Finding Pharmacophore Mappings

## Finding Mappings

Potential mappings of the pharmacophore onto the molecule are found as follows:

1. Lists of all matches the molecule has for each of the pharmacophore's features are created
2. All possible combinations of these matches are generated

At this stage in the search process, the pharmacophore distances are not used. The only constraint on the mappings is that a single atom may not be involved in more than one feature in the mapping. This improves efficiency by removing degenerate pharmacophores from consideration.