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Toolkit Development Platform

Programming Libraries for Creating Custom Applications, Scripts and Web Services

The OpenEye toolkits are programming libraries, commonly called software development kits (SDKs), for creating custom applications, scripts and/or web services. All of the toolkits are developed in C++ to ensure exceptional performance but are also available to developers in Python, Java, and .NET for maximum flexibility and utility. Each toolkit has its own well documented and stable API with extensive examples. The toolkits are broadly categorized into two major suites: Cheminformatics and Modeling.

Supported Platforms

After several failed attempts with open source software, I resorted to a commercial solution. The best tool I found for parsing XYZ files and assigning bond orders was the OEChem toolkit from OpenEye Scientific Software. Using OEChem, I could parse the XYZ files and correctly assign bond orders. - Pat Walters, Practical Cheminformatics
OE_toolkits_2022_updated_w_SiteHopper v2
The OpenEye Toolkit Ecosystem.


The Modeling suite of toolkits provides the core functionality underlying OpenEye's defining principle that shape & electrostatics are the two fundamental descriptors determining intermolecular interactions. Many of the toolkits in the Modeling suite are directly associated with specific OpenEye applications and can, therefore, be used to create new or extend existing functionality associated with those applications.

  • OEChem TK Core chemistry handling and representation as well as molecule file I/O
  • FastROCS™ TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
  • OEDocking TK Molecular docking and scoring
  • Omega TK Conformer generation
  • Shape TK 3D shape description, optimization, and overlap
  • SiteHopper TK Rapid Comparison of Protein Binding Sites
  • Spicoli TK Surface generation, manipulation, and interrogation
  • Spruce TK Protein preparation and modeling
  • Szybki TK Force field based focused optimization and Entropy estimations
  • OEFF TK Force fields and general optimization tools
  • Szmap TK Understanding water interactions in a binding site
  • Zap TK Calculate Poisson-Boltzmann electrostatic potentials
  • Bioisostere TK 3D fragment similarity, lead optimization, and analog generation


The Cheminformatics suite of toolkits provides the core foundation upon which all the OpenEye applications and remaining toolkits are built.

  • OEChem TK Core chemistry handling and representation as well as molecule file I/O
  • OEDepict TK 2D Molecule rendering and depiction
  • Grapheme™ TK Advanced molecule rendering and report generation
  • GraphSim TK 2D molecular similarity (e.g. fingerprints)
  • Lexichem TK name-to-structure, structure-to-name, foreign language translation
  • MolProp TK Molecular property calculation and filtering
  • Quacpac TK Tautomer enumeration and charge assignment
  • MedChem TK Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics


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