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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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- ir-frequencies |
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- ir-intensities |
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annotations_creators: |
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- crowdsourced |
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pretty_name: pubchemqc-pm6 |
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size_categories: |
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- 10K<n<300M |
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source_datasets: |
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- pubchem |
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- pubchemqc-pm6 |
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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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viewer: false |
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configs: |
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- config_name: pm6opt |
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data_files: |
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- split: train |
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path: "data/pm6opt/train/*.json" |
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default: true |
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- config_name: pm6opt_chon300nosalt |
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data_files: |
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- split: train |
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path: "data/pm6opt_chon300nosalt/train/*.json" |
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- config_name: pm6opt_chon500nosalt |
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data_files: |
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- split: train |
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path: "data/pm6opt_chon500nosalt/train/*.json" |
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- config_name: pm6opt_chnops500nosalt |
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data_files: |
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- split: train |
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path: "data/pm6opt_chnops500nosalt/train/*.json" |
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- config_name: pm6opt_chnopsfcl300nosalt |
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data_files: |
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- split: train |
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path: "data/pm6opt_chnopsfcl300nosalt/train/*.json" |
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- config_name: pm6opt_chnopsfcl500nosalt |
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data_files: |
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- split: train |
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path: "data/pm6opt_chnopsfcl500nosalt/train/*.json" |
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- config_name: pm6opt_chnopsfclnakmgca500 |
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data_files: |
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- split: train |
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path: "data/pm6opt_chnopsfclnakmgca500/train/*.json" |
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--- |
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|
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# PubChemQC PM6 Dataset |
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|
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## Table of Contents |
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|
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- [PubChemQC PM6 Dataset](#pubchemqc-pm6-dataset) |
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- [Table of Contents](#table-of-contents) |
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- [Dataset Description](#dataset-description) |
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- [Dataset Summary](#dataset-summary) |
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- [Dataset Structure](#dataset-structure) |
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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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- [Initial Data Collection and Normalization](#initial-data-collection-and-normalization) |
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- [Personal and Sensitive Information](#personal-and-sensitive-information) |
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- [Considerations for Using the Data](#considerations-for-using-the-data) |
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- [Social Impact of Dataset](#social-impact-of-dataset) |
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- [Additional Information](#additional-information) |
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- [Dataset Curators](#dataset-curators) |
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- [Licensing Information](#licensing-information) |
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- [Citation Information](#citation-information) |
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- [Contributions](#contributions) |
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|
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## Dataset Description |
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|
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- **Homepage:** https://nakatamaho.riken.jp/pubchemqc.riken.jp/pm6_datasets.html |
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- **Repository:** https://nakatamaho.riken.jp/pubchemqc.riken.jp/pm6_datasets.html |
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- **Paper:** https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00740 |
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- **Point of Contact:** [Maho Nakata]([email protected]) |
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- **Point of Contact:** [Mohammad Mostafanejad]([email protected]) |
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- **Point of Contact:** [MolSSI-AI Hub]([email protected]) |
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|
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### Dataset Summary |
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|
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The **PubChemQC PM6** dataset consists of optimized molecular geometries |
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and electronic properties calculated by the PM6 method for 94.0% of the 91.6 million |
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molecules cataloged in PubChem Compounds retrieved on August 29, 2016. In addition to |
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neutral states, the cationic, anionic, and spin flipped electronic states of respectively |
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56.2%, 49.7%, and 41.3% of the molecules have also been studied. As such, the grand total |
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of the PM6 calculations amounted to 221 million. |
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|
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## Dataset Structure |
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|
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### Data Instances |
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|
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An example of a data instance is as follows: |
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```json |
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{ |
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"cid": 1, |
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"state": "S0", |
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"pubchem-inchi": "InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3", |
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"pubchem-charge": 0, |
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"pubchem-version": "20160829", |
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"name": "000000001.PM6.S0", |
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"coordinates": [4.543146, -2.8411939999999998, -1.641861, ..., 4.345637], |
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"atomic-numbers": [6, 6, 8, ..., 1], |
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"atom-count": 31, |
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"heavy-atom-count": 14, |
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"core-electrons": [0, 0, 0,..., 0], |
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"version": "2.0", |
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"obabel-inchi": "InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3/t8-/m0/s1", |
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"pm6-obabel-canonical-smiles": "[O]C(=O)C[C@@H](C[N](C)(C)C)OC(=O)C", |
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"charge": 0, |
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"energy-beta-gap": 8.458931156643, |
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"energy-beta-homo": -8.8325434733795, |
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"energy-beta-lumo": -0.37361231673649903, |
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"energy-alpha-gap": 8.458931156643, |
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"energy-alpha-homo": -8.8325434733795, |
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"energy-alpha-lumo": -0.37361231673649903, |
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"total-energy": -7.558832783207512, |
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"enthalpy": -0.021744, |
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"homos": [40], |
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"orbital-energies": [ |
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[-34.149199782348006, |
