Protonation and Formal Charges

The program has been implemented on top of the Gorina [15] toolkit library. All chemical substructures have been hard-coded for performance reasons. The program can handle 2-D or 3-D SDFiles and will, in the latter case, produce correct 3-D coordinates for all hydrogens being changed in the process. 

By default, Permute would generate all possible combinations of protonation states at all of these functional groups when contained in a molecule. A number of additional rules are used to prevent unreasonable combinations and combinatorial explosion  

This set of rules stops isomer generation whenever one rule is violated. It implicitly restricts the total number of isomers generated also. 

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