Abstract
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.
Highlights
Two major types of chemical objects are at the core of the cheminformatics—chemical structures and structure transformations
By elaborating the details of the A Reaction Transform Language (SMIRKS) processing logic, we hope to provide to Ambit-SMIRKS users insight into its use and assist with obtaining correct results from chemical point of view
Comparison between Ambit‐SMIRKS and other open‐source chemoinformatics tools We present comparison between Ambit-SMIRKS and two popular open source chemoinformatics packages, supporting chemical transformations based on Smiles Arbitrary Target Specification (SMARTS)/SMIRKS
Summary
Two major types of chemical objects are at the core of the cheminformatics—chemical structures and structure transformations (reactions). SMILES provide concise and efficient way to describe the molecular structures (i.e. reactants and products) on topological level, while SMARTS expressions and SMIRKS atoms mappings allow specification of exact chemical transformation logic. Another SMIRKS advantage is that it is easy and efficient for manual coding of the chemical reactions as well as for computer handling. The basic functionality of Ambit-SMIRKS is implemented by 3 major Java classes SMIRKSReaction, SMIRKSManager, StereoChemUtils and additional utilities for handling H atoms and reaction search (Fig. 1). The options include the following operations (switched on/off by the corresponding flags): clearing of atom hybridization, aromaticity and H atoms before processing, atom typing and configuration, adding of implicit H atoms, aromaticity detection, conversion of implicit H atom to explicit or vice versa
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