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bio-molecular-descriptors
Maintainer FreedomIntelligence · Last updated April 1, 2026
Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer descriptors. Use when featurizing molecules for machine learning or filtering by drug-likeness criteria.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-molecular-descriptors
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: AllChem.GetMorganFingerprintAsBitVect(), Descriptors.MolWt(), QED.qed() (RDKit).
- Calculate molecular fingerprints for my compound library" → Compute structural fingerprints (Morgan/ECFP, MACCS keys) and physicochemical descriptors (Lipinski, QED, TPSA) for molecules, producing feature vectors for similarity analysis or ML models. Python: AllChem.GetMorganFingerprintAsBitVect(), Descriptors.MolWt(), QED.qed() (RDKit).
- Calculate fingerprints and physicochemical properties for molecules.
- ecfp4 = AllChem.GetMorganFingerprintAsBitVect(mol, radius=2, nBits=2048) ecfp6 = AllChem.GetMorganFingerprintAsBitVect(mol, radius=3, nBits=2048).
Source Doc
Excerpt From SKILL.md
Morgan Fingerprints (ECFP)
Goal: Generate circular fingerprints that encode local chemical environments for similarity searching and ML models.
Approach: Use GetMorganFingerprintAsBitVect with a chosen radius (2 for ECFP4, 3 for ECFP6) and bit length, optionally including chirality information.
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles('CCO')
## With stereochemistry information
ecfp4_chiral = AllChem.GetMorganFingerprintAsBitVect(
mol, radius=2, nBits=2048, useChirality=True
)
## As count vector (for some ML methods)
ecfp4_counts = AllChem.GetMorganFingerprint(mol, radius=2)
Use cases
- Use when featurizing molecules for machine learning or filtering by drug-likeness criteria.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- molecular-io - Load molecules for descriptor calculation
- similarity-searching - Use fingerprints for similarity
- admet-prediction - Predict ADMET from descriptors
- machine-learning/biomarker-discovery - ML on molecular features
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