---
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
---
### <details><summary>Cite this dataset </summary>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</details>  
#### This dataset has been curated and formatted for the ColabFit Exchange  
#### This dataset is also available on the ColabFit Exchange:  
https://materials.colabfit.org/id/DS_qpqczxvnj5bo_0  
#### Visit the ColabFit Exchange to search additional datasets by author, description, element content and more.  
https://materials.colabfit.org
<br><hr>  
# 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  
  
<br>
<hr>  

# 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).  
<br>
#### ColabFit Exchange documentation includes descriptions of content and example code for parsing parquet files:  
- [Parquet parsing: example code](https://materials.colabfit.org/docs/how_to_use_parquet)  
- [Dataset info schema](https://materials.colabfit.org/docs/dataset_schema)  
- [Configuration schema](https://materials.colabfit.org/docs/configuration_schema)  
- [Configuration set schema](https://materials.colabfit.org/docs/configuration_set_schema)  
- [Configuration set to configuration mapping schema](https://materials.colabfit.org/docs/cs_co_mapping_schema)