AL
Data & Repro
alphafold
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FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-molecular-io
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-molecular-io
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: Chem.MolFromSmiles(), Chem.SDMolSupplier() (RDKit).
- Load my chemical library into Python" → Parse molecular file formats (SMILES, SDF, MOL2, PDB) into RDKit molecule objects for programmatic access, standardization, and format conversion. Python: Chem.MolFromSmiles(), Chem.SDMolSupplier() (RDKit).
- Read, write, and convert molecular file formats with structure standardization.
- mol = Chem.MolFromSmiles('CCO').
Source Doc
Excerpt From SKILL.md
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')
Use cases
- Use when loading chemical libraries, converting formats, or preparing molecules for analysis.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- molecular-descriptors - Calculate properties after loading
- similarity-searching - Compare loaded molecules
- virtual-screening - Prepare ligands for docking
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