Merge pull request #736 from padix-key/rdkit

Add interface to RDKit

.github/workflows/test_and_deploy.yml

@@ -23,6 +23,7 @@ env:
     --durations=50
     --ignore={project}//tests//sequence//align//test_statistics.py
     --ignore={project}//tests//application
+    --ignore={project}//tests//interface
     --ignore={project}//tests//database
     --ignore={project}//tests//test_doctest.py
     --ignore={project}//tests//test_modname.py
@@ -223,6 +224,7 @@ jobs:
           tests//test_modname.py
           tests//database
           tests//application
+          tests//interface
 
 
   test-muscle5:

doc/conf.py

@@ -67,6 +67,7 @@
     "sphinx.ext.doctest",
     "sphinx.ext.mathjax",
     "sphinx.ext.linkcode",
+    "sphinx.ext.intersphinx",
     "sphinxcontrib.bibtex",
     "sphinx_gallery.gen_gallery",
     "sphinx_design",
@@ -111,6 +112,10 @@
 
 notfound_urls_prefix = "/latest/"
 
+intersphinx_mapping = {"rdkit": ("https://www.rdkit.org/docs/", None)}
+intersphinx_timeout = 60
+
+
 #### HTML ####
 
 html_theme = "pydata_sphinx_theme"

doc/switcher.py

@@ -5,60 +5,31 @@
 __author__ = "Patrick Kunzmann"
 __all__ = ["create_switcher_json"]
 
-import functools
 import json
-import re
-from dataclasses import dataclass
 import requests
+from packaging.version import Version
 import biotite
 
 RELEASE_REQUEST = "https://api.github.com/repos/biotite-dev/biotite/releases"
 BIOTITE_URL = "https://www.biotite-python.org"
-SEMVER_TAG_REGEX = r"^v?(\d+)\.(\d+)\.(\d+)"
-
-
-@functools.total_ordering
-@dataclass(frozen=True)
-class Version:
-    major: ...
-    minor: ...
-    patch: ...
-
-    @staticmethod
-    def from_tag(tag):
-        match = re.match(SEMVER_TAG_REGEX, tag)
-        if match is None:
-            raise ValueError(f"Invalid tag: {tag}")
-        major, minor, patch = map(int, match.groups())
-        return Version(major, minor, patch)
-
-    def __str__(self):
-        return f"{self.major}.{self.minor}.{self.patch}"
-
-    def __ge__(self, other):
-        return (self.major, self.minor, self.patch) >= (
-            other.major,
-            other.minor,
-            other.patch,
-        )
 
 
 def _get_previous_versions(min_tag, n_versions, current_version):
     # The current version might already be released on GitHub
     # -> request one more version than necessary
     response = requests.get(RELEASE_REQUEST, params={"per_page": n_versions + 1})
     release_data = json.loads(response.text)
-    versions = [Version.from_tag(release["tag_name"]) for release in release_data]
+    versions = [Version(release["tag_name"]) for release in release_data]
     applicable_versions = [
         version
         for version in versions
-        if version >= Version.from_tag(min_tag) and version < current_version
+        if version >= Version(min_tag) and version < current_version
     ]
     return applicable_versions[:n_versions]
 
 
 def _get_current_version():
-    return Version(*biotite.__version_tuple__[:3])
+    return Version(biotite.__version__)
 
 
 def create_switcher_json(file_path, min_tag, n_versions):
@@ -81,7 +52,7 @@ def create_switcher_json(file_path, min_tag, n_versions):
         versions.append(current_version)
     versions.sort()
     for version in versions:
-        if version.patch != 0:
+        if version.micro != 0:
             # Documentation is not uploaded for patch versions
             continue
         version_config.append(

doc/tutorial/index.rst

@@ -103,4 +103,5 @@ provided by the mentioned subpackages.
     database/index
     sequence/index
     structure/index
-    application/index
+    application/index
+    interface/index

doc/tutorial/interface/index.rst

@@ -0,0 +1,38 @@
+:sd_hide_title: true
+
+.. include:: /tutorial/preamble.rst
+
+##########################
+``interface`` subpackage
+##########################
+
+Connecting the ecosystem - The ``interface`` subpackage
+=======================================================
+
+.. currentmodule:: biotite.interface
+
+In the last section we learned that :mod:`biotite.application` encapsulates entire
+external application runs with subsequent calls of ``start()`` and ``join()``.
+In contrast :mod:`biotite.interface` provides flexible interfaces to other Python
+packages in the bioinformatics ecosystem.
+Its purpose is to convert between native Biotite objects, such as :class:`.AtomArray`
+and :class:`.Sequence`, and the corresponding objects in the respective interfaced
+package.
+Each interface is located in a separate subpackage with the same name as the
+interfaced package.
+For example, the interface to ``rdkit`` is placed in the subpackage
+:mod:`biotite.interface.rdkit`.
+
+.. note::
+
+    Like in :mod:`biotite.application`, the interfaced Python packages are not
+    dependencies of the ``biotite`` package.
+    Hence, they need to be installed separately.
+
+The following chapters will give you an overview of the different interfaced packages.
+
+.. toctree::
+    :maxdepth: 1
+    :hidden:
+
+    rdkit

