Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add GPTomics/bioSkills --skill molecular-iogit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/gptomics/bioskills/molecular-io)<a href="https://agentmods.dev/skills/gptomics/bioskills/molecular-io"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/molecular-io/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/gptomics/bioskills/molecular-io"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/molecular-io.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00101 | $0.03894 |
| Opus 5 | $0.00051 | $0.01947 |
| Sonnet 5 | $0.00020 | $0.00779 |
| Haiku 4.5 | $0.00010 | $0.00389 |
Grade A, and why
bio-molecular-io scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
subprocess.run(['obabel', 'docked.pdbqt', '-O', 'docked.sdf'], check=True) Copies of this mod
1 near-identical copy found in the catalogue:
- bio-molecular-io — 92% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 270 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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>thenhelp(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 |
|---|---|---|---|---|---|
| SMILES | 2D | Atom chirality @/@@; double-bond / and \ |
Atom-local formal charges | Compact, web-friendly, fast parse | Loses absolute coordinates; aromatic perception ambiguous across toolkits; tautomers not canonical |
| InChI | 2D | /b, /t, /m, /s stereo sublayers |
/q charge and /p added/removed-proton sublayers; /p is not a pH model |
Canonical by construction; cross-toolkit identity | Standard InChI normalizes mobile-H forms; limited organometallic stereo; large molecules may require special handling |
| SDF V2000 | 2D/3D | Wedge bonds | M CHG line | Industry default; metadata via tags | 999-atom limit; cannot encode multi-component reactions; query atoms ambiguous |
| SDF V3000 | 2D/3D | Wedge + stereo flag | Inline charge | No atom limit; query support; rich properties | Some software (legacy) cannot read; verbose |
| MOL2 (Tripos) | 3D | Common records rely on 3D coordinates and toolkit perception; no portable explicit stereo field | Per-atom partial | SYBYL atom types preserved for docking | Atom-type dialects diverge (SYBYL vs Corina); RDKit MOL2 parser brittle |
| PDB | 3D | None | None standard | Universal protein format | No bond orders; aromatic perception lost; ligand names truncated to 3 chars |
| PDBQT | 3D | None | Gasteiger / AD4 | AutoDock-ready; torsion tree encoded | Specific to docking; no aromaticity layer |
| BinaryCIF (MMTF retired) | 3D | Encoded | Encoded | BinaryCIF (.bcif) is the current compact structural format; RCSB stopped serving MMTF files on July 2, 2024 and recommends BinaryCIF (RCSB PDB 2024) |
Not all toolkits parse; binary format |
| CDX/CDXML | 2D | Drawing | Drawing | ChemDraw native | Not a structural format; converts unreliably |
| InChIKey | Hash | Stereo layer | n/a | Database key, fast lookup | Collision probability depends on key block and collection size; cannot recover structure |
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 270 lines · 101 tokens per session scan A d6a5f24e0fae
bio-molecular-io is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 24d ago), licensed MIT. It adds 101 tokens to every session and 3,894 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other skills, from other repositories
instrument-data-to-allotrope
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…
exploratory-data-analysis
Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain…
matlab
Build, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.
phylogenetics
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
research-engineer
An uncompromising Academic Research Engineer. Operates with absolute scientific rigor, objective criticism, and zero flair. Focuses on theoretical correctness, formal verification, and optimal implementation across any required technology.
mapping-to-snomed
Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED CT, run an ECL…