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Agent skill

Structure Fetch

by Hello-QM in Hello-QM/catgo-LRG

Fetch crystal structures from Materials Project/OPTIMADE databases and molecules from PubChem.

AGPL-3.0Auto-check passedResearch & Science

Install Structure Fetch

skills CLI
$ npx skills add Hello-QM/catgo-LRG --skill structure-fetch -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install Hello-QM/catgo-LRG structure-fetch --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/structure-fetch .claude/skills/structure-fetch && rm -rf skills-src

Use ~/.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/

Facts

Skill name
structure-fetch
GitHub stars
205
Token cost
~1.2k tokens
SKILL.md length
443 words
Files
1
Skills in repo
75
Repo updated
First seen
Licence
AGPL-3.0

At a glance

Fetch crystal structures from Materials Project/OPTIMADE databases and molecules from PubChem.

  • Works in 5 steps: Search for the bulk crystal → Load the desired polymorph → Verify it loaded correctly → …
  • Tasks that involve Physical and earth sciences
  • SKILL.md covers When to Use, Data Sources, MCP Tool Examples and Workflow: Search -> Select ->…, plus 3 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Structure Fetch is an agent skill from Hello-QM/catgo-LRG. Fetch crystal structures from Materials Project/OPTIMADE databases and molecules from PubChem. Search, select, and load structures into the CatGO viewer.

Its SKILL.md is about 1.2k 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 Physical and earth sciences. The repository describes itself as: AI-driven workbench for computational materials science — interactive 3D structure viewer, natural-language CatBot assistant, visual DAG workflow engine, HPC job submission… The licence is AGPL-3.0.

When your agent uses it

  • Tasks that involve Physical and earth sciences

Example prompts

  • “/structure-fetch”

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. Search for the bulk crystal
  2. Load the desired polymorph
  3. Verify it loaded correctly
  4. Build a slab for surface chemistry
  5. Place an adsorbate

What it can do on your machine

Read from SKILL.md and the folder at commit fd6291b. 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 json).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    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

Structure Fetch loads about 1.2k tokens when it runs. Until then it costs about 42 tokens; SKILL.md has 443 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~42
When it runs · the whole SKILL.md, loaded when a task matches
~1.2k

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 Hello-QM/catgo-LRG at commit fd6291b, republished under its AGPL-3.0 licence (© Hello-QM). 443 words, ~1,227 tokens.

Download SKILL.mdSave it as .claude/skills/structure-fetch/SKILL.md (or your agent's skills folder).
name
structure-fetch
description
Fetch crystal structures from Materials Project/OPTIMADE databases and molecules from PubChem. Search, select, and load structures into the CatGO viewer.

Structure Fetching Skill

When to Use

Use this skill when the user wants to:

  • Load a known crystal structure (e.g., "get TiO2 rutile")
  • Search for materials by composition or elements
  • Fetch a molecule by name or formula from PubChem
  • Browse structures from OPTIMADE-compliant databases

Data Sources

SourceTool actionWhat it has
Materials Projectcatgo_fetch(action: "crystal")~150k inorganic crystals, DFT-relaxed
Alexandriacatgo_fetch(action: "search", provider: "alexandria")~5M structures, PBE/PBEsol
MC3Dcatgo_fetch(action: "search", provider: "mc3d")Curated crystal database
2DMatPediacatgo_fetch(action: "search", provider: "twodmatpedia")2D materials
PubChemcatgo_fetch(action: "molecule")~110M molecules, 3D conformers

MCP Tool Examples

Fetch a crystal by formula (Materials Project)
json
catgo_fetch(action: "crystal", formula: "TiO2", provider: "mp")

This loads the lowest-energy TiO2 structure from Materials Project directly into the viewer. The formula is automatically normalized for OPTIMADE (alphabetical element order: "O2Ti").

Fetch a specific structure by ID
json
catgo_fetch(action: "crystal", structure_id: "mp-2657", provider: "mp")
Search for structures (returns list, does not auto-load)
json
catgo_fetch(action: "search", formula: "Fe2O3", provider: "mp", limit: 10)

Returns a list of matching structures with IDs, space groups, and energies. The user then picks one to load:

json
catgo_fetch(action: "crystal", structure_id: "mp-19770", provider: "mp")
Search by elements (any compound containing these elements)
json
catgo_fetch(action: "search", elements: ["Ti", "O"], provider: "mp", limit: 5)

This finds all compounds containing Ti and O (TiO2, Ti2O3, SrTiO3, etc.).

Search across multiple providers
json
catgo_fetch(action: "search", formula: "BaTiO3", provider: "alexandria", limit: 5)
Fetch a molecule from PubChem

By name:

json
catgo_fetch(action: "molecule", query: "aspirin")

By formula:

json
catgo_fetch(action: "molecule", query: "C6H12O6")

By PubChem CID:

json
catgo_fetch(action: "molecule", cid: 2244)
Add a molecule to existing structure

To add a molecule into the current structure (e.g., adding an adsorbate above a surface), use catgo_structure instead:

json
catgo_structure(action: "add_molecule", query: "water", count: 1)

This fetches from PubChem and merges into the current viewer structure. For multiple copies (e.g., a water layer):

json
catgo_structure(action: "add_molecule", query: "water", count: 5, spacing: 2.8)

