bio-molecular-io
Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.
npx skills add BioTender-max/awesome-bio-agent-skills --skill 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 2024.09+, Open Babel 3.1.1+, ChEMBL structure_pipeline 1.2+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `obabel -V`; `obabel -L formats` 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 Parse, write, and convert molecular file formats. Most downstream errors trace back to silent I/O issues: incorrect aromaticity perception, lost stereochemistry, mishandled charges, dropped stereo bonds, or non-canonical tautomers. This skill enumerates each format's failure modes and prescribes the correct toolchain for each scenario. For full standardization (canonicalization, salt stripping, tautomer enumeration) see `chemoinformatics/molecular-standardization`. For generating 3D conformers from parsed 2D molecules, see `chemoinformatics/conformer-generation`. ## Format Taxonomy | Format | Dim | Stereo | Charges | Strength | Fails when | |--------|-----|--------|---------|----------|-----
- Version Compatibility
- Format Taxonomy
- Aromaticity Perception (most common silent error)
- Stereochemistry Layers
- Reading SMILES with Stereo Preservation
- Reading SDF with Property Carryover
- Open Babel for MOL2 / PDBQT
- InChI for Canonical Identity
- Per-Format Failure Modes
- SMILES -- ambiguous aromaticity
- SDF V2000 -- atom count >999
- SDF -- wedge bond orientation lost
- PDB ligand -- no bond orders
- MOL2 -- SYBYL atom type dialect
What does the bio-molecular-io skill do?
Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill 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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.