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@@ -25,6 +25,7 @@ The core of the dataset is 530,601 SwissProt proteins with associated substructu
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  - `dataset_splits/` - dataset splits (train/val/test) for the SwissProt and debug datasets. Splits are available for both sequenced-based clustering (AFDB50) and structure-based clustering (FoldSeek cluster). See [FoldSeek cluster](https://afdb-cluster.steineggerlab.workers.dev/) for more information.
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  - `sequences/` - FASTA file of SwissProt protein sequences and files associated with dataset selection.
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  - `afdb_structures/` - Placeholder default directory for downloading protein structures in PDB format from AlphaFold DB. This is the default search location for protein structures, but can be configured per-run using the `data.struct_template` parameter if you already have a AFDB download elsewhere.
 
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  ## Model-specific data
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  Currently, Magneton incorporates two models that utilize protein structure as an input: SaProt and ProSST. These models both use structure tokens to represent the protein structure, and we precompute these structure tokens for the Magneton SwissProt dataset to speed up the training process. The `generated_data/` directory contains these files.
 
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  - `dataset_splits/` - dataset splits (train/val/test) for the SwissProt and debug datasets. Splits are available for both sequenced-based clustering (AFDB50) and structure-based clustering (FoldSeek cluster). See [FoldSeek cluster](https://afdb-cluster.steineggerlab.workers.dev/) for more information.
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  - `sequences/` - FASTA file of SwissProt protein sequences and files associated with dataset selection.
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  - `afdb_structures/` - Placeholder default directory for downloading protein structures in PDB format from AlphaFold DB. This is the default search location for protein structures, but can be configured per-run using the `data.struct_template` parameter if you already have a AFDB download elsewhere.
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+ To load the datasets, please refer to our [GitHub repo](https://github.com/rcalef/magneton), or if you would prefer to directly load the JSONL files into your own environment, please refer to [this implementation](https://github.com/rcalef/magneton/blob/main/magneton/core_types.py#L190) of loading `Protein` objects from JSONL.
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  ## Model-specific data
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  Currently, Magneton incorporates two models that utilize protein structure as an input: SaProt and ProSST. These models both use structure tokens to represent the protein structure, and we precompute these structure tokens for the Magneton SwissProt dataset to speed up the training process. The `generated_data/` directory contains these files.