Fragmenter fragments molecules based on predefined cleavage rules. The cleavage rules are given in form of reaction molecules in the configuration XML.
The Fragmenter class itself is mainly responsible for the command line interface, while you should instantiate its ExhaustiveFragmenter for API access. This class implements an exhaustive way of finding all possible fragmentations with the specified parameters. Some of these can be specified in API methods:
There is a configurable cleavage revision mechanism that can filter out some of the cleavages. This can be implemented by extending the CutBonReviser class and implementing its revise(int a1, int a2) method. Currently only the RECAP method is available, which is implemented by the Recap class. Its parameters can be set in the corresponding section of the configuration XML as well as by parameter setter methods.
The fragmentation is divided into two parts:
fragment(List coll, Molecule mol) includes these two steps for convenience.
A typical API usage example can be found in the ExhaustiveFragmenter class header.