Datasets:
Update README.md
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README.md
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@@ -40,7 +40,47 @@ This dataset contains hallucinated cyclic peptide scaffold structures (in CIF fo
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- **Repository:** https://zenodo.org/records/15164650
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- **Paper [optional]:** Rettie, S.A., Campbell, K.V., Bera, A.K. et al. Cyclic peptide structure prediction and design using AlphaFold2. *Nature Communications* **16**, 4730 (2025). https://doi.org/10.1038/s41467-025-59940-7
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##
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### Direct Use
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- **Repository:** https://zenodo.org/records/15164650
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- **Paper [optional]:** Rettie, S.A., Campbell, K.V., Bera, A.K. et al. Cyclic peptide structure prediction and design using AlphaFold2. *Nature Communications* **16**, 4730 (2025). https://doi.org/10.1038/s41467-025-59940-7
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## Quickstart Usage
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### Install HuggingFace Datasets package
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Each subset can be loaded into python using the Huggingface [datasets](https://huggingface.co/docs/datasets/index) library.
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First, from the command line install the `datasets` library
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$ pip install datasets
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then, from within python load the datasets library
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>>> import datasets
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### Load dataset
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Load the 'RosettaCommons/AfCycDesign' datasets.
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>>> AfCycDesign = datasets.load_dataset('RosettaCommons/AfCycDesign')
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Downloading readme: 9.67kB [00:00, 3.57MB/s]
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Downloading data: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 2.94M/2.94M [00:00<00:00, 6.99MB/s]
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Downloading data: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████| 544/544 [00:00<00:00, 4.22kB/s]
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Generating afcycpep_hallucinated split: 100%|███████████████████████████████████████████████████████████████| 20656/20656 [00:00<00:00, 246500.54 examples/s]
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Generating afcycpep_experimental split: 100%|█████████████████████████████████████████████████████████████████████████| 8/8 [00:00<00:00, 3582.58 examples/s]
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and the dataset is loaded as a datasets.arrow_dataset.Dataset
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>>> AfCycDesign
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DatasetDict({
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afcycpep_hallucinated: Dataset({
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features: ['ID', 'sequence', 'nmer', 'rosetta_score', 'hf_path', 'Type'],
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num_rows: 20656
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})
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afcycpep_experimental: Dataset({
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features: ['ID', 'sequence', 'nmer', 'rosetta_score', 'hf_path', 'Type'],
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num_rows: 8
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})
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})
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which is a column oriented format that can be accessed directly, converted in to a pandas.DataFrame, or parquet format, e.g.
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>>> AfCycDesign.data.column('sequence')
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>>> AfCycDesign.to_pandas()
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>>> AfCycDesign.to_parquet("dataset.parquet")
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### Direct Use
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