1. Introduction

This is the documentation for the OpenEye Shape toolkit. Shape and associated color functions allow a rigorous and rapid comparison of the shape of 2 molecules to get similarity. This comparison can be in an arbitrary alignment provided by some outside source, or the optimum overlap between the 2 molecules can be maximized then the resulting overlap properties can be calculated.

Also, while most discussions will involve the comparison of two small molecules, most of the algorithms work on grids as well.

In all the examples below, when considering the two species to be compared, we will use the following naming convention. The object that is stationary will be known as the reference and the object being compared will be called the fit object. This technology is the same as found in OpenEye's application, ROCS, where these 2 objects are also sometimes referred to as the query and dbase molecule, respectively.

Subsections

1.1 History

				Shape Toolkit Java Programming Manual

				Shape Toolkit Java Programming Manual