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Integrating xyz2mol Into The RDKit Core (GSoC 2022) #5557

Merged
merged 55 commits into from Oct 6, 2022
Merged

Integrating xyz2mol Into The RDKit Core (GSoC 2022) #5557

merged 55 commits into from Oct 6, 2022

Commits on Jul 13, 2022

  1. Added xyz2mol file parser and tests

    Sreya Gogineni committed Jul 13, 2022
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  2. pulled changes from master onto branch

    Sreya Gogineni committed Jul 13, 2022
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  3. Merge pull request #1 from gosreya/localb 

    Added file parser.
    @gosreya
    gosreya committed Jul 13, 2022
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  4. deleted some comments

    Sreya Gogineni committed Jul 13, 2022
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  5. Merge pull request #2 from gosreya/localb 

    deleted some comments
    @gosreya
    gosreya committed Jul 13, 2022
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  6. Delete file parser

    @gosreya
    gosreya committed Jul 13, 2022
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  7. Delete file parser test

    @gosreya
    gosreya committed Jul 13, 2022
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  8. Revert "Localb"

    @gosreya
    gosreya committed Jul 13, 2022
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  9. Merge pull request #3 from gosreya/revert-1-localb 

    Revert "Localb"
    @gosreya
    gosreya committed Jul 13, 2022
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  10. adding all files again

    Sreya Gogineni committed Jul 13, 2022
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  11. adding file parser and test

    Sreya Gogineni committed Jul 13, 2022
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Commits on Jul 15, 2022

  1. Updated empty string check 

    Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
    @gosreya @greglandrum
    gosreya and greglandrum committed Jul 15, 2022
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  2. Updated atom initialization 

    Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
    @gosreya @greglandrum
    gosreya and greglandrum committed Jul 15, 2022
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Commits on Jul 16, 2022

  1. Allow zero-atom molecule object 

    Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
    @gosreya @greglandrum
    gosreya and greglandrum committed Jul 16, 2022
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Commits on Jul 21, 2022

  1. file parser improvements and added 0-atom mol test

    Sreya Gogineni committed Jul 21, 2022
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Commits on Jul 26, 2022

  1. added xyz block parser and other fixes

    Sreya Gogineni committed Jul 26, 2022
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Commits on Jul 30, 2022

  1. Merge pull request #5 from gosreya/twig 

    Added file parser and accompanied tests
    @gosreya
    gosreya committed Jul 30, 2022
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  2. Added the DetermineBonds library with atomic connectivity determination

    Sreya Gogineni committed Jul 30, 2022
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Commits on Aug 26, 2022

  1. atomic connectivity updates including EHT methhod addition

    Sreya Gogineni committed Aug 26, 2022
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Commits on Aug 31, 2022

  1. incorporated more suggestions

    Sreya Gogineni committed Aug 31, 2022
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Commits on Sep 6, 2022

  1. Merge pull request #6 from gosreya/twig 

    Added the DetermineBonds library with atomic connectivity determination
    @gosreya
    gosreya committed Sep 6, 2022
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  2. adding buggy version of determine bond ordering

    Sreya Gogineni committed Sep 6, 2022
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  3. added documentation for determineBonds() use

    Sreya Gogineni committed Sep 6, 2022
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  4. fixed unfavorable oxygen bond ordering

    Sreya Gogineni committed Sep 6, 2022
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Commits on Sep 7, 2022

  1. suggested updates

    Sreya Gogineni committed Sep 7, 2022
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Commits on Sep 10, 2022

  1. additional error checking and added determine bond ordering radical t… 

    …esting
    Sreya Gogineni committed Sep 10, 2022
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  2. divided test files into categories

    Sreya Gogineni committed Sep 10, 2022
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  3. added determineBonds() combining connectivity and bond ordering

    Sreya Gogineni committed Sep 10, 2022
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Commits on Sep 11, 2022

  1. Merge pull request #8 from gosreya/twig 

    Added determineBondOrdering() function
    @gosreya
    gosreya committed Sep 11, 2022
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  2. edited determineBonds.h documentation, added readme

    Sreya Gogineni committed Sep 11, 2022
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  3. small grammar fixes

    Sreya Gogineni committed Sep 11, 2022
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  4. more tiny fixes

    Sreya Gogineni committed Sep 11, 2022
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  5. one less letter

    Sreya Gogineni committed Sep 11, 2022
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  6. Merge pull request #9 from gosreya/twig 

    Added README.md and minor documentation changes
    @gosreya
    gosreya committed Sep 11, 2022
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  7. Merge branch 'rdkit:master' into gsoc2022

    @gosreya
    gosreya committed Sep 11, 2022
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  8. another typo fix

    Sreya Gogineni committed Sep 11, 2022
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  9. Merge pull request #10 from gosreya/twig 

    typo fix
    @gosreya
    gosreya committed Sep 11, 2022
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Commits on Sep 14, 2022

  1. make the xyz2mol functionality optional

    @greglandrum
    greglandrum committed Sep 14, 2022
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  2. Merge remote-tracking branch 'origin/master' into gsoc2022

    @greglandrum
    greglandrum committed Sep 14, 2022
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  3. enable that for the CI builds

    @greglandrum
    greglandrum committed Sep 14, 2022
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  4. Update CMakeLists.txt 

    Co-authored-by: Sreya Gogineni <74024376+gosreya@users.noreply.github.com>
    @greglandrum @gosreya
    greglandrum and gosreya committed Sep 14, 2022
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  5. Merge pull request #11 from greglandrum/gsoc2022 

    make the new code optional
    @gosreya
    gosreya committed Sep 14, 2022
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Commits on Sep 16, 2022

  1. array to vector

    Sreya Gogineni committed Sep 16, 2022
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  2. Merge pull request #12 from gosreya/post 

    array to vector
    @gosreya
    gosreya committed Sep 16, 2022
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Commits on Sep 20, 2022

  1. get windows DLL builds working

    @greglandrum
    greglandrum committed Sep 20, 2022
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  2. Merge pull request #13 from greglandrum/gsoc2022 

    get windows DLL builds working
    @gosreya
    gosreya committed Sep 20, 2022
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Commits on Sep 23, 2022

  1. rename determineBondOrder -> determineBondOrders

    @greglandrum
    greglandrum committed Sep 23, 2022
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  2. run clang-format

    @greglandrum
    greglandrum committed Sep 23, 2022
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  3. add python wrappers 

    rename determineBondOrder->determineBondOrders
    @greglandrum
    greglandrum committed Sep 23, 2022
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  4. expose XYZ parsers to python

    @greglandrum
    greglandrum committed Sep 23, 2022
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Commits on Sep 24, 2022

  1. Merge pull request #14 from greglandrum/gsoc2022 

    initial version of the python wrappers
    @gosreya
    gosreya committed Sep 24, 2022
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Commits on Oct 5, 2022

  1. Merge remote-tracking branch 'origin/master' into gsoc2022

    @greglandrum
    greglandrum committed Oct 5, 2022
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  2. changes in response to review

    @greglandrum
    greglandrum committed Oct 5, 2022
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  3. Merge pull request #15 from greglandrum/gsoc2022 

    code review changes
    @gosreya
    gosreya committed Oct 5, 2022
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  4. Merge branch 'master' into gsoc2022

    @greglandrum
    greglandrum committed Oct 5, 2022
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