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Protein_ligand graph support & junction tree feature #164

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Protein_ligand graph support & junction tree feature #164

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Commits on Apr 13, 2022

  1. add mol support

    @yuanqidu
    yuanqidu committed Apr 13, 2022
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Commits on Apr 14, 2022

  1. add rdkit as optional dependency

    @a-r-j
    a-r-j committed Apr 14, 2022
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  2. lint atomic edges

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    a-r-j committed Apr 14, 2022
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  3. lint distance

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    a-r-j committed Apr 14, 2022
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  4. lint graphs

    @a-r-j
    a-r-j committed Apr 14, 2022
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  5. lint atom type

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    a-r-j committed Apr 14, 2022
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  6. lint tests

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    a-r-j committed Apr 14, 2022
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  7. additional node features from rdkit

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    a-r-j committed Apr 14, 2022
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  8. additional vocabularies to atoms

    @a-r-j
    a-r-j committed Apr 14, 2022
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Commits on Apr 15, 2022

  1. add more RDKit constants

    @a-r-j
    a-r-j committed Apr 15, 2022
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  2. refactor config matching utils to reduce duplication

    @a-r-j
    a-r-j committed Apr 15, 2022
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  3. add molecule graph config to yaml parser

    @a-r-j
    a-r-j committed Apr 15, 2022
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  4. lint edge funcs

    @a-r-j
    a-r-j committed Apr 15, 2022
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  5. add bond-based edge feature funcs

    @a-r-j
    a-r-j committed Apr 15, 2022
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  6. add additional Rdkit node features

    @a-r-j
    a-r-j committed Apr 15, 2022
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  7. add feature __init__

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    a-r-j committed Apr 15, 2022
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  8. add molecule __init__

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    a-r-j committed Apr 15, 2022
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  9. lint graphs

    @a-r-j
    a-r-j committed Apr 15, 2022
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  10. fix rdkit constants

    @a-r-j
    a-r-j committed Apr 15, 2022
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  11. add molecule module to docs

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    a-r-j committed Apr 15, 2022
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  12. fix rdkit constants

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    a-r-j committed Apr 15, 2022
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  13. fix rdkit type hint

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    a-r-j committed Apr 15, 2022
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  14. refactor config utils to prevent circular import

    @a-r-j
    a-r-j committed Apr 15, 2022
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  15. add names to graphs

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    a-r-j committed Apr 15, 2022
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  16. add global mol descriptors

    @a-r-j
    a-r-j committed Apr 15, 2022
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  17. add add_hs flag

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    a-r-j committed Apr 15, 2022
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  18. fix feature funcs

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    a-r-j committed Apr 15, 2022
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  19. add descriptor vocab

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    a-r-j committed Apr 15, 2022
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  20. update changelog

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    a-r-j committed Apr 15, 2022
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  21. add molecule tutorial

    @a-r-j
    a-r-j committed Apr 15, 2022
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  22. add molecule tutorial to docs

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    a-r-j committed Apr 15, 2022
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  23. Merge branch 'master' into master

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    a-r-j committed Apr 15, 2022
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  24. update path to config parser utils

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    a-r-j committed Apr 15, 2022
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  25. resolve merge

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    a-r-j committed Apr 15, 2022
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Commits on Apr 16, 2022

  1. add additional molecular graph tests

    @a-r-j
    a-r-j committed Apr 16, 2022
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  2. Merge branch 'master' into master

    @a-r-j
    a-r-j committed Apr 16, 2022
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Commits on Apr 17, 2022

  1. add plotting functions for molecules

    @a-r-j
    a-r-j committed Apr 17, 2022
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  2. :wqMerge branch 'master' of https://github.com/yuanqidu/graphein into… 

    … pr/yuanqidu/157
    @a-r-j
    a-r-j committed Apr 17, 2022
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  3. update mol tutorial with 3d plots

    @a-r-j
    a-r-j committed Apr 17, 2022
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  4. add molecule visualisation to docs

    @a-r-j
    a-r-j committed Apr 17, 2022
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  5. fix molecule notebooks in docs

    @a-r-j
    a-r-j committed Apr 17, 2022
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  6. update docs with refactored config

    @a-r-j
    a-r-j committed Apr 17, 2022
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Commits on Apr 19, 2022

  1. update node naming to including element symbol

    @a-r-j
    a-r-j committed Apr 19, 2022
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  2. Merge branch 'a-r-j:master' into master

    @yuanqidu
    yuanqidu committed Apr 19, 2022
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Commits on Apr 24, 2022

  1. junction added & protein_ligand support added

    @yuanqidu
    yuanqidu committed Apr 24, 2022
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Commits on Apr 26, 2022

  1. clean and refactored codes & comments added

    @yuanqidu
    yuanqidu committed Apr 26, 2022
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Commits on Apr 27, 2022

  1. add __init__ to new test submodules

    @a-r-j
    a-r-j committed Apr 27, 2022
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  2. add prody as extras dependency

    @a-r-j
    a-r-j committed Apr 27, 2022
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Commits on May 9, 2022

  1. fix error where multiple occurences of the same ligand would be treat… 

    …ed as one ligand
    @a-r-j
    a-r-j committed May 9, 2022
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  2. Merge branch 'master' into master

    @a-r-j
    a-r-j committed May 9, 2022
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Commits on Jun 30, 2022

  1. Merge branch 'master' into master

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    a-r-j committed Jun 30, 2022
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Commits on Jul 2, 2022

  1. remove unnecessary pdbs

    @a-r-j
    a-r-j committed Jul 2, 2022
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  2. remove unnecessary pdbs

    @a-r-j
    a-r-j committed Jul 2, 2022
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Commits on Jul 6, 2022

  1. refactor JT computation

    @a-r-j
    a-r-j committed Jul 6, 2022
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  2. refactor JT computation (remove old code)

    @a-r-j
    a-r-j committed Jul 6, 2022
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  3. remove duplicated code in features/sequence

    @a-r-j
    a-r-j committed Jul 6, 2022
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  4. remove unneeded data files

    @a-r-j
    a-r-j committed Jul 6, 2022
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Commits on Aug 23, 2023

  1. Merge branch 'master' into master

    @a-r-j
    a-r-j committed Aug 23, 2023
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Aug 23, 2023
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