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PDBManager
- Bug fixes, adding necessary changes to export only first PDB model, and merging-in latest updates from master
#309
Commits on Feb 21, 2023
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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>
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Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…
…nto pr/amorehead/272-1
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Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…
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Add extra documentation around clustering function, and address small…
… formatting issues
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Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…
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Commits on Feb 28, 2023
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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
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Commits on Mar 1, 2023
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Commits on Mar 11, 2023
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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>
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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
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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>
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Switch to miniconda for build (a-r-j#278)
* switch to miniconda for build * update docker build * switch to checkout v3
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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>
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Commits on Mar 12, 2023
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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>
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Commits on Mar 14, 2023
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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>
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* 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>
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Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…
…nto pr/amorehead/272-1
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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>
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Default to export model 1's chains only in PDBManager, and clean-up n…
…otebook and utilities
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Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…
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Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…
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Merge branch 'pdb_manager' of https://github.com/amorehead/graphein i…
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Support MMTF & rename pdb_path to path throughout (a-r-j#293)
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Prep for 1.7.0 release (a-r-j#292)
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Consistent conversion to undirected graphs (a-r-j#301)
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* 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>
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Export only first model of each downloaded PDB file, and typecast mod…
…el_id column to str to avoid to_pdb() errors
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Add fix for scenario where downloaded PDB files do not contain ATOMs …
…for an entry's listed chains
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