The Visual Interactivity Design of the Chemical Reaction Map in RMapViewer

Abstract

RMapViewer (Reaction Map Viewer) is an interactive visual environment for exploring a large network of chemical reaction paths, called the reaction map. The chemical reaction map consists of a set of atomic isomorphic 3-D structural configuration states that are theoretically derived by using the quantum mechanics. Each node is associated with its theoretically derived potential energy, and is connected with one or more other nodes via a transition link. The difference between the energy of two linked nodes represents necessary energy to transform the structural state on the one end to the adjacent state on the other end. The reaction map has been designed to support a user (i.e., a chemist) in exploring the map in a variety of ways, such as to find out possible molecule structures within a certain number of transitional steps from a focused node, or compare the energy values of possible transition paths between given two nodes. This paper describes RMapViewer by illustrating how a user interacts with the system through the different types of visualizations of the reaction map, sorting schemes, and transitional animations along with the model of a user's cognitive process in exploring the reaction map.