diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index f2993190..b08a3f8c 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -20,12 +20,18 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.10"
-      - run: |
-          pip install rdkit
-          pip install -e ".[docs]"
+      - name: Install poetry
+        uses: abatilo/actions-poetry@v2
+      - name: Define a cache for the virtual environment based on the dependencies lock file
+        uses: actions/cache@v3
+        with:
+          path: ./.venv
+          key: venv-${{ hashFiles('poetry.lock') }}
+      - name: Install the package with doc dependencies
+        run: poetry install --with docs
       - run: |
           cd doc
-          make html
+          poetry run sphinx-build -b html . _build/html
       - name: Deploy pages
         uses: peaceiris/actions-gh-pages@v3
         with:
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 2e03abec..58b2957c 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -25,14 +25,19 @@ jobs:
         uses: actions/setup-python@v3
         with:
           python-version: "3.10"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install build
+      - name: Install poetry
+        uses: abatilo/actions-poetry@v2
+      - name: Define a cache for the virtual environment based on the dependencies lock file
+        uses: actions/cache@v3
+        with:
+          path: ./.venv
+          key: venv-${{ hashFiles('poetry.lock') }}
+      - name: Install the package with doc dependencies
+        run: poetry install --without docs,tests
       - name: Build package
-        run: python -m build
+        run: poetry build
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: ${{ secrets.PYPI_USERNAME }}
           password: ${{ secrets.PYPI_PASSWORD }}
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 5829bc6b..8bd168bd 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -18,10 +18,13 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.10"
-
+      - name: Install poetry
+        uses: abatilo/actions-poetry@v2
+      - name: Define a cache for the virtual environment based on the dependencies lock file
+        uses: actions/cache@v3
+        with:
+          path: ./.venv
+          key: venv-${{ hashFiles('poetry.lock') }}
       - run: |
-          pip install rdkit==2023.09.6
-          pip install -e ".[tests]"
-          pip install pre-commit
-          pre-commit install && pre-commit run --all
-      - run: pytest --cov=pdbeccdutils
+          poetry install --with tests
+          poetry run pytest --cov=pdbeccdutils
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9ba84bde..0cb60ead 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,15 +13,25 @@ repos:
       - id: fix-byte-order-marker
       - id: end-of-file-fixer
       - id: check-ast
+      - id: no-commit-to-branch
 
-  - repo: https://github.com/ambv/black
-    rev: 22.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.5 # Ruff version.
     hooks:
-      - id: black
-
-  - repo: https://github.com/pycqa/flake8
-    rev: 3.9.1
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+  - repo: https://github.com/dzhu/rstfmt
+    rev: v0.0.14
     hooks:
-      - id: flake8
-        args: ["--max-line-length=88", "--ignore=E501,W503"]
-        exclude: \.cif$
+      - id: rstfmt
+        name: rST Formatter
+  - repo: https://github.com/python-poetry/poetry
+    rev: "1.8.2"
+    hooks:
+      - id: poetry-check
+      - id: poetry-lock
+        args:
+          - "--no-update"
+          - "--check"
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 754363ba..6c0663ad 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,12 @@
 # Changelog
 
+## RELEASE 0.8.6 - Oct 28, 2024
+
+### Features
+* Enable parsing of a subset of CCDs from the Chemical Component Dictionary
+* Added CCDC to UniChem resources
+
+
 ## RELEASE 0.8.5 - May 26, 2024
 
 ### Features
diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 00000000..6a4136c7
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,53 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Kunnakkattu"
+  given-names: "Ibrahim Roshan"
+  orcid: "https://orcid.org/0000-0002-8646-0969"
+- family-names: "Pravda"
+  given-names: "Lukas"
+- family-names: "Yuan"
+  given-names: "Qi"
+- family-names: "S.Smart"
+  given-names: "Oliver"
+- family-names: "Nadzirin"
+  given-names: "Nurul"
+- family-names: "Anyango"
+  given-names: "Stephen"
+- family-names: "Nair"
+  given-names: "Sreenath"
+
+title: "PDBe CCDUtils"
+version: 0.8.5
+date-released: 22/05/2024
+url: "https://github.com/PDBeurope/ccdutils"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Kunnakkattu"
+    given-names: "Ibrahim Roshan"
+    orcid: "https://orcid.org/0000-0002-8646-0969"
+  - family-names: "Choudhary"
+    given-names: "Preeti"
+    orcid: "https://orcid.org/0000-0003-2340-3278"
+  - family-names: "Pravda"
+    given-names: "Lukas"
+  - family-names: "Yuan"
+    given-names: "Qi"
+  - family-names: "S.Smart"
+    given-names: "Oliver"
+  - family-names: "Nadzirin"
+    given-names: "Nurul"
+  - family-names: "Anyango"
+    given-names: "Stephen"
+  - family-names: "Nair"
+    given-names: "Sreenath"
+  - family-names: "Velankar"
+    given-names: "Sameer"
+    orcid: "https://orcid.org/0000-0002-8439-5964"
+  doi: "10.1186/s13321-023-00786-w"
+  journal: "Journal of Cheminformatics"
+  month: 12
+  title: "PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank"
+  volume: 15
+  year: 2023
diff --git a/README.md b/README.md
index f5c20596..7db98478 100644
--- a/README.md
+++ b/README.md
@@ -1,76 +1,83 @@
-[![CodeFactor](https://www.codefactor.io/repository/github/pdbeurope/ccdutils/badge/master)](https://www.codefactor.io/repository/github/pdbeurope/ccdutils/overview/master)  ![PYPi](https://img.shields.io/pypi/v/pdbeccdutils?color=green&style=flat)  ![GitHub](https://img.shields.io/github/license/pdbeurope/ccdutils)   ![ccdutils documentation](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20documentation/badge.svg) ![ccdutils tests](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20tests/badge.svg)
+[![CodeFactor](https://www.codefactor.io/repository/github/PDBeurope/ccdutils/badge/master)](https://www.codefactor.io/repository/github/PDBeurope/ccdutils/overview/master)  ![PYPi](https://img.shields.io/pypi/v/pdbeccdutils?color=green&style=flat)  ![GitHub](https://img.shields.io/github/license/PDBeurope/ccdutils)   ![ccdutils documentation](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20documentation/badge.svg) ![ccdutils tests](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20tests/badge.svg) ![PyPI Downloads](https://img.shields.io/pypi/dm/pdbeccdutils)
+
 
