graphein

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Some modules reference optional dependencies. These messages are communicated to users via this function: https://github.com/a-r-j/graphein/blob/840ec27dc82684cce5cab9e3604062ce852ae4aa/graphein/utils/utils.py#L326 We should add an `extras` arg to this function indicating whether or not the dependency...

a-r-j

As identified in #239 we should switch to [PyDSSP](https://github.com/ShintaroMinami/PyDSSP) for easier install and (likely) speed improvements.

a-r-j

Networkx to pyg conversion loses track or edge features

1

**Describe the bug** The conversion from a network to a pytorch geometric object is corrupted: - The edge features is given as a list of string instead of a list...

manonreau

Fix ml dataset

1

Fixed some issues in the `ProteinGraphDataset` class, such as - checking for bad uniprot IDs for alphafold structure download (believe this was also fixed by @a-r-j in another func with...

kamurani

`ProteinGraphDataset` for pairs of proteins?

3

I was wondering if there's an elegant (easy) way to use the inbuilt `ProteinGraphDataset` class for making a PyTorch dataloader that can supply proteins in *pairs*, with an associated label....

kamurani

convert_nx_to_pyg doubles edge_index but not kind

2

**Describe the bug** Using GraphFormatConvertor to go from nx to pyg graph results in a doubling of the number of edges indicated by edge_index (this means we are going from...

l-Dr-MR-l

[cleanup] change logging levels to debug to declutter output

1

#### Reference Issues/PRs #### What does this implement/fix? Explain your changes Set logging level down to `DEBUG` from `INFO` and `WARNING` at some places due to unnecessary terminal output there...

kierandidi

Add AYA to constants #387

1

#### Reference Issues/PRs #387 #### What does this implement/fix? Explain your changes Adds `AYA` to lists of modified residues. #### What testing did you do to verify the changes in...

a-r-j

TypeError: construct_graph() got an unexpected keyword argument 'pdb_path'

2

Dear , I got an error message: from graphein.protein.graphs import construct_graph g = construct_graph(config=config, pdb_path=str(protein_path)+str(pdb_ID)+".pdb") TypeError: construct_graph() got an unexpected keyword argument 'pdb_path' Can you take a look at the...

zhaoxuetong

Error occurred while constructing edges from pdb files

1

The bug information provided is as follows, what can I do to overcome it? Please help me，Thank you ``` File "protein_pretrain.py", line 60, in protein_graph g = construct_graph(config=config, path=str(protein_path)+str(pdb_ID)+".pdb") File...

Runinthenight