LEMONS (Library for the Enumeration of MOdular Natural Structures) is a library for the enumeration of hypothetical modular natural product structures. A second library of modified structures can be generated based on the first library, and the first and second libraries can be compared using chemical fingerprints.
The most simple use case for LEMONS involves specifying parameters for the generation of a single library of scaffolds:
--initial_monomers monomers used to construct the original scaffolds
--initial_reactions tailoring reactions used to construct the original scaffolds
--max_size the maximum size, in monomers, of a scaffold
--min_size the minimum size, in monomers, of a scaffold
--library_size the size of the library to generate
A modified library of scaffolds can also be generated by varying parameters:
--add_reactions add tailoring reactions to the modified scaffolds
--remove_reactions reverse the chemistry catalyzed by these reactions from the modified scaffolds
--swap_reactions change the site of these tailoring reactions on the modified scaffolds
--swap_monomers monomers to substitute into the modified scaffolds
--swaps the number of monomer substitutions to execute
The -w flag writes all generated libraries, while the -f flag generates chemical fingerprints and ranks Tanimoto coefficients between original and modified structures.
To see a full list of options, do:
$ java -jar lemons.jar --help
LEMONS is designed to be easily extensible. Templates for the addition of new natural product monomers (MonomerSetTemplate.java) and tailoring reactions (ReactionTemplate.java) are provided to facilitate the addition of new functionality to LEMONS.