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