merge and fix docs doc

.coveragerc

@@ -13,6 +13,3 @@ exclude_lines =
     # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:
-
-    # OpenBabel2
-    except ImportError:

CHANGELOG.md

@@ -8,17 +8,32 @@
 Date:            XXX/XX/XXX
 Contributors:    @RMeli
 
+### Improved
+
+* Documentation on loading RDKit and Open Babel molecules [PR #77 | @RMeli]
+
 ### Changed
 
 * Version of several GitHub actions [PR #76 | @RMeli]
 * Versioneer to `0.28` [PR #76 | @RMeli]
 * Minimum Python version to `3.7` to match CI [PR #76 | @RMeli]
 * Code according to `black==23.3.0` [PR #76 | @RMeli]
 
+### Added
+
+* Pin to `sphinx<7` to avoid compatibility with RTD theme [PR #77 | @RMeli] 
+
 ### Removed
 
+* Outdated information about RDKit from the documentation [PR #84 | @RMeli]
+* Support for Open Babel 2 [PR #84 | @RMeli]
 * LGTM badge and code annotations [PR #76 | @RMeli]
 
+### Added
+
+* `extras_require` to `setup.py` for RDKit and Open Babel [PR #84 | @RMeli]
+* Error message when `spyrmsd` is used as module but neither OpenBabel nor RDKit are installed [PR #81 | @RMeli]
+
 ------------------------------------------------------------------------------
 
 ## Version 0.5.2

README.md

@@ -39,6 +39,8 @@ If you find `spyrmsd` useful, please consider citing the following paper:
 
 _Note_: `spyrmsd` will install [NetworkX](https://networkx.github.io/) (multi-platform). You can install [graph-tool](https://graph-tool.skewed.de/) on macOS and Linux for higher performance.
 
+_Note_: If `spyrmsd` is used as a standalone tool, it is required to install either [RDKit](https://rdkit.org/) or [Open Babel](http://openbabel.org/). Neither is automatically installed with `pip` nor `conda`.
+
 ### PyPI
 
 ```bash
@@ -80,8 +82,6 @@ Additionally, one of the following packages is required to use `spyrmsd` as a st
 * [Open Babel](http://openbabel.org/)
 * [RDKit](https://rdkit.org/)
 
-_Note_: [RDKit](https://rdkit.org/) is not available on PyPI ([Why the RDKit isn't available on PyPi](https://rdkit.blogspot.com/2019/11/why-rdkit-isnt-available-on-pypi.html)). See [RDKit Installation](http://www.rdkit.org/docs/Install.html) for installation instructions.
-
 ## Usage
 
 ### Standalone Tool

devtools/conda-envs/spyrmsd-all.yaml

@@ -33,7 +33,7 @@ dependencies:
   - codecov
 
   # Doc
-  - sphinx
+  - sphinx<7
   - sphinx_rtd_theme
   - pip:
     - duecredit

devtools/conda-envs/spyrmsd-docs.yaml

@@ -17,5 +17,5 @@ dependencies:
   - rdkit
 
   # Doc
-  - sphinx
+  - sphinx<7
   - sphinx_rtd_theme

docs/README.md

@@ -4,7 +4,7 @@ The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/m
 
 ## Installation
 
-Ensure that Sphinx and the ReadTheDocs theme are installed:
+Ensure that Sphinx and the [Read the Docs](https://sphinx-rtd-theme.readthedocs.io/en/stable/index.html) theme are installed:
 
 ```bash
 conda install sphinx sphinx_rtd_theme
@@ -20,6 +20,15 @@ Create API documentation automatically with `sphinx-apidoc`:
 sphinx-apidoc -f -M -e  -T -o source/api ../spyrmsd
 ```
 
+### Convert Tutorial Jupyter Notebooks to HTML
+
+Jupyter Notebooks need to be converted to HTML:
+
+```bash
+pip install pandoc
+jupyter nbconvert --to rst tutorial.ipynb  
+```
+
 ### Build Documentation
 
 Use the `Makefile` to compile static HTML pages:

docs/source/installation.rst

@@ -59,13 +59,9 @@ Additionally, one of the following packages is required to use ``spyrmsd`` as a
 * `Open Babel`_
 * RDKit_
 
-.. note::
-   RDKit_ has to be installed using ``conda`` (see `Why the RDKit isn't available on PyPi`_).
-
 .. _PyPI: https://pypi.org/project/spyrmsd/
 .. _conda-forge: https://github.com/conda-forge/spyrmsd-feedstock
 .. _RDKit: https://rdkit.org/
-.. _Why the RDKit isn't available on PyPi: https://rdkit.blogspot.com/2019/11/why-rdkit-isnt-available-on-pypi.html
 .. _Open Babel: http://openbabel.org/
 .. _graph-tool: https://graph-tool.skewed.de/
 .. _NetworkX: https://networkx.github.io/

docs/source/tutorials/tutorial.ipynb

@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -9,21 +10,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
     "from spyrmsd import io, rmsd"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "### OpenBabel or RDKit"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -37,13 +40,15 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "### Loading Molecules"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -52,14 +57,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
     "ref = io.loadmol(\"molecules/1a4k_ligand.sdf\")"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -68,21 +74,82 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
     "mols = io.loadallmols(\"molecules/1a4k_dock.sdf\")"
    ]
   },
   {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Loading RDKit or OpenBabel Molecules"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "`spyrmsd` natively supports Open Babel and RDKit (if installed). The `Molecule` class provides `from_openbabel()` and `from_rdkit()` constructors."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "<frozen importlib._bootstrap>:241: RuntimeWarning: to-Python converter for std::__1::pair<double, double> already registered; second conversion method ignored.\n",
+      "[18:44:03] Molecule does not have explicit Hs. Consider calling AddHs()\n",
+      "[18:44:03] Molecule does not have explicit Hs. Consider calling AddHs()\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "[0.019162902039384797]"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from rdkit import Chem\n",
+    "from rdkit.Chem import AllChem\n",
+    "\n",
+    "rdmol1 = Chem.MolFromSmiles(\"c1ccccc1\")\n",
+    "rdmol2 = Chem.MolFromSmiles(\"c1ccccc1\")\n",
+    "AllChem.EmbedMolecule(rdmol1)\n",
+    "AllChem.EmbedMolecule(rdmol2)\n",
+    "\n",
+    "from spyrmsd.molecule import Molecule\n",
+    "from spyrmsd.rmsd import rmsdwrapper\n",
+    "\n",
+    "mol1 = Molecule.from_rdkit(rdmol1)\n",
+    "mol2 = Molecule.from_rdkit(rdmol2)\n",
+    "\n",
+    "rmsdwrapper(mol1, mol2)"
+   ]
+  },
+  {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "### Removing Hydrogen Atoms"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -91,7 +158,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -100,7 +167,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -109,13 +176,15 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "## Symmetry-Corrected RMSD"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -124,7 +193,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -135,7 +204,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -145,6 +214,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -153,7 +223,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -178,13 +248,15 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "### Minimum RMSD"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -193,14 +265,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[1.2012368667355435, 1.0533413220699535, 1.153253104575529, 1.036542688936588, 0.8407673221224143, 1.1758143217869736, 0.7817315189656655, 1.0933314311267845, 1.0260767175206462, 0.9586369647000478]\n"
+      "[1.2012368667355435, 1.0533413220699535, 1.153253104575529, 1.036542688936588, 0.8407673221224187, 1.1758143217869736, 0.7817315189656655, 1.0933314311267845, 1.0260767175206462, 0.9586369647000478]\n"
      ]
     }
    ],
@@ -235,7 +307,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,