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Improved PubChem Fingerprinter through comparission to the CACTVS_SUB… #973

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merged 1 commit into from Apr 27, 2023

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@johnmay johnmay commented Apr 24, 2023

…STRUCTURE_KEYS field in PubChem SDfiles.

  • Add an option to use the more correct "ESSSR" ring set - now we have this option
  • Count implicit hydrogens, SMARTS patterns are already implicit/explicit ambivalent
  • Use integers for atomic number count lookups
  • Tweak the "isSaturated" definition based on checked examples

Fixes #970 - larger scale testing could find more differences to address.

…STRUCTURE_KEYS field in PubChem SDfiles.

- Add an option to use the more correct "ESSSR" ring set - now we have this option
- Count implicit hydrogens, SMARTS patterns are already implicit/explicit ambivalent
- Use integers for atomic number count lookups
- Tweak the "isSaturated" definition based on checked examples
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sonarcloud bot commented Apr 24, 2023

@johnmay
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johnmay commented Apr 24, 2023

Not going to fix those code smells - mostly IAtom.C instead of IElement.C but that is cleaner IMO

@egonw egonw merged commit 82d8098 into main Apr 27, 2023
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discrepancy between CDK results and fingerprint extracted directly from pubchem website
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