RAG Implementation
wshobson/agents
Build retrieval-augmented generation systems: pick a vector database and embedding model, choose retrieval and reranking strategies, and start from a LangGraph pipeline.
Automate molecular simulations with the ChemGraph agentic framework
Install Chemgraph Agent Guide
$ npx skills add wentorai/research-plugins --skill chemgraph-agent-guide -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install wentorai/research-plugins chemgraph-agent-guide --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/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/domains/chemistry/chemgraph-agent-guide .claude/skills/chemgraph-agent-guide && 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 "chemgraph-agent-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/chemgraph-agent-guide into .claude/skills/chemgraph-agent-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemgraph-agent-guide", 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/wentorai/research-plugins/tree/main/skills/domains/chemistry/chemgraph-agent-guideType 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 wentorai/research-plugins --skill chemgraph-agent-guide -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install wentorai/research-plugins chemgraph-agent-guide --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/domains/chemistry/chemgraph-agent-guide .agents/skills/chemgraph-agent-guide && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "chemgraph-agent-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/chemgraph-agent-guide into .agents/skills/chemgraph-agent-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemgraph-agent-guide", 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 wentorai/research-plugins --skill chemgraph-agent-guide -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install wentorai/research-plugins chemgraph-agent-guide --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/domains/chemistry/chemgraph-agent-guide .cursor/skills/chemgraph-agent-guide && 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 "chemgraph-agent-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/chemgraph-agent-guide into .cursor/skills/chemgraph-agent-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemgraph-agent-guide", 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/wentorai/research-plugins.git --path skills/domains/chemistry/chemgraph-agent-guide--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 wentorai/research-plugins --skill chemgraph-agent-guide -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install wentorai/research-plugins chemgraph-agent-guide --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/domains/chemistry/chemgraph-agent-guide .gemini/skills/chemgraph-agent-guide && 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 "chemgraph-agent-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/chemgraph-agent-guide into .gemini/skills/chemgraph-agent-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemgraph-agent-guide", 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 wentorai/research-plugins chemgraph-agent-guideInstalls 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 wentorai/research-plugins --skill chemgraph-agent-guide -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/domains/chemistry/chemgraph-agent-guide .github/skills/chemgraph-agent-guide && 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 "chemgraph-agent-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/chemgraph-agent-guide into .github/skills/chemgraph-agent-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemgraph-agent-guide", 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 wentorai/research-plugins --skill chemgraph-agent-guide -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install wentorai/research-plugins chemgraph-agent-guide --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/domains/chemistry/chemgraph-agent-guide .opencode/skills/chemgraph-agent-guide && 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 "chemgraph-agent-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/chemgraph-agent-guide into .opencode/skills/chemgraph-agent-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chemgraph-agent-guide", 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
chemgraph-agent-guide- GitHub stars
- 298
- Used in
- 1 other repo
- Token cost
- ~894 tokens
- SKILL.md length
- 205 words
- Files
- 1
- Skills in repo
- 405
- Repo updated
- First seen
- Licence
- MIT
At a glance
Automate molecular simulations with the ChemGraph agentic framework
- Works in 4 steps: Parser Agent — Interprets natural… → Structure Agent — Generates/retrieves… → Calculator Agent — Selects and runs… → …
- AI & LLM Engineering work in your project
- SKILL.md covers Overview, Installation, Core Capabilities and Agent Architecture, plus 3 more sections
- Calls pip and docker
What it does
Chemgraph Agent Guide is an agent skill from wentorai/research-plugins. Automate molecular simulations with the ChemGraph agentic framework
Its SKILL.md is about 890 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in AI & LLM Engineering. It works with LangGraph. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.
When your agent uses it
- AI & LLM Engineering work in your project
Example prompts
- “/chemgraph-agent-guide”
Requirements
- Python 3
- Docker
Workflow steps
4 steps, taken from the first numbered list in SKILL.md.
