Molecode
AtomFlow-AI/MoleCode
A skill your agent uses for deterministic molecule understanding, graph-level editing, generation, and validation with MoleCode — an explicit Mermaid graph in which every atom and bond is a typed…
Convert between IUPAC names, SMILES strings, molecular formulas, and common names for chemical compounds.
Install Chemical Structure Converter
$ npx skills add aipoch/medical-research-skills --skill chemical-structure-converter -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aipoch/medical-research-skills chemical-structure-converter --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/scientific-skills/Other/chemical-structure-converter .claude/skills/chemical-structure-converter && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "chemical-structure-converter" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/chemical-structure-converter into .claude/skills/chemical-structure-converter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemical-structure-converter", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/chemical-structure-converterType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add aipoch/medical-research-skills --skill chemical-structure-converter -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aipoch/medical-research-skills chemical-structure-converter --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/scientific-skills/Other/chemical-structure-converter .agents/skills/chemical-structure-converter && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "chemical-structure-converter" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/chemical-structure-converter into .agents/skills/chemical-structure-converter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemical-structure-converter", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aipoch/medical-research-skills --skill chemical-structure-converter -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aipoch/medical-research-skills chemical-structure-converter --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/scientific-skills/Other/chemical-structure-converter .cursor/skills/chemical-structure-converter && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "chemical-structure-converter" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/chemical-structure-converter into .cursor/skills/chemical-structure-converter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemical-structure-converter", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/aipoch/medical-research-skills.git --path scientific-skills/Other/chemical-structure-converter--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add aipoch/medical-research-skills --skill chemical-structure-converter -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aipoch/medical-research-skills chemical-structure-converter --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/scientific-skills/Other/chemical-structure-converter .gemini/skills/chemical-structure-converter && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "chemical-structure-converter" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/chemical-structure-converter into .gemini/skills/chemical-structure-converter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemical-structure-converter", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install aipoch/medical-research-skills chemical-structure-converterInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add aipoch/medical-research-skills --skill chemical-structure-converter -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/scientific-skills/Other/chemical-structure-converter .github/skills/chemical-structure-converter && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "chemical-structure-converter" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/chemical-structure-converter into .github/skills/chemical-structure-converter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemical-structure-converter", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aipoch/medical-research-skills --skill chemical-structure-converter -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aipoch/medical-research-skills chemical-structure-converter --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/scientific-skills/Other/chemical-structure-converter .opencode/skills/chemical-structure-converter && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "chemical-structure-converter" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/chemical-structure-converter into .opencode/skills/chemical-structure-converter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemical-structure-converter", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
chemical-structure-converter- GitHub stars
- 1.9k
- Token cost
- ~1.7k tokens
- SKILL.md length
- 630 words
- Files
- 3 (incl. scripts)
- Skills in repo
- 578
- Repo updated
- First seen
- Licence
- MIT
At a glance
Convert between IUPAC names, SMILES strings, molecular formulas, and common names for chemical compounds.
- Works in 3 steps: Multi-Format Conversion → SMILES Validation → Batch Processing
- Tasks that involve Drug discovery and cheminformatics
- SKILL.md covers Input Validation, Quick Check, Workflow and Core Capabilities, plus 7 more sections
- Runs Python scripts from its folder; calls python; reaches pubchem.ncbi.nlm.nih.gov and chemspider.com
What it does
Chemical Structure Converter is an agent skill from aipoch/medical-research-skills. Convert between IUPAC names, SMILES strings, molecular formulas, and common names for chemical compounds. Supports SMILES validation, batch processing, structure standardization, and cheminformatics database preparation for drug discovery workflows.
Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files, including scripts (for example `chemical-structure-converter_audit_result_v4.json` and `scripts/main.py`).
It sits in Research & Science, covering Drug discovery and cheminformatics and Data pipelines and ETL. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.
When your agent uses it
- Tasks that involve Drug discovery and cheminformatics
- Tasks that involve Data pipelines and ETL
Example prompts
- “/chemical-structure-converter”
Requirements
- Python 3
Workflow steps
3 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
pubchem.ncbi.nlm.nih.govchemspider.com
Also links to:
opensmiles.orgrdkit.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Chemical Structure Converter loads about 1.7k tokens when it runs. Until then it costs about 70 tokens; SKILL.md has 630 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 630 words, ~1,708 tokens.
Download SKILL.mdSave it as
.claude/skills/chemical-structure-converter/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.- name
- chemical-structure-converter
- description
- Convert between IUPAC names, SMILES strings, molecular formulas, and common names for chemical compounds. Supports SMILES validation, batch processing, structure standardization, and cheminformatics database preparation for drug discovery workflows.