doc/tutorial/interface/rdkit.rst

@@ -0,0 +1,66 @@
+.. include:: /tutorial/preamble.rst
+
+Interface to RDKit
+==================
+
+.. currentmodule:: biotite.interface.rdkit
+
+`RDKit <https://www.rdkit.org/>`_ is a popular cheminformatics package
+and thus can be used to supplement *Biotite* with a variety of functionalities focused
+on small molecules, such as conversion from/to textual representations
+(e.g. *SMILES* and *InChI*) and visualization as structural formulas.
+Basically, the :mod:`biotite.interface.rdkit` subpackage provides only two functions:
+:func:`to_mol()` to obtain a :class:`rdkit.Chem.rdchem.Mol` from an :class:`.AtomArray`
+and :func:`from_mol()` for the reverse direction.
+The rest happens within the realm of *RDKit*.
+This tutorial will only give a small glance on how the interface can be used.
+For comprehensive documentation refer to the
+`RDKit documentation <https://www.rdkit.org/docs/>`_.
+
+First example: Depiction as structural formula
+----------------------------------------------
+*RDKit* allows rendering structural formulas using
+`pillow <https://pillow.readthedocs.io/en/stable/>`_.
+For a proper structural formula, we need to compute proper 2D coordinates first.
+
+.. jupyter-execute::
+
+    import biotite.interface.rdkit as rdkit_interface
+    import biotite.structure.info as struc
+    from rdkit.Chem.Draw import MolToImage
+    from rdkit.Chem.rdDepictor import Compute2DCoords
+    from rdkit.Chem.rdmolops import RemoveHs
+
+    penicillin = struc.residue("PNN")
+    mol = rdkit_interface.to_mol(penicillin)
+    # We do not want to include explicit hydrogen atoms in the structural formula
+    mol = RemoveHs(mol)
+    Compute2DCoords(mol)
+    image = MolToImage(mol, size=(600, 400))
+    display(image)
+
+Second example: Creating a molecule from SMILES
+-----------------------------------------------
+Although the *Chemical Component Dictionary* accessible from
+:mod:`biotite.structure.info` already provides all compounds found in the PDB,
+there are a myriad of compounds out there that are not part of it.
+One way to to obtain them as :class:`.AtomArray` is passing a *SMILES* string to
+*RDKit* to obtain the topology of the molecule and then computing the coordinates.
+
+.. jupyter-execute::
+
+    from rdkit.Chem import MolFromSmiles
+    from rdkit.Chem.rdDistGeom import EmbedMolecule
+    from rdkit.Chem.rdForceFieldHelpers import UFFOptimizeMolecule
+    from rdkit.Chem.rdmolops import AddHs
+
+    ERTAPENEM_SMILES = "C[C@@H]1[C@@H]2[C@H](C(=O)N2C(=C1S[C@H]3C[C@H](NC3)C(=O)NC4=CC=CC(=C4)C(=O)O)C(=O)O)[C@@H](C)O"
+
+    mol = MolFromSmiles(ERTAPENEM_SMILES)
+    # RDKit uses implicit hydrogen atoms by default, but Biotite requires explicit ones
+    mol = AddHs(mol)
+    # Create a 3D conformer
+    conformer_id = EmbedMolecule(mol)
+    UFFOptimizeMolecule(mol)
+    ertapenem = rdkit_interface.from_mol(mol, conformer_id)
+    print(ertapenem)

environment.yml

@@ -22,6 +22,7 @@ dependencies:
   - msgpack-python >=0.5.6
   - networkx >=2.0
   - numpy >=2.0
+  - packaging >=24.0
   - requests >=2.12
   # Testing
   - pytest >=7.0
@@ -53,3 +54,6 @@ dependencies:
   - pydot >=1.4
   - scikit-learn >=0.18
   - scipy >=1.8.0
+  - pip:
+    # Conda provides no recent version of RDKit (required for biotite.interface)
+    - rdkit

pyproject.toml

@@ -27,7 +27,7 @@ dependencies = [
   "requests >= 2.12",
   "msgpack >= 0.5.6",
   "networkx >= 2.0",
-  "requests >= 2.12",
+  "packaging >= 24.0",
 ]
 dynamic = ["version"]
 

src/biotite/interface/__init__.py

@@ -0,0 +1,19 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+This subpackage provides interfaces to other Python packages in the bioinformatics
+ecosystem.
+Its purpose is to convert between native Biotite objects, such as :class:`.AtomArray`
+and :class:`.Sequence`, and the corresponding objects in the respective interfaced
+package.
+In contrast to :mod:`biotite.application`, where an entire application run is handled
+under the hood, :mod:`biotite.interface` only covers the object conversion, allowing
+for more flexibility.
+"""
+
+__name__ = "biotite.interface"
+__author__ = "Patrick Kunzmann"
+
+from .warning import *

src/biotite/interface/rdkit/__init__.py

@@ -0,0 +1,15 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+This subpackage provides an interface to the `RDKit <https://www.rdkit.org/>`_
+cheminformatics package.
+It allows conversion between :class:`.AtomArray` and :class:`rdkit.Chem.rdchem.Mol`
+objects.
+"""
+
+__name__ = "biotite.interface.rdkit"
+__author__ = "Patrick Kunzmann"
+
+from .mol import *