- Parser Agent — Interprets natural language into chemistry tasks
- Structure Agent — Generates/retrieves molecular structures (SMILES, PDB, CIF)
- Calculator Agent — Selects and runs appropriate simulation backend
- Analysis Agent — Processes results and generates reports
What it can do on your machine
Read from SKILL.md and the folder at commit bf44b3c. 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
Shell commands in SKILL.md call:
pipdocker
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
github.comwiki.fysik.dtu.dk
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
Chemgraph Agent Guide loads about 894 tokens when it runs. Until then it costs about 22 tokens; SKILL.md has 205 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); files beside SKILL.md are not scanned.
SKILL.md
The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 205 words, ~894 tokens.
Download SKILL.mdSave it as
.claude/skills/chemgraph-agent-guide/SKILL.md (or your agent's skills folder).- name
- chemgraph-agent-guide
- description
- Automate molecular simulations with the ChemGraph agentic framework
ChemGraph Agent Guide
Overview
ChemGraph is an agentic framework from Argonne National Lab that automates molecular simulation workflows using LLMs. Built on LangGraph and ASE (Atomic Simulation Environment), it enables natural language control of computational chemistry tasks — structure generation, geometry optimization, thermochemistry, and more. Supports DFT (NWChem, ORCA), semi-empirical (xTB), and ML potentials (MACE).
Installation
pip install chemgraph
# Or via Docker
docker pull ghcr.io/argonne-lcf/chemgraph:latestCore Capabilities
Natural Language Chemistry
from chemgraph import ChemGraphAgent
agent = ChemGraphAgent(
llm_provider="anthropic",
calculator="xtb", # fast semi-empirical
)
# Natural language molecular tasks
result = agent.run("Optimize the geometry of caffeine and calculate its vibrational frequencies")
print(result.energy)
print(result.frequencies)
# Thermochemistry
result = agent.run("Calculate the enthalpy of formation of ethanol at 298K")
print(f"ΔHf = {result.enthalpy:.2f} kJ/mol")Supported Calculators
| Calculator | Type | Speed | Accuracy |
|---|---|---|---|
| xTB (TBLite) | Semi-empirical | Fast | Moderate |
| MACE | ML potential | Fast | Good |
| NWChem | Ab initio DFT | Slow | High |
| ORCA | Ab initio/DFT | Slow | High |
| UMA | Universal ML | Fast | Good |
Workflow Automation
# Multi-step workflow
workflow = agent.create_workflow([
"Generate 3D structure of aspirin from SMILES",
"Optimize geometry with DFT/B3LYP/6-31G*",
"Calculate IR spectrum",
"Identify key functional group vibrations",
])
results = workflow.execute()
# Reaction pathway
pathway = agent.run(
"Find the transition state for the Diels-Alder reaction "
"between butadiene and ethylene"
)Integration with ASE
from ase.io import read
from chemgraph.calculators import get_calculator
# Use ChemGraph's calculator with ASE directly
atoms = read("molecule.xyz")
calc = get_calculator("xtb")
atoms.calc = calc
energy = atoms.get_potential_energy()
forces = atoms.get_forces()Agent Architecture
ChemGraph uses LangGraph's state machine to orchestrate:
- Parser Agent — Interprets natural language into chemistry tasks
- Structure Agent — Generates/retrieves molecular structures (SMILES, PDB, CIF)
- Calculator Agent — Selects and runs appropriate simulation backend
- Analysis Agent — Processes results and generates reports
Use Cases
- High-throughput screening: Automated property calculation for molecular libraries
- Reaction discovery: Transition state finding and reaction pathway analysis
- Materials design: Optimize structures for target properties
- Education: Natural language interface for learning computational chemistry
Requirements
- Python 3.10+
- At least one calculator backend (xTB recommended for getting started)
- LLM API key (Anthropic, OpenAI, or local)
References
© wentorai, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/domains/chemistry/chemgraph-agent-guide of wentorai/research-plugins.
