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.

OEChem TK is available in C++ and is wrapped for Python and Java. OEChem TK is required to access all our other toolkits and provides molecule handling in all the OpenEye applications.

To aid new users of OEChem TK, a large number of example programs illustrating the use of some of the most powerful functions of OEChem TK are provided. These programs perform a number of useful tasks, such as MCS detection, molecule fragmentation and ligand extraction from PDB files, as well as forming the basis for customized programs.

OEChem TK has been used as the basis for molecular handling in Pubchem [1] and in BREED [2], for small molecule clustering with MCS [3] and for fingerprinting protein-ligand interaction [4].

OEChem TK incorporates the chemistry models used by the main software providers.
One advantage of robust multiple chemistry perception is data integrity: OEChem TK is
able to navigate through file formats with no loss of information, as shown by the
reliability of the file format conversion application that comes with OEChem TK, BABEL.

Features

• Facile management of molecules, atoms, bonds, and conformers
• Conformational and frame-of-reference coordinate transformations
• Maximum common substructure and exact substructure searching
• Extremely fast 2D similarity using LINGOS [5]
• Perception of aromaticity with multiple models
• Chemical reaction parsing and processing
• Tetrahedral and E/Z stereochemistry recognition
• Ring perception and Kekulization
• Molecular normalization and canonicalization
• Multiconformer molecule handling
• Support for residues and bases
• Ability to store and recall generic primitives or user-defined objects on molecules, atoms, bonds, or conformers

For OEChem TK and All OpenEye Products

• Multiple file format handling: robust reading and specification-compliant writing of: SMILES, SLN, SDF, MOL, MOL2, PDB, FASTA, MOPAC, MacroModel, XYZ, CCP4, XPLOR, and OEBinary.
• Platform independence: support for Linux, Windows, Mac OS X and many flavors of Unix in both 32 and 64 bit.

[1] http://pubchem.ncbi.nlm.nih.gov/
[2] Pierce, A.C., Rao, G. and Bemis, G.W., J. Med. Chem. 2004, 47, 2768.
[3] Stahl, M. and Mauser, H., J. Chem. Inf. Model., 2005, 45, 542.
[4] Marcou, G. and Rognan, D. J., Chem. Inf. Model., 2007, 47, 195.
[5] Grant, J. A., Haigh, J. A., Pickup, B. T., Nicholls, A., and Sayle, R. A., J. Chem. Inf. Model, 2006, 46, 1912.