Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

PDBManager - Bug fixes, adding necessary changes to export only first PDB model, and merging-in latest updates from master #309

Merged
merged 154 commits into from
Apr 22, 2023

Commits on Feb 21, 2023

  1. Fix graph sequence (atomistic graphs in `initialise_graph_with_metada…

    …ta` had duplicated residues) (a-r-j#268)
    
    * Fix param name typo in function docstring
    
    * fix: atomistic graph only has sequence residues for CA atom in `initialise_graph_with_metadata`
    
    * fix: avoid changing dataframe when extracting rows
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * add: test sequence feature in graphs
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * fix graph sequence feature (a-r-j#268)
    
    * fix matplotlib deprecation
    
    * fix test bug
    
    * change build to ubuntu-latest
    
    * remove unecessary selection
    
    ---------
    
    Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com>
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Arian Jamasb <arjamasb@gmail.com>
    4 people authored Feb 21, 2023
    Configuration menu
    Copy the full SHA
    acaef3a View commit details
    Browse the repository at this point in the history

Commits on Feb 25, 2023

  1. Configuration menu
    Copy the full SHA
    6a10c9d View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    3012ffe View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    d304a06 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    228946f View commit details
    Browse the repository at this point in the history
  5. Remove unused test

    amorehead committed Feb 25, 2023
    Configuration menu
    Copy the full SHA
    a2f1424 View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    a6d2137 View commit details
    Browse the repository at this point in the history
  7. Configuration menu
    Copy the full SHA
    052801b View commit details
    Browse the repository at this point in the history

Commits on Feb 26, 2023

  1. add deposition date parsing

    a-r-j committed Feb 26, 2023
    Configuration menu
    Copy the full SHA
    685a2e6 View commit details
    Browse the repository at this point in the history
  2. remove pdb.py

    a-r-j committed Feb 26, 2023
    Configuration menu
    Copy the full SHA
    abeef32 View commit details
    Browse the repository at this point in the history
  3. add chain extraction util

    a-r-j committed Feb 26, 2023
    Configuration menu
    Copy the full SHA
    5412622 View commit details
    Browse the repository at this point in the history
  4. add chain writing method

    a-r-j committed Feb 26, 2023
    Configuration menu
    Copy the full SHA
    e4ffe3d View commit details
    Browse the repository at this point in the history
  5. Configuration menu
    Copy the full SHA
    ae8a246 View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    f520f98 View commit details
    Browse the repository at this point in the history
  7. Configuration menu
    Copy the full SHA
    22122b3 View commit details
    Browse the repository at this point in the history
  8. Fix up SonarCloud concerns

    amorehead committed Feb 26, 2023
    Configuration menu
    Copy the full SHA
    c4d8de4 View commit details
    Browse the repository at this point in the history

Commits on Feb 27, 2023

  1. Configuration menu
    Copy the full SHA
    67bc788 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    3b42dab View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    9ed7171 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    1878f78 View commit details
    Browse the repository at this point in the history
  5. Configuration menu
    Copy the full SHA
    67524a8 View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    d252d2e View commit details
    Browse the repository at this point in the history
  7. add additional properties

    a-r-j committed Feb 27, 2023
    Configuration menu
    Copy the full SHA
    81e4c23 View commit details
    Browse the repository at this point in the history
  8. Configuration menu
    Copy the full SHA
    279ad3e View commit details
    Browse the repository at this point in the history
  9. Configuration menu
    Copy the full SHA
    1baf309 View commit details
    Browse the repository at this point in the history
  10. Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…

    …nto pr/amorehead/272-1
    a-r-j committed Feb 27, 2023
    Configuration menu
    Copy the full SHA
    e27c11c View commit details
    Browse the repository at this point in the history
  11. Configuration menu
    Copy the full SHA
    408ab6a View commit details
    Browse the repository at this point in the history
  12. Configuration menu
    Copy the full SHA
    f9e8d8d View commit details
    Browse the repository at this point in the history
  13. Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…

    …nto pr/amorehead/272-1
    a-r-j committed Feb 27, 2023
    Configuration menu
    Copy the full SHA
    bf36dc2 View commit details
    Browse the repository at this point in the history
  14. Configuration menu
    Copy the full SHA
    af2818b View commit details
    Browse the repository at this point in the history
  15. Configuration menu
    Copy the full SHA
    b6c52d8 View commit details
    Browse the repository at this point in the history
  16. Configuration menu
    Copy the full SHA
    407a80c View commit details
    Browse the repository at this point in the history
  17. Configuration menu
    Copy the full SHA
    f6e4e40 View commit details
    Browse the repository at this point in the history
  18. Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…