 # pdbeccdutils
 
-* A set of python tools to deal with PDB chemical components definitions
-  for small molecules, taken from the [wwPDB Chemical Component Dictionary](https://www.wwpdb.org/data/ccd) and [wwPDB The Biologically Interesting Molecule Reference Dictionary](https://www.wwpdb.org/data/bird)
+An RDKit-based python toolkit for parsing and processing small molecule definitions in [wwPDB Chemical Component Dictionary](https://www.wwpdb.org/data/ccd) and [wwPDB The Biologically Interesting Molecule Reference Dictionary](https://www.wwpdb.org/data/bird).`pdbeccdutils` provides streamlined access to all metadata of small molecules in the PDB and offers a set of convenient methods to compute various properties of small molecules using RDKIt such as 2D depictions, 3D conformers, physicochemical properties, matching common fragments and scaffolds, mapping to small-molecule databases using UniChem.
+
+## Features
 
-* The tools use:
-  * [RDKit](http://www.rdkit.org/) for chemistry. Presently tested with `2022.09.4`
+* `gemmi` CCD read/write.
+* Generation of 2D depictions (`No image available` generated if the flattening cannot be done) along with the quality check.
+* Generation of 3D conformations.
+* Fragment library search (PDBe hand-curated library, ENAMINE, DSI).
+* Chemical scaffolds (Murcko scaffold, Murcko general, BRICS).
+* Lightweight implementation of [parity method](https://doi.org/10.1016/j.str.2018.02.009) by Jon Tyzack.
+* RDKit molecular properties per component.
+* UniChem mapping.
+* Generating complete representation of multiple [Covalently Linked Components (CLC)](https://www.ebi.ac.uk/pdbe/news/introducing-covalently-linked-components)
+
+## Dependencies
+
+  * [RDKit](http://www.rdkit.org/) for small molecule representation. Presently tested with `2023.9.6`
   * [GEMMI](https://gemmi.readthedocs.io/en/latest/index.html) for parsing mmCIF files.
   * [scipy](https://www.scipy.org/) for depiction quality check.
   * [numpy](https://www.numpy.org/) for molecular scaling.
   * [networkx](https://networkx.org/) for bound-molecules.
 
-* Please note that the project is under active development.
 
-## Installation instructions
+## Installation
 
-* `pdbeccdutils` requires RDKit to be installed.
-  The official RDKit documentation has [installation instructions for a variety of platforms](http://www.rdkit.org/docs/Install.html).
-  For Linux/macOS this is most easily done using the Anaconda Python with commands similar to:
+create a [virtual environment](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/#create-and-use-virtual-environments) and install using pip
 
-  ```console
-  conda create -n rdkit-env rdkit python=3.9
-  conda activate rdkit-env
-  ```
-
-* Once you have installed RDKit, as described above then install `pdbeccdutils` using `pip`:
-
-  ```console
+  ```bash
   pip install pdbeccdutils
   ```
 
-## Features
+## Contribution
+We encourage you to contribute to this project. The package uses [poetry](https://python-poetry.org/) for packaging and dependency management. You can develop locally using:
 
-* `gemmi` CCD read/write.
-* Generation of 2D depictions (`No image available` generated if the flattening cannot be done) along with the quality check.
-* Generation of 3D conformations.
-* Fragment library search (PDBe hand-curated library, ENAMINE, DSI).
-* Chemical scaffolds (Murcko scaffold, Murcko general, BRICS).
-* Lightweight implementation of [parity method](https://doi.org/10.1016/j.str.2018.02.009) by Jon Tyzack.
-* RDKit molecular properties per component.
-* UniChem mapping.
+```bash
+git clone https://github.com/PDBeurope/ccdutils.git
+cd ccdutils
+pip install poetry
+poetry install --with tests,docs
+pre-commit install
+```
 
-## TODO list
+The pre-commit hook will run linting, formatting and update `poetry.lock`. The `poetry.lock` file will lock all dependencies and ensure that they match pyproject.toml versions.
 
-* Add more unit/regression tests to get higher code coverage.
-* Further improvements of the documentation.
+To add a new dependency
 
+```bash
+# Latest resolvable version
+poetry add <package>
 
-## Documentation
+# Optionally fix a version
+poetry add <package>@<version>
+```
+
+To change a version of a dependency, either edit pyproject.toml and run:
 
-The documentation depends on the following packages:
+```bash
+poetry sync --with dev
+```
 
-* `sphinx`
-* `sphinx_rtd_theme`
-* `myst-parser`
-* `sphinx-autodoc-typehints`
+or
 
-Note that `sphinx` needs to be a part of the virtual environment, if you want to generate documentation by yourself.
-Otherwise it cannot pick `rdkit` module. `sphinx_rtd_theme` is a theme providing nice `ReadtheDocs` mobile friendly style.
+```bash
+poetry add <package>@<version>
+```
 
-* Generate *.rst* files to be included as a part of the documentation. Inside the directory `pdbeccdutils/doc` run the following commands to generate documentation.
-* Alternatively, use the `myst-parser` package to get the Markdown working.
 
- Use the following to generate initial markup files to be used by sphinx.  This needs to be used when adding another sub-packages.
+## Documentation
 
-```console
-sphinx-apidoc -f -o /path/to/output/dir ../pdbeccdutils/
-```
+The documentation is generated using `sphinx` in `sphinx_rtd_theme` and hosted on GitHub Pages. To generate the documentation locally,
 
-Use this to re-generate the documentation from the doc/ directory:
+```bash
+cd doc
+poetry run sphinx-build -b html . _build/html
 
-```console
-make html
+# See the documentation at http://localhost:8080.
+python -m http.server 8080 -d _build/html
 ```
diff --git a/doc/conf.py b/doc/conf.py
index dcaa4a73..9d8d4ae9 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -13,7 +13,7 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 
-import pdbeccdutils
+import importlib.metadata
 
