bio-molecular-descriptors
Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.
npx skills add BioTender-max/awesome-bio-agent-skills --skill molecular-descriptors --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: RDKit 2024.09+, numpy 1.26+, pandas 2.2+, mapchiral 0.1+ (MAP4), mhfp 1.9+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Molecular Descriptors Featurize molecules for similarity search, QSAR, virtual screening, or ML. The fingerprint or descriptor choice is **chemotype-aware**: ECFP4 dominates drug-like organic similarity, AtomPair and TopologicalTorsion outperform for scaffold hopping, MAP4/MHFP6 win on metabolomics-scale chemical diversity, and 3D conformer-based descriptors are essential when shape and stereochemistry matter. For canonicalization before featurization, see `chemoinformatics/molecular-standardization`. For 3D-only descriptors, see `chemoinformatics/conformer-generation`. ## Fingerprint Taxonomy | Fingerprint | Type | Radius/Path | Bits | Use case | Fails when | |-------------|------|-------------|------|----------|------------| | Morgan
- Version Compatibility
- Fingerprint Taxonomy
- Bit vs Count Vectors
- Morgan / ECFP Radius Math
- FCFP vs ECFP
- 3D Descriptors and Conformer Dependence
- Partial Charge Methods
- MAP4 and MHFP6 for Diverse Libraries
- Physicochemical Descriptors
- Drug-Likeness Rule Sets
- QED (Weighted Drug-Likeness)
- Common Errors
- References
- Related Skills
What does the bio-molecular-descriptors skill do?
Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill molecular-descriptors --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.