Fix graph sequence (atomistic graphs in initialise_graph_with_metadata had duplicated residues)
#268
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@a-r-j where abouts should I put the tests that I came up with? |
https://github.com/a-r-j/graphein/blob/master/tests/protein/test_graphs.py |
a-r-j
reviewed
Feb 19, 2023
graphein/protein/graphs.py
Outdated
| @@ -493,6 +493,13 @@ def initialise_graph_with_metadata( | |||
| sequence = protein_df.loc[protein_df["chain_id"] == c][ | |||
| "residue_name" | |||
| ].str.cat() | |||
| elif granularity == "atom": | |||
| protein_df = protein_df.loc[protein_df["atom_name"] == "CA"] | |||
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Hmm, is keeping the CA subset of protein_df not problematic downstream?
Do we not want to store this in a temporary variable (if at all, can we not just add the atom_name selection into L499 when we select by chain ID?
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Yep, 100%. My bad, I forgot that when it's passed to the graph construction it only passes a reference to it.
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…st PDB model, and merging-in latest updates from `master` (#309) * Fix graph sequence (atomistic graphs in `initialise_graph_with_metadata` had duplicated residues) (#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 (#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> * Add dataset splits functionality and add new documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Resolve merge conflicts with remote * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove unused test * Address lingering SonarCloud concerns * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add deposition date parsing * remove pdb.py * add chain extraction util * add chain writing method * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * After fixing merge conflicts, add more filters and add time-based splits * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix up SonarCloud concerns * Improve verbiage surrounding PDB resolutions * Simplify code and improve variable names * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Track names of splits in df_splits * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix column naming during merging of DataFrame splits * add additional properties * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * refactor clustering to allow file caching and overwriting * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add description to assert statements * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add extra documentation around clustering function, and address small formatting issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add method to write selection to CSV * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * improve from_fasta documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Enable code reuse for length filters * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Minor documentation changes to FASTA write-out function * Add ability to perform most API calls for a subset of splits * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update .gitignore * Fix missing download call, and add more documentation to download functions * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix small bug when merging different splits together * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix bug in length filtering functions, fix print bugs in utils, and add ability to write-out PDB files after selecting a subset of chains to include in them * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix string formatting * Update PDB write-out logic and documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add PDB download workaround for PDBs that can no longer be downloaded * Make exception more specific * Add TQDM for data split exporting * Add improved error message for non standard node funcs #274 (#275) * Add improved error message for non standard node funcs #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> * clean up unused files and move docs from root (#276) * clean up unused files and move docs from root * remove setup.cfg * prelim path support #269 (#277) * prelim path support #269 * fix import error 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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. 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selection * fix chain selection typehint * Update changelog --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add NLW as a nonstandard residue * Export only first model of each downloaded PDB file, and typecast model_id column to str to avoid to_pdb() errors * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Track split names for edge cases in dataset splitting * Add fix for scenario where downloaded PDB files do not contain ATOMs for an entry's listed chains * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Cam <73625486+kamurani@users.noreply.github.com> 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> Co-authored-by: Anton Bushuiev 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…st PDB model, and merging-in latest updates from `master` (#311) * add PDB manager #270 * add download method * add clustering utilities * `PDBManager` - Bug fixes, adding necessary changes to export only first PDB model, and merging-in latest updates from `master` (#309) * Fix graph sequence (atomistic graphs in `initialise_graph_with_metadata` had duplicated residues) (#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 (#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> * Add dataset splits functionality and add new documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Resolve merge conflicts with remote * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove unused test * Address lingering SonarCloud concerns * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add deposition date parsing * remove pdb.py * add chain extraction util * add chain writing method * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * After fixing merge conflicts, add more filters and add time-based splits * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix up SonarCloud concerns * Improve verbiage surrounding PDB resolutions * Simplify code and improve variable names * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Track names of splits in df_splits * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix column naming during merging of DataFrame splits * add additional properties * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * refactor clustering to allow file caching and overwriting * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add description to assert statements * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add extra documentation around clustering function, and address small formatting issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add method to write selection to CSV * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * improve from_fasta documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Enable code reuse for length filters * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Minor documentation changes to FASTA write-out function * Add ability to perform most API calls for a subset of splits * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update .gitignore * Fix missing download call, and add more documentation to download functions * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix small bug when merging different splits together * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix bug in length filtering functions, fix print bugs in utils, and add ability to write-out PDB files after selecting a subset of chains to include in them * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix string formatting * Update PDB write-out logic and documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add PDB download workaround for PDBs that can no longer be downloaded * Make exception more specific * Add TQDM for data split exporting * Add improved error message for non standard node funcs #274 (#275) * Add improved error message for non standard node funcs #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> * clean up unused files and move docs from root (#276) * clean up unused files and move docs from root * remove setup.cfg * prelim path support #269 (#277) * prelim path support #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> * Switch to miniconda for build (#278) * switch to miniconda for build * update docker build * switch to checkout v3 * Improve altloc handling (#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> * Df processing #216 (#222) * docstrings and df processing funcs #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 * 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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Default to export model 1's chains only in PDBManager, and clean-up notebook and utilities * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add tutorial nblink * add tutorial to datasets sections * mv pdb data to ml API * rm pyg dataset import * rm unused code * fix annotation * add MMTF download format * refactor dependency utils * refactor graphein.utils.utils.import_message * refactor graphein.protein.utils.is_tool * update .gitignore * ignore cif too * ignore cif too * ignore foldcomp files * catch straggling erroneous imports * ignore mol2 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update folding utils * add max batch option * add foldcomp utils * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add notebook updates [WIP] 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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> * Add graphein install to tutorial notebook #306 * Tensor fixes (#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> * Add NLW as a nonstandard residue * Export only first model of each downloaded PDB file, and typecast model_id column to str to avoid to_pdb() errors * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Track split names for edge cases in dataset splitting * Add fix for scenario where downloaded PDB files do not contain ATOMs for an entry's listed chains * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Cam <73625486+kamurani@users.noreply.github.com> 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> Co-authored-by: Anton Bushuiev <67932762+anton-bushuiev@users.noreply.github.com> Co-authored-by: Ryan Greenhalgh <35999546+rg314@users.noreply.github.com> * Add structure format parameter to allow mmtf manipulation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update changelog --------- Co-authored-by: Alex Morehead <acmwhb@missouri.edu> Co-authored-by: Cam <73625486+kamurani@users.noreply.github.com> 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: Anton Bushuiev <67932762+anton-bushuiev@users.noreply.github.com> Co-authored-by: Ryan Greenhalgh <35999546+rg314@users.noreply.github.com>
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Fixes #267
This ensures that atomistic level graphs have the same sequence (for each
cinchain_ids) as those created withCAor residue granularity.Tested with an assertion (comparing sequences from residue and atomistic graphs).