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updates the Readme file
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README.md
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---
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license:
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- cc-by-4.0
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license_link: https://creativecommons.org/licenses/by/4.0
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tags:
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- homo-lumo-gaps
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- energy
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- dipole-moments
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- quantum-chemistry
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- pubchem
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- small-molecules
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annotations_creators:
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- crowdsourced
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pretty_name: pubchemqc-b3lyp
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size_categories:
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- 10K<n<100M
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source_datasets:
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- pubchem
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- pubchemqc-b3lyp
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task_categories:
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- tabular-regression
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- other
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task_ids:
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- tabular-single-column-regression
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configs:
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- config_name: b3lyp_pm6
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- config_name: b3lyp_pm6_chon300nosalt
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- config_name: b3lyp_pm6_chon500nosalt
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- config_name: b3lyp_pm6_chnopsfcl300nosalt
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- config_name: b3lyp_pm6_chnopsfcl500nosalt
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- config_name: b3lyp_pm6_chnopsfclnakmgca500
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---
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## Table of Contents
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- [Data Instances](#data-instances)
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- [Data Fields](#data-fields)
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- [Data Splits and Configurations](#data-splits-and-configurations)
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- [Dataset Creation](#dataset-creation)
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- [Curation Rationale](#curation-rationale)
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- [Source Data](#source-data)
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### Dataset Summary
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The presented **PubChemQC B3LYP/6-31G
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properties of 85,938,443 molecules, encompassing a broad spectrum of molecules from
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essential compounds to biomolecules with a molecular weight up to 1000. These molecules
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account for 94.0% of the original PubChem Compound catalog as of August 29, 2016.
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The electronic properties, including orbitals, orbital energies, total energies, dipole
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moments, and other pertinent properties, were computed by using the B3LYP/6-31G
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methods.
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## Dataset Structure
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### Data Fields
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-
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### Data Splits and Configurations
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The dataset has only one
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has six configurations/subsets:
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## Dataset Creation
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### Curation Rationale
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-
The present version of PubChemQC B3LYP/6-31G
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from its original Postgresql database, transformed into a dictionary and
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stored in the
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### Source Data
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The link to the original PubChemQC B3LYP/6-31G
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found [here](https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html)
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#### Initial Data Collection and Normalization
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Other than the changes detailed in Sec. [Curation Rationale](#curation-rationale),
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no data modification has been performed on the PubChemQC B3LYP/6-31G
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### Personal and Sensitive Information
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The PubChemQC B3LYP/6-31G
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## Considerations for Using the Data
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### Social Impact of Dataset
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The PubChemQC B3LYP/6-31G
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## Additional Information
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journal = {Journal of Chemical Information and Modeling},
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pages = {5734-5754},
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publisher = {American Chemical Society},
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title = {{PubChemQC B3LYP/6-31G*//PM6 Data Set: The Electronic Structures of 86 Million Molecules
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Using B3LYP/6-31G* Calculations}},
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volume = {63},
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url = {https://pubs.acs.org/doi/abs/10.1021/acs.jcim.3c00899},
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### Contributions
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- **Mohammad Mostafanejad**, The Molecular Sciences Software Institute (MolSSI)
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---
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license:
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- cc-by-4.0
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license_link: https://creativecommons.org/licenses/by/4.0
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tags:
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+
- homo-lumo-gaps
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+
- energy
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+
- dipole-moments
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- quantum-chemistry
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+
- pubchem
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+
- small-molecules
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annotations_creators:
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- crowdsourced
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pretty_name: pubchemqc-b3lyp
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size_categories:
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- 10K<n<100M
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source_datasets:
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- pubchem
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- pubchemqc-b3lyp
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task_categories:
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- tabular-regression
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- other
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task_ids:
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- tabular-single-column-regression
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configs:
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- config_name: b3lyp_pm6
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data_files:
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- split: train
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path: "data/b3lyp_pm6/train/*.json"
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default: true
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- config_name: b3lyp_pm6_chon300nosalt
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data_files:
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- split: train
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path: "data/b3lyp_pm6_chon300nosalt/train/*.json"
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- config_name: b3lyp_pm6_chon500nosalt
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data_files:
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- split: train
