## Generating Structures

Three-dimensional structures are generated for a mapping by:

1. Creating an initial set of coordinates by embedding the updated bounds matrix for each mapping [Crippen1981]
2. Cleaning up the embedded structures using the Universal Force Field (UFF).[Rappe1992, Casewit1992] The optimization is done with constraints to ensure that the final structure still satisfies the pharmacophore.
3. Aligning the cleaned conformation to the reference pharmacophore.[Heisterberg1990]

Whenever possible, multiple aligned conformations are generated for each mapping. This provides the user with an overview of the ways in which the probe molecule can satisfy the pharmacophore.<>