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pdbeccdutils

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library1.0.3pypypiunverified

A toolkit to parse and process small molecules (chemical components) from the wwPDB Chemical Component Dictionary (CCD), including PRD and CLC entries. Current version 1.0.3, updated to work with modern RDKit and NumPy. Releases are irregular but focused on bug fixes and dependency updates.

data
pip install pdbeccdutils
github ↗package ↗docs ↗
INSTALL
IMPORT
SIG · PDBECCDUTILS
P
pdbeccdutils
datapythonv1.0.3
Install
11.2s avg
Import
—
Disk
362MB
Pass rate
7/ 10
Env Coverage7 / 10
glibc
3.9–3.13
musl
3.9–3.13
Install & Compatibility
Where this runs
tested against v1.0.3 · pip install
no network on importno background threads
Install × environment matrix
Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux
musl
glibc
py 3.10
✕ build_error
✓ 11.4s
py 3.11
✓ —
✓ 11.1s
py 3.12
✓ —
✓ 11.3s
py 3.13
✕ build_error
✓ 11.3s
py 3.9
✕ build_error
✓ 11.1s
362MB installed
● package 362MB
Code
Verified usage

Verified import paths — ran on the pinned version, not inferred.

PDBeComponent
✓ from pdbeccdutils import PDBeComponent
✗ from pdbeccdutils.core.component import PDBeComponent

Basic usage: download and inspect a chemical component from the PDB.

from pdbeccdutils.core.component import PDBeComponent from pdbeccdutils.helpers import download_components # Download a component by CCD code comp = PDBeComponent('ATP') # ATP as example print(comp.code, comp.name)
Debug
Known issues
breakingVersion 1.0.0 introduced breaking changes: updated RDKit and NumPy dependencies, and fixed a 2D depiction error. Code written for v0.8.x may not work without adjustments.
fix
Check RDKit version compatibility and update depiction calls if needed.
affects: <1.0.0
gotchaThe download_components helper requires an active internet connection; it fetches data from wwPDB. Offline use is not supported.
fix
Ensure network access when using download_components; cache results locally if needed.
affects: all
Upgrade
Version history
1.0.3latest on PyPI · released Feb 19, 2026
Audit
Dependencies
rdkitrequiredRequired for chemical structure handling
numpyrequiredRequired for numerical operations
Agent activity
2 hits · last 30 days
node
2
Resources
githubhttps://github.com/PDBeurope/ccdutils ↗
packagehttps://pypi.org/project/pdbeccdutils/ ↗
docshttps://pdbeurope.github.io/ccdutils/ ↗