--- license: - cc-by-4.0 size_categories: - n<10K source_datasets: - pm7 task_categories: - tabular-regression - other task_ids: - tabular-single-column-regression pretty_name: pm7 license_link: https://creativecommons.org/licenses/by/4.0 tags: - heat-of-formation - dipole-moments - entropy - energy - pm7 - crystals - small-molecules - organometallics dataset_info: config_name: pm7 features: - name: title dtype: string - name: name dtype: string - name: mopac-id dtype: int64 - name: net-charge dtype: int64 - name: spin-multiplicity dtype: int64 - name: openbabel-canonical-smiles dtype: string - name: openbabel-version dtype: string - name: rdkit-canonical-smiles dtype: string - name: rdkit-version dtype: string - name: oechem-canonical-smiles dtype: string - name: oechem-version dtype: string - name: mopac-keywords sequence: string - name: description dtype: string - name: atomic-indices sequence: int64 - name: atomic-numbers sequence: int64 - name: atomic-symbols sequence: string - name: coordinates sequence: float64 - name: bonds sequence: int64 - name: enthalpy-of-formation dtype: float64 - name: enthalpy-of-formation-error dtype: string - name: enthalpy-of-formation-reference dtype: string - name: enthalpy-of-formation-units dtype: string - name: ionization-energy dtype: float64 - name: ionization-energy-error dtype: string - name: ionization-energy-reference dtype: string - name: ionization-energy-units dtype: string - name: entropy dtype: float64 - name: entropy-units dtype: string - name: constant-pressure-heat-capacity dtype: float64 - name: constant-pressure-heat-capacity-units dtype: string - name: diople-moment dtype: float64 - name: dipole-moment-reference dtype: string - name: dipole-moment-units dtype: string - name: mopac-reference-energy dtype: float64 - name: mopac-reference-energy-units dtype: string splits: - name: train num_bytes: 6848753 num_examples: 4617 download_size: 2180033 dataset_size: 6848753 configs: - config_name: pm7 data_files: - split: train path: data/train-* default: true --- # PM7 Dataset ## Table of Contents - [PM7 Dataset](#pm7-dataset) - [Table of Contents](#table-of-contents) - [Dataset Description](#dataset-description) - [Dataset Summary](#dataset-summary) - [Dataset Structure](#dataset-structure) - [Data Instances](#data-instances) - [Data Fields](#data-fields) - [Data Splits and Configurations](#data-splits-and-configurations) - [How to Use the Dataset](#how-to-use-the-dataset) - [Prerequisites](#prerequisites) - [Accessing the Data](#accessing-the-data) - [Dataset Creation](#dataset-creation) - [Curation Rationale](#curation-rationale) - [Source Data](#source-data) - [Initial Data Collection and Normalization](#initial-data-collection-and-normalization) - [Personal and Sensitive Information](#personal-and-sensitive-information) - [Considerations for Using the Data](#considerations-for-using-the-data) - [Social Impact of Dataset](#social-impact-of-dataset) - [Additional Information](#additional-information) - [Dataset Curators](#dataset-curators) - [Licensing Information](#licensing-information) - [Citation Information](#citation-information) - [Contributions](#contributions) ## Dataset Description - **Homepage:** http://openmopac.net - **Repository:** https://github.com/openmopac/mopac - **Paper:** https://doi.org/10.1007/s00894-012-1667-x - **Point of Contact:** [James J. P. Stewart](MrMopac@openmopac.net) - **Point of Contact:** [Paul Saxe](psaxe@vt.edu) - **Point of Contact:** [Mohammad Mostafanejad](smostafanejad@vt.edu) - **Point of Contact:** [MolSSI-AI Hub](hub@molssi.org) ### Dataset Summary PM7 is a modern semi-empirical method with broad applications in chemical space including organic molecules, organometallics and solid-state crystalline compounds. The parameterization process involved adopting a diverse set of experimental and high-level ab initio reference data. The