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EZ Isomerism and R/S chirality continued #45

Merged
merged 18 commits into from
Sep 11, 2024
Merged

EZ Isomerism and R/S chirality continued #45

merged 18 commits into from
Sep 11, 2024

Commits on May 3, 2024

  1. EZ isomerism and chirality

    @fgrunewald
    fgrunewald committed May 3, 2024
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Commits on Jun 12, 2024

  1. Apply suggestions from code review 

    address comments

Co-authored-by: Peter C Kroon <pckroon@users.noreply.github.com>
    @fgrunewald @pckroon
    fgrunewald and pckroon committed Jun 12, 2024
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Commits on Jun 21, 2024

  1. proper ring sorting and implicit hydrogen

    @fgrunewald
    fgrunewald committed Jun 21, 2024
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  2. Merge branch 'master' into isomerism

    @fgrunewald
    fgrunewald committed Jun 21, 2024
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  3. fix bond order

    @fgrunewald
    fgrunewald committed Jun 21, 2024
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Commits on Jul 11, 2024

  1. Merge remote-tracking branch 'origin/master' into isomerism

    @pckroon
    pckroon committed Jul 11, 2024
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  2. Clean up tetrahedral chirality 

    Allows for implicit hydrogens, and add test cases from opensmiles
    @pckroon
    pckroon committed Jul 11, 2024
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  3. Move explicit hydrogen accounting to after chirality assignment 

    Also, adapt add/remove explicit hydrogen functions to correct the stereo of the parent
    @pckroon
    pckroon committed Jul 11, 2024
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  4. Fix typo's

    @pckroon
    pckroon committed Jul 11, 2024
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Commits on Sep 2, 2024

  1. Make annotate_ez_isomers private. Make remove_explicit_hydrogens awar… 

    …e of EZ chirality
    @pckroon
    pckroon committed Sep 2, 2024
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  2. Add tests for chirality corner cases

    @pckroon
    pckroon committed Sep 2, 2024
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  3. Push coverage, fix issues with removing explicit EZchirality hydrogens

    @pckroon
    pckroon committed Sep 2, 2024
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  4. Add a few nobranch pragmas for malformatted smiles

    @pckroon
    pckroon committed Sep 2, 2024
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Commits on Sep 3, 2024

  1. Add stereochemistry to readme

    @pckroon
    pckroon committed Sep 3, 2024
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Commits on Sep 4, 2024

  1. Make the writer print a warning when it's losing stereochemical infor… 

    …mation
    @pckroon
    pckroon committed Sep 4, 2024
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  2. Correct writer warning for stereochemical info

    @pckroon
    pckroon committed Sep 4, 2024
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Commits on Sep 11, 2024

  1. Remove leftover comment

    @pckroon
    pckroon committed Sep 11, 2024
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  2. Rename tetrehedral RS stereo attribute from "stereo" to "rs_isomer"

    @pckroon
    pckroon committed Sep 11, 2024
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