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A small bug in the creating_datasets_from_the_pdb.ipynb #306

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pengzhangzhi opened this issue Apr 17, 2023 · 1 comment
Closed

A small bug in the creating_datasets_from_the_pdb.ipynb #306

pengzhangzhi opened this issue Apr 17, 2023 · 1 comment

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@pengzhangzhi
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Hi @amorehead and @a-r-j,

from rich import inspect
!pip install graphein
from graphein.ml.datasets import PDBManager

manager = PDBManager(root_dir=".")
inspect(manager, methods=True)
@a-r-j
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a-r-j commented Apr 17, 2023

Thanks for spotting that! I will add it :)

a-r-j added a commit that referenced this issue Apr 17, 2023
@a-r-j
Add graphein install to tutorial notebook #306
a48acc4
@a-r-j a-r-j closed this as completed Apr 17, 2023
amorehead pushed a commit to amorehead/graphein that referenced this issue Apr 18, 2023
@a-r-j @amorehead
Add graphein install to tutorial notebook a-r-j#306
6eace97
a-r-j added a commit that referenced this issue Apr 22, 2023
@amorehead @kamurani
@pre-commit-ci @a-r-j @anton-bushuiev @rg314
PDBManager - Bug fixes, adding necessary changes to export only fir…
807196e 
…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

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* add: test sequence feature in graphs

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fix graph sequence feature (#268)

* fix matplotlib deprecation

* fix test bug

* change build to ubuntu-latest

* remove unecessary selection

---------

Co-authored-by: Cam <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Arian Jamasb <[email protected]>

* Add dataset splits functionality and add new documentation

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* Resolve merge conflicts with remote

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Remove unused test

* Address lingering SonarCloud concerns

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* 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

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* 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

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* Track names of splits in df_splits

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Fix column naming during merging of DataFrame splits

* add additional properties

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* refactor clustering to allow file caching and overwriting

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* add description to assert statements

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Add extra documentation around clustering function, and address small formatting issues

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* add method to write selection to CSV

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* improve from_fasta documentation

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Enable code reuse for length filters

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* 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

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* Update .gitignore

* Fix missing download call, and add more documentation to download functions

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Fix small bug when merging different splits together

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* 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

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* Fix string formatting

* Update PDB write-out logic and documentation

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* 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

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---------

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* 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

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* Update changelog

---------

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* 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

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* bump torch versions in CI

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* Try fixing graph attributes

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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---------

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* Minor patch `convert_nx_to_pyg` #280 (#281)

* nx_to_pyg bug fix #280

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* changes for 1.6.0 (#279)

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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 <[email protected]>

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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---------

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)

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---------

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

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Co-authored-by: Cam <[email protected]>
Co-authored-by: Cam <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Arian Jamasb <[email protected]>
Co-authored-by: Anton Bushuiev <[email protected]>
Co-authored-by: Ryan Greenhalgh <[email protected]>
a-r-j added a commit that referenced this issue Apr 28, 2023
@a-r-j @amorehead
@kamurani @pre-commit-ci @anton-bushuiev @rg314
PDBManager - Bug fixes, adding necessary changes to export only fir…
e982aa1 
…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

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* add: test sequence feature in graphs

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fix graph sequence feature (#268)

* fix matplotlib deprecation

* fix test bug

* change build to ubuntu-latest

* remove unecessary selection

---------

Co-authored-by: Cam <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Arian Jamasb <[email protected]>

* 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

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* Remove unused test

* Address lingering SonarCloud concerns

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* 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

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* 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

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* Fix column naming during merging of DataFrame splits

* add additional properties

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* refactor clustering to allow file caching and overwriting

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* add description to assert statements

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Add extra documentation around clustering function, and address small formatting issues

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* add method to write selection to CSV

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* improve from_fasta documentation

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* Enable code reuse for length filters

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Minor documentation changes to FASTA write-out function

* Add ability to perform most API calls for a subset of splits

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* Update .gitignore

* Fix missing download call, and add more documentation to download functions

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* Fix small bug when merging different splits together

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* 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

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* Fix string formatting

* Update PDB write-out logic and documentation

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* 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

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---------

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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* Update changelog

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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

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* 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

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