Ambit-SMIRKS is an open source software, enabling structure transformation via the SMIRKS language and implemented as an extension of Ambit-SMARTS. As part of the Ambit project it builds on top of The Chemistry Development Kit (The CDK). Ambit-SMIRKS provides the following functionalities: parsing of SMIRKS linear notations into internal reaction (transformation) representations based on The CDK objects, application of the stored reactions against target (reactant) molecules for actual transformation of the target chemical objects, reaction searching, stereo information handling, product post-processing, etc. The transformations can be applied on various sites of the reactant molecule in several modes: single, non-overlapping, non-identical, non-homomorphic or externally specified list of sites utilizing efficient substructure searching algorithm. Ambit-SMIRKS handles the molecules stereo information and supports basic chemical stereo elements implemented in The CDK library. The full SMARTS logical expressions syntax for reactions specification is supported, including recursive SMARTS expressions as well as additional syntax extensions. Since its initial development for the purpose of metabolite generation within Toxtree, the Ambit-SMIRKS module was used in various chemoinformatics projects, both developed by the authors of the package and by external teams. We show several use cases of the Ambit-SMIRKS software including standardization of large chemical databases and pathway transformation database and prediction. Ambit-SMIRKS is distributed as a Java library under LGPL license. More information on use cases and applications, including download links is available at http://ambit.sourceforge.net/smirks.

Presently, software tools for retrosynthetic analysis are widely used by organic, medicinal, and computational chemists. Rule-based systems extensively use collections of retro-reactions (transforms). While there are many public datasets with reactions in synthetic direction (usually non-generic reactions), there are no publicly-available databases with generic reactions in computer-readable format which can be used for the purposes of retrosynthetic analysis. Here we present RetroTransformDB-a dataset of transforms, compiled and coded in SMIRKS line notation by us. The collection is comprised of more than 100 records, with each one including the reaction name, SMIRKS linear notation, the functional group to be obtained, and the transform type classification. All SMIRKS transforms were tested syntactically, semantically, and from a chemical point of view in different software platforms. The overall dataset design and the retrosynthetic fitness were analyzed and curated by organic chemistry experts. The RetroTransformDB dataset may be used by open-source and commercial software packages, as well as chemoinformatics tools.

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