haneulpark commited on
Commit
a337049
·
verified ·
1 Parent(s): 5d70aab

Update README.md

Browse files
Files changed (1) hide show
  1. README.md +41 -1
README.md CHANGED
@@ -40,7 +40,47 @@ This dataset contains hallucinated cyclic peptide scaffold structures (in CIF fo
40
  - **Repository:** https://zenodo.org/records/15164650
41
  - **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
42
 
43
- ## Uses
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
44
 
45
  ### Direct Use
46
 
 
40
  - **Repository:** https://zenodo.org/records/15164650
41
  - **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
42
 
43
+ ## Quickstart Usage
44
+ ### Install HuggingFace Datasets package
45
+ Each subset can be loaded into python using the Huggingface [datasets](https://huggingface.co/docs/datasets/index) library.
46
+ First, from the command line install the `datasets` library
47
+
48
+ $ pip install datasets
49
+
50
+ then, from within python load the datasets library
51
+
52
+ >>> import datasets
53
+
54
+
55
+ ### Load dataset
56
+ Load the 'RosettaCommons/AfCycDesign' datasets.
57
+
58
+ >>> AfCycDesign = datasets.load_dataset('RosettaCommons/AfCycDesign')
59
+ Downloading readme: 9.67kB [00:00, 3.57MB/s]
60
+ Downloading data: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 2.94M/2.94M [00:00<00:00, 6.99MB/s]
61
+ Downloading data: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████| 544/544 [00:00<00:00, 4.22kB/s]
62
+ Generating afcycpep_hallucinated split: 100%|███████████████████████████████████████████████████████████████| 20656/20656 [00:00<00:00, 246500.54 examples/s]
63
+ Generating afcycpep_experimental split: 100%|█████████████████████████████████████████████████████████████████████████| 8/8 [00:00<00:00, 3582.58 examples/s]
64
+
65
+ and the dataset is loaded as a datasets.arrow_dataset.Dataset
66
+
67
+ >>> AfCycDesign
68
+ DatasetDict({
69
+ afcycpep_hallucinated: Dataset({
70
+ features: ['ID', 'sequence', 'nmer', 'rosetta_score', 'hf_path', 'Type'],
71
+ num_rows: 20656
72
+ })
73
+ afcycpep_experimental: Dataset({
74
+ features: ['ID', 'sequence', 'nmer', 'rosetta_score', 'hf_path', 'Type'],
75
+ num_rows: 8
76
+ })
77
+ })
78
+
79
+ which is a column oriented format that can be accessed directly, converted in to a pandas.DataFrame, or parquet format, e.g.
80
+
81
+ >>> AfCycDesign.data.column('sequence')
82
+ >>> AfCycDesign.to_pandas()
83
+ >>> AfCycDesign.to_parquet("dataset.parquet")
84
 
85
  ### Direct Use
86