Toolkit Development Platform



Programming Library for Chemistry and Cheminformatics

OEChem TK is a programming library for chemistry and cheminformatics that is fast and flexible. OEChem TK has many simple yet powerful functions that handle the details of working with small molecules, as well as an expanding number of functions for dealing with proteins. High-level functions provide simplicity while low-level functions provide flexibility.  

The OEChem TK also includes two sub-libraries designed to handle macromolecules (OEBio) and grids (OEGrid).

Key Features of OEBio:

    • protein residue, the primary, secondary and tertiary structure hierarchy perception
    • crystal symmetry handling
    • sequence alignment
    • management of torsions, rotamer libraries, and alternate conformations
Key Features of OEGrid:
    • support for the following grid file formats: Grasp, GRD (OpenEye Binary format), CCP4, XPLOR

For more detailed information on OEChem TK, check out the links below:

 Documentation   >   Evaluate

OEChem TK incorporates the chemistry models used by the main software providers.

OEChem TK incorporates the chemistry models used by the main software providers.

  File Format read write 
  OpenEye's binary Yes Yes
  MDL Mol Yes Yes
  MDL SD Yes Yes
  MDL RDF Yes No
  Protein Databank PDB  Yes Yes
  Tripos Sybyl mol2 Yes Yes
  Canonical SMILES Yes Yes
  Canonical isomeric SMILES Yes Yes
  InChi No Yes
  InChiKey  No Yes
  FASTA protein sequence Yes Yes
  Macromodel Yes Yes
  XMol XYZ Yes Yes
One advantage of robust multiple chemistry perception is data integrity: OEChem TK is able to navigate through file formats with no loss of information. The table above shows the common molecule file formats supported by OEChem. 


  • Facile management of molecules, atoms, bonds, and conformers
  • Conformational and frame-of-reference coordinate transformations
  • Maximum common substructure
  • Substructure searching based on SMARTS or MDL query
  • Perception of aromaticity with multiple models
  • Chemical reaction parsing and processing
  • Library generation based on SMIRKS or MDL reaction
  • Tetrahedral and E/Z stereochemistry recognition
  • CIP atom and bond stereo perception
  • Ring perception and Kekulization
  • Molecular canonicalization
  • Multiconformer molecule handling
  • Ability to store and recall generic primitives or user-defined objects on molecules, atoms, bonds, or conformers


The Cheminformatics suite of toolkits provides the core foundation upon which all of the OpenEye applications and remaining toolkits are built. The Cheminformatics suite is a collection of seven individual yet interdependent toolkits that are described in the table below.

  Toolkit Major Functionality
  FastROCS TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
  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 
  MedChem TK Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics
  MolProp TK Molecular property calculation and filtering 
  Quacpac TK Tautomer enumeration and charge assignment


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.

  Toolkit Major Functionality
  OEChem TK Core chemistry handling and representation as well as molecule file I/O
  OEDocking TK Molecular docking and scoring
  Omega TK Conformer generation
  Shape TK 3D shape description, optimization, and overlap
  Spicoli TK Surface generation, manipulation, and interrogation
  Spicoli TK Surface generation, manipulation, and interrogation
  Spruce TK Protein preparation and modeling
  Szybki TK General purpose optimization with MMFF94
  Szmap TK Understanding water interactions in a binding site
  Zap TK Calculate Poisson-Boltzmann electrostatic potentials


  1. Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints Gilles Marcou, Didier Rognan. J. Chem. Inf. Model., 2007, 47 (1), 195-207.
  2. Database Clustering with a Combination of Fingerprint and Maximum Common Substructure MethodsMartin Stahl, Harald Mauser. J. Chem. Inf. Model., 2005, 45 (3), 542-548.