--smallest-transformation-only doesn't work for some transformations #61

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opened 2025-10-14 17:04:20 -06:00 by navan · 0 comments

navan commented

2025-10-14 17:04:20 -06:00

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Originally created by @mahendra-awale on 11/4/2019

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.

*Originally created by @mahendra-awale on 11/4/2019* 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.