{"id":24218,"library":"pdbeccdutils","title":"PDBe CCD Utils","description":"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.","status":"active","version":"1.0.3","language":"python","source_language":"en","source_url":"https://github.com/PDBeurope/ccdutils","tags":["pdb","chemistry","small-molecules","bioinformatics","structural-biology"],"install":[{"cmd":"pip install pdbeccdutils","lang":"bash","label":"Install from PyPI"}],"dependencies":[{"reason":"Required for chemical structure handling","package":"rdkit","optional":false},{"reason":"Required for numerical operations","package":"numpy","optional":false}],"imports":[{"note":"PDBeComponent is in the core.component submodule, not top-level.","wrong":"from pdbeccdutils import PDBeComponent","symbol":"PDBeComponent","correct":"from pdbeccdutils.core.component import PDBeComponent"}],"quickstart":{"code":"from pdbeccdutils.core.component import PDBeComponent\nfrom pdbeccdutils.helpers import download_components\n\n# Download a component by CCD code\ncomp = PDBeComponent('ATP')  # ATP as example\nprint(comp.code, comp.name)","lang":"python","description":"Basic usage: download and inspect a chemical component from the PDB."},"warnings":[{"fix":"Check RDKit version compatibility and update depiction calls if needed.","message":"Version 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.","severity":"breaking","affected_versions":"<1.0.0"},{"fix":"Ensure network access when using download_components; cache results locally if needed.","message":"The download_components helper requires an active internet connection; it fetches data from wwPDB. Offline use is not supported.","severity":"gotcha","affected_versions":"all"}],"env_vars":null,"last_verified":"2026-05-01T00:00:00.000Z","next_check":"2026-07-30T00:00:00.000Z","problems":[{"fix":"Use: from pdbeccdutils.core.component import PDBeComponent","cause":"PDBeComponent is not exposed at package level; it is in the core.component submodule.","error":"ImportError: cannot import name 'PDBeComponent' from 'pdbeccdutils'"},{"fix":"Ensure you are using v0.8.4 or later; if problem persists, the molecule may be invalid.","cause":"Sanitisation may fail for some molecules; v0.8.4 introduced non-sanitised fallback.","error":"RDKit ERROR: [14:11:29] Cannot find matching atom for bond ..."}],"ecosystem":"pypi","meta_description":null,"install_score":null,"install_tag":null,"quickstart_score":null,"quickstart_tag":null}