Merge pull request #18 from OpenDrugDiscovery/isolated_at_en

Isolated at en

.gitignore

@@ -148,3 +148,4 @@ cookie.txt
 *.csv
 *.txt
 *.sh
+.DS_Store

docs/API/available_datasets.md

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+# Available Datasets
+
+::: openqdc.datasets

docs/API/isolated_atom_energies.md

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+# Isolated atoms energy
+
+This page contains the isolated atom energies.
+
+::: openqdc.utils.atomization_energies

docs/_overrides/main.html

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+{% extends "base.html" %}
+
+{% block content %}
+{{ super() }}
+
+<style>
+    .jp-RenderedHTMLCommon p {
+        font-size: .8rem;
+        line-height: 1.6;
+    }
+
+    .jp-RenderedHTMLCommon li {
+        font-size: .8rem;
+        line-height: 1.6;
+    }
+
+    .jp-RenderedHTMLCommon h1 {
+        margin: 0 0 1.25em;
+        color: var(--md-default-fg-color--light);
+        font-weight: 300;
+        font-size: 2em;
+        line-height: 1.3;
+        letter-spacing: -0.01em;
+    }
+
+    .jp-RenderedHTMLCommon h2 {
+        margin: 1.6em 0 .64em;
+        font-weight: 300;
+        font-size: 1.965em;
+        line-height: 1.4;
+        letter-spacing: -0.01em;
+    }
+
+    .jp-RenderedHTMLCommon h3 {
+        margin: 1.6em 0 .8em;
+        font-weight: 400;
+        font-size: 1.57em;
+        line-height: 1.5;
+        letter-spacing: -0.01em;
+    }
+
+    .jp-RenderedHTMLCommon hr {
+        border: none;
+    }
+</style>
+{% endblock content %}

docs/css/custom.css

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+/* Indentation. */
+div.doc-contents:not(.first) {
+    padding-left: 25px;
+    border-left: 4px solid rgba(230, 230, 230);
+    margin-bottom: 80px;
+  }
+
+  /* Don't capitalize names. */
+  h5.doc-heading {
+    text-transform: none !important;
+  }
+
+  /* Don't use vertical space on hidden ToC entries. */
+  .hidden-toc::before {
+    margin-top: 0 !important;
+    padding-top: 0 !important;
+  }
+
+  /* Don't show permalink of hidden ToC entries. */
+  .hidden-toc a.headerlink {
+    display: none;
+  }
+
+  /* Avoid breaking parameters name, etc. in table cells. */
+  td code {
+    word-break: normal !important;
+  }
+
+  /* For pieces of Markdown rendered in table cells. */
+  td p {
+    margin-top: 0 !important;
+    margin-bottom: 0 !important;
+  }

docs/datasets.md

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+# Overview of Datasets
+
+<!-- Create a table with the following columns
+1. Name of Dataset (with reference of paper) [Dataset Name](paper link)
+2. Number of Molecules
+3. Number of Conformers
+4. Average Conformer to Molecule Ratio (in 2 lines)
+5. Labels
+6. QM Level of Theory
+ -->
+
+We provide support for the following publicly available QM Datasets.
+
+| Dataset | # Molecules | # Conformers | Average Conformers per Molecule | Force Labels | Atom Types | QM Level of Theory | Off-Equilibrium Conformations|
+| --- | --- | --- | --- | --- | --- | --- | --- |
+| [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 | |
+| [QM7X](https://www.nature.com/articles/s41597-021-00812-2) |  6,950 | 4,195,237 | 603 | Yes | 7 | PBE0+MBD | Yes |

docs/index.md

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+# openQDC
+
+Open Quantum Data Commons
+
+## Setup Datasets
+
+Use the scripts in `setup/` to download the datasets. For more information, see the [README](setup/README.md) in the `setup/` directory.
+
+# Install the library in dev mode
+```bash
+# Install the deps
+mamba env create -n qdc -f env.yml
+
+# Activate the environment
+mamba activate  qdc
+
+# Install the qdc library in dev mode
+pip install -e .
+
+```
+
+## Development lifecycle
+
+### Tests
+
+You can run tests locally with:
+
+```bash
+pytest .
+```