    …nto pr/amorehead/272-1
    a-r-j committed Feb 27, 2023
    Configuration menu
    Copy the full SHA
    7821d9f View commit details
    Browse the repository at this point in the history
  19. Configuration menu
    Copy the full SHA
    59b95b2 View commit details
    Browse the repository at this point in the history
  20. Configuration menu
    Copy the full SHA
    3b7d4c9 View commit details
    Browse the repository at this point in the history
  21. Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…

    …nto pr/amorehead/272-1
    a-r-j committed Feb 27, 2023
    Configuration menu
    Copy the full SHA
    7797e29 View commit details
    Browse the repository at this point in the history
  22. Configuration menu
    Copy the full SHA
    7a66e91 View commit details
    Browse the repository at this point in the history
  23. Configuration menu
    Copy the full SHA
    7a6ff72 View commit details
    Browse the repository at this point in the history
  24. Configuration menu
    Copy the full SHA
    49b594d View commit details
    Browse the repository at this point in the history
  25. Configuration menu
    Copy the full SHA
    624ed1b View commit details
    Browse the repository at this point in the history
  26. Configuration menu
    Copy the full SHA
    a36c960 View commit details
    Browse the repository at this point in the history
  27. Configuration menu
    Copy the full SHA
    88f5f14 View commit details
    Browse the repository at this point in the history
  28. Update .gitignore

    amorehead committed Feb 27, 2023
    Configuration menu
    Copy the full SHA
    45c5a6f View commit details
    Browse the repository at this point in the history
  29. Configuration menu
    Copy the full SHA
    44663bb View commit details
    Browse the repository at this point in the history
  30. Configuration menu
    Copy the full SHA
    ed6c3e4 View commit details
    Browse the repository at this point in the history
  31. Configuration menu
    Copy the full SHA
    fd56f47 View commit details
    Browse the repository at this point in the history
  32. Configuration menu
    Copy the full SHA
    8df967c View commit details
    Browse the repository at this point in the history

Commits on Feb 28, 2023

  1. Fix bug in length filtering functions, fix print bugs in utils, and a…

    …dd ability to write-out PDB files after selecting a subset of chains to include in them
    amorehead committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    540662b View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    0c4c39e View commit details
    Browse the repository at this point in the history
  3. Fix string formatting

    amorehead committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    9eac3e9 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    8462fa5 View commit details
    Browse the repository at this point in the history
  5. Configuration menu
    Copy the full SHA
    0fb19cc View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    2ba6c99 View commit details
    Browse the repository at this point in the history

Commits on Mar 1, 2023

  1. Configuration menu
    Copy the full SHA
    587f900 View commit details
    Browse the repository at this point in the history

Commits on Mar 2, 2023

  1. Configuration menu
    Copy the full SHA
    055a192 View commit details
    Browse the repository at this point in the history

Commits on Mar 11, 2023

  1. Add improved error message for non standard node funcs a-r-j#274 (a-r…

    …-j#275)
    
    * Add improved error message for non standard node funcs a-r-j#274
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    a-r-j and pre-commit-ci[bot] authored Mar 11, 2023
    Configuration menu
    Copy the full SHA
    b8a69a9 View commit details
    Browse the repository at this point in the history
  2. clean up unused files and move docs from root (a-r-j#276)

    * clean up unused files and move docs from root
    
    * remove setup.cfg
    a-r-j authored Mar 11, 2023
    Configuration menu
    Copy the full SHA
    edaf836 View commit details
    Browse the repository at this point in the history
  3. prelim path support a-r-j#269 (a-r-j#277)

    * prelim path support a-r-j#269
    
    * fix import error
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * Update changelog
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    a-r-j and pre-commit-ci[bot] authored Mar 11, 2023
    Configuration menu
    Copy the full SHA
    b9f6dc4 View commit details
    Browse the repository at this point in the history
  4. Switch to miniconda for build (a-r-j#278)

    * switch to miniconda for build
    
    * update docker build
    
    * switch to checkout v3
    a-r-j authored Mar 11, 2023
    Configuration menu
    Copy the full SHA
    16095f0 View commit details
    Browse the repository at this point in the history
  5. Improve altloc handling (a-r-j#263)

    * Fix bug in `add_k_nn_edges`.
    
    `kneighbors_graph(X=dist_mat, ...)` is wrong since `X` may not be a distance matrix. This leads to wrong results which may be similar to correct ones.
    
