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Error occurred while Constructing edges when reading PDB file.

7

The error message is as follows: ``` Constructing edges... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0% -:--:-- Traceback (most recent call last): File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3803, in get_loc return self._engine.get_loc(casted_key) File "pandas/_libs/index.pyx", line 138, in...

1412140736

`pip install` fails on fresh `python==3.11` and `python==3.10` conda environment

1

On a clean conda environment created with `conda create -n env_name python==3.11` on Linux, and then ``` pip install graphein graphein ``` I get the following: ``` [04/05/24 12:07:30] WARNING...

kamurani

[pre-commit.ci] pre-commit autoupdate

1

updates: - [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)

pre-commit-ci[bot]

[fix] change progressbar for pdb download

1

#### What does this implement/fix? Explain your changes When using the download_pdb_multiprocessing function, a progress bar for each individual download would be created. This was quite confusing since the progress...

kierandidi

Can not find a function ProteinGraph function anymore

4

I was trying to reproduce the notebooks to train the PSCDB data set but I can not find this function: from graphein.construct_graphs import ProteinGraph Any way you can help me...

velocirraptor23

Feat/coord mask and logging change

1

#### Reference Issues/PRs #### What does this implement/fix? Explain your changes 1. Enables the user to also get a atom37 coordinate mask if needed for their protein (while maintaining backward...

kierandidi

Error in tdc_developability.ipynb notebook

1

I was trying to follow this notebook but in the part for training (Creating Datasets) I got this error: File [/cluster/ddu/cmmartinez001/graphein/notebooks/../graphein/ml/conversion.py:274](http://localhost:8083/lab/tree/graphein/notebooks/graphein/graphein/ml/conversion.py#line=273), in GraphFormatConvertor.convert_nx_to_pyg(self, G) 264 """ 265 Converts ``NetworkX`` graph...

velocirraptor23

add additional hetatm info to pyg parser

1

#### Reference Issues/PRs #### What does this implement/fix? Explain your changes Imposes a better data structure on hetatm metadata with additional fields when using `protein_to_pyg`. #### What testing did you...

a-r-j

In order to exclude residues less than _long_interaction_threshold_, the code checks for _residue_number_ value in the pdb dataframe. The _residue_number_ value is identical for residues with insertion codes. Therefore, it...

tsjain

ERROR 'NoneType' object has no attribute 'nodes'. WARNING can't convert np.ndarray of type numpy.str_.

2

Hi, I'm using Graphein on Google Colab, I have a list of PDB ids `pdb_ids` and I'm using `ProteinGraphDataset(...)` to create a dataset. ``` !pip install graphein[extras] torch-geometric ``` ```...

PabloExperimental