current dataset, curated by the Molecular Sciences Software Institute, attempts to provide a ready-to-use version of the PM7 dataset for the computational molecular science and machine learning community. ## Dataset Structure ### Data Instances An example of a data instance is as follows: ```json {'title': 'MOPAC_54/PM7_reference', 'name': '1,1,1-Trifluoroethane', 'mopac-id': 54, 'net-charge': 0, 'spin-multiplicity': 1, 'openbabel-canonical-smiles': 'CC(F)(F)F', 'openbabel-version': '3.1.0', 'rdkit-canonical-smiles': 'CC(F)(F)F', 'rdkit-version': '2024.03.5', 'oechem-canonical-smiles': 'CC(F)(F)F', 'oechem-version': '20240905', 'mopac-keywords': ['SYMMETRY', 'PM7'], 'description': '1,1,1-Trifluoroethane\nI=13.8 IR=LLNBS82 D=2.32 H=-178.9 HR=NIST DR=MCC1963 S=66.9 CP=18.69', 'atomic-indices': [1, 2, 3, 4, 5, 6, 7, 8], 'atomic-numbers': [6, 6, 9, 9, 9, 1, 1, 1], 'atomic-symbols': ['C', 'C', 'F', 'F', 'F', 'H', 'H', 'H'], 'coordinates': [0.0, 0.0, 0.0, ..., -0.41029998660087585, -0.8860999941825867, 0.5116000175476074], 'bonds': [1, 7, 1, 1, 2, 1, 1, 6, 1, 1, 8, 1, 2, 5, 1, 2, 4, 1, 2, 3, 1], 'enthalpy-of-formation': -748.5176, 'enthalpy-of-formation-error': None, 'enthalpy-of-formation-reference': None, 'enthalpy-of-formation-units': 'kJ/mol', 'ionization-energy': 13.8, 'ionization-energy-error': None, 'ionization-energy-reference': None, 'ionization-energy-units': 'eV', 'entropy': 279.9096, 'entropy-units': 'J/mol/K', 'constant-pressure-heat-capacity': 78.19896000000001, 'constant-pressure-heat-capacity-units': 'J/mol/K', 'diople-moment': 2.32, 'dipole-moment-reference': 'MCC1963', 'dipole-moment-units': 'D', 'mopac-reference-energy': -731.158184, 'mopac-reference-energy-units': 'kJ/mol'} ``` ### Data Fields | Field | Description | | ------------------------------------- | --------------------------------------------------------------- | | title | Title line in the MOPAC input/SDF file | | name | Name of the molecule | | mopac-id | MOPAC ID of the molecule | | net-charge | Net charge of the molecule | | spin-multiplicity | Spin multiplicity of the molecule | | openbabel-canonical-smiles | Canonical SMILES string generated by OpenBabel | | openbabel-version | Version of OpenBabel used to generate the canonical SMILES | | rdkit-canonical-smiles | Canonical SMILES string generated by RDKit | | rdkit-version | Version of RDKit used to generate the canonical SMILES | | oechem-canonical-smiles | Canonical SMILES string generated by OpenEye OEChem | | oechem-version | Version of OpenEye OEChem used to generate the canonical SMILES | | mopac-keywords | Keywords used in the MOPAC input file | | description | Description of the molecule | | atomic-indices | Atomic indices of the atoms in the molecule | | atomic-numbers | Atomic numbers of the atoms in the molecule | | atomic-symbols | Atomic symbols of the atoms in the molecule | | coordinates | Atomic coordinates of the atoms in the molecule | | bonds | Bond information of the molecule | | enthalpy-of-formation | Enthalpy of formation of the molecule | | enthalpy-of-formation-error | Error in the enthalpy of formation | | enthalpy-of-formation-reference | Reference for the enthalpy of formation | | enthalpy-of-formation-units | Units of the enthalpy of formation | | ionization-energy | Ionization energy of the molecule | | ionization-energy-error | Error in the ionization energy | | ionization-energy-reference | Reference for the ionization energy | | ionization-energy-units | Units of the ionization energy | | entropy | Entropy of the molecule | | entropy-units | Units of the entropy | | constant-pressure-heat-capacity | Constant pressure heat capacity of the molecule | | constant-pressure-heat-capacity-units | Units of the constant pressure heat capacity | | diople-moment | Dipole moment of the molecule | | dipole-moment-reference | Reference for the dipole moment | | dipole-moment-units | Units of the dipole moment | | mopac-reference-energy | Reference energy of the molecule | | mopac-reference-energy-units | Units of the reference energy | ### Data Splits and Configurations The dataset has only one `train` split. Currently, the PM7 dataset has one configuration/subset: - `pm7` (default) ## How to Use the Dataset ### Prerequisites We recommend isolating your work in a virtualenv or conda environment. You can create a new conda environment, `pm7`, ```bash conda create -n pm7 python=3.12 ``` and activate it using the following command ```bash conda activate pm7 ``` Once the conda environment is activated, you can install the dependencies in it as shown below ```bash pip install datasets huggingface_hub ``` ### Accessing the Data Once the required packages are installed, you can run the following code to access the data ```python # import the modules from datasets import load_dataset # load the dataset with streaming hub_ds = load_dataset(path="molssiai-hub/pm7", name="pm7", split="train", cache_dir="./tmp") # fetch a random batch of 32 samples from the dataset ds = hub_ds.shuffle(seed=1234).select(range(32)) ``` The argument `name` by default is set to `pm7`. The `split` must be set to `train` as it is the only split in our dataset. The `cache_dir` allows us to store the Hugging Face datasets' and models' artifacts in a non-default directory (by default, it is set to `~/.cache/huggingface`). The `shuffle` method shuffles the dataset with a seed of 1234, and the `select` method selects the first 32 samples from the shuffled dataset. ## Dataset Creation ### Curation Rationale The present version of PM7 dataset has been extracted from the [pm7.sdf.gz](https://huggingface.co/datasets/molssiai-hub/pm7/blob/main/pm7.sdf.gz) file, transformed into a dictionary and stored in the `.json` format. The SDF file was generated using [Simulation Environment for Atomistic and Molecular Modeling (SEAMM)](https://github.com/molssi-seamm) software. The SEAMM flowchart for processing the PM7 dataset from the MOPAC input files can be found on Zenodo. ### Source Data The PM7 dataset (and the corresponding SDF file) was generated using the MOPAC input files hosted in [MOPAC GitHub repository](https://github.com/openmopac/mopac/tree/main/data/normal). #### Initial Data Collection and Normalization Other than the changes detailed in Sec. [Curation Rationale](#curation-rationale), no data modification has been performed on the PM7 dataset. ### Personal and Sensitive Information The PM7 dataset does not involve any personal or sensitive information. ## Considerations for Using the Data ### Social Impact of Dataset The PM7 dataset paves the way for applications in (in)organic chemistry, solid-state physics and materials science, among others. ## Additional Information ### Dataset Curators - **James J. P. Stewart**, Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO, 80921, USA - **Paul Saxe**, The Molecular Sciences Software Institute (MolSSI), Blacksburg, VA, 24060, USA - **Mohammad Mostafanejad**, The Molecular Sciences Software Institute (MolSSI), Blacksburg, VA, 24060, USA ### Licensing Information [Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0) ### Citation Information ```tex @article{Stewart:2013:1, author = {Stewart, James J. P.}, doi = {10.1007/S00894-012-1667-X}, journal = {Journal of Molecular Modeling}, pages = {1-32}, publisher = {Springer}, title = {Optimization of parameters for semiempirical methods VI: More modifications to the NDDO approximations and re-optimization of parameters}, volume = {19}, url = {https://link.springer.com/article/10.1007/s00894-012-1667-x}, year = {2013} } ``` ### Contributions - **James J. P. Stewart**, Stewart Computational Chemistry - **Paul Saxe**, The Molecular Sciences Software Institute (MolSSI) - **Mohammad Mostafanejad**, The Molecular Sciences Software Institute (MolSSI)