    * Extend `add_k_nn_edges`.
    
    * Add types to docstring
    
    * Update changelog
    
    * Add `kind_name` argument
    
    * Test `filter_distmat`
    
    * Set default value of `long_interaction_threshold` to 0
    
    * Fix filtering bug in `add_k_nn_edges`
    
    * Test `add_k_nn_edges`
    
    * Refactor with `add_edge`
    
    * Fix bug for empty `edges_to_excl`
    
    * Improve `convert_nx_to_pyg`
    
    * Fix bug in `plot_pyg_data`
    
    * Test `convert_nx_to_pyg` on multimers
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * Update `CHANGELOG.md`
    
    * Fix version in `CHANGELOG.md`
    
    * Handle corner cases
    
    * Handle NaNs in coordinatess
    
    * Add PyG install to CI
    
    * typo in CI config
    
    * bump torch versions in CI
    
    * make pyg-related tests conditional pyg installation
    
    * Try fixing graph attributes
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * Fix typo and extend amino acid 3to1, 1to3 mappings
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * Adapt imports of amino acid codes
    
    * add semicolon to version
    
    * remove wildcard version number for pyyaml
    
    * fix typo
    
    * fix additonal typos
    
    * Extend aggregation to vectors
    
    * Implement `aggregate_feature_over_residues`
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * Add docstring and aggregation type
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * import literal from typing extensions
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * Add missing `median` in exception message
    
    * Fix `nullcontext`
    
    * fix dataset test
    
    * fix division by zero errors in edge colouring
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * update changlelog
    
    * Separate and improve `remove_alt_locs`
    
    Removal of alt_locs is separeted from removal of insertions. Additionaly, now alt_locs with hihger occupancies are left
    
    * Test `remove_alt_locs`
    
    * Rename test
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * Set `insertions=True` by default
    
    * Make `alt_locs` configurable (TODO `include` case)
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * use typing_extensions literal for 3.7 compatibility
    
    * use typing extensions literal for 3.7 compatibility
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * improve hbond donor/acceptor assignment robustnness
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * replace trailing ":" in insertions
    
    * fix test and hbond granularity inference
    
    * Add altloc identifer to node ID
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * fix tests
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * fix test
    
    * fix test
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * actually fix test
    
    * update changelog
    
    * Fix typo
    
    ---------
    
    Co-authored-by: Arian Jamasb <arjamasb@gmail.com>
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    3 people authored Mar 11, 2023
    Configuration menu
    Copy the full SHA
    ea79ad1 View commit details
    Browse the repository at this point in the history

Commits on Mar 12, 2023

  1. Df processing a-r-j#216 (a-r-j#222)

    * docstrings and df processing funcs a-r-j#216
    
    * dcstrings
    
    * add test
    
    * lint test
    
    * fix test
    
    * fix typo in test
    
    * Update changelog
    
    * fix typo in test
    
    * fix broken test
    
    * fix broken test
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * add hetatm removal to test
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * use atomic granularity
    
    * fix syntax error
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * fix bugs in test
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * fix test
    
    * typo
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    a-r-j and pre-commit-ci[bot] authored Mar 12, 2023
    Configuration menu
    Copy the full SHA
    b308a58 View commit details
    Browse the repository at this point in the history

Commits on Mar 14, 2023

  1. Minor patch convert_nx_to_pyg a-r-j#280 (a-r-j#281)

    * nx_to_pyg bug fix a-r-j#280
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * update changelog
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Arian Jamasb <arjamasb@gmail.com>
    3 people authored Mar 14, 2023
    Configuration menu
    Copy the full SHA
    1e2764b View commit details
    Browse the repository at this point in the history

Commits on Mar 18, 2023

  1. changes for 1.6.0 (a-r-j#279)

    * changes for 1.6.0
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    a-r-j and pre-commit-ci[bot] authored Mar 18, 2023
    Configuration menu
    Copy the full SHA
    82d3ba3 View commit details
    Browse the repository at this point in the history

Commits on Mar 21, 2023

  1. Configuration menu
    Copy the full SHA
    35d1064 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    ff675bd View commit details
    Browse the repository at this point in the history
  3. add initial tests

    a-r-j committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    9ae9375 View commit details
    Browse the repository at this point in the history
  4. update changelog

    a-r-j authored Mar 21, 2023
    Configuration menu
    Copy the full SHA
    054ff60 View commit details
    Browse the repository at this point in the history
  5. add tutorial notebook

    a-r-j committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    8bb6e63 View commit details
    Browse the repository at this point in the history
  6. Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…

