RMeli · RMeli · Dec 20, 2025 · Dec 20, 2025 · Dec 20, 2025 · Dec 20, 2025
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -12,7 +12,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
     - uses: actions/checkout@v5

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -25,18 +25,14 @@ jobs:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
         python-version: ["3.11", "3.12", "3.13", "3.14"]
-        chemlib: [obabel, rdkit]
+        chemlib: [rdkit]
         graphlib: [nogt, all]
         exclude:
           # graph-tool does not work on Windows
           - {os: "windows-latest", graphlib: "all"}
           # Don't run without graph-tool on Ubuntu and macOS
           - {os: "ubuntu-latest", graphlib: "nogt"}
           - {os: "macos-latest", graphlib: "nogt"}
-          # Open Babel has not been updated for Python 3.13 and 3.14
-          - {chemlib: "obabel", python-version: "3.13"}
-          - {chemlib: "obabel", python-version: "3.14"}
-
     steps:
     - uses: actions/checkout@v5
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ Contributors: @RMeli
 
 ### Removed
 
+* support for Open Babel [PR #151 | @RMeli]
 * Python `3.9` and `3.10` from CI [PR #147 | @RMeli]
 
 ## Version 0.9.0

diff --git a/README.md b/README.md
@@ -41,7 +41,7 @@ If you find `spyrmsd` useful, please consider citing the following paper:
 > `spyrmsd` will install [rustworkx] (multi-platform) when using `pip` or `conda`. You can install other backends manually.
 
 > [!WARNING]
-> 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`.
+> If `spyrmsd` is used as a standalone tool, it is required to install [RDKit](https://rdkit.org/). It is not automatically installed with `pip` nor `conda`.
 
 ### PyPI
 
@@ -84,9 +84,8 @@ One of the following graph libraries is required:
 
 #### Standalone Tool
 
-Additionally, one of the following packages is required to use `spyrmsd` as a standalone tool:
+Additionally, following package is required to use `spyrmsd` as a standalone tool:
 
-* [Open Babel](http://openbabel.org/)
 * [RDKit](https://rdkit.org/)
 
 ## Usage

diff --git a/devtools/conda-envs/spyrmsd-all.yaml b/devtools/conda-envs/spyrmsd-all.yaml
@@ -22,7 +22,6 @@ dependencies:
   - scikit-learn
 
   # Chemistry
-  - openbabel
   - rdkit
 
   # Plotting

diff --git a/devtools/conda-envs/spyrmsd-docs.yaml b/devtools/conda-envs/spyrmsd-docs.yaml
@@ -15,7 +15,6 @@ dependencies:
   - rustworkx
 
   # Chemistry
-  - openbabel
   - rdkit
 
   # Doc

diff --git a/devtools/conda-envs/spyrmsd-test-obabel-all.yaml b/devtools/conda-envs/spyrmsd-test-obabel-all.yaml
diff --git a/devtools/conda-envs/spyrmsd-test-obabel-nogt.yaml b/devtools/conda-envs/spyrmsd-test-obabel-nogt.yaml
diff --git a/docs/source/api/spyrmsd.constants.rst b/docs/source/api/spyrmsd.constants.rst
@@ -3,5 +3,5 @@ spyrmsd.constants module
 
 .. automodule:: spyrmsd.constants
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.due.rst b/docs/source/api/spyrmsd.due.rst
@@ -3,5 +3,5 @@ spyrmsd.due module
 
 .. automodule:: spyrmsd.due
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.exceptions.rst b/docs/source/api/spyrmsd.exceptions.rst
@@ -3,5 +3,5 @@ spyrmsd.exceptions module
 
 .. automodule:: spyrmsd.exceptions
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.graph.rst b/docs/source/api/spyrmsd.graph.rst
@@ -3,5 +3,5 @@ spyrmsd.graph module
 
 .. automodule:: spyrmsd.graph
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.graphs.gt.rst b/docs/source/api/spyrmsd.graphs.gt.rst
@@ -3,5 +3,5 @@ spyrmsd.graphs.gt module
 
 .. automodule:: spyrmsd.graphs.gt
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.graphs.nx.rst b/docs/source/api/spyrmsd.graphs.nx.rst
@@ -3,5 +3,5 @@ spyrmsd.graphs.nx module
 
 .. automodule:: spyrmsd.graphs.nx
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.graphs.rst b/docs/source/api/spyrmsd.graphs.rst
@@ -3,8 +3,8 @@ spyrmsd.graphs package
 
 .. automodule:: spyrmsd.graphs
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
 
