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88 changes: 51 additions & 37 deletions README.md
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# openQDC

Open Quantum Data Commons
<div align="center">
<img src="docs/assets/logo-title.png" width="100%">
</div>

<p align="center">
<b>openQDC - Open Quantum Data Commons </b> <br />
</p>
<p align="center">
<a href="https://docs.openqdc.io/" target="_blank">
Docs
</a> |
<a href="https://openqdc.io/" target="_blank">
Homepage
</a>
</p>

---

[![license](https://licensebuttons.net/l/by-nc/4.0/80x15.png)](https://github.com/valence-labs/openQDC/blob/main/LICENSE)

### Installing openQDC

```bash
git clone [email protected]:OpenDrugDiscovery/openQDC.git
cd openQDC
Expand Down Expand Up @@ -59,39 +74,38 @@ We provide support for the following publicly available QM Potential Energy Data

# Potential Energy

| Dataset | # Molecules | # Conformers | Average Conformers per Molecule | Force Labels | Atom Types | QM Level of Theory | Off-Equilibrium Conformations|
| --- | --- | --- | --- | --- | --- | --- | --- |
| [ANI](https://pubs.rsc.org/en/content/articlelanding/2017/SC/C6SC05720A) | 57,462 | 20,000,000 | 348 | No | 4 | ωB97x:6-31G(d) | Yes |
| [GEOM](https://www.nature.com/articles/s41597-022-01288-4) | 450,000 | 37,000,000 | 82 | No | 18 | GFN2-xTB | No |
| [Molecule3D](https://arxiv.org/abs/2110.01717) | 3,899,647 | 3,899,647 | 1 | No | 5 | B3LYP/6-31G* | No |
| [NablaDFT](https://pubs.rsc.org/en/content/articlelanding/2022/CP/D2CP03966D) | 1,000,000 | 5,000,000 | 5 | No | 6 | ωB97X-D/def2-SVP | |
| [OrbNet Denali](https://arxiv.org/abs/2107.00299) | 212,905 | 2,300,000 | 11 | No | 16 | GFN1-xTB | Yes |
| [PCQM_PM6](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00740) | | | 1| No| | PM6 | No
| [PCQM_B3LYP](https://arxiv.org/abs/2305.18454) | 85,938,443|85,938,443 | 1| No| | B3LYP/6-31G* | No
| [QMugs](https://www.nature.com/articles/s41597-022-01390-7) | 665,000 | 2,000,000 | 3 | No | 10 | GFN2-xTB, ωB97X-D/def2-SVP | No |
| [QM7X](https://www.nature.com/articles/s41597-021-00812-2) | 6,950 | 4,195,237 | 603 | Yes | 7 | PBE0+MBD | Yes |
| [SN2RXN](https://pubs.acs.org/doi/10.1021/acs.jctc.9b00181) | 39 | 452709 | 11,600 | Yes | 6 | DSD-BLYP-D3(BJ)/def2-TZVP | |
| [SolvatedPeptides](https://doi.org/10.1021/acs.jctc.9b00181) | | 2,731,180 | | Yes | | revPBE-D3(BJ)/def2-TZVP | |
| [Spice](https://arxiv.org/abs/2209.10702) | 19,238 | 1,132,808 | 59 | Yes | 15 | ωB97M-D3(BJ)/def2-TZVPPD | Yes |
| [tmQM](https://pubs.acs.org/doi/10.1021/acs.jcim.0c01041) | 86,665 | 86,665| 1| No | | TPSSh-D3BJ/def2-SVP | |
| [Transition1X](https://www.nature.com/articles/s41597-022-01870-w) | | 9,654,813| | Yes | | ωB97x/6–31 G(d) | Yes |
| [WaterClusters](https://doi.org/10.1063/1.5128378) | 1 | 4,464,740| | No | 2 | TTM2.1-F | Yes|

| Dataset | # Molecules | # Conformers | Average Conformers per Molecule | Force Labels | Atom Types | QM Level of Theory | Off-Equilibrium Conformations |
| ----------------------------------------------------------------------------- | ----------- | ------------ | ------------------------------- | ------------ | ---------- | -------------------------- | ----------------------------- |
| [ANI](https://pubs.rsc.org/en/content/articlelanding/2017/SC/C6SC05720A) | 57,462 | 20,000,000 | 348 | No | 4 | ωB97x:6-31G(d) | Yes |
| [GEOM](https://www.nature.com/articles/s41597-022-01288-4) | 450,000 | 37,000,000 | 82 | No | 18 | GFN2-xTB | No |
| [Molecule3D](https://arxiv.org/abs/2110.01717) | 3,899,647 | 3,899,647 | 1 | No | 5 | B3LYP/6-31G\* | No |
| [NablaDFT](https://pubs.rsc.org/en/content/articlelanding/2022/CP/D2CP03966D) | 1,000,000 | 5,000,000 | 5 | No | 6 | ωB97X-D/def2-SVP | |
| [OrbNet Denali](https://arxiv.org/abs/2107.00299) | 212,905 | 2,300,000 | 11 | No | 16 | GFN1-xTB | Yes |
| [PCQM_PM6](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00740) | | | 1 | No | | PM6 | No |
| [PCQM_B3LYP](https://arxiv.org/abs/2305.18454) | 85,938,443 | 85,938,443 | 1 | No | | B3LYP/6-31G\* | No |
| [QMugs](https://www.nature.com/articles/s41597-022-01390-7) | 665,000 | 2,000,000 | 3 | No | 10 | GFN2-xTB, ωB97X-D/def2-SVP | No |
| [QM7X](https://www.nature.com/articles/s41597-021-00812-2) | 6,950 | 4,195,237 | 603 | Yes | 7 | PBE0+MBD | Yes |
