pdbeccdutils

What it is and what it does

pdbeccdutils is an RDKit-based toolkit for working with small molecule definitions in the Protein Data Bank. It provides streamlined access to metadata and chemical properties from the wwPDB Chemical Component Dictionary (CCD) and Biologically Interesting Molecule Reference Dictionary (PRD), and includes methods to generate 2D and 3D depictions, compute physicochemical properties, identify common fragments and scaffolds, and map molecules to external databases via UniChem.

The package is built on top of RDKit, GEMMI, SciPy, NumPy, and NetworkX. It is actively maintained, supports Python 3.10 through 3.14, and runs on macOS, Windows, and Unix-like systems. It is suitable for structural biology workflows, cheminformatics pipelines, and applications that need to query or analyze PDB ligands programmatically.

Use it for:

• Extract and analyze ligand properties from PDB structures in automated workflows.
• Generate 2D depictions and 3D conformations for small molecules in the CCD.
• Search for common chemical fragments and Murcko scaffolds in ligand datasets.
• Map PDB ligands to external small-molecule databases using UniChem.
• Process covalently linked components (CLC) as complete molecular representations.
• Compute RDKit molecular properties for ligands in structural biology pipelines.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

Parse and process small molecule definitions from the wwPDB Chemical Component Dictionary and Biologically Interesting Molecule Reference Dictionary, with RDKit-based tools for 2D/3D depiction, property computation, and fragment/scaffold analysis.

Yes. pdbeccdutils is actively maintained, has no known vulnerabilities, installs with low friction, and is licensed permissively. Install it if you work with PDB ligands, need to compute molecular properties or depictions for small molecules, or want to integrate wwPDB chemical data into a cheminformatics pipeline. The compiled dependencies (RDKit, GEMMI) may require build tools, but wheels are available for common platforms.

Install

pdbeccdutils on PyPI

pip install pdbeccdutils

uv add pdbeccdutils

poetry add pdbeccdutils

Installing pdbeccdutils

Before you install

Low install friction with a pure-wheel distribution. Active maintenance (last commit 2026-07-21, release 45 days ago) and broad Python support (3.10–3.14). Depends on compiled packages (RDKit, GEMMI, SciPy) that may require build tools on some systems, but the toolkit itself installs cleanly.

License in practice

Licensed under Apache License 2.0 (permissive). No restrictions on commercial or private use; you may modify and distribute freely under the same license terms.

Quickstart

pip install pdbeccdutils

from pdbeccdutils.core import ccd_reader

# Parse a chemical component from the CCD
component = ccd_reader.read_pdb("LIG")

Requires RDKit and GEMMI as compiled dependencies; installation may need a C++ compiler or pre-built wheels for your platform.

Verify before relying

• Whether UniChem mapping requires network access or a local database.
• Performance characteristics when processing large numbers of molecules or complex covalently linked components.
• Exact version of RDKit currently tested (description mentions 2023.9.6 but does not specify if newer versions are supported).

Package facts

Evidence: pdbeccdutils-1.0.4-py3-none-any.whl

Keywords: PDB, ligand, small molecule, complex, CCD, PRD, CLC

Tags

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