CMLSnap : Animated reaction mechanisms

Abstract

Reactions with many steps can be represented by a single XML-based table of the atoms, bonds and electrons. For each step the complete Chemical Markup Language 1 representation of all components is obtained and a snapshot representing the end point of the step is generated. These snapshots can then be combined to give an animated description of the complete reaction, both in "2D" chemical structure diagrams and in three dimensions. Here we demonstrate the method's power with enzymatic reactions. It should be noted that readers of this paper will benefit from having an SVG (Scalable Vector Graphics) viewer plugin.