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Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation
Nikolay Kochev1,2, Svetlana Avramova1, Nina Jeliazkova3
1Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 24 Tsar Assen St., 4000, Plovdiv, Bulgaria.
Journal of Cheminformatics
|August 22, 2018
Summary
Ambit-SMIRKS is an open-source Java software that transforms chemical structures using the SMIRKS language. It enables efficient reaction application, searching, and stereo handling for various chemoinformatics applications.
Area of Science:
- Chemoinformatics
- Computational Chemistry
- Software Development
Background:
- Chemical structure transformation is crucial for various chemoinformatics tasks.
- Existing tools may lack comprehensive features for reaction application and searching.
- The SMIRKS language provides a powerful way to define chemical transformations.
Purpose of the Study:
- To introduce Ambit-SMIRKS, an open-source software for chemical structure transformation.
- To provide a robust platform for applying SMIRKS-defined reactions to molecules.
- To showcase the versatility of Ambit-SMIRKS in diverse chemoinformatics projects.
Main Methods:
- Implementation as a Java library extending Ambit-SMARTS and The Chemistry Development Kit (The CDK).
- Parsing SMIRKS notations into internal reaction representations.
- Applying transformations using various site selection modes and substructure searching.
- Handling stereo information and supporting advanced SMARTS syntax.
Main Results:
- Ambit-SMIRKS successfully parses and applies SMIRKS transformations.
- The software handles molecular stereo information and supports complex SMARTS expressions.
- Demonstrated use cases include metabolite generation, database standardization, and pathway prediction.
- The module is integrated into various chemoinformatics projects.
Conclusions:
- Ambit-SMIRKS offers a comprehensive solution for chemical structure transformation.
- Its flexibility and feature set make it valuable for diverse chemoinformatics applications.
- The open-source nature and LGPL license facilitate widespread adoption and development.
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