OESystem::OEIterBase<OEChem::OEMolBase> *
OEMatchedPairApplyTransforms(const OEChem::OEMolBase &mol, OEMatchedPairAnalyzer &mmp,
                             int chemcontext=OEMatchedPairContext::Default,
                             unsigned int minMMPThreshold=0)

The OEMatchedPairApplyTransforms function will take the matched pair analysis provided by the OEMatchedPairAnalyzer engine to generate a set of transformations to apply to the input molecule. The output molecule(s) will be annotated with SD data that identifies the original pair of molecules from the matched pair indexing, any data associated with those original molecules, and the transformation that resulted in the output molecule. The context argument controls the amount of chemistry information that should be used in constructing the transformation reaction, see OEMatchedPairContext. The minMMPThreshold argument will only apply transformations that meet or exceed the specified number of matched pairs. A minMMPThreshold value of 0 will apply transformations regardless of the number of matched pairs associated with them.