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base repository: cdk/cdk
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  • 13 commits
  • 7 files changed
  • 1 contributor

Commits on Mar 30, 2017

  1. Cache AdjList computation - useful for when we fire lots of SMARTS at…

    … one molecule. In future this should be handed off to the user to manage, this will be easier when AtomRef is introduced.
    johnmay committed Mar 30, 2017
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  2. SMARTS mass matching semantics, 0 = unspecified. Attempting to update…

    … the grammar was not successful.
    johnmay committed Mar 30, 2017
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  3. Minor optimisation we test either the ring connectivity or number or …

    …rings. In the case of R0 we can also check connectivity. [!R0] = [R]
    johnmay committed Mar 30, 2017
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  5. Safe SMARTS optimizations - reorder pattern to be more efficient with…

    …out changing the meaning.
    johnmay committed Mar 30, 2017
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  6. Use VF matcher.

    johnmay committed Mar 30, 2017
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  7. Basic non-compatible SMARTS changes. We implement bit1 and allow bit3…

    … and bi18 to also match the aromatic atoms.
    johnmay committed Mar 30, 2017
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  9. Count aromatic rings at the same time. When MDL say aromatic they rea…

    …lly only mean benzene/pyridine - using the correct arom model this change has no change of results.
    johnmay committed Mar 30, 2017
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  11. Remove check for rings >= 8M bit101. bit101 is described as 8M ring b…

    …ut was actually matching >= 8. Removing this and only checking for 8M rings affects a large number of molecules.
    johnmay committed Mar 30, 2017
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  12. Replace recursive patterns, the alternatives provided by the recursiv…

    …e patterns should usually be matched, e.g. bit118: ACH2CH2A is not equivalent to *1~[#6H2]~[#6H2]~1. This is confirmed by other MACCS implementations (T.J. O'Donnell, Design and use of relational databases in chemistry). There are a lot of changes in MACCS FP generate because recursive SMARTS were incorrectly used: *~[#6H2]~[#6H2]~* matches the SMILES OCCO once uniquely, whilst [$(*~[#6H2]~[#6H2]~*)] matches it twice.
    johnmay committed Mar 30, 2017
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  13. FIxed FP size.

    johnmay committed Mar 30, 2017
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