pyocl-idor 0.8.2__tar.gz

pyocl_idor-0.8.2/.gitattributes

@@ -0,0 +1,4 @@
+* text=auto eol=lf
+*.bat text eol=crlf
+*.jar -text
+*.class -text

pyocl_idor-0.8.2/.github/workflows/release.yml

@@ -0,0 +1,127 @@
+name: CI and PyPI release
+
+on:
+  push:
+    branches: ["**"]
+    tags: ["v*"]
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build and validate distributions
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7.0.1
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - uses: actions/setup-python@v7.0.0
+        with:
+          python-version: "3.12"
+      - name: Install build tools
+        run: python -m pip install build twine
+      - name: Build wheel and source distribution
+        run: python -m build
+      - name: Validate package metadata
+        run: python -m twine check --strict dist/*
+      - name: Check bundled Java files and release version
+        env:
+          IS_RELEASE: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') }}
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: |
+          python - <<'PY'
+          from email.parser import Parser
+          import os
+          from pathlib import Path
+          from packaging.version import Version
+          from zipfile import ZipFile
+
+          wheel, = Path("dist").glob("*.whl")
+          with ZipFile(wheel) as archive:
+              names = archive.namelist()
+              required = {
+                  "pyocl/lib/openchemlib-2026.2.1.jar",
+                  "pyocl/java/CustomObjectInputStream.class",
+                  "pyocl/java/ParallelSimilaritySearch.class",
+                  "pyocl/java/ParallelSimilaritySearch$Query.class",
+                  "pyocl/java/ParallelSimilaritySearch$Result.class",
+              }
+              missing = required.difference(names)
+              if missing:
+                  raise SystemExit(f"Missing Java files: {sorted(missing)}")
+              bundled_jars = {name for name in names if name.endswith(".jar")}
+              if bundled_jars != {"pyocl/lib/openchemlib-2026.2.1.jar"}:
+                  raise SystemExit(f"Unexpected bundled JARs: {sorted(bundled_jars)}")
+              metadata_file, = [name for name in names if name.endswith(".dist-info/METADATA")]
+              metadata = Parser().parsestr(archive.read(metadata_file).decode())
+              version = Version(metadata["Version"])
+
+          if os.environ["IS_RELEASE"] == "true":
+              expected = Version(os.environ["RELEASE_TAG"][1:])
+              if expected.local is not None or expected.is_devrelease:
+                  raise SystemExit("Release tags must use a public release version")
+              if version != expected:
+                  raise SystemExit(f"Built version {version} does not match tag {expected}")
+          print(f"Validated {metadata['Name']} {version}")
+          PY
+      - uses: actions/upload-artifact@v7.0.2
+        with:
+          name: distributions
+          path: dist/*
+          if-no-files-found: error
+
+  test:
+    name: Test wheel (${{ matrix.os }}, Python ${{ matrix.python }})
+    needs: build
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python: ["3.10", "3.12"]
+    steps:
+      - uses: actions/checkout@v7.0.1
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@v7.0.0
+        with:
+          python-version: ${{ matrix.python }}
+      - uses: actions/setup-java@v6.0.1
+        with:
+          distribution: temurin
+          java-version: "21"
+      - uses: actions/download-artifact@v8.0.1
+        with:
+          name: distributions
+          path: dist
+      - name: Install built wheel and test dependencies
+        shell: bash
+        run: python -m pip install dist/*.whl pytest
+      - name: Test installed package outside the checkout
+        working-directory: ${{ runner.temp }}
+        shell: bash
+        run: python -m pytest --import-mode=importlib "$GITHUB_WORKSPACE/tests" -q
+
+  publish:
+    name: Publish to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    needs: [build, test]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/pyocl-idor/
+    permissions:
+      id-token: write
+    concurrency:
+      group: pypi-${{ github.ref }}
+      cancel-in-progress: false
+    steps:
+      - uses: actions/download-artifact@v8.0.1
+        with:
+          name: distributions
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@v1.14.2

pyocl_idor-0.8.2/.gitignore

@@ -0,0 +1,10 @@
+__pycache__/
+*.pyc
+.env
+.DS_Store
+build/
+dist/
+*.egg-info/
+docs/_build/
+docs/pyocl*.rst
+_version.py