 # region Project information
 project = "pdbeccdutils"
@@ -21,9 +21,9 @@
 author = "Protein Data Bank in Europe"
 
 # The short X.Y version
-version = pdbeccdutils.__version__
+version = importlib.metadata.version("pdbeccdutils")
 # The full version, including alpha/beta/rc tags
-release = pdbeccdutils.__version__
+release = importlib.metadata.version("pdbeccdutils")
 
 # endregion
 
diff --git a/pdbeccdutils/__init__.py b/pdbeccdutils/__init__.py
deleted file mode 100644
index af46754d..00000000
--- a/pdbeccdutils/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-__version__ = "0.8.5"
diff --git a/pdbeccdutils/computations/parity_method.py b/pdbeccdutils/computations/parity_method.py
index 2018bc85..3832cc97 100644
--- a/pdbeccdutils/computations/parity_method.py
+++ b/pdbeccdutils/computations/parity_method.py
@@ -5,6 +5,8 @@
 from rdkit import Chem
 from rdkit.Chem import rdFMCS
 
+from pdbeccdutils.helpers import mol_tools
+from rdkit.Chem import BondType
 from pdbeccdutils.core.models import ParityResult
 
 
@@ -88,8 +90,17 @@ def compare_molecules(template, query, thresh=0.01, exact_match=False):
         ParityResult: Result of the PARITY comparison.
     """
 
-    template_atoms = template.GetNumAtoms()
-    query_atoms = query.GetNumAtoms()
+    template_copy = Chem.RWMol(template)
+    query_copy = Chem.RWMol(query)
+
+    # changing bondtype from DATIVE to ZERO as the SMARTS with DATIVE bondtype were missing
+    # substructures using GetSubstructMatches (e.g. HEM)
+    # refer rdkit github issue https://github.com/rdkit/rdkit/issues/7280
+    mol_tools.change_bonds_type(template_copy, BondType.DATIVE, BondType.ZERO)
+    mol_tools.change_bonds_type(query_copy, BondType.DATIVE, BondType.ZERO)
+
+    template_atoms = template_copy.GetNumAtoms()
+    query_atoms = query_copy.GetNumAtoms()
 
     min_num_atoms = min(template_atoms, query_atoms)
     max_sim_score = float(min_num_atoms) / float(
@@ -101,7 +112,7 @@ def compare_molecules(template, query, thresh=0.01, exact_match=False):
 
     if not exact_match:
         mcs_graph = rdFMCS.FindMCS(
-            [template, query],
+            [template_copy, query_copy],
             bondCompare=rdFMCS.BondCompare.CompareAny,
             atomCompare=rdFMCS.AtomCompare.CompareAny,
             timeout=40,
@@ -109,7 +120,7 @@ def compare_molecules(template, query, thresh=0.01, exact_match=False):
         )
     else:
         mcs_graph = rdFMCS.FindMCS(
-            [template, query],
+            [template_copy, query_copy],
             bondCompare=rdFMCS.BondCompare.CompareOrderExact,
             atomCompare=rdFMCS.AtomCompare.CompareElements,
             timeout=40,
diff --git a/pdbeccdutils/core/boundmolecule.py b/pdbeccdutils/core/boundmolecule.py
index 41037506..d1a7ad17 100644
--- a/pdbeccdutils/core/boundmolecule.py
+++ b/pdbeccdutils/core/boundmolecule.py
@@ -46,7 +46,7 @@ def infer_bound_molecules(structure, to_discard, assembly=False):
         bm = BoundMolecule(subgraph)
         bound_molecules.append(bm)
 
-    bound_molecules = sorted(bound_molecules, key=lambda l: -len(l.graph.nodes))
+    bound_molecules = sorted(bound_molecules, key=lambda item: -len(item.graph.nodes))
     return bound_molecules
 
 
diff --git a/pdbeccdutils/core/ccd_reader.py b/pdbeccdutils/core/ccd_reader.py
index 2c18e0b2..3365e570 100644
--- a/pdbeccdutils/core/ccd_reader.py
+++ b/pdbeccdutils/core/ccd_reader.py
@@ -101,7 +101,7 @@ def read_pdb_cif_file(path_to_cif: str, sanitize: bool = True) -> CCDReaderResul
 
 
 def read_pdb_components_file(
-    path_to_cif: str, sanitize: bool = True
+    path_to_cif: str, sanitize: bool = True, include: list[str] = []
 ) -> Dict[str, CCDReaderResult]:
     """
     Process multiple compounds stored in the wwPDB CCD
@@ -112,6 +112,8 @@ def read_pdb_components_file(
             multiple ligands in it.
         sanitize (bool): Whether or not the components should be sanitized
             Defaults to True.
+        include (list[str]): List of CCDs to be parsed. By default it is empty and parse
+        all the CCDs. If a list of CCDs provided, will only parse them
 
     Raises:
         ValueError: if the file does not exist.
@@ -124,15 +126,14 @@ def read_pdb_components_file(
         raise ValueError("File '{}' does not exists".format(path_to_cif))
 
     result_bag = {}
-
     for block in cif.read(path_to_cif):
-        try:
-            result_bag[block.name] = _parse_pdb_mmcif(block, sanitize)
-        except CCDUtilsError as e:
-            logging.error(
-                f"ERROR: Data block {block.name} not processed. Reason: ({str(e)})."
-            )
-
+        if (block.name in include) or (len(include) == 0):
+            try:
+                result_bag[block.name] = _parse_pdb_mmcif(block, sanitize)
+            except CCDUtilsError as e:
+                logging.error(
+                    f"ERROR: Data block {block.name} not processed. Reason: ({str(e)})."
+                )
     return result_bag
 
 
diff --git a/pdbeccdutils/core/ccd_writer.py b/pdbeccdutils/core/ccd_writer.py
index be541d82..a4082619 100644
--- a/pdbeccdutils/core/ccd_writer.py
+++ b/pdbeccdutils/core/ccd_writer.py
@@ -22,6 +22,7 @@
     CCDUtilsError: If deemed format is not supported or an unrecoverable
         error occurres.
 """
+
 import json
 import logging
 import math
@@ -31,7 +32,7 @@
 from xml.etree import ElementTree as ET
 from xml.etree.ElementTree import Element, SubElement
 
