We now discuss limitations of the ( ) subgraph matching algorithm and ( ) replacement routine as implemented in PoreMatMod.jl. First, the subgraph matching algorithm is unable to distinguish among stereoisomers or conformations of flexible moieties, as the graph representation of a fragment is invariant to stereoisomerism and conformation changes. By imposing other geometrybased constraints on matches, such a budget on the sum of pairwise distances between the corresponding atoms after aligning the query with its matching substructure of the parent-thereby quantifying the quality of the spatial overlay-it is possible to distinguish among stereoisomers and conformations. Second, replacement of a query fragment with a replacement fragment bearing no structural commonalities ("overlap") with it is presently not possible because there is no basis for automatically defining the optimality of the alignment of the replacement fragment with the parent crystal structure. Third, as the child structure inherits the unit cell of the parent structure, PoreMatMod.jl cannot currently handle replacements that require expansion/contraction of the unit cell. E.g., it cannot replace a linker of a MOF with a shorter or longer linker, as then the unit cell would need to contract/expand to accommodate it.