| [SN2RXN](https://pubs.acs.org/doi/10.1021/acs.jctc.9b00181) | 39 | 452709 | 11,600 | Yes | 6 | DSD-BLYP-D3(BJ)/def2-TZVP | |
| [SolvatedPeptides](https://doi.org/10.1021/acs.jctc.9b00181) | | 2,731,180 | | Yes | | revPBE-D3(BJ)/def2-TZVP | |
| [Spice](https://arxiv.org/abs/2209.10702) | 19,238 | 1,132,808 | 59 | Yes | 15 | ωB97M-D3(BJ)/def2-TZVPPD | Yes |
| [tmQM](https://pubs.acs.org/doi/10.1021/acs.jcim.0c01041) | 86,665 | 86,665 | 1 | No | | TPSSh-D3BJ/def2-SVP | |
| [Transition1X](https://www.nature.com/articles/s41597-022-01870-w) | | 9,654,813 | | Yes | | ωB97x/6–31 G(d) | Yes |
| [WaterClusters](https://doi.org/10.1063/1.5128378) | 1 | 4,464,740 | | No | 2 | TTM2.1-F | Yes |

# Interaction energy

We also provide support for the following publicly available QM Noncovalent Interaction Energy Datasets.

| Dataset |
| --- |
| [DES370K](https://www.nature.com/articles/s41597-021-00833-x) |
| [DES5M](https://www.nature.com/articles/s41597-021-00833-x) |
| Dataset |
| ------------------------------------------------------------------------------------------------------------------- |
| [DES370K](https://www.nature.com/articles/s41597-021-00833-x) |
| [DES5M](https://www.nature.com/articles/s41597-021-00833-x) |
| [Metcalf](https://pubs.aip.org/aip/jcp/article/152/7/074103/1059677/Approaches-for-machine-learning-intermolecular) |
| [DESS66](https://www.nature.com/articles/s41597-021-00833-x) |
| [DESS66x8](https://www.nature.com/articles/s41597-021-00833-x) |
| [Splinter](https://www.nature.com/articles/s41597-023-02443-1) |
| [X40](https://pubs.acs.org/doi/10.1021/ct300647k) |
| [L7](https://pubs.acs.org/doi/10.1021/ct400036b) |
| [DESS66](https://www.nature.com/articles/s41597-021-00833-x) |
| [DESS66x8](https://www.nature.com/articles/s41597-021-00833-x) |
| [Splinter](https://www.nature.com/articles/s41597-023-02443-1) |
| [X40](https://pubs.acs.org/doi/10.1021/ct300647k) |
| [L7](https://pubs.acs.org/doi/10.1021/ct400036b) |

# CI Status

Expand All @@ -100,15 +114,15 @@ The CI runs tests and performs code quality checks for the following combination
- The three major platforms: Windows, OSX and Linux.
- The four latest Python versions.

| | `main` |
| --------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Lib build & Testing | [![test](https://github.com/valence-labs/openQDC/actions/workflows/test.yml/badge.svg)](https://github.com/valence-labs/openQDC/actions/workflows/test.yml) |
| Code Sanity (linting and type analysis) | [![code-check](https://github.com/valence-labs/openQDC/actions/workflows/code-check.yml/badge.svg)](https://github.com/valence-labs/openQDC//actions/workflows/code-check.yml) |
| Documentation Build | [![doc](https://github.com/valence-labs/openQDC/actions/workflows/doc.yml/badge.svg)](https://github.com/valence-labs/openQDC/actions/workflows/doc.yml) |
| Pre-Commit | [![pre-commit](https://github.com/valence-labs/openQDC/actions/workflows/pre-commit-ci.yml/badge.svg)](https://github.com/valence-labs/openQDC/actions/workflows/pre-commit-ci.yml) |

| | `main` |
| --------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Lib build & Testing | [![test](https://github.com/valence-labs/openQDC/actions/workflows/test.yml/badge.svg)](https://github.com/valence-labs/openQDC/actions/workflows/test.yml) |
| Code Sanity (linting and type analysis) | [![code-check](https://github.com/valence-labs/openQDC/actions/workflows/code-check.yml/badge.svg)](https://github.com/valence-labs/openQDC//actions/workflows/code-check.yml) |
| Documentation Build | [![doc](https://github.com/valence-labs/openQDC/actions/workflows/doc.yml/badge.svg)](https://github.com/valence-labs/openQDC/actions/workflows/doc.yml) |
| Pre-Commit | [![pre-commit](https://github.com/valence-labs/openQDC/actions/workflows/pre-commit-ci.yml/badge.svg)](https://github.com/valence-labs/openQDC/actions/workflows/pre-commit-ci.yml) |

# How to cite

All data presented in the OpenQDC are already published in scientific journals, full reference to the respective paper is attached to each dataset class. When citing data obtained from OpenQDC, you should cite both the original paper(s) the data come from and our paper on OpenQDC itself. The reference is:

ADD REF HERE LATER
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