-import pdbeccdutils
+import importlib.metadata
 import rdkit
 import gemmi
 from gemmi import cif
@@ -123,7 +124,7 @@ def to_pdb_str(
         f"HEADER    {conf_type.name} coordinates",
         f" for PDB-CCD {component.id}",
         f"COMPND    {component.id}",
-        f"AUTHOR    pdbccdutils {pdbeccdutils.__version__}",
+        f"AUTHOR    pdbccdutils {importlib.metadata.version('pdbeccdutils')}",
         f"AUTHOR    RDKit {rdkit.__version__}",
     ]
 
@@ -496,7 +497,7 @@ def to_json_str(component: Component, remove_hs=True, conf_type=ConformerType.Id
 
     temp = to_json_dict(component, remove_hs, conf_type)
     temp["rdkit_version"] = rdkit.__version__
-    temp["pdbeccdutils_version"] = pdbeccdutils.__version__
+    temp["pdbeccdutils_version"] = importlib.metadata.version("pdbeccdutils")
 
     return json.dumps(temp)
 
@@ -1125,7 +1126,7 @@ def _add_sw_info_cif(cif_block_copy):
         cif.quote_list(
             [
                 "pdbeccdutils",
-                pdbeccdutils.__version__,
+                importlib.metadata.version("pdbeccdutils"),
                 "Wrapper to provide 2D templates and molecular fragments.",
             ]
         )
@@ -1179,8 +1180,8 @@ def _add_fragments_and_scaffolds_cif(component, cif_block_copy):
             f"S{i+1}",
             "scaffold",
             smiles,
-            inchi or None,
-            inchikey or None,
+            inchi,
+            inchikey,
         ]
         substructure_loop.add_row(cif.quote_list(new_row))
 
@@ -1225,7 +1226,8 @@ def _add_rdkit_properties_cif(component, cif_block_copy):
         from gemmi.
     """
     category = "_pdbe_chem_comp_rdkit_properties."
-    cif_block_copy.set_pairs(category, {"comp_id": component.id})
+    if component.physchem_properties:
+        cif_block_copy.set_pairs(category, {"comp_id": component.id})
 
     for k, v in component.physchem_properties.items():
         cif_block_copy.set_pairs(
diff --git a/pdbeccdutils/core/clc_reader.py b/pdbeccdutils/core/clc_reader.py
index 63e5585a..8e72c646 100644
--- a/pdbeccdutils/core/clc_reader.py
+++ b/pdbeccdutils/core/clc_reader.py
@@ -93,7 +93,6 @@ def read_pdb_cif_file(
 
 
 def infer_multiple_chem_comp(path_to_cif, bm, bm_id, sanitize=True):
-
     """Args:
         path_to_cif: Path to input structure
         bm: bound-molecules identified from input structure
@@ -152,7 +151,7 @@ def infer_multiple_chem_comp(path_to_cif, bm, bm_id, sanitize=True):
 
     properties = CCDProperties(
         id=bm_id,
-        name=bm.name,
+        name=mol_tools.rdkit_object_property(mol, "name"),
         formula=CalcMolFormula(mol),
         modified_date=date.today(),
         pdbx_release_status=pdbx_release_status,
@@ -204,6 +203,7 @@ def _parse_pdb_mmcif(
     _parse_pdb_conformers(mol, bm_atoms)
     _parse_pdb_bonds(mol, bm, cif_block, errors)
     _add_connections(mol, bm, errors)
+    _parse_pdb_entity(mol, bm, cif_block)
     mol = _handle_hydrogens(mol)
     return (mol, warnings, errors)
 
@@ -368,6 +368,18 @@ def _add_connections(
             errors.append(f"Duplicit bond {atom_1} - {atom_2}")
 
 
+def _parse_pdb_entity(mol, bm, cif_block):
+    if "_entity." not in cif_block.get_mmcif_category_names():
+        return
+
+    entities = cif_block.find("_entity.", ["id", "pdbx_description"])
+    bm_entities = list({residue.ent_id for residue in bm.nodes()})
+    if len(bm_entities) == 1:
+        for row in entities:
+            if cif.as_string(row["_entity.id"]) == bm_entities[0]:
+                mol.SetProp("name", cif.as_string(row["pdbx_description"]))
+
+
 def get_chem_comp_bonds(cif_block: cif.Block, residue: str):
     """Returns _chem_comp_bond associated with a residue
 
@@ -527,7 +539,8 @@ def _parse_clc_mmcif(cif_block, sanitize=True):
     ccd_reader._handle_implicit_hydrogens(mol)
 
     if sanitize:
-        sanitized = mol_tools.sanitize(mol)
+        sanitized_result = mol_tools.sanitize(mol)
+        mol, sanitized = sanitized_result.mol, sanitized_result.status
 
     descriptors = ccd_reader._parse_pdb_descriptors(
         cif_block, "_pdbx_chem_comp_descriptor.", "descriptor"
diff --git a/pdbeccdutils/core/clc_writer.py b/pdbeccdutils/core/clc_writer.py
index 737604f8..69706999 100644
--- a/pdbeccdutils/core/clc_writer.py
+++ b/pdbeccdutils/core/clc_writer.py
@@ -10,7 +10,7 @@
 from xml.etree import ElementTree as ET
 from xml.etree.ElementTree import Element, SubElement
 
-import pdbeccdutils
+import importlib.metadata
 from pdbeccdutils.core.component import Component
 from pdbeccdutils.core.exceptions import CCDUtilsError
 from pdbeccdutils.core.models import ConformerType
@@ -96,7 +96,7 @@ def to_pdb_str(
         f"HEADER    {conf_type.name} coordinates",
         f" for PDB-CLC {component.id}",
         f"COMPND    {component.id}",
-        f"AUTHOR    pdbccdutils {pdbeccdutils.__version__}",
+        f"AUTHOR    pdbccdutils {importlib.metadata.version('pdbeccdutils')}",
         f"AUTHOR    RDKit {rdkit.__version__}",
     ]
 