Open the folder on GitHubat commit bf44b3c
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Chemgraph Agent Guide 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 |
|---|---|---|---|---|---|---|
| Chemgraph Agent Guide this skillwentorai/research-plugins | 298 | 1 repos | ~894 | Automated safety check: Pass | MIT | |
| RAG Implementationwshobson/agents | 40k | 10 repos | ~1.1k | Automated safety check: Pass | MIT | |
| Langgraph Agent Patternssoba-labs/langchain-agent-skills | 107 | — | ~3.6k | Automated safety check: Pass | MIT | |
| AI EngineerDokhacgiakhoa/Agent-Skills-4-Vibe-Coding-CLI | 507 | — | ~1.1k | Automated safety check: Pass | Custom licence | |
| Langgraph Error Handlingsoba-labs/langchain-agent-skills | 107 | — | ~1.5k | Automated safety check: Pass | MIT | |
| Port From Langgraphstrands-agents/harness-sdk | 8.7k | — | ~200 | Automated safety check: Pass | Apache-2.0 |
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Langgraph Agent Patterns
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AI Engineer
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Principal AI Architect and Machine Learning Engineer. An agent skill from Dokhacgiakhoa/Agent-Skills-4-Vibe-Coding-CLI.
Langgraph Error Handling
soba-labs/langchain-agent-skills
Implement LangGraph error handling with current v1 patterns.
Port From Langgraph
strands-agents/harness-sdk
Migrate a LangGraph application to Strands Agents while preserving its external entrypoint, routing, persistence, interrupts, limits, and tracing.
- Official
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Related
Works with
Categories
Questions about Chemgraph Agent Guide
What does Chemgraph Agent Guide do?
Automate molecular simulations with the ChemGraph agentic framework. Chemgraph Agent Guide is an agent skill from wentorai/research-plugins.
When should I use Chemgraph Agent Guide?
Chemgraph Agent Guide fits situations like: AI & LLM Engineering work in your project.
How do I install Chemgraph Agent Guide in Claude Code?
Run `npx skills add wentorai/research-plugins --skill chemgraph-agent-guide -a claude-code`. Or copy the skill folder (skills/domains/chemistry/chemgraph-agent-guide in wentorai/research-plugins) into .claude/skills/chemgraph-agent-guide in your project. Claude Code loads it when a task matches its description.
How do I install Chemgraph Agent Guide in Codex?
Run `npx skills add wentorai/research-plugins --skill chemgraph-agent-guide -a codex`. Or copy the skill folder (skills/domains/chemistry/chemgraph-agent-guide in wentorai/research-plugins) into .agents/skills/chemgraph-agent-guide in your project. Codex loads it when a task matches its description.
Can I use Chemgraph Agent Guide 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 wentorai/research-plugins --skill chemgraph-agent-guide -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/chemgraph-agent-guide, .gemini/skills/chemgraph-agent-guide, .github/skills/chemgraph-agent-guide and .opencode/skills/chemgraph-agent-guide in your project.
What does Chemgraph Agent Guide need to run?
Going by SKILL.md and its folder, Chemgraph Agent Guide needs the command-line tools its instructions call (pip and docker). Our summary lists: Python 3; Docker.
Does Chemgraph Agent Guide access the network?
SKILL.md names 2 domains. As links in the text: github.com and wiki.fysik.dtu.dk. This is read from the text; nothing was executed.
Is Chemgraph Agent Guide 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. Review the folder before installing.
What licence does Chemgraph Agent Guide use?
Chemgraph Agent Guide is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Chemgraph Agent Guide use?
About 894 tokens (SKILL.md is roughly 3.6k 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 Chemgraph Agent Guide?
Skills that share tags, products or a category with Chemgraph Agent Guide: RAG Implementation (wshobson/agents, 40k stars), Langgraph Agent Patterns (soba-labs/langchain-agent-skills, 107 stars), AI Engineer (Dokhacgiakhoa/Agent-Skills-4-Vibe-Coding-CLI, 507 stars) and Langgraph Error Handling (soba-labs/langchain-agent-skills, 107 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Chemgraph Agent Guide?
wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 skills in this directory. The repository was last updated on June 19, 2026.
Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.