 Submodules
 ----------
@@ -14,3 +14,4 @@ Submodules
 
    spyrmsd.graphs.gt
    spyrmsd.graphs.nx
+   spyrmsd.graphs.rx
diff --git a/docs/source/api/spyrmsd.graphs.rx.rst b/docs/source/api/spyrmsd.graphs.rx.rst
@@ -0,0 +1,7 @@
+spyrmsd.graphs.rx module
+========================
+
+.. automodule:: spyrmsd.graphs.rx
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.hungarian.rst b/docs/source/api/spyrmsd.hungarian.rst
@@ -3,5 +3,5 @@ spyrmsd.hungarian module
 
 .. automodule:: spyrmsd.hungarian
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.io.rst b/docs/source/api/spyrmsd.io.rst
@@ -3,5 +3,5 @@ spyrmsd.io module
 
 .. automodule:: spyrmsd.io
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.molecule.rst b/docs/source/api/spyrmsd.molecule.rst
@@ -3,5 +3,5 @@ spyrmsd.molecule module
 
 .. automodule:: spyrmsd.molecule
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.optional.obabel.rst b/docs/source/api/spyrmsd.optional.obabel.rst
diff --git a/docs/source/api/spyrmsd.optional.rdkit.rst b/docs/source/api/spyrmsd.optional.rdkit.rst
@@ -3,5 +3,5 @@ spyrmsd.optional.rdkit module
 
 .. automodule:: spyrmsd.optional.rdkit
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.optional.rst b/docs/source/api/spyrmsd.optional.rst
@@ -3,14 +3,13 @@ spyrmsd.optional package
 
 .. automodule:: spyrmsd.optional
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
 
 Submodules
 ----------
 
 .. toctree::
    :maxdepth: 4
 
-   spyrmsd.optional.obabel
    spyrmsd.optional.rdkit
diff --git a/docs/source/api/spyrmsd.parallel.rst b/docs/source/api/spyrmsd.parallel.rst
@@ -0,0 +1,7 @@
+spyrmsd.parallel module
+=======================
+
+.. automodule:: spyrmsd.parallel
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.qcp.rst b/docs/source/api/spyrmsd.qcp.rst
@@ -3,5 +3,5 @@ spyrmsd.qcp module
 
 .. automodule:: spyrmsd.qcp
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.rmsd.rst b/docs/source/api/spyrmsd.rmsd.rst
@@ -3,5 +3,5 @@ spyrmsd.rmsd module
 
 .. automodule:: spyrmsd.rmsd
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/api/spyrmsd.rst b/docs/source/api/spyrmsd.rst
@@ -3,8 +3,8 @@ spyrmsd package
 
 .. automodule:: spyrmsd
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
 
 Subpackages
 -----------
@@ -28,6 +28,7 @@ Submodules
    spyrmsd.hungarian
    spyrmsd.io
    spyrmsd.molecule
+   spyrmsd.parallel
    spyrmsd.qcp
    spyrmsd.rmsd
    spyrmsd.utils
diff --git a/docs/source/api/spyrmsd.utils.rst b/docs/source/api/spyrmsd.utils.rst
@@ -3,5 +3,5 @@ spyrmsd.utils module
 
 .. automodule:: spyrmsd.utils
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -7,7 +7,7 @@ Installation
 Installation
 ------------
 
-Installing ``spyrmsd`` with ``pip``, ``conda`` or from source will install the package as a library. In order to install the package as a standalone tool, `Open Babel`_ or RDKit_ need to be installed as well (see :ref:`Dependencies`).
+Installing ``spyrmsd`` with ``pip``, ``conda`` or from source will install the package as a library. In order to install the package as a standalone tool, RDKit_ needs to be installed as well (see :ref:`Dependencies`).
 
 pip
 ~~~
@@ -56,13 +56,11 @@ Standalone Tool
 
 Additionally, one of the following packages is required to use ``spyrmsd`` as a standalone tool:
 
-* `Open Babel`_
 * RDKit_
 
 .. _PyPI: https://pypi.org/project/spyrmsd/
 .. _conda-forge: https://github.com/conda-forge/spyrmsd-feedstock
 .. _RDKit: https://rdkit.org/
-.. _Open Babel: http://openbabel.org/
 .. _graph-tool: https://graph-tool.skewed.de/
 .. _NetworkX: https://networkx.github.io/
 .. _numpy: https://numpy.org/
-Original file line number
+Diff line change
@@ Expand Up / @@ -15,7 +15,6 @@ dependencies: @@
       - rustworkx
       # Chemistry
-      - openbabel
       - rdkit
       # Doc
@@ Expand Down @@