Datasets:

colabfit
/

rQM9

configs:
  - config_name: default
    data_files: co/*.parquet
  - config_name: info
    data_files: ds.parquet
license: cc-by-4.0
tags:
  - molecular dynamics
  - mlip
  - interatomic potential
pretty_name: rQM9

Cite this dataset
Zeng, C., Jin, J., Karypis, G., Transtrum, M., Tadmor, E. B., Hennig, R. G., Roitberg, A., Martiniani, S., and Liu, M. rQM9. ColabFit, 2025. https://doi.org/None

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This dataset is also available on the ColabFit Exchange:

https://materials.colabfit.org/id/DS_qpqczxvnj5bo_0

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Dataset Name

rQM9

Description

133885 molecular structures from the QM9 with revised bond and charges in the SDF format. Bond information can be gathered from the metadata column of the parquet files, a map where the key bonds contains the bond indices as they appear in the final rows of an SDF molecule block. If additional charges are present, these are contained under the key charge_info. rQM9 is derived from DeepChem's QM9 SDF dataset and rectifies the original dataset's net-charge discrepancies and invalid bond orders by enforcing correct valency-charge configurations. Nevertheless, a subset of molecules remains problematic, as they either fail RDKit sanitization or fragment into multiple components. The zero-based indices of these unresolved molecules are provided in a NumPy file in the original data file.

Dataset authors

Cheng Zeng, Jirui Jin, George Karypis, Mark Transtrum, Ellad B. Tadmor, Richard G. Hennig, Adrian Roitberg, Stefano Martiniani, Mingjie Liu

Publication

https://doi.org/10.48550/arXiv.2505.21469

Original data link

https://huggingface.co/datasets/colabfit/rQM9

License

CC-BY-4.0

Number of unique molecular configurations

133885

Number of atoms

2407753

Elements included

C, F, H, N, O

Properties included

Usage

ds.parquet : Aggregated dataset information.
co/ directory: Configuration rows each include a structure, calculated properties, and metadata.
cs/ directory : Configuration sets are subsets of configurations grouped by some common characteristic. If cs/ does not exist, no configurations sets have been defined for this dataset.
cs_co_map/ directory : The mapping of configurations to configuration sets (if defined).

Cite this dataset Zeng, C., Jin, J., Karypis, G., Transtrum, M., Tadmor, E. B., Hennig, R. G., Roitberg, A., Martiniani, S., and Liu, M. rQM9. ColabFit, 2025. https://doi.org/None