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    PROGRAMMING LIBRARY FOR CHEMISTRY AND CHEMINFORMATICS


    OEChem TK


    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).

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

    Features

    • 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
    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
    CIF/mmCIF Yes Yes
     
    Note: Includes support for updated formats of PDBx/mmCIF file for protein structures

    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 link below:

    Documentation

    Cheminformatics

    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.


    • 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

    Modeling

    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.

    • 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
    • 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 General purpose optimization with MMFF94
    • Szmap TK Understanding water interactions in a binding site
    • Zap TK Calculate Poisson-Boltzmann electrostatic potentials
    • SiteHopper TK Rapid Comparison of Protein Binding Sites

    References

    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 Methods Martin Stahl, Harald Mauser. J. Chem. Inf. Model., 2005, 45 (3), 542-548.

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