- license
- MIT
- author
- AIPOCH
Chemical Structure Converter
Interconvert between different chemical structure representations including IUPAC names, SMILES strings, molecular formulas, and common names. Essential for cheminformatics workflows, database standardization, and compound registration in drug discovery and chemical research.
Key Capabilities:
- Multi-Format Conversion: IUPAC names, SMILES, InChI, molecular formulas
- SMILES Validation: Validate SMILES syntax for structural correctness
- Batch Processing: Process multiple compounds for database standardization
- Identifier Lookup: Retrieve all available identifiers for known compounds
- Structure Standardization: Normalize chemical representations for consistency
Input Validation
This skill accepts: compound names (common or IUPAC), SMILES strings, or InChI identifiers. Batch input via CSV or plain text list is also supported.
If the request does not involve converting or validating chemical structure identifiers — for example, asking to predict biological activity, perform docking, or interpret spectra — do not proceed. Instead respond:
"Chemical Structure Converter is designed to interconvert chemical identifiers (names, SMILES, formulas). Please provide a compound name or SMILES string. For other cheminformatics tasks, use a more appropriate tool."
Quick Check
python -m py_compile scripts/main.py
python scripts/main.py --helpWorkflow
- Confirm the input identifier type (name, SMILES, IUPAC) and desired output format.
- Validate that the request matches the documented scope; stop if the task requires unsupported assumptions.
- Run the script or apply the documented conversion path with only the inputs available.
- Return a structured result separating assumptions, deliverables, risks, and unresolved items.
- If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.
Fallback: If no identifier is provided, respond: "No chemical identifier provided. Please supply a compound name (--name), SMILES string (--smiles), or IUPAC name (--iupac). Cannot convert without an input identifier."
Core Capabilities
1. Multi-Format Conversion
from scripts.main import ChemicalStructureConverter
converter = ChemicalStructureConverter()
data = converter.name_to_identifiers("aspirin")
# → IUPAC: 2-acetoxybenzoic acid, SMILES: CC(=O)Oc1ccccc1C(=O)O, Formula: C9H8O4, MW: 180.16| From → To | Use Case |
|---|---|
| Name → SMILES | Literature to database |
| SMILES → IUPAC | Machine to human readable |
| IUPAC → SMILES | Chemical registration |
| SMILES → Formula | Quick MW calculation |
2. SMILES Validation
is_valid, message = converter.validate_smiles("CC(=O)Oc1ccccc1C(=O)O")
# → True, "Valid SMILES syntax"| Check | Example Error |
|---|---|
| Parentheses | C(=O — missing closing |
| Ring closures | C1CC — ring not closed |
| Atom validity | @ — invalid character |
3. Batch Processing
for compound in compound_list:
data = converter.name_to_identifiers(compound)
if not data:
print(f"Warning: '{compound}' not found in database")CLI Usage
# Convert by compound name
python scripts/main.py --name aspirin
# Convert SMILES to IUPAC
python scripts/main.py --smiles "CC(=O)Oc1ccccc1C(=O)O"
# Validate SMILES
python scripts/main.py --smiles "CCO" --validate
# List all compounds
python scripts/main.py --listParameters
| Parameter | Type | Required | Description |
|---|---|---|---|
--name, -n | string | No | Compound name |
--smiles, -s | string | No | SMILES string |
--iupac, -i | string | No | IUPAC name |
--validate | flag | No | Validate SMILES syntax |
--list, -l | flag | No | List available compounds |
Show full SKILL.md (269 more words)Show less
Output Requirements
Every final response must make these explicit:
- Objective or requested deliverable
- Inputs used (identifier type and value) and assumptions introduced
- Conversion method applied
- Core result: all available identifiers (SMILES, IUPAC, formula, MW)
- Constraints and risks (local database limited; novel compounds may not be found)
- Unresolved items and next-step checks (validate against PubChem for critical work)
Error Handling
- If no identifier is provided, list the required input options and request clarification.
- If a compound is not found in the local database, flag it and provide direct lookup URLs:
https://pubchem.ncbi.nlm.nih.gov/compound/{compound_name}andhttps://www.chemspider.com/Search.aspx?q={compound_name}. For programmatic lookup, query the PubChem REST API:https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{name}/JSON. The script should automatically query this endpoint when a compound is not found locally. - If
scripts/main.pyfails, report the failure point and provide manual fallback guidance. - Do not fabricate SMILES strings, molecular weights, or identifiers.
