A "--smallest-transformation-only" option doesn't produce desirable result with some transformations. It seems that there is conflict between --smallest-transformation-only option (use during indexing) with --min-heavies-per-const-frag option (use during fragmentation)
For example, if one considers this transformation [:1]C(=O)Nc1ccccc1>>[:1]C(=O)Nc1cccnc1, it is clearly reducible to [:1]c1ccccc1>>[:1]c1cccnc1.
However, if someone sets the option --min-heavies-per-const-frag == 9 (during fragmentation step), then the output is [:1]C(=O)Nc1ccccc1>>[:1]C(=O)Nc1cccnc1 and not the [:1]c1ccccc1>>[:1]c1cccnc1.
This is possibly because, a number of heavy atoms in fragment [:1]C(=O)Nc1ccccc1 (or [:1]C(=O)Nc1cccnc1) <=min-heavies-per-const-frag and hence there is no further fragmentation possible for this fragments and hence it's not reducible.
A "--smallest-transformation-only" option doesn't produce desirable result with some transformations. It seems that there is conflict between --smallest-transformation-only option (use during indexing) with --min-heavies-per-const-frag option (use during fragmentation)
For example, if one considers this transformation [:1]C(=O)Nc1ccccc1>>[:1]C(=O)Nc1cccnc1, it is clearly reducible to [:1]c1ccccc1>>[:1]c1cccnc1.
However, if someone sets the option --min-heavies-per-const-frag == 9 (during fragmentation step), then the output is [:1]C(=O)Nc1ccccc1>>[:1]C(=O)Nc1cccnc1 and not the [:1]c1ccccc1>>[:1]c1cccnc1.
This is possibly because, a number of heavy atoms in fragment [:1]C(=O)Nc1ccccc1 (or [:1]C(=O)Nc1cccnc1) <=min-heavies-per-const-frag and hence there is no further fragmentation possible for this fragments and hence it's not reducible.