Merge pull request #112 from valence-labs/3bpa

3bpa dataset

README.md

@@ -1,8 +1,25 @@
-# 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
@@ -57,41 +74,55 @@ 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
+
+The CI runs tests and performs code quality checks for the following combinations:
+
+- 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) |
 
 # 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/e0_dispatcher.md

@@ -0,0 +1 @@
+::: openqdc.datasets.energies

docs/API/properties.md

@@ -0,0 +1,3 @@
+# Defined properties for datasets
+
+:::openqdc.datasets.properties

docs/API/statistics.md

@@ -0,0 +1 @@
+::: openqdc.datasets.statistics

docs/index.md

@@ -9,17 +9,17 @@ OpenQDC is a python library to work with quantum datasets. It's a package aimed
 - 🧠 Performance matters: read and write multiple formats (memmap, zarr, xyz, etc).
 - 📈 Data: have access to 1.5+ billion datapoints
 
-Visit our website at TOFILL <IDK>.
+Visit our website at https://openqdc.io .
 
 ## Installation
 
 Use mamba:
 
 ```bash
-mamba install -c conda-forge openqdc
+conda install -c conda-forge openqdc
 ```
 
-_**Tips:** You can replace `mamba` by `conda`._
+_**Tips:** You can replace `conda` by `mamba`._
 
 _**Note:** We highly recommend using a [Conda Python distribution](https://github.com/conda-forge/miniforge) to install OpenQDC. The package is also pip installable if you need it: `pip install openqdc`._
 
@@ -58,7 +58,7 @@ dataset.calculate_descriptors(
 
 ## How to cite
 
-Please cite OpenQDC if you use it in your research: [![DOI](zenodo_badge)](zenodo_link).
+Please cite OpenQDC if you use it in your research: [![Pending Publication](Pending Publication)](Pending Publication).
 
 ## Compatibilities
 

docs/usage.md

@@ -37,6 +37,14 @@ for data in dataset.as_iter(atoms=True):
     break
 ```
 
+or if you want to just iterate over the data:
+
+```python
+for data in dataset:
+    print(data) # dict of arrays
+    break
+```
+
 ## Lazy loading
 
 OpenQDC uses lazy loading to dynamically expose all its API without imposing a long import time during `import openqdc as qdc`. In case of trouble you can always disable lazy loading by setting the environment variable `OPENQDC_DISABLE_LAZY_LOADING` to `1`.

env.yml

@@ -14,6 +14,7 @@ dependencies:
   - s3fs
   - pydantic
   - python-dotenv
+  - httpx
 
 
   # Scientific

mkdocs.yml

@@ -1,8 +1,8 @@
 site_name: "OpenQDC"
-site_description: "I don't know... Something about data and Quantum stuff I guess :D"
+site_description: "Harness the power of quantum chemistry in one line of code."
 repo_url: "https://github.com/valence-labs/openQDC"
 repo_name: "openQDC"
-copyright: Copyright 2023 Valence Labs
+copyright: Copyright 2024 Valence Labs
 
 site_url: "https://github.com/valence-labs/openQDC"
 remote_branch: "gh-pages"
@@ -25,7 +25,11 @@ nav:
   - API:
     - QM methods: API/methods.md
     - Normalization regressor: API/regressor.md
-    - Main class: API/basedataset.md
+    - Main classes:
+      - BaseDataset: API/basedataset.md
+      - Available Properties: API/properties.md
+      - e0 Dispatcher: API/e0_dispatcher.md
+      - Statistics: API/statistics.md
     - Format loading: API/formats.md
     - Datasets:
       - Potential Energy:

openqdc/__init__.py

@@ -21,6 +21,7 @@ def get_project_root():
     "ANI1CCX_V2": "openqdc.datasets.potential.ani",
     "ANI1X": "openqdc.datasets.potential.ani",
     "ANI2X": "openqdc.datasets.potential.ani",
+    "BPA": "openqdc.datasets.potential.bpa",
     "Spice": "openqdc.datasets.potential.spice",
     "SpiceV2": "openqdc.datasets.potential.spice",
     "SpiceVL2": "openqdc.datasets.potential.spice",
@@ -118,6 +119,7 @@ def __dir__():
     # POTENTIAL
     from .datasets.potential.alchemy import Alchemy
     from .datasets.potential.ani import ANI1, ANI1CCX, ANI1CCX_V2, ANI1X, ANI2X
+    from .datasets.potential.bpa import BPA
     from .datasets.potential.comp6 import COMP6
     from .datasets.potential.dummy import Dummy, PredefinedDataset
     from .datasets.potential.gdml import GDML

openqdc/datasets/base.py

@@ -237,7 +237,13 @@ def force_methods(self):
         return list(compress(self.energy_methods, self.force_mask))
 
     @property
-    def e0s_dispatcher(self):
+    def e0s_dispatcher(self) -> AtomEnergies:
+        """
+        Property to get the object that dispatched the isolated atom energies of the QM methods.
+
+        Returns:
+            Object wrapping the isolated atom energies of the QM methods.
+        """
         if not hasattr(self, "_e0s_dispatcher"):
             # Automatically fetch/compute formation or regression energies
             self._e0s_dispatcher = AtomEnergies(self, **self.regressor_kwargs)