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…
PNNL cheminformatics LLM agent for molecular analysis. An agent skill from wentorai/research-plugins.
Install Cactus Cheminformatics Guide
$ npx skills add wentorai/research-plugins --skill cactus-cheminformatics-guide -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install wentorai/research-plugins cactus-cheminformatics-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/cactus-cheminformatics-guide .claude/skills/cactus-cheminformatics-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 "cactus-cheminformatics-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/cactus-cheminformatics-guide into .claude/skills/cactus-cheminformatics-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "cactus-cheminformatics-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/cactus-cheminformatics-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 cactus-cheminformatics-guide -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install wentorai/research-plugins cactus-cheminformatics-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/cactus-cheminformatics-guide .agents/skills/cactus-cheminformatics-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 "cactus-cheminformatics-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/cactus-cheminformatics-guide into .agents/skills/cactus-cheminformatics-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "cactus-cheminformatics-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 cactus-cheminformatics-guide -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install wentorai/research-plugins cactus-cheminformatics-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/cactus-cheminformatics-guide .cursor/skills/cactus-cheminformatics-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 "cactus-cheminformatics-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/cactus-cheminformatics-guide into .cursor/skills/cactus-cheminformatics-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "cactus-cheminformatics-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/cactus-cheminformatics-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 cactus-cheminformatics-guide -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install wentorai/research-plugins cactus-cheminformatics-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/cactus-cheminformatics-guide .gemini/skills/cactus-cheminformatics-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 "cactus-cheminformatics-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/cactus-cheminformatics-guide into .gemini/skills/cactus-cheminformatics-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "cactus-cheminformatics-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 cactus-cheminformatics-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 cactus-cheminformatics-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/cactus-cheminformatics-guide .github/skills/cactus-cheminformatics-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 "cactus-cheminformatics-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/cactus-cheminformatics-guide into .github/skills/cactus-cheminformatics-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "cactus-cheminformatics-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 cactus-cheminformatics-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 cactus-cheminformatics-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/cactus-cheminformatics-guide .opencode/skills/cactus-cheminformatics-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 "cactus-cheminformatics-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/chemistry/cactus-cheminformatics-guide into .opencode/skills/cactus-cheminformatics-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "cactus-cheminformatics-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
cactus-cheminformatics-guide- GitHub stars
- 298
- Used in
- 1 other repo
- Token cost
- ~641 tokens
- SKILL.md length
- 104 words
- Files
- 1
- Skills in repo
- 405
- Repo updated
- First seen
- Licence
- MIT
At a glance
PNNL cheminformatics LLM agent for molecular analysis. An agent skill from wentorai/research-plugins.
- Works in 5 steps: Molecular analysis: Property calculation… → Drug screening: Lipinski/Veber rule… → Similarity search: Find analogs in… → …
- Tasks that involve Drug discovery and cheminformatics
- SKILL.md covers Overview, Usage, Similarity Search and Substructure Analysis, plus 2 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Cactus Cheminformatics Guide is an agent skill from wentorai/research-plugins. PNNL cheminformatics LLM agent for molecular analysis
Its SKILL.md is about 640 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 Research & Science, covering Drug discovery and cheminformatics. 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
- Tasks that involve Drug discovery and cheminformatics
Example prompts
- “/cactus-cheminformatics-guide”
Requirements
- Python 3
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Molecular analysis: Property calculation via natural language
- Drug screening: Lipinski/Veber rule checking
- Similarity search: Find analogs in chemical databases
- Structure analysis: Substructure and functional group ID
- Chemical education: Interactive chemistry exploration
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
No scripts in the folder and no shell commands in SKILL.md (its code samples are python).
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.comrdkit.orgpnnl.gov
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
Cactus Cheminformatics Guide loads about 641 tokens when it runs. Until then it costs about 21 tokens; SKILL.md has 104 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). 104 words, ~641 tokens.
Download SKILL.mdSave it as
.claude/skills/cactus-cheminformatics-guide/SKILL.md (or your agent's skills folder).- name
- cactus-cheminformatics-guide
- description
- PNNL cheminformatics LLM agent for molecular analysis
CACTUS Cheminformatics Agent Guide
Overview
CACTUS is a cheminformatics LLM agent developed at Pacific Northwest National Laboratory (PNNL) that provides AI-assisted molecular analysis, property prediction, and chemical reasoning. It wraps RDKit, molecular databases, and ML models behind a conversational interface, enabling researchers to query molecular properties, perform similarity searches, and run cheminformatics workflows using natural language.
Usage
from cactus import ChemAgent
agent = ChemAgent(llm_provider="anthropic")
# Natural language chemistry queries
result = agent.ask(
"What is the molecular weight and LogP of aspirin? "
"Is it drug-like by Lipinski's rules?"