@@ -421,7 +421,7 @@ def _write_pdb_clc_cif_atoms(cif_block, component):
             f"{model_atom.z:.3f}",
             res_info.GetResidueName(),
             residue_numbers[atom.GetProp("residue_id")],
-            mol_tools.get_component_atom_id(atom),
+            mol_tools.rdkit_object_property(atom, "component_atom_id"),
             str(atom.GetIdx() + 1),
         ]
 
diff --git a/pdbeccdutils/core/component.py b/pdbeccdutils/core/component.py
index 6d3dd4fb..a3f2ead2 100644
--- a/pdbeccdutils/core/component.py
+++ b/pdbeccdutils/core/component.py
@@ -464,11 +464,12 @@ def export_2d_svg(
         Raises:
             CCDUtilsError: If bond or atom does not exist.
         """
-        get_atom_name = (
-            lambda a: a.GetProp("name")
-            if a.HasProp("name")
-            else a.GetSymbol() + str(a.GetIdx())
-        )
+
+        def get_atom_name(atom):
+            if atom.HasProp("name"):
+                return atom.GetProp("name")
+            else:
+                return f"{atom.GetSymbol()}{atom.GetIdx()}"
 
         if self.mol2D is None:
             drawing.save_no_image(file_name, self.id, width)
@@ -520,7 +521,7 @@ def export_2d_svg(
             self.mol2D, drawer, file_name, wedge_bonds, atom_highlight, bond_highlight
         )
 
-        mol_tools.change_bonds_type(self.mol2D, BondType.ZERO, BondType.ZERO)
+        mol_tools.change_bonds_type(self.mol2D, BondType.ZERO, BondType.DATIVE)
 
     def export_2d_annotation(self, file_name: str, wedge_bonds: bool = True) -> None:
         """Generates 2D depiction in JSON format with annotation of
diff --git a/pdbeccdutils/core/depictions.py b/pdbeccdutils/core/depictions.py
index 17a94d87..a33dc513 100755
--- a/pdbeccdutils/core/depictions.py
+++ b/pdbeccdutils/core/depictions.py
@@ -20,6 +20,7 @@
 quality
 
 """
+
 import logging
 import math
 import os
@@ -118,7 +119,7 @@ def depict_molecule(
 
         results = results + template_res
 
-        results.sort(key=lambda l: (l.score, l.source))
+        results.sort(key=lambda item: (item.score, item.source))
 
         if results:
             to_return = results[0]
diff --git a/pdbeccdutils/core/models.py b/pdbeccdutils/core/models.py
index 29a5515e..95f8fd12 100755
--- a/pdbeccdutils/core/models.py
+++ b/pdbeccdutils/core/models.py
@@ -230,7 +230,7 @@ class ParityResult:
 @dataclass
 class CCDProperties:
     """
-    Properties of the component comming from _chem_comp namespace.
+    Properties of the component coming from _chem_comp namespace.
 
     Args:
         id (str): _chem_comp.id
@@ -308,7 +308,7 @@ def __eq__(self, other) -> bool:
 class BoundMolecule:
     def __init__(self, graph):
         self.graph = graph
-        self.nodes = sorted(self.graph, key=lambda l: (int(l.res_id), l.chain))
+        self.nodes = sorted(self.graph, key=lambda item: (int(item.res_id), item.chain))
 
     @property
     def id(self) -> str:
@@ -362,7 +362,7 @@ def to_dict(self):
             dict of `str`: dict representation of the object
         """
 
-        nodes = sorted(self.graph, key=lambda l: (int(l.res_id), l.chain))
+        nodes = sorted(self.graph, key=lambda item: (int(item.res_id), item.chain))
 
         results_bag = {}
         results_bag["residues"] = [x.to_dict() for x in nodes]
diff --git a/pdbeccdutils/core/prd_writer.py b/pdbeccdutils/core/prd_writer.py
index 7f65c5d7..098f9017 100644
--- a/pdbeccdutils/core/prd_writer.py
+++ b/pdbeccdutils/core/prd_writer.py
@@ -22,10 +22,11 @@
     CCDUtilsError: If deemed format is not supported or an unrecoverable
         error occurres.
 """
+
 import json
 import math
 from pathlib import Path
-import pdbeccdutils
+import importlib.metadata
 import rdkit
 import gemmi
 from gemmi import cif
@@ -119,7 +120,7 @@ def to_pdb_str(
         f"HEADER    {conf_type.name} coordinates",
         f" for PDB-PRD {component.id}",
         f"COMPND    {component.id}",
-        f"AUTHOR    pdbccdutils {pdbeccdutils.__version__}",
+        f"AUTHOR    pdbccdutils {importlib.metadata.version('pdbeccdutils')}",
         f"AUTHOR    RDKit {rdkit.__version__}",
     ]
 
diff --git a/pdbeccdutils/helpers/drawing.py b/pdbeccdutils/helpers/drawing.py
index 07c650f3..2a2fde1c 100644
--- a/pdbeccdutils/helpers/drawing.py
+++ b/pdbeccdutils/helpers/drawing.py
@@ -15,8 +15,7 @@
 # specific language governing permissions and limitations
 # under the License.
 
-"""Module helper providing drawing functionality based on RDKit
-"""
+"""Module helper providing drawing functionality based on RDKit"""
 
 import os
 import re
diff --git a/pdbeccdutils/helpers/helper.py b/pdbeccdutils/helpers/helper.py
index aa3a5ab3..46d4b90b 100644
--- a/pdbeccdutils/helpers/helper.py
+++ b/pdbeccdutils/helpers/helper.py
@@ -15,8 +15,7 @@
 # specific language governing permissions and limitations
 # under the License.
 