pyocl_idor-0.8.2/LICENSE

@@ -0,0 +1,32 @@
+/*
+* Copyright (c) 1997 - 2016
+* Actelion Pharmaceuticals Ltd.
+* Gewerbestrasse 16
+* CH-4123 Allschwil, Switzerland
+*
+* All rights reserved.
+*
+* Redistribution and use in source and binary forms, with or without
+* modification, are permitted provided that the following conditions are met:
+*
+* 1. Redistributions of source code must retain the above copyright notice, this
+*    list of conditions and the following disclaimer.
+* 2. Redistributions in binary form must reproduce the above copyright notice,
+*    this list of conditions and the following disclaimer in the documentation
+*    and/or other materials provided with the distribution.
+* 3. Neither the name of the the copyright holder nor the
+*    names of its contributors may be used to endorse or promote products
+*    derived from this software without specific prior written permission.
+*
+* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*
+*/

pyocl_idor-0.8.2/MANIFEST.in

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+recursive-include pyocl/lib *
+recursive-include pyocl/java *

pyocl_idor-0.8.2/PKG-INFO

@@ -0,0 +1,102 @@
+Metadata-Version: 2.4
+Name: pyocl-idor
+Version: 0.8.2
+Summary: OpenChemLib via python
+Author-email: Julien Hazemann <julien.hazemann@idorsia.com>, Manuel Sellner <manuel.sellner@idorsia.com>, Thomas Liphardt <thomas.liphardt@idorsia.com>
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: jpype1>=1.5.1
+Requires-Dist: numba>=0.61.0
+Dynamic: license-file
+
+# PyOCL
+
+## Description
+
+The PyOCL (Python OpenChemLib) is a python wrapper for the Java-based [OpenChemLib](https://github.com/Actelion/openchemlib).
+
+
+## Prerequisites
+
+Environment variable ```JAVA_HOME``` must point to a Java 21 or newer runtime.
+The bundled PyOCL helper classes require Java 21. E.g.
+```bash
+export JAVA_HOME=/path/to/jdk-21
+```
+
+## Dependencies
+
+Some functionalities of PyOCL require RDKit or pandas to be installed (conversion between OCL StereoMolecules and RDKit molecules, conversion between DataWarrior dwar files and pandas dataframes).  
+If you need these functionalities, you have to install RDKit and/or pandas separately:
+
+```bash
+pip install pandas==2.2.3
+pip install rdkit==2024.3.6
+```
+
+## Installation
+
+1. Generate and activate virtual environment:
+```bash
+# Conda
+conda create -n pyocl python=3.10
+conda activate pyocl
+
+# Python venv
+python -m venv venv
+. venv/bin/activate  # Command for Linux
+.\venv\Scripts\activate  # Command for Windows
+```
+
+2. Install PyOCL:
+```bash
+# From PyPI
+python -m pip install pyocl-idor
+
+# From cloned repository
+git clone https://github.com/actelion/pyocl.git
+python -m pip install pyocl/
+
+# Directly from GitHub with pip
+python -m pip install git+https://github.com/actelion/pyocl.git
+```
+
+The PyPI distribution is named `pyocl-idor`; Python imports use `pyocl`, for
+example `from pyocl.chem import StereoMolecule`.
+
+## Documentation
+
+You can build a local version of the full PyOCL documentation:
+
+```bash
+# Create environment and install dependencies
+conda create -n pyocl python=3.10
+conda activate pyocl
+git clone https://github.com/actelion/pyocl.git
+python -m pip install pyocl/ sphinx==8.1.3 sphinx-rtd-theme==3.0.2 pandas==2.2.3 rdkit==2024.3.6
+
+# Build documentation
+cd pyocl/docs/
+sphinx-apidoc -o . ../pyocl
+make html  # Command for Linux
+.\make.bat html  # Command for Windows
+```
+
+This creates the directory `docs/_build/html` in which you can find a file called `index.html`. You can open this file in your browser to access the documentation.
+
+This package also contains tutorials about specific functionalities of PyOCL. While they are covered in the html version of the documentation, there is also a **Python script** and a **Jupyter notebook** for each of the tutorials. These files can be found in `docs/tutorials`.
+
+## CI and PyPI releases
+
+The GitHub Actions workflow in `.github/workflows/release.yml` builds a wheel and
+source distribution on branch pushes and pull requests. It checks package
+metadata and bundled Java files, then tests the installed wheel on Linux,
+Windows, and macOS with Python 3.10 and 3.12 and Java 21. The Java setup action
+sets `JAVA_HOME` and adds Java to `PATH` in every test job.
+
+Pushing a version tag such as `v0.8.2` also publishes the tested distributions to
+PyPI under the distribution name `pyocl-idor`. Branch pushes, pull requests, and
+manual workflow runs run the checks
+without publishing. Versions are derived from Git tags by `setuptools_scm`;
+the release build must match the pushed tag.

