Synthesizer processes a sequence of reactions taking their reactants from and putting their products into predefined molecule sets. The purpose is to generate a set of synthetically feasible molecules which can be generated from a set of input molecules by repeatedly using a set of specified reactions.
The SynthesisGraph describes the reaction scheme: each reaction is represented as a directed graph edge with an array of reactant MoleculeSet objects as start node and an array of product MoleculeSet objects as end node. The SynthesisAlgorithm describes how this synthesis graph is used to process the reactions: the order of the reactions and the molecule selection mechanism to be used when taking the reactants from the corresponding molecule sets. Currently 3 such algorithms are implemented:
The SynthesisGraph and the SynthesisAlgorithm are specified in the configuration XML.
Synthesizer can be created to run in memory mode, file mode or database mode.
API usage example using database mode can be found in the Synthesizer class header.