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  • 9 commits
  • 18 files changed
  • 2 contributors

Commits on Aug 19, 2015

  1. Representation independant type assignment for nitro groups.

    Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
    johnmay authored and egonw committed Aug 19, 2015
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  2. Internal API additions allow us to pass back which bonds are aromatic…

    … by MMFF's model. Ideally we would seperate out the aromaticity to a optional preprocessing step but at the moment the aromaticity needs to be assigned after the initial symbolic types.
    
    Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
    johnmay authored and egonw committed Aug 19, 2015
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  3. Map symbolic types HOCS and HON down to integer type 21. These appear…

    … in the validation suite and labelled as *new* in the parameter files but do not appear in the papers.
    
    Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
    johnmay authored and egonw committed Aug 19, 2015
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  4. Internal class for MMFF Parameter Loading - duplicates/replaces some …

    …functionality of the ForceFieldConfigurator/MMFF94BasedParameterSetReader.
    
    Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
    johnmay authored and egonw committed Aug 19, 2015
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  5. Correct citation id.

    Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
    johnmay authored and egonw committed Aug 19, 2015
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  6. New MMFF partial charges implementation. Relocate tests from descript…

    …or and rebase using SMILES (required due to InChI standardisations).
    
    Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
    johnmay authored and egonw committed Aug 19, 2015
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  7. Delegate existing MMFF partial charge methods to new implementation.

    Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
    johnmay authored and egonw committed Aug 19, 2015
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  8. Deprecate implementations and ignore failing tests of old methods.

    Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
    johnmay authored and egonw committed Aug 19, 2015
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  9. Include copyright statements and some cleanup after review.

    Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
    johnmay authored and egonw committed Aug 19, 2015
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