-"""Generic helper functions that may be re-used
-"""
+"""Generic helper functions that may be re-used"""
 
 import os
 import sys
@@ -28,7 +27,7 @@
 
 import rdkit
 
-import pdbeccdutils
+import importlib.metadata
 
 
 def bond_pdb_order(value_order):
@@ -97,7 +96,7 @@ def set_up_logger(args: argparse.Namespace) -> logging.Logger:
     if not args.no_header:
         logging.info("PDBeBm pipeline using:")
         logging.info(
-            f"pdbeccdutils core v. {pdbeccdutils.__version__}, RDKit v. {rdkit.__version__}"
+            f"pdbeccdutils core v. {importlib.metadata.version('pdbeccdutils')}, RDKit v. {rdkit.__version__}"
         )
         logging.info("Settings:")
         for k, v in vars(args).items():
@@ -145,7 +144,6 @@ def requests_retry_session(
     status_forcelist=(429, 500, 502, 503, 504),
     session=None,
 ):
-
     session = session or requests.Session()
     retry = Retry(
         total=retries,
diff --git a/pdbeccdutils/helpers/mol_tools.py b/pdbeccdutils/helpers/mol_tools.py
index d1428bca..a16473a3 100644
--- a/pdbeccdutils/helpers/mol_tools.py
+++ b/pdbeccdutils/helpers/mol_tools.py
@@ -258,9 +258,11 @@ def inchikey_from_inchi(inchi: str) -> str:
     Returns:
         str: the InChIKey or '' if there was an error finding it.
     """
-
-    inchikey = rdkit.Chem.inchi.InchiToInchiKey(inchi)
-    return inchikey if inchikey else None
+    try:
+        inchikey = rdkit.Chem.inchi.InchiToInchiKey(inchi)
+        return inchikey
+    except Exception:
+        return None
 
 
 def mol_from_inchi(inchi: str) -> MolFromRDKit:
@@ -295,18 +297,14 @@ def mol_from_inchi(inchi: str) -> MolFromRDKit:
     return mol_result
 
 
-def get_component_atom_id(atom):
-    """Gets component atom id.
+def rdkit_object_property(object, property: str):
+    """Returns the value of property set to the rdkit object
 
     Args:
-        atom (rdkit.Chem.rdchem.Atom): rdkit atom.
+        object: rdkit.Chem.rdchem object with GetProp
 
-    Returns:
-        str: Name of the atom.
     """
-    return (
-        atom.GetProp("component_atom_id") if atom.HasProp("component_atom_id") else None
-    )
+    return object.GetProp(property) if object.HasProp(property) else None
 
 
 def correct_atom_coords(conformer, atom_id):
diff --git a/pdbeccdutils/scripts/process_components_cif_cli.py b/pdbeccdutils/scripts/process_components_cif_cli.py
index c63b8105..7a8a3ff3 100755
--- a/pdbeccdutils/scripts/process_components_cif_cli.py
+++ b/pdbeccdutils/scripts/process_components_cif_cli.py
@@ -28,12 +28,13 @@
 
 https://gitlab.ebi.ac.uk/pdbe/release/pdbechem
 """
+
 import argparse
 import logging
 import os
 from pathlib import Path
 
-import pdbeccdutils
+import importlib.metadata
 import rdkit
 from pdbeccdutils.core import ccd_reader, ccd_writer, prd_reader, prd_writer
 from pdbeccdutils.core.component import Component
@@ -454,7 +455,7 @@ def main():
     logging.basicConfig(level=lvl, format=frm, datefmt="%a, %d %b %Y %H:%M:%S")
     logging.info("PDBeChem pipeline using:")
     logging.info(
-        f"pdbeccdutils core v. {pdbeccdutils.__version__}, RDKit v. {rdkit.__version__}"
+        f"pdbeccdutils core v. {importlib.metadata.version('pdbeccdutils')}, RDKit v. {rdkit.__version__}"
     )
 
     logging.info("Settings:")
diff --git a/pdbeccdutils/scripts/setup_pubchem_library_cli.py b/pdbeccdutils/scripts/setup_pubchem_library_cli.py
index dfa51a4c..5ca1d315 100644
--- a/pdbeccdutils/scripts/setup_pubchem_library_cli.py
+++ b/pdbeccdutils/scripts/setup_pubchem_library_cli.py
@@ -2,6 +2,7 @@
 the pdbeccdutils. Based on the inchikey provided in the CCD
 a corresponding 2D layout is downloaded from PubChem database.
 """
+
 import argparse
 import os
 import sys
diff --git a/pdbeccdutils/tests/conftest.py b/pdbeccdutils/tests/conftest.py
index 1482c909..1e609a4d 100644
--- a/pdbeccdutils/tests/conftest.py
+++ b/pdbeccdutils/tests/conftest.py
@@ -1,5 +1,5 @@
-"""Common fixtures shared among all the tests
-"""
+"""Common fixtures shared among all the tests"""
+
 import pytest
 from pdbeccdutils.core import ccd_reader, clc_reader
 from pdbeccdutils.core.fragment_library import FragmentLibrary
diff --git a/pdbeccdutils/tests/test_bound_molecule.py b/pdbeccdutils/tests/test_bound_molecule.py
index 37d321f0..b3fcc55e 100644
--- a/pdbeccdutils/tests/test_bound_molecule.py
+++ b/pdbeccdutils/tests/test_bound_molecule.py
@@ -1,5 +1,4 @@
-"""Common fixtures shared among all the tests
-"""
+"""Common fixtures shared among all the tests"""
 
 import json
 import pytest
diff --git a/pdbeccdutils/tests/test_clc_reader.py b/pdbeccdutils/tests/test_clc_reader.py
index 4850cad7..23d3589c 100644
--- a/pdbeccdutils/tests/test_clc_reader.py
+++ b/pdbeccdutils/tests/test_clc_reader.py
@@ -1,6 +1,7 @@
 """
 load 6lq4_updated.cif from file and test important cif item.
 """
+
 import pytest
 from pdbeccdutils.core import clc_reader
 from pdbeccdutils.core.models import ReleaseStatus
diff --git a/pdbeccdutils/tests/test_fragment_library.py b/pdbeccdutils/tests/test_fragment_library.py
index 3f5a0b3e..6023d485 100644
--- a/pdbeccdutils/tests/test_fragment_library.py
+++ b/pdbeccdutils/tests/test_fragment_library.py
@@ -1,5 +1,4 @@
-"""Test fragment library functionality
-"""
+"""Test fragment library functionality"""
 