    …nto pr/amorehead/272-1
    a-r-j committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    3a316ba View commit details
    Browse the repository at this point in the history
  7. Configuration menu
    Copy the full SHA
    e1ac7b0 View commit details
    Browse the repository at this point in the history

Commits on Mar 22, 2023

  1. add module-level import

    a-r-j committed Mar 22, 2023
    Configuration menu
    Copy the full SHA
    a4969d6 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    efb3bc4 View commit details
    Browse the repository at this point in the history

Commits on Mar 25, 2023

  1. Configuration menu
    Copy the full SHA
    7335baa View commit details
    Browse the repository at this point in the history
  2. fix download checker

    a-r-j committed Mar 25, 2023
    Configuration menu
    Copy the full SHA
    f8ad185 View commit details
    Browse the repository at this point in the history
  3. actually fix download checker

    a-r-j committed Mar 25, 2023
    Configuration menu
    Copy the full SHA
    f8ae78e View commit details
    Browse the repository at this point in the history
  4. add availability filter

    a-r-j committed Mar 25, 2023
    Configuration menu
    Copy the full SHA
    1436907 View commit details
    Browse the repository at this point in the history

Commits on Mar 27, 2023

  1. FoldComp ML Datasets (a-r-j#284)

    * add foldcomp dataset util
    
    * clean up
    
    * add import warnings
    
    * add foldcomp dataset extra dependencies
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * exclude foldcomp from notebook tests. download too big :(
    
    * update changelog
    
    * add lightning datamodule wrapper
    
    * add transform functionality
    
    * docs: add new module to API reference
    
    * update notebook
    
    * fix: fix paths issue on setup
    
    * add foldcomp dataset tutorial to docs
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * add stage param to setup
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    a-r-j and pre-commit-ci[bot] authored Mar 27, 2023
    Configuration menu
    Copy the full SHA
    bf53b26 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    c0cdaf0 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    b7226a0 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    5ff520e View commit details
    Browse the repository at this point in the history
  5. add tutorial nblink

    a-r-j committed Mar 27, 2023
    Configuration menu
    Copy the full SHA
    e65935d View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    0c96f38 View commit details
    Browse the repository at this point in the history
  7. mv pdb data to ml API

    a-r-j committed Mar 27, 2023
    Configuration menu
    Copy the full SHA
    4d1007c View commit details
    Browse the repository at this point in the history
  8. rm pyg dataset import

    a-r-j committed Mar 27, 2023
    Configuration menu
    Copy the full SHA
    64ec09f View commit details
    Browse the repository at this point in the history
  9. rm unused code

    a-r-j committed Mar 27, 2023
    Configuration menu
    Copy the full SHA
    96f3ac5 View commit details
    Browse the repository at this point in the history
  10. fix annotation

    a-r-j committed Mar 27, 2023
    Configuration menu
    Copy the full SHA
    618bcee View commit details
    Browse the repository at this point in the history

Commits on Mar 29, 2023

  1. add MMTF download format

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    8d5ca7a View commit details
    Browse the repository at this point in the history
  2. refactor dependency utils

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    d8e5c62 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    142c8d9 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    25f576c View commit details
    Browse the repository at this point in the history
  5. update .gitignore

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    bd4c60c View commit details
    Browse the repository at this point in the history
  6. ignore cif too

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    746ad26 View commit details
    Browse the repository at this point in the history
  7. ignore cif too

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    98f0075 View commit details
    Browse the repository at this point in the history
  8. ignore foldcomp files

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    0a09b00 View commit details
    Browse the repository at this point in the history
  9. Configuration menu
    Copy the full SHA
    5ad764c View commit details
    Browse the repository at this point in the history
  10. ignore mol2

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    fe84d40 View commit details
    Browse the repository at this point in the history
  11. Configuration menu
    Copy the full SHA
    be63c6d View commit details
    Browse the repository at this point in the history
  12. update folding utils

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    dd7ce39 View commit details
    Browse the repository at this point in the history
  13. add max batch option

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    9737fd6 View commit details
    Browse the repository at this point in the history
  14. add foldcomp utils

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    9b6c832 View commit details
    Browse the repository at this point in the history
  15. Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…

    …nto pr/amorehead/272-1
    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    a899352 View commit details
    Browse the repository at this point in the history
  16. Configuration menu
    Copy the full SHA
    2bf820d View commit details
    Browse the repository at this point in the history
  17. add notebook updates [WIP]