)
print(result.answer)
# Aspirin (CC(=O)Oc1ccccc1C(=O)O):
# MW: 180.16, LogP: 1.24
# Lipinski: PASS (MW<500, LogP<5, HBD=1≤5, HBA=4≤10)
# Molecular property calculation
props = agent.calculate_properties(
smiles="CC(=O)Oc1ccccc1C(=O)O",
properties=["mw", "logp", "tpsa", "hbd", "hba", "rotatable"],
)
print(props)Similarity Search
# Find similar molecules
similar = agent.similarity_search(
query_smiles="CC(=O)Oc1ccccc1C(=O)O", # Aspirin
database="chembl",
threshold=0.7, # Tanimoto similarity
max_results=10,
)
for mol in similar:
print(f"{mol.name}: {mol.smiles} "
f"(similarity: {mol.tanimoto:.3f})")Substructure Analysis
# Substructure search
matches = agent.substructure_search(
pattern="c1ccccc1C(=O)O", # Benzoic acid motif
database="drugbank",
max_results=20,
)
# Functional group identification
groups = agent.identify_functional_groups(
smiles="CC(=O)Oc1ccccc1C(=O)O"
)
# ["ester", "carboxylic_acid", "aromatic_ring"]Use Cases
- Molecular analysis: Property calculation via natural language
- Drug screening: Lipinski/Veber rule checking
- Similarity search: Find analogs in chemical databases
- Structure analysis: Substructure and functional group ID
- Chemical education: Interactive chemistry exploration
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/cactus-cheminformatics-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
Cactus Cheminformatics 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 |
|---|---|---|---|---|---|---|
| Cactus Cheminformatics Guide this skillwentorai/research-plugins | 298 | 1 repos | ~641 | 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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Predicts how small molecules bind to a protein with DiffDock, covering batch docking, pose ranking by confidence and checks on the results; not for binding affinity.
Biomedical Analysis Dispatch
xjtulyc/MedgeClaw
Routes bioinformatics, drug discovery, clinical and multi-omics tasks from a chat interface to Claude Code sessions running K-Dense scientific skills, with a live dashboard per task.
Biopipelines
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Design and run computational protein and ligand workflows on a GPU: binder and enzyme design, de novo backbone generation, inverse folding and sequence redesign, structure prediction, protein-ligand…
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Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment.
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Related
Categories
Questions about Cactus Cheminformatics Guide
What does Cactus Cheminformatics Guide do?
PNNL cheminformatics LLM agent for molecular analysis. An agent skill from wentorai/research-plugins. Cactus Cheminformatics Guide is an agent skill from wentorai/research-plugins.
When should I use Cactus Cheminformatics Guide?
Cactus Cheminformatics Guide fits situations like: tasks that involve Drug discovery and cheminformatics.
How do I install Cactus Cheminformatics Guide in Claude Code?
Run `npx skills add wentorai/research-plugins --skill cactus-cheminformatics-guide -a claude-code`. Or copy the skill folder (skills/domains/chemistry/cactus-cheminformatics-guide in wentorai/research-plugins) into .claude/skills/cactus-cheminformatics-guide in your project. Claude Code loads it when a task matches its description.
How do I install Cactus Cheminformatics Guide in Codex?
Run `npx skills add wentorai/research-plugins --skill cactus-cheminformatics-guide -a codex`. Or copy the skill folder (skills/domains/chemistry/cactus-cheminformatics-guide in wentorai/research-plugins) into .agents/skills/cactus-cheminformatics-guide in your project. Codex loads it when a task matches its description.
Can I use Cactus Cheminformatics 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 cactus-cheminformatics-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/cactus-cheminformatics-guide, .gemini/skills/cactus-cheminformatics-guide, .github/skills/cactus-cheminformatics-guide and .opencode/skills/cactus-cheminformatics-guide in your project.
What does Cactus Cheminformatics Guide need to run?
SKILL.md names no scripts, command-line tools or credentials: Cactus Cheminformatics Guide is instructions for the agent only. Our summary lists: Python 3.
Does Cactus Cheminformatics Guide access the network?
SKILL.md names 3 domains. As links in the text: github.com, rdkit.org and pnnl.gov. This is read from the text; nothing was executed.
Is Cactus Cheminformatics 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 Cactus Cheminformatics Guide use?
Cactus Cheminformatics 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 Cactus Cheminformatics Guide use?
About 641 tokens (SKILL.md is roughly 2.6k 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 Cactus Cheminformatics Guide?
Skills that share tags, products or a category with Cactus Cheminformatics Guide: 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 Cactus Cheminformatics 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.