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CoLibri: help

Note that this help page is under construction. Instead of a comprehensive user guide, which nobody reads..., we intend to respond here quickly to questions and feedback which we get from users. So, if anything is missing here, please send us a note!


  • CoLibri:
    is a toolkit comprised of multiple components, the reaction synthesizer, the fragment space merger and FTrees-FS, read below what is what
  • reaction synthesizer:
    a command line tool that takes one or more reaction definitions as an input and generates an individual fragment space for every one of them. In addition the reaction synthesizer can enumerate product molecules for a reaction
  • fragment space merger:
    a command line tool that takes the output of the reaction synthesizer (multiple individual fragment spaces) and merges them to a single concise fragment space
  • FTrees-FS:
    an extension module to the similarity search method FTrees, which works with a fragment space as input to search through
  • BioSphere:
    an amazing KNIME® workflow that contains and exemplifies the use of all CoLibri components
  • KnowledgeSpace™:
    a public domain fragment space absed on literature reactions and trusted vendor reagents


This tutorial explains how to define reactions properly, so that they can be processed with the CoLibri tools. The basis of the description is the KNIME® environment, but you may easily extrapolate from there to command line use:

How to add your reactions to generate a chemical space in KNIME®

getting started

As a novice we recommend you to obtain KNIME® and install our amazing workflow BioSphere. This KNIME® workflow contains and exemplifies the use of all CoLibri components.

command line options

As usual use --help to get a list of all command line options.


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