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    ea0812d View commit details
    Browse the repository at this point in the history
  18. Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…

    …nto pr/amorehead/272-1
    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    c82a344 View commit details
    Browse the repository at this point in the history
  19. Configuration menu
    Copy the full SHA
    4a3bf5c View commit details
    Browse the repository at this point in the history
  20. remove datasets init

    a-r-j committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    cdcce18 View commit details
    Browse the repository at this point in the history
  21. Configuration menu
    Copy the full SHA
    88c6d91 View commit details
    Browse the repository at this point in the history

Commits on Mar 30, 2023

  1. add PDBmanager to __init__

    a-r-j authored Mar 30, 2023
    Configuration menu
    Copy the full SHA
    9e3315e View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    9b11370 View commit details
    Browse the repository at this point in the history
  3. fix oligomeric filtering

    a-r-j committed Mar 30, 2023
    Configuration menu
    Copy the full SHA
    4f47c6b View commit details
    Browse the repository at this point in the history
  4. update notebook

    a-r-j committed Mar 30, 2023
    Configuration menu
    Copy the full SHA
    81d4359 View commit details
    Browse the repository at this point in the history
  5. fix dataset init

    a-r-j committed Mar 30, 2023
    Configuration menu
    Copy the full SHA
    86d5118 View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    5f1c525 View commit details
    Browse the repository at this point in the history
  7. Configuration menu
    Copy the full SHA
    e572f40 View commit details
    Browse the repository at this point in the history
  8. Configuration menu
    Copy the full SHA
    eacff28 View commit details
    Browse the repository at this point in the history
  9. add mmseqs to CI build

    a-r-j committed Mar 30, 2023
    Configuration menu
    Copy the full SHA
    8417a0e View commit details
    Browse the repository at this point in the history
  10. rollback dssp install to conda

    a-r-j committed Mar 30, 2023
    Configuration menu
    Copy the full SHA
    d1d713d View commit details
    Browse the repository at this point in the history
  11. Configuration menu
    Copy the full SHA
    d727656 View commit details
    Browse the repository at this point in the history
  12. fix code smell

    a-r-j committed Mar 30, 2023
    Configuration menu
    Copy the full SHA
    4115bd5 View commit details
    Browse the repository at this point in the history
  13. fix metrics

    a-r-j committed Mar 30, 2023
    Configuration menu
    Copy the full SHA
    51ca8f6 View commit details
    Browse the repository at this point in the history

Commits on Mar 31, 2023

  1. shorten line lengths

    a-r-j committed Mar 31, 2023
    Configuration menu
    Copy the full SHA
    33926b6 View commit details
    Browse the repository at this point in the history
  2. add minimum scipy version

    a-r-j committed Mar 31, 2023
    Configuration menu
    Copy the full SHA
    6f7f0c3 View commit details
    Browse the repository at this point in the history
  3. remove python 3.7 from CI

    a-r-j committed Mar 31, 2023
    Configuration menu
    Copy the full SHA
    4f25b5c View commit details
    Browse the repository at this point in the history
  4. Add Torch 2.0.0 to CI

    a-r-j authored Mar 31, 2023
    Configuration menu
    Copy the full SHA
    dc6112d View commit details
    Browse the repository at this point in the history
  5. Configuration menu
    Copy the full SHA
    78379f9 View commit details
    Browse the repository at this point in the history
  6. add torch cluster install to CI

    a-r-j committed Mar 31, 2023
    Configuration menu
    Copy the full SHA
    52efc31 View commit details
    Browse the repository at this point in the history
  7. Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…

    …nto pr/amorehead/272-1
    a-r-j committed Mar 31, 2023
    Configuration menu
    Copy the full SHA
    cdbfef3 View commit details
    Browse the repository at this point in the history
  8. update dockerfile to torch 2.0

    a-r-j committed Mar 31, 2023
    Configuration menu
    Copy the full SHA
    9aae6e9 View commit details
    Browse the repository at this point in the history
  9. Configuration menu
    Copy the full SHA
    418669c View commit details
    Browse the repository at this point in the history
  10. Configuration menu
    Copy the full SHA
    6a9a234 View commit details
    Browse the repository at this point in the history
  11. Configuration menu
    Copy the full SHA
    37ab1ec View commit details
    Browse the repository at this point in the history
  12. Configuration menu
    Copy the full SHA
    0a8affb View commit details
    Browse the repository at this point in the history
  13. Configuration menu
    Copy the full SHA
    ef5b811 View commit details
    Browse the repository at this point in the history
  14. Configuration menu
    Copy the full SHA
    ae1a524 View commit details
    Browse the repository at this point in the history
  15. update test ignores

    a-r-j committed Mar 31, 2023
    Configuration menu
    Copy the full SHA
    160409b View commit details
    Browse the repository at this point in the history
  16. Configuration menu
    Copy the full SHA
    b19df0d View commit details
    Browse the repository at this point in the history
  17. Configuration menu
    Copy the full SHA
    cd4db9e View commit details
    Browse the repository at this point in the history