Workflow: Search -> Select -> Load -> Build

A typical session for setting up a catalysis calculation:

  1. Search for the bulk crystal:
json
catgo_fetch(action: "search", formula: "RuO2", provider: "mp", limit: 5)
  1. Load the desired polymorph:
json
catgo_fetch(action: "crystal", structure_id: "mp-825", provider: "mp")
  1. Verify it loaded correctly:
json
catgo_view(action: "get_state")
  1. Build a slab for surface chemistry:
json
catgo_structure(action: "slab", miller_index: [1, 1, 0],
                min_slab_size: 10.0, min_vacuum_size: 15.0)
  1. Place an adsorbate:
json
catgo_structure(action: "add_molecule", query: "OH")
Show full SKILL.md (167 more words)Show less

Formula Normalization

OPTIMADE requires formulas in alphabetical element order:

  • User says "TiO2" -> query sends "O2Ti"
  • User says "Fe2O3" -> query sends "Fe2O3" (already alphabetical)
  • User says "H2O" -> query sends "H2O" (already alphabetical)

Unicode subscripts are automatically converted: TiO₂ -> TiO2.

The catgo_fetch tool handles this normalization internally. You do not need to manually reorder formulas.

Provider-Specific Notes

Materials Project (mp)
  • Highest quality: structures are DFT-relaxed with standardized settings
  • Has computed properties: band gap, formation energy, stability
  • Preferred for common inorganic materials
Alexandria
  • Largest database (~5M structures)
  • Good for finding exotic compositions
  • PBE and PBEsol relaxed
PubChem
  • Molecules only (no periodic structures)
  • 3D conformers from MMFF94 or experimental data
  • Returns the first conformer; may not be the global minimum
  • Always optimize the geometry after fetching for DFT work

Common Mistakes

  • Searching with non-alphabetical formula on OPTIMADE (handled automatically)
  • Expecting PubChem molecules to be DFT-optimized (they are not)
  • Loading a crystal when a molecule is needed, or vice versa
  • Not checking catgo_view(action: "get_state") after loading to confirm the structure is correct

© Hello-QM, AGPL-3.0. 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 .claude/skills/structure-fetch of Hello-QM/catgo-LRG.

Open the folder on GitHubat commit fd6291b

Compare with similar skills

Structure Fetch 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.

Structure Fetch compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Structure Fetch this skillHello-QM/catgo-LRG205—~1.2kAutomated safety check: PassAGPL-3.0
Cantera Ignition DelayK-Dense-AI/scientific-agent-skills48k2 repos~2.2kAutomated safety check: PassMIT
AstropyzLanqing/codex-claude-academic-skills4.6k14 repos~2.9kAutomated safety check: PassBSD-3-Clause
PymatgenzLanqing/codex-claude-academic-skills4.6k12 repos~5kAutomated safety check: PassMIT
Weathertrpc-group/trpc-agent-go1.8k9 repos~591Automated safety check: PassApache-2.0
Pymol VisualizationChatMol/ChatMol372—~1.2kAutomated safety check: PassMIT

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Categories

Questions about Structure Fetch

What does Structure Fetch do?

Fetch crystal structures from Materials Project/OPTIMADE databases and molecules from PubChem. Structure Fetch is an agent skill from Hello-QM/catgo-LRG. Fetch crystal structures from Materials Project/OPTIMADE databases and molecules from PubChem.

When should I use Structure Fetch?

Structure Fetch fits situations like: tasks that involve Physical and earth sciences.

How do I install Structure Fetch in Claude Code?

Run `npx skills add Hello-QM/catgo-LRG --skill structure-fetch -a claude-code`. Or copy the skill folder (.claude/skills/structure-fetch in Hello-QM/catgo-LRG) into .claude/skills/structure-fetch in your project. Claude Code loads it when a task matches its description.

How do I install Structure Fetch in Codex?

Run `npx skills add Hello-QM/catgo-LRG --skill structure-fetch -a codex`. Or copy the skill folder (.claude/skills/structure-fetch in Hello-QM/catgo-LRG) into .agents/skills/structure-fetch in your project. Codex loads it when a task matches its description.

Can I use Structure Fetch 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 Hello-QM/catgo-LRG --skill structure-fetch -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/structure-fetch, .gemini/skills/structure-fetch, .github/skills/structure-fetch and .opencode/skills/structure-fetch in your project.

What does Structure Fetch need to run?

SKILL.md names no scripts, command-line tools or credentials: Structure Fetch is instructions for the agent only.

Does Structure Fetch access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Structure Fetch 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 Structure Fetch use?

Structure Fetch is published under the AGPL-3.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Structure Fetch use?

About 1.2k tokens (SKILL.md is roughly 4.9k 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 Structure Fetch?

Skills that share tags, products or a category with Structure Fetch: Cantera Ignition Delay (K-Dense-AI/scientific-agent-skills, 48k stars), Astropy (zLanqing/codex-claude-academic-skills, 4.6k stars), Pymatgen (zLanqing/codex-claude-academic-skills, 4.6k stars) and Weather (trpc-group/trpc-agent-go, 1.8k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Structure Fetch?

Hello-QM (a GitHub user) maintains it in Hello-QM/catgo-LRG, which has 205 GitHub stars. The repository holds 75 skills in this directory. The repository was last updated on September 22, 2026.

Source: Hello-QM/catgo-LRG on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.