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README.md
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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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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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- `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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