- Batch mode: Include a summary line:
X/N compounds converted successfully, Y failed (list failed compound names). - Database versioning: The local compound database version is tracked in
DB_VERSIONinscripts/main.py. To add compounds, update theCOMPOUND_DBdict and incrementDB_VERSION.
Common Pitfalls
- Ambiguous names: Use CAS numbers or specific synonyms for unambiguous lookup
- Stereochemistry omitted: Specify @/@@ in SMILES for chiral compounds
- Hydrates vs anhydrous: Always specify form (e.g., "caffeine anhydrous")
- Duplicate entries: Deduplicate by canonical SMILES when building databases
- Character encoding: Use UTF-8 for IUPAC names with special characters
SMILES Quick Reference
C= aliphatic carbon,c= aromatic carbon== double bond,#= triple bond()= branching,[]= explicit valence/charge@= anticlockwise (S),@@= clockwise (R)
References
- PubChem: https://pubchem.ncbi.nlm.nih.gov
- ChemSpider: http://www.chemspider.com
- SMILES Specification: http://opensmiles.org
- RDKit Documentation: https://www.rdkit.org/docs/
Known Limitation: Local database contains common compounds only. Integrate PubChem API for production use.
© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 2 other files (scripts) in scientific-skills/Other/chemical-structure-converter of aipoch/medical-research-skills.
- SKILL.md
- chemical-structure-converter_audit_result_v4.json
- scripts/main.py
Open the folder on GitHubat commit 686e09d
Compare with similar skills
Chemical Structure Converter next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Chemical Structure Converter this skillaipoch/medical-research-skills | 1.9k | — | ~1.7k | Automated safety check: Pass | MIT | |
| MolecodeAtomFlow-AI/MoleCode | 306 | — | ~1.9k | Automated safety check: Pass | MIT | |
| Drug DiscoveryTommy-yw/RunbookHermes | 546 | 1 repos | ~2.3k | Automated safety check: Pass | MIT | |
| DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3k | Automated safety check: Notes | MIT | |
| Biomedical Analysis Dispatchxjtulyc/MedgeClaw | 617 | 1 repos | ~2k | Automated safety check: Pass | None | |
| Biopipelineslocbp-uzh/biopipelines | 109 | — | ~2.4k | Automated safety check: Pass | MIT |
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Categories
Questions about Chemical Structure Converter
What does Chemical Structure Converter do?
Convert between IUPAC names, SMILES strings, molecular formulas, and common names for chemical compounds. Chemical Structure Converter is an agent skill from aipoch/medical-research-skills. Convert between IUPAC names, SMILES strings, molecular formulas, and common names for chemical compounds.
When should I use Chemical Structure Converter?
Chemical Structure Converter fits situations like: tasks that involve Drug discovery and cheminformatics; tasks that involve Data pipelines and ETL.
How do I install Chemical Structure Converter in Claude Code?
Run `npx skills add aipoch/medical-research-skills --skill chemical-structure-converter -a claude-code`. Or copy the skill folder (scientific-skills/Other/chemical-structure-converter in aipoch/medical-research-skills) into .claude/skills/chemical-structure-converter in your project. Claude Code loads it when a task matches its description.
How do I install Chemical Structure Converter in Codex?
Run `npx skills add aipoch/medical-research-skills --skill chemical-structure-converter -a codex`. Or copy the skill folder (scientific-skills/Other/chemical-structure-converter in aipoch/medical-research-skills) into .agents/skills/chemical-structure-converter in your project. Codex loads it when a task matches its description.
Can I use Chemical Structure Converter in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill chemical-structure-converter -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/chemical-structure-converter, .gemini/skills/chemical-structure-converter, .github/skills/chemical-structure-converter and .opencode/skills/chemical-structure-converter in your project.
What does Chemical Structure Converter need to run?
Going by SKILL.md and its folder, Chemical Structure Converter needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Chemical Structure Converter access the network?
SKILL.md names 4 domains. In commands or code: pubchem.ncbi.nlm.nih.gov and chemspider.com; the agent is likely to contact these when it follows the instructions. As links in the text: opensmiles.org and rdkit.org. This is read from the text; nothing was executed.
Is Chemical Structure Converter safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Chemical Structure Converter use?
Chemical Structure Converter is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Chemical Structure Converter use?
About 1.7k tokens (SKILL.md is roughly 6.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Chemical Structure Converter?
Skills that share tags, products or a category with Chemical Structure Converter: Molecode (AtomFlow-AI/MoleCode, 306 stars), Drug Discovery (Tommy-yw/RunbookHermes, 546 stars), DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars) and Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Chemical Structure Converter?
aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,937 GitHub stars. The repository holds 578 skills in this directory. The repository was last updated on September 17, 2026.
Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.