Introduction

2D structure diagrams can be considered to be the “natural language” of chemists, since the graphical representation allows molecules to be instantly conceivable.

Historically, 2D representations have mainly been used to visualize the connection table of molecular graphs. However, projecting 3D information into the 2D layout and displaying various atom and bond properties on the molecular diagram open up a novel way to present information to chemists.

The Grapheme TK provides several representation schemes that allow visualization of complex molecular interactions and properties in a clear and coherent 2D format that is the most natural to chemists.

Oxford dictionary definition

grapheme /’grafēm/

The smallest meaningful contrastive unit in a writing system.

Wiki definition

A grapheme is the smallest semantically distinguishing unit in a written language, analogous to the phonemes of spoken languages. A grapheme may or may not carry meaning by itself, and may or may not correspond to a single phoneme.

Graphemes include alphabetic letters, typographic ligatures, Chinese characters, numerical digits, punctuation marks, and other individual symbols of any of the world’s writing systems. The word grapheme is derived from Greek γράφω gráphō (“write”), and the suffix -eme, by analogy with phoneme and other names of emic units.

Note

This manual provides examples about molecule annotations, drawing 2D molecule surfaces and displaying atom properties on a property map. However, the basic concepts of molecule depiction and image handling are discussed in the OEDepict TK manual. Therefore, studying the OEDepict TK manual is highly recommended prior to reading this documentation.