inaccurate explicit/implicit hydrogen handling in fingerprints
Open
Bingo
Priority: High
- Dominant language
- C++
- Stars
- 406
- Forks
- 134
- Avg merge
- 2d 11h
- Merged PRs (30d)
- 24
Description
Using the 'sub' fingerprint for substructure search prefiltering produces false negatives where the hydrogen count is specified in the SMARTS query.
Examples:
Query:
`[*:1]-[OHX2]`
Targets:
`N1C[C@@H](O)CO1.Cl`
`C(F)(F)(F)C(CN)O.Cl`
Query:
`[*:1]-[NHX3]-[*:2]`
Target:
`C(NCC)(C(C)(C)O)=O`
Performing the SMARTS matching produces hits in all cases. The prefiltering works after adding explicit hydrogens to the targets. I suggest to neglect `[H]` in the SMARTS during the sub fingerprint generation as `[H]` includes the implicit hydrogens as well according to the Daylight spec.
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