{"categories":[{"label":"Bio-Informatics","url":"https://skillfed.io/packages/category/scientific-engineering-bio-informatics"},{"label":"Chemistry","url":"https://skillfed.io/packages/category/scientific-engineering-chemistry"}],"enrichment":{"capability":"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.","skillfed_tags":["structural-biology","cheminformatics","pdb-data"],"use_cases":["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."],"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.\n\nThe 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.","worth_installing":"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."},"id":"pdbeccdutils","links":{"html":"https://skillfed.io/packages/pdbeccdutils","md":"https://skillfed.io/packages/pdbeccdutils.md","pypi":"https://pypi.org/project/pdbeccdutils/"},"maintenance":{"status":"active"},"meta":{"latest_release":"2026-06-30","license_spdx":null,"license_treatment":"permissive","name":"pdbeccdutils","python_support":"supports_current","summary":"Toolkit to parse and process small molecules in wwPDB"},"popularity":{"monthly_downloads":238665,"position":8932,"tier":"top_15000"},"security":{"n_vulnerabilities":0},"version":"1.0.4"}