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DOCK uses several types of scoring functions to discriminate among orientations and molecules. Scoring is requested using the score_molecules parameter. The scoring functions are implemented with a hierarchical strategy. A master score class manages all scoring functions that DOCK uses. Any of the DOCK scoring functions can be selected as the primary and/or the secondary scoring function. The primary scoring function is used during rigid orienting, anchor-and-grow steps, and minimization, which typically make many calls to the scoring function. The secondary scoring function is used in the final minimization, scoring, and ranking of the molecules.