README.md

---
language:
  - en
tags:
  - chemistry
  - biology
pretty_name: >-
  Processed NCI Open Compounds Structures for Docking, Cofold, and Affinity
  Prediction
size_categories:
  - 100K<n<1M

configs:
  - config_name: default
    data_files:
      - split: train
        path: nci_compounds.tsv
    delimiter: "\t"
---

# Curated NCI Open Compounds dataset

A curated set of the NCI Open Compounds with compatible mol2 and pdbqt files safe for cofolding and docking applications

## Quickstart Usage

### Install HuggingFace Datasets package

Each subset can be loaded into python using the Huggingface [datasets](https://huggingface.co/docs/datasets/index) library.
First, from the command line install the `datasets` library

    $ pip install datasets

Optionally set the cache directory, e.g.

    $ HF_HOME=${HOME}/.cache/huggingface/
    $ export HF_HOME

then, from within python load the datasets library

    >>> import datasets

### Load model datasets
   
To load one of the `NCI_Open_Compounds` model datasets, use `datasets.load_dataset(...)`:

    >>> dataset_tag = "train"
    >>> dataset_models = datasets.load_dataset(
      path = "leebecca/NCI_Open_Compounds",
      name = f"{dataset_tag}_models",
      data_dir = f"{dataset_tag}")['train']

and the dataset is loaded as a `datasets.arrow_dataset.Dataset`

    >>> dataset_models
    Dataset({
        features: [    
          'NSC',
          'duplicate_idx',
          'CID',
          'SID',
          'CAS',
          'entry_id',
          'entry_name',
          'name',
          'formula',
          'smiles',
          'mw',
          'tot_q',
          'tot_abs_q',
          'chiralities_consistent',
          'chiral_flag',
          'flags',
          'charging_adjusted_penalty',
          'ionization_penalty',
          'ionization_penalty_charging',
          'ionization_penalty_neutral',
          'state_penalty',
          'energy',
          'tautomer_probability',
          'input_file',
          'structure_evaluation',
          'chemistry_notes',
          'pka_notes'
        ],
        num_rows: 445794
    })


## Dataset Details

### Dataset Description
The set contains ligprep output of the minimized 3D structures, expanded to include possible protonation states and tautomers capped at 3 per ligand.


- **Acknowledgements:**
We kindly acknowledge RosettaCommons

### Dataset Sources
https://wiki.nci.nih.gov/spaces/NCIDTPdata/pages/155844992/Chemical+Data

## Uses

### Out-of-Scope Use


### Source Data

## Citation

## Dataset Card Authors
Becca Lee (beccalee5@g.ucla.edu)