pyocl_idor-0.8.2/README.md

@@ -0,0 +1,90 @@
+# PyOCL
+
+## Description
+
+The PyOCL (Python OpenChemLib) is a python wrapper for the Java-based [OpenChemLib](https://github.com/Actelion/openchemlib).
+
+
+## Prerequisites
+
+Environment variable ```JAVA_HOME``` must point to a Java 21 or newer runtime.
+The bundled PyOCL helper classes require Java 21. E.g.
+```bash
+export JAVA_HOME=/path/to/jdk-21
+```
+
+## Dependencies
+
+Some functionalities of PyOCL require RDKit or pandas to be installed (conversion between OCL StereoMolecules and RDKit molecules, conversion between DataWarrior dwar files and pandas dataframes).  
+If you need these functionalities, you have to install RDKit and/or pandas separately:
+
+```bash
+pip install pandas==2.2.3
+pip install rdkit==2024.3.6
+```
+
+## Installation
+
+1. Generate and activate virtual environment:
+```bash
+# Conda
+conda create -n pyocl python=3.10
+conda activate pyocl
+
+# Python venv
+python -m venv venv
+. venv/bin/activate  # Command for Linux
+.\venv\Scripts\activate  # Command for Windows
+```
+
+2. Install PyOCL:
+```bash
+# From PyPI
+python -m pip install pyocl-idor
+
+# From cloned repository
+git clone https://github.com/actelion/pyocl.git
+python -m pip install pyocl/
+
+# Directly from GitHub with pip
+python -m pip install git+https://github.com/actelion/pyocl.git
+```
+
+The PyPI distribution is named `pyocl-idor`; Python imports use `pyocl`, for
+example `from pyocl.chem import StereoMolecule`.
+
+## Documentation
+
+You can build a local version of the full PyOCL documentation:
+
+```bash
+# Create environment and install dependencies
+conda create -n pyocl python=3.10
+conda activate pyocl
+git clone https://github.com/actelion/pyocl.git
+python -m pip install pyocl/ sphinx==8.1.3 sphinx-rtd-theme==3.0.2 pandas==2.2.3 rdkit==2024.3.6
+
+# Build documentation
+cd pyocl/docs/
+sphinx-apidoc -o . ../pyocl
+make html  # Command for Linux
+.\make.bat html  # Command for Windows
+```
+
+This creates the directory `docs/_build/html` in which you can find a file called `index.html`. You can open this file in your browser to access the documentation.
+
+This package also contains tutorials about specific functionalities of PyOCL. While they are covered in the html version of the documentation, there is also a **Python script** and a **Jupyter notebook** for each of the tutorials. These files can be found in `docs/tutorials`.
+
+## CI and PyPI releases
+
+The GitHub Actions workflow in `.github/workflows/release.yml` builds a wheel and
+source distribution on branch pushes and pull requests. It checks package
+metadata and bundled Java files, then tests the installed wheel on Linux,
+Windows, and macOS with Python 3.10 and 3.12 and Java 21. The Java setup action
+sets `JAVA_HOME` and adds Java to `PATH` in every test job.
+
+Pushing a version tag such as `v0.8.2` also publishes the tested distributions to
+PyPI under the distribution name `pyocl-idor`. Branch pushes, pull requests, and
+manual workflow runs run the checks
+without publishing. Versions are derived from Git tags by `setuptools_scm`;
+the release build must match the pushed tag.

pyocl_idor-0.8.2/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

pyocl_idor-0.8.2/docs/conf.py

@@ -0,0 +1,38 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../pyocl'))
+
+project = 'PyOCL'
+copyright = '2024, Julien Hazemann, Thomas Liphardt, Manuel Sellner'
+author = 'Julien Hazemann, Thomas Liphardt, Manuel Sellner'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.viewcode",
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+language = "EN"
+
+pygments_style = "default"
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']

pyocl_idor-0.8.2/docs/getting_started.rst

@@ -0,0 +1,17 @@
+Getting Started
+===============
+
+This page details how to use PyOCL.
+
+Installation
+------------
+
+You can install PyOCL either from pip or from GitHub:
+
+.. code:: bash
+
+    # Install with pip
+    python -m pip install pyocl-idor
+
+    # Install from GitHub
+    python -m pip install git+https://github.com/idorsia/pyocl.git