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path: "data/b3lyp_pm6_chon500nosalt/train/*.json"
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- config_name: b3lyp_pm6_chnopsfcl300nosalt
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data_files:
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- split: train
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path: "data/b3lyp_pm6_chnopsfcl300nosalt/train/*.json"
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- config_name: b3lyp_pm6_chnopsfcl500nosalt
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data_files:
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- split: train
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path: "data/b3lyp_pm6_chnopsfcl500nosalt/train/*.json"
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- config_name: b3lyp_pm6_chnopsfclnakmgca500
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data_files:
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- split: train
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path: "data/b3lyp_pm6_chnopsfclnakmgca500/train/*.json"
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---
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# PubChemQC-B3LYP/6-31G\*//PM6 Dataset
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## Table of Contents
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- [Data Instances](#data-instances)
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- [Data Fields](#data-fields)
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- [Data Splits and Configurations](#data-splits-and-configurations)
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- [How to Use the Dataset](#how-to-use-the-dataset)
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- [Prerequisites](#prerequisites)
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- [Accessing the Data](#accessing-the-data)
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- [Dataset Creation](#dataset-creation)
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- [Curation Rationale](#curation-rationale)
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- [Source Data](#source-data)
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### Dataset Summary
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The presented **PubChemQC B3LYP/6-31G\*//PM6** data set is composed of the electronic
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properties of 85,938,443 molecules, encompassing a broad spectrum of molecules from
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essential compounds to biomolecules with a molecular weight up to 1000. These molecules
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account for 94.0% of the original PubChem Compound catalog as of August 29, 2016.
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The electronic properties, including orbitals, orbital energies, total energies, dipole
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+
moments, and other pertinent properties, were computed by using the B3LYP/6-31G\* and PM6
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methods.
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## Dataset Structure
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### Data Fields
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| Field | Description |
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| ------------------------------- | ------------------------------------------------------------------------------------------------------------------------------ |
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| cid | Pubchem Compound ID |
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| state | Electronic state |
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| pubchem-inchi | InChI extracted from PubChem Compound entry |
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| pubchem-charge | Molecular charge extracted from PubChem Compound entry |
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| pubchem-version | PubChem Compound database version |
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| name | Name of the input file used for the B3LYP/6-31G\*//PM6 calculation |
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| coordinates | Cartesian coordinates of the molecular geometry optimized with PM6 method in Angstroem |
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| atomic-numbers | An array of atomic numbers |
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| atom-count | Number of atoms in the molecule |
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| heavy-atom-count | Number of heavy atoms in the molecule |
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| core-electrons | Number of core electrons in each atom's pseudopotentials |
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| bond-order | Bond order |
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| connection-indices | Connection indices between atoms |
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| formula | Chemical formula |
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| version | Version number |
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| obabel-inchi | InChI of the structure generated by Open Babel |
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| pm6-obabel-canonical-smiles | Canonical SMILES for the structure generated by Open Babel |
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| charge | Molecular charge |
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| energy-beta-gap | HOMO-LUMO energy gap for beta spin orbitals |
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| energy-beta-homo | Energy of the highest-occupied molecular orbital (HOMO) of beta spin symmetry |
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| energy-beta-lumo | Energy of the lowest-unoccupied molecular orbital (LUMO) of beta spin symmetry |
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| energy-alpha-gap | HOMO-LUMO energy gap for alpha spin orbitals |
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| energy-alpha-homo | Energy of the highest-occupied molecular orbital (HOMO) of alpha spin symmetry |
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| energy-alpha-lumo | Energy of the lowest-unoccupied molecular orbital (LUMO) of alpha spin symmetry |
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| total-energy | Total electronic energy of the molecule calculated at the B3LYP/6-31G\* level of theory |
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| homos | 1D index array of the highest occupied molecular orbital (HOMO) with one (two) element(s) for the (un)restricted wavefunctions |
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| orbital-energies | 1D array of orbital energies in hartree with one (two) member(s) for the (un)restricted wavefunction |
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| mo-count | Number of molecular orbitals |
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| basis-count | Number of basis functions |
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| multiplicity | Spin multiplicity |
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| molecular-mass | Molecular mass |
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| number-of-atoms | Number of atoms in the molecule |
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| lowdin-partial-charges | Lowdin partial atomic charges |
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| mulliken-partial-charges | Mulliken partial atomic charges |
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| dipole-moment | Dipole moment |
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| pubchem-multiplicity | Spin multiplicity of the molecule extracted from PubChem Compound |
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| pubchem-obabel-canonical-smiles | Canonical SMILES of the molecule extracted from PubChem Compound generated by Open Babel |
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| pubchem-isomeric-smiles | Isomeric SMILES of the molecule extracted from PubChem Compound calculated by the OpenEye's OEChem Toolkit |
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| pubchem-molecular-weight | Molecular weight extracted from the PubChem Compound entry |
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| pubchem-molecular-formula | Molecular formula extracted from the PubChem Compound entry |
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### Data Splits and Configurations
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The dataset has only one `train` split. The PubChemQC B3LYP/6-31G\*//PM6 dataset
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has six configurations/subsets:
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+
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- `b3lyp_pm6` (default)
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+
- `b3lyp_pm6_chon300nosalt`
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- `b3lyp_pm6_chon500nosalt`
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- `b3lyp_pm6_chnopsfcl300nosalt`
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- `b3lyp_pm6_chnopsfcl500nosalt`
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- `b3lyp_pm6_chnopsfclnakmgca500`
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+
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## How to Use the Dataset
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### Prerequisites
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We recommend isolating your work in a virtualenv or conda environment.
