to get my requirement done efficiently. For example I have fuzzy logic, genetic algorithm etc

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    "i think it will result in a lot of time consumption" - don't think. Benchmark. –  Jul 13 '13 at 12:14
  • Or at least give more details. Are you wanting to list all possible chains of in-between steps? Or just those in the shortest chains? How long are typical chains? Extremely long chains? – Teepeemm Jul 14 '13 at 19:43

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Concerning genetic algorithms, it's a quite good tool for multiparametric optimization. But, surely, you need to evaluate kinetic parameters for each reaction, not only reaction mechanism framework. Also, thermodynamic data is needed for each intermediate species. So, you have tons of parameters - you need tons of experimental data to evaluate these parameters correctly. If you already have your own reaction set, from which reactions should be taken, you can generate full kinetic mechanism (with all pathways) and further implement the reduction of chemical mechanisms technique. There are different reduction techniques, which are not for discussing on stackoverflow. Also, if your reaction parameters are estimated (so reactions are ready to deal with), you can generate different schemes with GA - e.g. with binary genes - 0 - this reaction won't be included into scheme, 1 - will be included.

John_West
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