 import os
 
diff --git a/pdbeccdutils/tests/test_load_eoh_cif.py b/pdbeccdutils/tests/test_load_eoh_cif.py
index 759545b0..e901f7a0 100644
--- a/pdbeccdutils/tests/test_load_eoh_cif.py
+++ b/pdbeccdutils/tests/test_load_eoh_cif.py
@@ -1,6 +1,7 @@
 """
 load EOH.cif from file and test important cif item.
 """
+
 import pytest
 
 from pdbeccdutils.core import ccd_reader, ccd_writer
diff --git a/pdbeccdutils/tests/test_parity.py b/pdbeccdutils/tests/test_parity.py
index 4297e3ad..26827f28 100644
--- a/pdbeccdutils/tests/test_parity.py
+++ b/pdbeccdutils/tests/test_parity.py
@@ -1,5 +1,4 @@
-"""Test of PARITY method
-"""
+"""Test of PARITY method"""
 
 import pytest
 
@@ -15,7 +14,7 @@ class TestParity:
         [
             ("MAN", "NAG", 0.74),
             ("NAD", "NAG", 0.09),
-            ("000", "000", 1.00),
+            ("HEM", "HEM", 1.00),
             ("SAC", "GOL", 0.50),
             ("MAN", "GLC", 1.00),
         ],
diff --git a/pdbeccdutils/tests/test_process_components_cif_cli.py b/pdbeccdutils/tests/test_process_components_cif_cli.py
index 0f9944bc..d66d9382 100644
--- a/pdbeccdutils/tests/test_process_components_cif_cli.py
+++ b/pdbeccdutils/tests/test_process_components_cif_cli.py
@@ -5,6 +5,7 @@
 http://dustinrcollins.com/testing-python-command-line-apps
 adapted to use nose then converted to pytest
 """
+
 import json
 import os
 import re
diff --git a/pdbeccdutils/tests/test_web_services.py b/pdbeccdutils/tests/test_web_services.py
index 746acef0..e1ba03d2 100644
--- a/pdbeccdutils/tests/test_web_services.py
+++ b/pdbeccdutils/tests/test_web_services.py
@@ -1,5 +1,4 @@
-"""Test of routine for retrieving 2D layouts of the CCDs.
-"""
+"""Test of routine for retrieving 2D layouts of the CCDs."""
 
 import os
 
diff --git a/pdbeccdutils/tests/test_write_img.py b/pdbeccdutils/tests/test_write_img.py
index 3e2db668..5bfa3b3a 100644
--- a/pdbeccdutils/tests/test_write_img.py
+++ b/pdbeccdutils/tests/test_write_img.py
@@ -1,6 +1,4 @@
-"""Unit tests for checking whether or not depictions are written properly.
-"""
-
+"""Unit tests for checking whether or not depictions are written properly."""
 
 import json
 import os
diff --git a/pdbeccdutils/utils/config.py b/pdbeccdutils/utils/config.py
index 885ebdcc..e0243d7b 100644
--- a/pdbeccdutils/utils/config.py
+++ b/pdbeccdutils/utils/config.py
@@ -1,16 +1,15 @@
-"""Package configuration with the paths to the templates
-"""
+"""Package configuration with the paths to the templates"""
+
 import os
-import pdbeccdutils
+from pathlib import Path
+
+
+def get_data_dir():
+    return Path(os.path.dirname(__file__)).parent / "data"
+
 
-general_templates = os.path.join(
-    os.path.dirname(pdbeccdutils.__file__), "data", "general_templates"
-)
-coordgen_templates = os.path.join(
-    os.path.dirname(pdbeccdutils.__file__), "data", "coordgen_templates"
-)
-fragment_library = os.path.join(
-    os.path.dirname(pdbeccdutils.__file__), "data", "fragment_library.tsv"
-)
+general_templates = os.path.join(get_data_dir(), "general_templates")
+coordgen_templates = os.path.join(get_data_dir(), "coordgen_templates")
+fragment_library = os.path.join(get_data_dir(), "fragment_library.tsv")
 
 DISCARDED_RESIDUES = {"HOH", "UNX"}
diff --git a/pdbeccdutils/utils/web_services.py b/pdbeccdutils/utils/web_services.py
index e69f76ac..6c42a69e 100644
--- a/pdbeccdutils/utils/web_services.py
+++ b/pdbeccdutils/utils/web_services.py
@@ -15,8 +15,7 @@
 # specific language governing permissions and limitations
 # under the License.
 
-"""module handling UniChem mapping
-"""
+"""module handling UniChem mapping"""
 
 from pdbeccdutils.helpers import helper
 
@@ -41,7 +40,6 @@
 all_resource = {
     "1": ("ChEMBL", "ChEMBL"),
     "2": ("DrugBank", "DrugBank"),
-    "3": ("PDBe", "Protein Data Bank in Europe"),
     "4": ("Guide to Pharmacology", "Guide to Pharmacology"),
     "5": ("PubChem DOTF", 'PubChem ("Drugs of the Future" subset'),
     "6": ("KEGG LIGAND", "KEGG (Kyoto Encyclopedia of Genes and Genomes) Ligand"),
@@ -82,6 +80,7 @@
     "47": ("rxnorm", "rxnorm"),
     "48": ("MedChemExpress", "MedChemExpress"),
     "49": ("Probes And Drugs", "Probes And Drugs"),
+    "50": ("CCDC", "CSD structures from the Cambridge Crystallographic Data Centre"),
 }
 
