README.md

---
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]([email protected])
- **Point of Contact:** [Paul Saxe]([email protected])
- **Point of Contact:** [Mohammad Mostafanejad]([email protected])
- **Point of Contact:** [MolSSI-AI Hub]([email protected])

### 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)