AL
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alphafold
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数据与复现
BI
bio-molecular-io
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use when loading chemical libraries, converting formats, or preparing molecules for analysis.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-molecular-io
- 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：Chem.MolFromSmiles()，Chem.SDMolSupplier() (RDKit)。
- Load my chemical 库 into Python" → Parse molecular file formats (SMILES，SDF，MOL2，PDB) into RDKit molecule objects ，用于 programmatic access，standardization，、 format conversion. Python：Chem.MolFromSmiles()，Chem.SDMolSupplier() (RDKit)。
- Read，write，、 convert molecular file formats ，支持 structure standardization。
- mol = Chem.MolFromSmiles('CCO')。
原始文档
SKILL.md 摘录
Supported Formats
| Format | Extension | Use Case |
|---|---|---|
| SMILES | .smi | Text representation, databases |
| SDF/MOL | .sdf, .mol | 3D structures, compound libraries |
| MOL2 | .mol2 | Docking, force field atoms |
| PDB | .pdb | Protein-ligand complexes |
Reading Molecules
Goal: Load molecules from SMILES strings, SDF files, or SMILES files into RDKit molecule objects.
Approach: Use Chem.MolFromSmiles for individual SMILES, SDMolSupplier for multi-molecule SDF files, and file iteration for SMILES files, filtering out parse failures.
from rdkit import Chem
from rdkit.Chem import AllChem
## From SDF file (single molecule)
mol = Chem.MolFromMolFile('molecule.mol')
适用场景
- 适合在loading chemical libraries，converting formats，或 preparing molecules ，用于 analysis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-descriptors - Calculate properties after loading
- similarity-searching - Compare loaded molecules
- virtual-screening - Prepare ligands for docking
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