Merge pull request #98 from OpenDrugDiscovery/develop

Release and update main

.github/workflows/code-check.yml

@@ -24,7 +24,7 @@ jobs:
 
       - name: Install black
         run: |
-          pip install black>=23
+          pip install black>=24
 
       - name: Lint
         run: black --check .

.github/workflows/test.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         os: ["ubuntu-latest"]
 
     runs-on: ${{ matrix.os }}
@@ -47,8 +47,11 @@ jobs:
       - name: Install library
         run: python -m pip install --no-deps .
 
+      - name: Check directory
+        run: ls
+
       - name: Run tests
-        run: pytest
+        run: python -m pytest
 
-      - name: Test building the doc
-        run: mkdocs build
+      #- name: Test building the doc
+      #  run: mkdocs build

README.md

@@ -19,6 +19,29 @@ You can run tests locally with:
 pytest
 ```
 
+### Documentation
+
+You can build the documentation locally with:
+
+```bash
+mkdocs serve
+```
+
+# Downloading Datasets
+
+A command line interface is available to download datasets or see which dataset is available, for more information please run openqdc --help.
+
+```bash
+# Display the available datasets
+openqdc datasets
+
+# Display the help message for the download command
+openqdc download --help
+
+# Download the Spice and QMugs dataset
+openqdc download Spice QMugs
+```
+
 # Overview of Datasets
 
 <!-- Create a table with the following columns
@@ -30,19 +53,45 @@ pytest
 6. QM Level of Theory
  -->
 
-We provide support for the following publicly available QM Datasets.
+We provide support for the following publicly available QM Potential Energy Datasets.
+
+# 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 | |
-| [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 |
-| [Spice](https://arxiv.org/abs/2209.10702) |  19,238 | 1,132,808 | 59 | Yes | 15 | ωB97M-D3(BJ)/def2-TZVPPD | Yes |
-| [ANI](https://pubs.rsc.org/en/content/articlelanding/2017/SC/C6SC05720A) |  57,462 | 20,000,000 | 348 | No | 4 | ωB97x:6-31G(d) | Yes |
-| [tmQM](https://pubs.acs.org/doi/10.1021/acs.jcim.0c01041) |  86,665 | |  | No | | TPSSh-D3BJ/def2-SVP | |
-| [DES370K](https://www.nature.com/articles/s41597-021-00833-x) | 3,700 | 370,000 | 100 | No | 20 | CCSD(T) | Yes |
-| [DES5M](https://www.nature.com/articles/s41597-021-00833-x) | 3,700 | 5,000,000 | 1351 | No | 20 | SNS-MP2 | Yes |
 | [OrbNet Denali](https://arxiv.org/abs/2107.00299) | 212,905 | 2,300,000 | 11 | No | 16 | GFN1-xTB | Yes |
-| [SN2RXN](https://pubs.acs.org/doi/10.1021/acs.jctc.9b00181) | 39 | 452709 | 11,600 | Yes | 6 | DSD-BLYP-D3(BJ)/def2-TZVP | |
+| [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)   |
+| [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)  |
+
+# 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

docs/API/methods.md

@@ -0,0 +1,3 @@
+# QM Methods
+
+::: openqdc.methods