TLDR:bbfilter

This tool (bbfilter) allows you to select building blocks that are compatible with a particular reaction scheme. To be compatible, a building block must possess the functional group required for the reaction. We call this inclusion SMARTS. At the same time, it must _not_ have functional groups that are incompatble with the reaction scheme. We call this exclusion SMARTS.

Examples of some inclusion SMARTS and exclusion SMARTS may be found on the chemistry commons (commons.docking.org) in the reactionClass page. http://commons.docking.org/reactionClass/

For example, for an amide coupling reaction, one reagent must have a carboxylic acid and the other must have an amine.

http://commons.docking.org/reactionClass/reaction_detail/AMIDE

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