graphein
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a-r-j
Protein Graph Library
Running the colab notebook 1.7.0 | Creating Datasets from the PDB and got `ModuleNotFoundError: No module named 'torch_geometric'` ``` ModuleNotFoundError Traceback (most recent call last) [](https://localhost:8080/#) in () 1 get_ipython().system('pip...
Here's a script to retrieve a mapping between RFAM families and PDB structure IDs. How could this be integrated into the codebase? There are two points that might need to...
Hi @a-r-j and @amorehead, I would like to propose a feature: PDB structure clustering. It would be useful for structure-related tasks like structure prediction and generation. Would you be interested...
We'd like to upgrade the torch verison in the Dockerfile to `pytorch/pytorch:2.0.0-cuda11.7-cudnn8-runtime`. However, this includes python 3.10 which is blocked by lack of `vmd-python` support for 3.10. https://github.com/Eigenstate/vmd-python/issues/46
#### Reference Issues/PRs Waiting on #272 #### What does this implement/fix? Explain your changes Dataset class for working with Sequence Datasets. Provides utilities for batch folding and embedding with ESM(Fold)....
Assuming the worst case scenario (using all of the uniprot predictions, approx 200m structures iirc), mapping graph/node labels into `Data`/`Protein` objects would have to be done when we `get` a...
Hello! I am doing some protein engineering work and would be nice to be able to be able to build graphs on protein mutations. For instance, it would be cool...
Files used to construct protein graphs must be in PDB format. Whereas, molecular graphs may also be constructed from MOL2 or SDF. Is it possible to add a protein graph...
Hi @a-r-j Happy 2023, I wish you great success with graphein and more! I am trying to build a protein mesh with surface descriptors (e.g. hydrophobicity). As an example, like...