 url_prefix = "https://www.ebi.ac.uk/unichem/rest/inchikey"
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 00000000..8da70c0f
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,1287 @@
+# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand.
+
+[[package]]
+name = "alabaster"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
+]
+
+[[package]]
+name = "babel"
+version = "2.16.0"
+description = "Internationalization utilities"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"},
+    {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
+]
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "certifi"
+version = "2024.8.30"
+description = "Python package for providing Mozilla's CA Bundle."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
+]
+
+[[package]]
+name = "cfgv"
+version = "3.4.0"
+description = "Validate configuration and produce human readable error messages."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
+    {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
+]
+
+[[package]]
+name = "charset-normalizer"
+version = "3.4.0"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+optional = false
+python-versions = ">=3.7.0"
+files = [
+    {file = "charset_normalizer-3.4.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:4f9fc98dad6c2eaa32fc3af1417d95b5e3d08aff968df0cd320066def971f9a6"},
+    {file = "charset_normalizer-3.4.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0de7b687289d3c1b3e8660d0741874abe7888100efe14bd0f9fd7141bcbda92b"},
+    {file = "charset_normalizer-3.4.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:5ed2e36c3e9b4f21dd9422f6893dec0abf2cca553af509b10cd630f878d3eb99"},
+    {file = "charset_normalizer-3.4.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:40d3ff7fc90b98c637bda91c89d51264a3dcf210cade3a2c6f838c7268d7a4ca"},
+    {file = "charset_normalizer-3.4.0-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:1110e22af8ca26b90bd6364fe4c763329b0ebf1ee213ba32b68c73de5752323d"},
+    {file = "charset_normalizer-3.4.0-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:86f4e8cca779080f66ff4f191a685ced73d2f72d50216f7112185dc02b90b9b7"},
+    {file = "charset_normalizer-3.4.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7f683ddc7eedd742e2889d2bfb96d69573fde1d92fcb811979cdb7165bb9c7d3"},
+    {file = "charset_normalizer-3.4.0-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:27623ba66c183eca01bf9ff833875b459cad267aeeb044477fedac35e19ba907"},
+    {file = "charset_normalizer-3.4.0-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:f606a1881d2663630ea5b8ce2efe2111740df4b687bd78b34a8131baa007f79b"},
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diff --git a/poetry.toml b/poetry.toml
new file mode 100644
index 00000000..53b35d37
--- /dev/null
+++ b/poetry.toml
@@ -0,0 +1,3 @@
+[virtualenvs]
+create = true
+in-project = true
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..4a5378a1
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,58 @@
+[tool.poetry]
+name = "pdbeccdutils"
+version = "0.8.6"
+description = "Toolkit to parse and process small molecules in wwPDB"
+authors = ["Protein Data Bank in Europe <pdbehelp@ebi.ac.uk>"]
+license = "Apache License 2.0."
+readme = "README.md"
+repository = "https://github.com/PDBeurope/ccdutils"
+documentation = "https://pdbeurope.github.io/ccdutils/"
+keywords = ["PDB", "ligand", "small molecule", "complex", "CCD", "PRD", "CLC"]
+classifiers=[
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+    "Operating System :: Unix",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Development Status :: 5 - Production/Stable",
+]
+
+[tool.poetry.dependencies]
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+rdkit = "2023.9.6"
+
+[tool.poetry.scripts]
+process_components_cif = "pdbeccdutils.scripts.process_components_cif_cli:main"
+setup_pubchem_library = "pdbeccdutils.scripts.setup_pubchem_library_cli:main"
+read_boundmolecule = "pdbeccdutils.scripts.boundmolecule_cli:run"
+
+[tool.poetry.group.tests.dependencies]
+pytest = "^8.3.2"
+pytest-cov = "^5.0.0"
+pre-commit = "^3.8.0"
+
+
+[tool.poetry.group.docs.dependencies]
+sphinx = "^7.0.0"
+sphinx-rtd-theme = "^2.0.0"
+sphinx-autodoc-typehints = "^2.3.0"
+sphinx-markdown-tables = "^0.0.17"
+myst-parser = "^4.0.0"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
diff --git a/setup.py b/setup.py
index c94fe7a2..60684932 100644
--- a/setup.py
+++ b/setup.py
@@ -1,72 +1,3 @@
-import os
+from setuptools import setup
 
-from setuptools import find_namespace_packages, setup
-
-
-def read(fname):
-    return open(os.path.join(os.path.dirname(__file__), fname)).read()
-
-
-def get_version(rel_path):
-    for line in read(rel_path).splitlines():
-        if line.startswith("__version__"):
-            delim = '"' if '"' in line else "'"
-            return line.split(delim)[1]
-
-    raise RuntimeError("Unable to find version string.")
-
-
-setup(
-    name="pdbeccdutils",
-    version=get_version("pdbeccdutils/__init__.py"),
-    description="Toolkit to deal with wwPDB chemical components definitions for small molecules.",
-    long_description=read("README.md"),
-    long_description_content_type="text/markdown",
-    project_urls={
-        "Source code": "https://github.com/PDBeurope/ccdutils",
-        "Documentation": "https://pdbeurope.github.io/ccdutils/",
-    },
-    author="Protein Data Bank in Europe",
-    author_email="pdbehelp@ebi.ac.uk",
-    license="Apache License 2.0.",
-    keywords="PDB CCD wwPDB small molecule",
-    url="http://pypi.python.org/pypi/pdbeccdutils/",
-    packages=find_namespace_packages(),
-    zip_safe=False,
-    include_package_data=True,
-    python_requires=">=3.9",
-    install_requires=["Pillow", "scipy", "numpy", "requests", "gemmi", "networkx"],
-    extras_require={
-        "tests": ["pytest", "pytest-cov", "pre-commit"],
-        "docs": [
-            "sphinx<7.0.0",
-            "sphinx_rtd_theme",
-            "sphinx-autodoc-typehints",
-            "sphinx-markdown-tables",
-            "myst-parser",
-        ],
-    },
-    entry_points={
-        "console_scripts": [
-            "process_components_cif=pdbeccdutils.scripts.process_components_cif_cli:main",
-            "setup_pubchem_library=pdbeccdutils.scripts.setup_pubchem_library_cli:main",
-            "read_boundmolecule=pdbeccdutils.scripts.boundmolecule_cli:run",
-        ]
-    },
-    classifiers=[
-        "License :: OSI Approved :: Apache Software License",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: Implementation :: CPython",
-        "Programming Language :: Python :: Implementation :: PyPy",
-        "Operating System :: Unix",
-        "Operating System :: MacOS",
-        "Operating System :: Microsoft :: Windows",
-        "Operating System :: POSIX",
-        "Intended Audience :: Science/Research",
-        "Intended Audience :: Developers",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-        "Topic :: Scientific/Engineering :: Chemistry",
-        "Development Status :: 5 - Production/Stable",
-    ],
-)
+setup()