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-32.51760513475, |
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-30.809274381311, |
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..., |
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6.947610830966 |
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] |
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], |
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"mo-count": 73, |
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"basis-count": 73, |
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"temperature": 298.15, |
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"multiplicity": 1, |
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"number-of-atoms": 31, |
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"mulliken-partial-charges": [-0.5888869999999999, |
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0.6862539999999999, |
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-0.580137, |
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..., |
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0.18249 |
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], |
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"dipole-moment": 13.22226250268841, |
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"frequencies": [26.1465, 37.9831, 50.1099, ..., 2779.2147], |
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"intensities": [0.771, 11.6909, 2.5082, ..., 111.8945], |
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"pubchem-multiplicity": 1, |
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"pubchem-obabel-canonical-smiles": "[O-]C(=O)CC(C[N+](C)(C)C)OC(=O)C", |
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"pubchem-isomeric-smiles": "CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C", |
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"pubchem-molecular-weight": 203.23558, |
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"pubchem-molecular-formula": "C9H17NO4" |
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} |
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``` |
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|
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### Data Fields |
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|
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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 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 | The number of core electrons in each atom's pseudopotentials | |
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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 using PM6 method | |
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| enthalpy | Enthalpy | |
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| homos | 1D index array of the highest occupied molecular orbital (HOMOs) 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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| temperature | Temperature (in K) | |
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| multiplicity | Spin multiplicity | |
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| number-of-atoms | Number of atoms in the molecule | |
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| mulliken-partial-charges | Mulliken partial atomic charges | |
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| dipole-moment | Dipole moment | |
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| frequencies | Infrared (IR) frequencies (in cm$^{-1}$) | |
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| intensities | Infrared intensities | |
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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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|
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### Data Splits and Configurations |
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The dataset has only one `train` split. The PubChemQC PM6 dataset |
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has seven configurations/subsets: |
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- `pm6opt` (default) |
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- `pm6opt_chon300nosalt` |
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- `pm6opt_chon500nosalt` |
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- `pm6opt_chnops500nosalt` |
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- `pm6opt_chnopsfcl300nosalt` |
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- `pm6opt_chnopsfcl500nosalt` |
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- `pm6opt_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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|
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# load the dataset with streaming |
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hub_ds = load_dataset(path="molssiai-hub/pubchemqc-pm6", |
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name="pm6opt", |
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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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|
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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 `pm6opt` 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-pm6/blob/main/pubchemqc-pm6.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 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. |
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|
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### Source Data |
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The link to the original PubChemQC PM6 dataset repository can be |
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found [here](https://nakatamaho.riken.jp/pubchemqc.riken.jp/pm6_datasets.html) |
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#### Initial Data Collection and Normalization |
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|
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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 PM6 dataset. |
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|
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### Personal and Sensitive Information |
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|
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The PubChemQC PM6 dataset does not involve any personal or sensitive information. |
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|
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## Considerations for Using the Data |
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|
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### Social Impact of Dataset |
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|
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The PubChemQC PM6 dataset paves the way for applications in drug discovery and materials science, among others. |
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|
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## Additional Information |
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### Dataset Curators |
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|
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- **Maho Nakata**, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan |
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- **Tomomi Shimazaki**, Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, JAPAN |
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- **Masatomo Hashimoto**, Software Technology and Artificial Intelligence Research Laboratory, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan |
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- **Toshiyuki Maeda**, Software Technology and Artificial Intelligence Research Laboratory, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan |
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|
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### Licensing Information |
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|
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[Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0) |
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|
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### Citation Information |
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```tex |
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@article{Nakata:2020:5891, |
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author = {Maho Nakata and Tomomi Shimazaki and Masatomo Hashimoto and Toshiyuki Maeda}, |
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doi = {10.1021/acs.jcim.0c00740}, |
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issn = {1549960X}, |
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issue = {12}, |
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journal = {Journal of Chemical Information and Modeling},W |
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month = {12}, |
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pages = {5891-5899}, |
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pmid = {33104339}, |
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publisher = {American Chemical Society}, |
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title = {PubChemQC PM6: Data Sets of 221 Million Molecules with Optimized Molecular Geometries and Electronic Properties}, |
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volume = {60}, |
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url = {https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00740}, |
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year = {2020}, |
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} |
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``` |
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### Contributions |
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- **Mohammad Mostafanejad**, The Molecular Sciences Software Institute (MolSSI) |
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|
