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bio-substructure-search
维护者 FreedomIntelligence · 最近更新 2026年4月1日
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.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-substructure-search
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- Python：mol.HasSubstructMatch()，Chem.MolFromSmarts() (RDKit)。
- Filter my 库 ，用于 compounds containing specific functional group" → Search molecular collections ，用于 substructure matches ，使用 SMARTS patterns，identifying compounds that contain specified chemical moieties，scaffolds，或 pharmacophore features. Python：mol.HasSubstructMatch()，Chem.MolFromSmarts() (RDKit)。
- Find molecules containing specific structural patterns ，使用 SMARTS。
- pattern = Chem.MolFromSmarts('[OH]') # Hydroxyl group has_hydroxyl = mol.HasSubstructMatch(pattern) print(f'Contains hydroxyl：{has_hydroxyl}')。
原始文档
SKILL.md 摘录
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 |
适用场景
- 适合在finding compounds containing specific chemical moieties 或 filtering libraries by structural features时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- molecular-io - Load molecules for searching
- similarity-searching - Fingerprint-based searching
- admet-prediction - Filter before ADMET analysis
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