pdbeccdutils
Toolkit to parse and process small molecules in wwPDB
Decision gist · record as of 2026-08-14
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.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires RDKit and GEMMI as compiled dependencies; installation may need a C++ compiler or pre-built wheels for your platform.
- 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).
License · maintenance · safety
Apache License 2.0. (permissive) — 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.
last release 2026-06-30 (45 days) · last repo commit 2026-07-21 · 83 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 238,665 downloads/mo, #8,932 on PyPI
Alternatives
Verify before relying
pip install pdbeccdutils
from pdbeccdutils.core import ccd_reader
# Parse a chemical component from the CCD
component = ccd_reader.read_pdb("LIG")- 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).
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 on it.
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
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.
Requires RDKit and GEMMI as compiled dependencies; installation may need a C++ compiler or pre-built wheels for your platform.
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")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
| License | Apache License 2.0. permissive |
| Python support | Supports the current Python release <4,>=3.10 |
| Install friction | Low. Pure-Python wheel |
| Runtime dependencies | 7 packagesgemminetworkxnumpypillowrdkitrequestsscipy |
| Maintenance | Actively maintained 45 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 238,665 / month, #8,932 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 5 - Production/StableIntended Audience :: DevelopersIntended Audience :: Science/ResearchLicense :: OSI Approved :: Apache Software LicenseLicense :: Other/Proprietary LicenseOperating System :: MacOSOperating System :: Microsoft :: WindowsOperating System :: POSIXOperating System :: UnixProgramming Language :: PythonProgramming Language :: Python :: 3Programming Language :: Python :: 3.10Programming Language :: Python :: 3.11Programming Language :: Python :: 3.12Programming Language :: Python :: 3.13Programming Language :: Python :: 3.14Programming Language :: Python :: 3.9Programming Language :: Python :: Implementation :: CPythonProgramming Language :: Python :: Implementation :: PyPyTopic :: Scientific/Engineering :: Bio-InformaticsTopic :: Scientific/Engineering :: Chemistry |
Evidence: pdbeccdutils-1.0.4-py3-none-any.whl
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