For unsupervised MMP analysis to be useful, the large volume of MMP and transform data must be filtered with analysis queries tuned to a user's interests. Matcher enables the most flexible such querying to-date, with control over both sides of the MMP transform (Figures and) and the environment around the transform. As we demonstrate in Figure , and as others have shown previously, the environment around the transform can dictate how a property changes. Sketched atoms can be highlighted as 'variable' (green highlight) or 'constant' (red highlight), which Matcher interprets as belonging to transform or environment, respectively. 'Variable' atoms can be designated as either exact structure or substructure, while 'constant' atoms always represent a substructure of the conserved environment in MMPs that are returned. Matcher respects the sketched point(s) of connection between 'variable' and 'constant' atoms, but also permits disconnected selections within a molecule or even over multiple fragments. Queries with no environment selection also work. Wildcard atoms are permitted. Any point of contact between 'variable' atoms and other atoms, whether designated as part of the 'constant' environment or not, is interpreted as a point of substitution on the 'variable' transform fragment. Up to three such points of substitution are supported in queries. Critically, the environment selection is not restricted to specific hard-coded patterns as in previous approaches. Users can select arbitrarily large, asymmetric, or disconnected environments, any of which could be critical for finding data of interest, such as MMPs from a specific chemical series, or MMPs with specific functional groups.