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BI
bio-substructure-search
Maintainer FreedomIntelligence · Last updated April 1, 2026
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matches with atom mapping. Use when finding compounds containing specific chemical moieties or filtering libraries by structural features.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-substructure-search
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: mol.HasSubstructMatch(), Chem.MolFromSmarts() (RDKit).
- Filter my library for compounds containing a specific functional group" → Search molecular collections for substructure matches using SMARTS patterns, identifying compounds that contain specified chemical moieties, scaffolds, or pharmacophore features. Python: mol.HasSubstructMatch(), Chem.MolFromSmarts() (RDKit).
- Find molecules containing specific structural patterns using SMARTS.
- pattern = Chem.MolFromSmarts('[OH]') # Hydroxyl group has_hydroxyl = mol.HasSubstructMatch(pattern) print(f'Contains hydroxyl: {has_hydroxyl}').
Source Doc
Excerpt From SKILL.md
Basic Substructure Search
from rdkit import Chem
mol = Chem.MolFromSmiles('c1ccc(O)cc1CCO')
## Get all matches (atom indices)
matches = mol.GetSubstructMatches(pattern)
print(f'Hydroxyl positions: {matches}')
Common SMARTS Patterns
| Pattern | SMARTS | Description |
|---|---|---|
| Hydroxyl | [OH] | Alcohol/phenol |
| Primary amine | [NH2] | Primary amine |
| Secondary amine | [NH1] | Secondary amine |
| Carboxylic acid | [CX3](=O)[OX2H1] | COOH |
| Amide | [CX3](=O)[NX3] | C(=O)N |
| Benzene | c1ccccc1 | Phenyl ring |
| Any aromatic | [a] | Any aromatic atom |
| Halogen | [F,Cl,Br,I] | Any halogen |
Use cases
- Use when finding compounds containing specific chemical moieties or filtering libraries by structural features.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- molecular-io - Load molecules for searching
- similarity-searching - Fingerprint-based searching
- admet-prediction - Filter before ADMET analysis
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