Programming Libraries for Naming & Depiction

Although modeling requires 3D structures, chemists often prefer identifying compounds by their name or 2D Kekulé drawing. To provide the chemical language more familiar to that audience, OpenEye offers programmers a complementary pair of toolkits.

Lexichem TK provides high conversion rates of chemical structures to chemical names and vice-versa, while Ogham TK [1] offers artful 2D rendering of chemical structures.

Picto is an example program that shows how Lexichem TK and Ogham TK
may be used to develop an application allowing naming and depiction on
the fly. Picto is not a product but is provided open sourced to licensees
of OEChem TK, Lexichem TK and Ogham TK.

Lexichem TK Features

• Converts connection tables (e.g. SMILES) to chemical names
• Converts chemical names to connection tables (e.g. SMILES)
• The toolkit comes with the applications mol2nam and nam2mol
• Supported nomenclature: IUPAC 79, IUPAC 93, IUPAC 200x, Chemical Abstracts (CAS), Traditional, Systematic, MDL/Beilstein AutoNom, OpenEye. Custom hybrid styles can be created
• Supported languages include: English (American), English (British), English (International), Japanese, Spanish, Swedish, German, French, Polish, Chinese, Hungarian and Russian.

Ogham TK Features

• Generates structure diagrams [2] (2D coordinates) suitable for rendering from connection tables (e.g. SMILES) or 3D structures
• Renders images (GIF, BMP, SVG or PostScript) from either generated or user-supplied structure diagrams
• Comes with example source code for generating JPEG and PNG images, and integration with TrollTech Qt
• Provides consistent (and specifiable) orientation of core substructures
• Offers a variety of display controls (color, size, optional use of superatoms or display hydrogens, style of representation for aromatic and dative bonds, arbitrary atom labels).

[1] The Ogham alphabet system of the ancient Irish is represented by lines, hashes and wedges; it is principally known for the inscription of names on standing stones.
[2] Helson, H.E., in "Reviews in Computational Chemistry", 1999, 13, 313—98, Eds. Lipkowitz, K.B, Boyd, D.B., Wiley-VCH Press.