bio-molecular-io
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-molecular-io --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: RDKit 2024.03+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Molecular I/O **"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. ## 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 in
- Version Compatibility
- Supported Formats
- Reading Molecules
- Writing Molecules
- Structure Standardization
- Open Babel Conversion
- Molecular Drawing
- Related Skills
What does the bio-molecular-io skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-molecular-io --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.