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You can create a new conda environment, `pubchemqc`,
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```bash
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conda create -n pubchemqc python=3.12
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```
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and activate it using the following command
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```bash
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conda activate pubchemqc
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```
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Once the conda environment is activated, you can
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install the dependencies in it as shown below
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```bash
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pip install huggingface_hub ijson
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```
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### Accessing the Data
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Once the required packages are installed, you can run the following code
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to access the data
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```python
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# import the modules
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from datasets import load_dataset
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# load the dataset with streaming
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hub_ds = load_dataset(path="molssiai-hub/pubchemqc-b3lyp",
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name="b3lyp_pm6",
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split="train",
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streaming=True,
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cache_dir="./tmp",
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trust_remote_code=True)
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# fetch a batch of 32 samples from the dataset
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ds = list(hub_ds.take(32))
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```
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The argument `name` by default is set to `b3lyp_pm6` which refers to
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the entire dataset. Other configurations (subsets), listed in
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Sec. [Data Splits and Configurations](#data-splits-and-configurations),
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can also be selected.
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The `split` must be set to `train` as it is the only split in our dataset.
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We recommend using `streaming=True` to avoid downloading the entire dataset
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on disk. The `cache_dir` allows us to store the Hugging Face datasets' and
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models' artifacts in a non-default directory (by default, it is set to
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`~/.cache/huggingface`). As we are using a custom
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[load script](https://huggingface.co/datasets/molssiai-hub/pubchemqc-b3lyp/blob/main/pubchemqc-b3lyp.py), the `trust_remote_code` argument should also be set to `True`.
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## Dataset Creation
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### Curation Rationale
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|
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+
The present version of PubChemQC B3LYP/6-31G\*//PM6 dataset has been extracted
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from its original Postgresql database, transformed into a dictionary and
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+
stored in the `.json` format.
|
| 320 |
|
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### Source Data
|
| 322 |
|
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+
The link to the original PubChemQC B3LYP/6-31G\*//PM6 dataset repository can be
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found [here](https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html)
|
| 325 |
|
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#### Initial Data Collection and Normalization
|
| 327 |
|
| 328 |
Other than the changes detailed in Sec. [Curation Rationale](#curation-rationale),
|
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+
no data modification has been performed on the PubChemQC B3LYP/6-31G\*//PM6 dataset.
|
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|
| 331 |
### Personal and Sensitive Information
|
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The PubChemQC B3LYP/6-31G\*//PM6 dataset does not involve any personal or sensitive information.
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## Considerations for Using the Data
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### Social Impact of Dataset
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The PubChemQC B3LYP/6-31G\*//PM6 dataset paves the way for applications in drug discovery and materials science, among others.
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## Additional Information
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journal = {Journal of Chemical Information and Modeling},
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pages = {5734-5754},
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publisher = {American Chemical Society},
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title = {{PubChemQC B3LYP/6-31G*//PM6 Data Set: The Electronic Structures of 86 Million Molecules
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Using B3LYP/6-31G* Calculations}},
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volume = {63},
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url = {https://pubs.acs.org/doi/abs/10.1021/acs.jcim.3c00899},
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### Contributions
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- **Mohammad Mostafanejad**, The Molecular Sciences Software Institute (MolSSI)
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