There is a newer version of the record available.

Published January 20, 2021 | Version 1.0
Software Open

Ambit-SLN: an open source software tool for processing of chemical objects via SLN linear notation

Authors/Creators

  • 1. University of Plovdiv, Faculty of Chemistry, Department of Analytical Chemistry and Computer Chemistry, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria
  • 2. Ideaconsult Ltd., 4 Angel Kanchev Str, 1000 Sofia, Bulgaria

Description

Ambit-SLN is a software library for chemoinformatics processing of chemical objects via linear notation SLN [1]. Ambit-SLN is developed as a part of the chemoinformatics platform AMBIT [2]. It is an open-source tool, distributed under LGPL license, written in Java and based on the Chemistry Development Kit [3].  Ambit-SLN includes a parser for the full SLN syntax of chemical structures and substructure search queries including support for macro and Markush atoms, global and local dictionaries and user defined properties which can be stored and used by the Ambit data model.
Ambit-SLN library implements functionalities for substructure matching based on SLN query string and utilities for conversion of SLN objects to other chemical formats such as SMILES and SMARTS. The functionality for Markush atom expansion can be used for generation of combinatorial structure sets.

The full capability of Ambit-SLN could be experienced using it as a Java library (see http://ambit.sourceforge.net/) with an APIs for accessing the functionality for SLN parsing, conversion utilities, substructure search utilities, macro atom expanding and Markush atom based combinatorial library generation. Here we present a console tool, ambit-sln.jar, available as command-line interface (CLI).

You can start using it right away with the console command:

             java -jar ambit-sln.jar -s CH3CH2O[charge=-1] -f ct.

Detailed usage examples are given in file Ambit-SLN-usage-examples.pdf.

 

References:

[1] R. Webster Homer, Jon Swanson, Robert J. Jilek, Tad Hurst, and Robert D. Clark SYBYL Line Notation (SLN): A Single Notation To Represent Chemical Structures, Queries, Reactions, and Virtual Libraries, J. Chem. Inf. Model. 2008, 48, 2294–2307

[2] N. Jeliazkova, V. Jeliazkov, AMBIT RESTful web services: an implementation of the OpenTox application programming interface, Journal of Cheminformatics 2011, 3:18, doi:10.1186/1758-2946-3-18

[3] E.L. Willighagen, J.W. Mayfield, J. Alvarsson, A. Berg, L. Carlsson, N. Jeliazkova, S. Kuhn, T. Pluskal, M. Rojas-Chertó, O. Spjuth, G. Torrance, C.T. Evelo, R. Guha, C. Steinbeck, J. Cheminform, 2017, 9(1), 33.

 

 

 

Notes

Ambit-SLN library includes several chemoinformatics functionalities: (1) Internal representation of the SLN string information as a SLNContainer object; (2) Parser for the full SLN syntax of chemical structures and substructure search queries including support for macro and Markush atoms, global and local dictionaries and user defined properties which can be stored and used by the Ambit data model; (3) Substructure searching based on SLN query string. Optionally, the substructure searching can be combined with molecular property matching (i.e. SLN CT attributes can be matched against the CDK molecular properties); (4) Configurable utilities for conversion of a SLNContainer object (i.e. object parsed from a SLN string) to the popular chemical formats such as SMILES (or structure represented as a CT and conversable to other chemical formats supported in CDK e.g. InChI or CML) and SMARTS for query structures or molecular fragments/templates; (5) Macro and Markush atoms representation and storage plus functionality for macro atoms expansion and generation of combinatorial structure sets based on Markush atoms.

Files

Ambit-SLN-usage-examples.pdf

Files (24.1 MB)

Name Size Download all
md5:bcb6765ac6b4627e4f517a6de5283cb3
164.0 kB Preview Download
md5:52e912f7aa483ec02de18a83d9fa48f0
23.9 MB Download
md5:23bfd73aab495b04f84a0b26ffe067bf
60 Bytes Download
md5:e18c6d701074f8cdc4ef6751be40a524
29 Bytes Download
md5:548b7d0e71703dc3c368132360bc3fb8
46 Bytes Download
md5:165771e4d06419cd04d74f15750d33f3
245 Bytes Preview Download