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@johnmay, is this one good to go too? |
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Not sure - lost track and need to review. Leave for now |
…class (Hydrogens.java) keeping all the logic together. We also improve the logic such that the user can have a single entry point and they specify how they want their hydrogens. I did flirt with the idea of making this very granualar (i.e. bitmask/enum set) but in the end I decided they are really only a few useful options and providing it's not too difficult to implement add any extra future logic that is okay. There are 5 options: Unsafe, Minimal, Explicit, Stereo, Depiction which do different things for different use cases (see doc).
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Rebased - This is good to go now. |
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This overhauls the hydrogen suppression/contraction logic placing it all in one place and adding new useful functionality and fixes some corner case. We now have an enum which controls how you would like your hydrogens stored/represented it has 5 options which are summarised by this diagram (included in the JavaDoc):
WIP as I need to think about the logic for "unsafe" a bit more.