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In addition to the pKa normalization mentioned above, Filter allows any number of additional molecular normalizations. Since normalizations are usually specific to a particular company or site, Filter provides the ability for users to input normalizations, such as the nitro tautomer state, but doesn't provide default implementations. Each normalization can be input as a SMIRKS reaction definition (one reaction per line) in a text file and entered into filter via the 'normalize' command-line parameter. All normalization transformations that can be appropriately applied to each molecule will be applied before each subsequent step in the filtering process.
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