Commits on Apr 18, 2023

  1. Update citation (a-r-j#287)

    * update citation
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    2 people authored and amorehead committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    fed750e View commit details
    Browse the repository at this point in the history
  2. Support MMTF & rename pdb_path to path throughout (a-r-j#293)

    * rename pdb_path to path throughout
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * install from biopandas bleeding edge
    
    * fix bleeding edge biopandas install
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * update to bleeding edge biopandas
    
    * [pre-commit.ci] pre-commit autoupdate (a-r-j#294)
    
    * [pre-commit.ci] pre-commit autoupdate
    
    updates:
    - [github.com/psf/black: 23.1.0 → 23.3.0](psf/black@23.1.0...23.3.0)
    
    * pin pandas to <2.0.0
    
    * Bump AF2 version
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Arian Jamasb <arjamasb@gmail.com>
    
    * update path in notebooks
    
    * Add missing import a-r-j#296 (a-r-j#297)
    
    * update changelog
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    2 people authored and amorehead committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    5d7dd0b View commit details
    Browse the repository at this point in the history
  3. Prep for 1.7.0 release (a-r-j#292)

    * update version string
    
    * update readme
    
    * update doc version
    
    * update changelog
    a-r-j authored and amorehead committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    75c7b88 View commit details
    Browse the repository at this point in the history
  4. Add autopublish workflow (a-r-j#298)

    * Add autopublish workflow
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    2 people authored and amorehead committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    e9935a5 View commit details
    Browse the repository at this point in the history
  5. update version for 1.7.0

    a-r-j authored and amorehead committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    e3b0c34 View commit details
    Browse the repository at this point in the history
  6. update workflow version

    a-r-j authored and amorehead committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    c40f8d0 View commit details
    Browse the repository at this point in the history
  7. remove rogue print statement (a-r-j#302)

    a-r-j authored and amorehead committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    36da0a2 View commit details
    Browse the repository at this point in the history
  8. Consistent conversion to undirected graphs (a-r-j#301)

    * Fix `convert_nx_to_pyg` to return undirected graph
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * Fix symmetrization of edges of different kinds
    
    * Clean
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * Fix case when `edge_index` is not desired
    
    * Test directed/undirected conversion consistency
    
    * Update contributors
    
    * Update CHANGELOG.md
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    2 people authored and amorehead committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    229e745 View commit details
    Browse the repository at this point in the history
  9. Configuration menu
    Copy the full SHA
    6eace97 View commit details
    Browse the repository at this point in the history
  10. Tensor fixes (a-r-j#307)

    * add PSW to nonstandard residues
    
    * improve insertion and non-standard residue handling
    
    * refactor chain selection
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * remove unused verbosity arg
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    * fix chain selection in tests
    
    * fix chain selection in tutorial notebook
    
    * fix notebook chain selection
    
    * fix chain selection typehint
    
    * Update changelog
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    2 people authored and amorehead committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    2d8a03e View commit details
    Browse the repository at this point in the history
  11. Add NLW as a nonstandard residue

    a-r-j authored and amorehead committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    81ca494 View commit details
    Browse the repository at this point in the history
  12. Export only first model of each downloaded PDB file, and typecast mod…

    …el_id column to str to avoid to_pdb() errors
    amorehead committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    9ad34ff View commit details
    Browse the repository at this point in the history
  13. Configuration menu
    Copy the full SHA
    594068d View commit details
    Browse the repository at this point in the history

Commits on Apr 19, 2023

  1. Configuration menu
    Copy the full SHA
    34fc210 View commit details
    Browse the repository at this point in the history

Commits on Apr 20, 2023

  1. Add fix for scenario where downloaded PDB files do not contain ATOMs …

    …for an entry's listed chains
    amorehead committed Apr 20, 2023
    Configuration menu
    Copy the full SHA
    126d12c View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    68b3e67 View commit details
    Browse the repository at this point in the history