pdbeccdutils

An RDKit-based python toolkit for parsing and processing small molecule definitions in wwPDB Chemical Component Dictionary and wwPDB The Biologically Interesting Molecule Reference Dictionary.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

• 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 by Jon Tyzack.
• RDKit molecular properties per component.
• UniChem mapping.
• Generating complete representation of multiple Covalently Linked Components (CLC)

Dependencies

• RDKit for small molecule representation. Presently tested with 2023.9.6
• GEMMI for parsing mmCIF files.
• scipy for depiction quality check.
• numpy for molecular scaling.
• networkx for bound-molecules.

Installation

create a virtual environment and install using pip

pip install pdbeccdutils

Contribution

We encourage you to contribute to this project. The package uses poetry for packaging and dependency management. You can develop locally using:

git clone https://github.com/PDBeurope/ccdutils.git
cd ccdutils
pip install poetry
poetry install --with tests,docs
pre-commit install

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.

To add a new dependency

# Latest resolvable version
poetry add <package>

# Optionally fix a version
poetry add <package>@<version>

To change a version of a dependency, either edit pyproject.toml and run:

poetry sync --with dev

or

poetry add <package>@<version>

Documentation

The documentation is generated using sphinx in sphinx_rtd_theme and hosted on GitHub Pages. To generate the documentation locally,

cd doc
poetry run sphinx-build -b html . _build/html

# See the documentation at http://localhost:8080.
python -m http.server 8080 -d _build/html