a-r-j graphein issues - Githubissues

a-r-j / graphein

Protein Graph Library

https://graphein.ai/

MIT License

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issues

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Keep all hetatms for all-atom graphs

#415 EvanKomp opened 3 weeks ago
3
I can't use "graphein.protein.features.sequence.propy.aa_dipeptide_composition" to extract protein sequence features

#414 Jrunchang closed 1 month ago
2
can't use functions to add sequence node features like aa_dipeptide_composition

#413 Jrunchang closed 1 month ago
0
[pre-commit.ci] pre-commit autoupdate

#412 pre-commit-ci[bot] closed 1 month ago
1
Bug in calculating edges based on k nearest neighbors

#410 tsjain opened 3 months ago
0
ERROR 'NoneType' object has no attribute 'nodes'. WARNING can't convert np.ndarray of type numpy.str_.

#409 PabloExperimental opened 3 months ago
2
hotfix greater than/less than operations in pdb_manager

#408 a-r-j closed 2 months ago
2
Pdb manager hotfix

#407 a-r-j closed 3 months ago
0
[pre-commit.ci] pre-commit autoupdate

#406 pre-commit-ci[bot] closed 1 month ago
1
V.1.7.7

#405 a-r-j closed 3 months ago
1
fix: improve support for newer `dssp` versions #403

#404 a-r-j closed 3 months ago
2
always add `dssp_version` argument

#403 edikedik closed 2 months ago
0
Feat/logging cif support

#402 kierandidi closed 3 months ago
1
Feat/coord mask and logging change

#401 kierandidi closed 4 months ago
1
Error in tdc_developability.ipynb notebook

#400 velocirraptor23 opened 5 months ago
1
Can not find a function ProteinGraph function anymore

#399 velocirraptor23 closed 1 month ago
5
[feat] add uniprot ecnumber and cath label options to pdb manager

#398 kierandidi closed 5 months ago
1
add additional hetatm info to pyg parser

#397 a-r-j closed 3 months ago
2
Fix cluster file loading bug in `pdb_data.py`

#396 amorehead closed 6 months ago
1
[fix] change progressbar for pdb download

#394 kierandidi closed 6 months ago
1
[pre-commit.ci] pre-commit autoupdate

#393 pre-commit-ci[bot] closed 6 months ago
1
convert_nx_to_pyg doubles edge_index but not kind

#392 l-Dr-MR-l opened 7 months ago
1
[cleanup] change logging levels to debug to declutter output

#391 kierandidi closed 6 months ago
1
Add AYA to constants #387

#390 a-r-j closed 3 months ago
2
TypeError: construct_graph() got an unexpected keyword argument 'pdb_path'

#389 zhaoxuetong closed 2 months ago
2
[feat] expose bfactors in protein_to_pyg function

#388 kierandidi closed 7 months ago
1
Error occurred while constructing edges from pdb files

#387 Runinthenight opened 7 months ago
1
[pre-commit.ci] pre-commit autoupdate

#386 pre-commit-ci[bot] closed 7 months ago
1
exposed fill_value to protein_to_pyg function

#385 kierandidi closed 7 months ago
2
Error occurred while Constructing edges when reading PDB file.

#384 1412140736 opened 7 months ago
7
[pre-commit.ci] pre-commit autoupdate

#383 pre-commit-ci[bot] closed 7 months ago
1
[fix] foldcomp datasets

#382 kierandidi closed 7 months ago
1
`pip install` fails on fresh `python==3.11` and `python==3.10` conda environment

#381 kamurani opened 7 months ago
1
Add PyG install to tutorial notebook #338

#380 a-r-j closed 7 months ago
2
remove typing_extension dependency

#378 kierandidi closed 8 months ago
3
change mmseqs pdb data path

#377 kierandidi closed 8 months ago
1
[pre-commit.ci] pre-commit autoupdate

#376 pre-commit-ci[bot] closed 8 months ago
1
Wire up `deprotonate` arg in `construct_graph` #374

#375 a-r-j closed 8 months ago
1
deprotonate=False not working?

#374 l-Dr-MR-l closed 8 months ago
5
keep_het parameter not working

#373 davidkastner closed 8 months ago
2
pin notebook version <7 #371

#372 a-r-j closed 7 months ago
3
docker compose fails to build due to jupyter nbextension

#371 avivko closed 7 months ago
3
Correct the judgment of hydrogen bonds

#370 Linsastar opened 8 months ago
5
error in the tutorial

#368 xiaopuren opened 9 months ago
1
[pre-commit.ci] pre-commit autoupdate

#367 pre-commit-ci[bot] closed 9 months ago
1
Bump version strings for 1.7.6 release

#365 a-r-j closed 9 months ago
1
update PDB urls to avoid deprecated ftp

#364 a-r-j closed 9 months ago
1
[pre-commit.ci] pre-commit autoupdate

#363 pre-commit-ci[bot] closed 10 months ago
1
[pre-commit.ci] pre-commit autoupdate

#362 pre-commit-ci[bot] closed 11 months ago
1
[pre-commit.ci] pre-commit autoupdate

#361 pre-commit-ci[bot] closed 11 months ago
1