Datasets:
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---
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)
|