pyocl_idor-0.8.2/docs/index.rst

@@ -0,0 +1,35 @@
+.. PyOCL documentation master file, created by
+   sphinx-quickstart on Fri Nov 15 17:30:00 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+PyOCL documentation
+===================
+
+PyOCL is a Python library that provides seamless access to the powerful cheminformatics capabilities of the Java-based OpenChemLib. 
+By wrapping OpenChemLib's Java classes, this project enables Python developers to leverage advanced chemical structure representation, 
+manipulation, and analysis tools directly within their Python workflows. The integration bridges the gap between Java's robust 
+cheminformatics ecosystem and Python's versatile data science and machine learning stack, making it an ideal tool for researchers, 
+chemists, and developers in computational chemistry and related fields.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   getting_started
+   tutorials
+
+
+.. toctree::
+   :maxdepth: 3
+
+   modules
+
+
+Indices and Tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

pyocl_idor-0.8.2/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

pyocl_idor-0.8.2/docs/modules.rst

@@ -0,0 +1,7 @@
+pyocl
+=====
+
+.. toctree::
+   :maxdepth: 4
+
+   pyocl

pyocl_idor-0.8.2/docs/tutorials/conformer_generation.ipynb

@@ -0,0 +1,84 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pyocl\n",
+    "from pyocl.chem.conf import ConformerSetGenerator\n",
+    "\n",
+    "\n",
+    "daridorexant = pyocl.convert.smiles_to_stereo_molecule(\"CC1=C(C=CC2=C1N=C(N2)[C@@]3(CCCN3C(=O)C4=C(C=CC(=C4)OC)N5N=CC=N5)C)Cl\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "confgen = ConformerSetGenerator(max_nr_confs=200)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "181\n"
+     ]
+    }
+   ],
+   "source": [
+    "conformer_set = confgen.generate_conformer_set(daridorexant)\n",
+    "print(len(conformer_set))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "0.00038681084215447145\n"
+     ]
+    }
+   ],
+   "source": [
+    "most_likely_conformers = conformer_set.sort_by_likelihood()[:100]\n",
+    "highest_likelihood = most_likely_conformers[0].get_likelihood()\n",
+    "print(highest_likelihood)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

pyocl_idor-0.8.2/docs/tutorials/conformer_generation.py

@@ -0,0 +1,18 @@
+import pyocl
+from pyocl.chem.conf import ConformerSetGenerator
+
+
+# Define molecule to create conformers for
+daridorexant = pyocl.convert.smiles_to_stereo_molecule("CC1=C(C=CC2=C1N=C(N2)[C@@]3(CCCN3C(=O)C4=C(C=CC(=C4)OC)N5N=CC=N5)C)Cl")
+
+# Initialize conformer set generator
+confgen = ConformerSetGenerator(max_nr_confs=200)
+
+# Generate set of conformers
+conformer_set = confgen.generate_conformer_set(daridorexant)
+print(len(conformer_set))
+
+# Sort by highest likelihood and get 100 most likely conformers
+most_likely_conformers = conformer_set.sort_by_likelihood()[:100]
+highest_likelihood = most_likely_conformers[0].get_likelihood()
+print(highest_likelihood)

pyocl_idor-0.8.2/docs/tutorials/conformer_generation.rst

@@ -0,0 +1,42 @@
+Conformer Generation
+====================
+
+This tutorial explains how to generate conformers for a given molecule.
+
+First, let's define the molecule we want to generate conformers for. We will do that using a SMILES string.
+
+.. code-block:: python
+
+    import pyocl
+    from pyocl.chem.conf import ConformerSetGenerator
+
+
+    daridorexant = pyocl.convert.smiles_to_stereo_molecule("CC1=C(C=CC2=C1N=C(N2)[C@@]3(CCCN3C(=O)C4=C(C=CC(=C4)OC)N5N=CC=N5)C)Cl")
+
+Next, we need to initialize the conformer set generator. This is done by using the wrapper for the :code:`ConformerSetGenerator` class.
+
+.. code-block:: python
+
+    confgen = ConformerSetGenerator(max_nr_confs=200)
+
+Now we are ready to actually generate conformers for our molecule.
+
+.. code-block:: python
+
+    conformer_set = confgen.generate_conformer_set(daridorexant)
+
+The output is an instance of the :code:`ConformerSet` class which contains :code:`Conformer` objects and has all the functionalities of a normal python set.
+
+.. code-block:: python
+
+    print(len(conformer_set))
+
+Let's say we are only interested in the 100 most likely conformers.
+
+.. code-block:: python
+
+    most_likely_conformers = conformer_set.sort_by_likelihood()[:100]
+    highest_likelihood = most_likely_conformers[0].get_likelihood()
+    print(highest_likelihood)
+
+For more details, see the API documentation for :class:`pyocl.chem.conf.conformer_set_generator.ConformerSetGenerator`, :class:`pyocl.chem.conf.conformer_set.ConformerSet`, and :class:`pyocl.chem.conf.conformer.Conformer`.