Arian Jamasb

Adding 200m structures to biopandas

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Small update to support AF2 v3. Very high structure:code ratio in this PR 😁

Type hints for PyG Data

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### 🚀 The feature, motivation and pitch Hiya, thanks for maintaining such a great project. I've often run into scenarios where I have multiple configurations of features used within a...

add ProteinsX dataset classes

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#### Reference Issues/PRs Adds dataloaders for the following built in datasets: #13 * `PROTEINS_METAL` * `PROTEINS_NUCLEIC` * `PROTEINS_LIGANDS` * `PROTEINS_NUCLEOTIDES` #### What does this implement/fix? Explain your changes #### What...

[WIP] Initial pass at GNN modelling feature

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#### What does this implement/fix? Explain your changes The goal of this feature is to provide an easy to use pipeline to perform GNN modelling experiments on protein graphs. Currently,...

Protein-Ligand Interaction Graphs

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Follow on issue for #155 We'd like to support Protein-Ligand Interaction Graphs eg as shown in this image from [this paper](https://pubs.acs.org/doi/10.1021/acs.jmedchem.1c01830).  Ideally we can keep this composable under the...

**Describe the solution you'd like** It’d be nice to be able to visualise the distribution of vector features in a manner decoupled from the structure. Perhaps in a way that...

Support for mmCIF Files

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**Is your feature request related to a problem? Please describe.** Currently, we only support PDB files as inputs for protein structure graphs. [Large complexes are now unavailable as PDBs.](https://www.rcsb.org/docs/general-help/structures-without-legacy-pdb-format-files): >...

**Describe the solution you'd like** * inputs for chain selection as a separate .txt file * Input as list of PDB codes (txt file) rather than PDB directory path

**Is your feature request related to a problem? Please describe.** [Currently](https://github.com/a-r-j/graphein/blob/0e6f075e716ae10b8afebf47cc0d8eada46d4f08/graphein/cli.py#L54) the CLI uses the normal `construct_graphs` function. Once the `dataloaders` PR (#71) is merged we can change this to...

**Is your feature request related to a problem? Please describe.** Now that we have a CLI (#113), it would be nice to provide some default configs implementing graph construction schemes...