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I'm trying to find a free automatic organic synthesis Linux command line program which take mol or smile files as input. I have random molecules and I'd like to know how difficult above a baseline they will be to synthesize. An implementation of synthetic accessibility and not a full step wise synthesis program would also be acceptable. Thanks for the help.

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    $\begingroup$ I would be very surprised if such a program exists for anything but a small subset of similarly structured molecules. Additionally, refer to the help section with respect to questions that are purely of a simulation nature. $\endgroup$ – bobthechemist Oct 24 '13 at 1:49
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    $\begingroup$ A general solution to this problem, by the way, would be literally worth zillions of dollars. $\endgroup$ – Richard Terrett Oct 24 '13 at 7:29
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    $\begingroup$ And probably a Nobel Prize (with its additional 8 million Swedish Kronor). $\endgroup$ – Ben Norris Oct 24 '13 at 11:07
  • $\begingroup$ @bobthechemist awh well then you can successfully be surprised as I found a solution. $\endgroup$ – user1464 Oct 24 '13 at 21:11
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The SAscore is now implemented in RDkit and available for download.

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    $\begingroup$ If you're wondering what "SAscore" is, see the following open-access article: "Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions" jcheminf.com/content/1/1/8 $\endgroup$ – user809695 Oct 25 '13 at 1:05

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