Customize and automate your tasks

Work more efficiently by creating your own workflows, automating common tasks, expanding Flare with Python modules and adding custom controls


Automate common tasks and customize the interface

The Python API gives full access to all the scientific capabilities of Flare, including the RDKitTM cheminformatics toolkit and to key elements in the main GUI interface. Use it to automate common tasks, customize the interface for your needs, or to develop or incorporate exciting new science.

Python extensions in Flare for structure-based design

Python extensions for Flare

The Flare Python API enables you to customize Flare with dedicated menus or new functionality. The freely available extensions provide additional, optional functionality that expand the extensive range of features in Flare. Whether developing your own extension or using one of ours we provide clear documentation and examples with support to ensure you have the right information to make the best decisions.

  • Customize and adapt Flare to your environment
  • Choose to add predicted properties into the Flare ligand table using a REST call to an in-house server or to create new context sensitive menu entries to enhance integration with internal information stores
Flare Python Cookbook

Ready-to-use recipes: learn to automate Flare experiments

Learn how to use the Flare Python API and start customizing and automating your tasks with the Flare Python Cookbook:

  • Remove and/or split proteins, protein chains, and biomolecules 
  • Prepare a large number of proteins and extract ligands from proteins
  • Export proteins and ligands
  • Modify and add property columns to the Ligands table
  • Organize ligands and conformations into customized roles
  • Run docking experiments on multiple proteins and their associated ligands

Script common tasks

Automate common tasks to significantly improve your productivity. Simple scripts enable you to do more:

  • Automatically scroll through and visualize ligands, ligand-protein complexes or proteins
  • Take snapshots from dynamics trajectories and minimize them prior to use in, for example, an ensemble docking experiment
  • Change ligand titles based on the parent protein or search for a subset and operate on only those
  • Automatically mutate specific ligand functional groups to create new analogues, for example find and mutate oxazoles to thiazoles
  • Find and highlight in the 3D viewer specific residues or residue interactions

Run Flare experiments from the command line

A dedicated Python binary (pyflare) enables you to access every Flare method from within a command line python script. Whether you choose to use the wide range of scripts provided, or write your own, pyflare enables you to achieve your research goals. 

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