Agent skill

Structure Builder

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

A skill your agent uses when the user asks to load, fetch, build, modify, or transform crystal/molecular structures.

AGPL-3.0Auto-check passed

Install Structure Builder

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

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

GitHub CLI
$ gh skill install Hello-QM/catgo-LRG structure-builder --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/catbot-plugin/skills/structure-builder .claude/skills/structure-builder && 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-builder
GitHub stars
205
Token cost
~700 tokens
SKILL.md length
256 words
Files
1
Skills in repo
75
Repo updated
First seen
Licence
AGPL-3.0

At a glance

A skill your agent uses when the user asks to load, fetch, build, modify, or transform crystal/molecular structures.

  • Works in 2 steps: Fetch bulk → 2. catgo_supercell (large… → catgo_build_defect → 4.…
  • The user asks to load
  • SKILL.md covers Loading Structures, Atom-Level Operations, Lattice and Cell Operations and Defect Engineering, plus 2 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Structure Builder is an agent skill from Hello-QM/catgo-LRG. Use when the user asks to load, fetch, build, modify, or transform crystal/molecular structures. Covers database import, supercell, defects, doping, intercalation, nanotubes, and atom-level editing.

Its SKILL.md is about 700 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

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

  • The user asks to load
  • Transform crystal/molecular structures

Example prompts

  • “/structure-builder”

Workflow steps

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

  1. Fetch bulk → 2. catgo_supercell (large enough to avoid defect-defect interaction) →
  2. catgo_build_defect → 4. catgo_structure_info

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.

    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 Builder loads about 700 tokens when it runs. Until then it costs about 54 tokens; SKILL.md has 256 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~54
When it runs · the whole SKILL.md, loaded when a task matches
~700

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). 256 words, ~700 tokens.

Download SKILL.mdSave it as .claude/skills/structure-builder/SKILL.md (or your agent's skills folder).
name
structure-builder
description
Use when the user asks to load, fetch, build, modify, or transform crystal/molecular structures. Covers database import, supercell, defects, doping, intercalation, nanotubes, and atom-level editing.

Structure Builder

Loading Structures

From Online Databases
  • catgo_fetch_crystal — Load crystal by formula or structure_id from OPTIMADE providers (mp=Materials Project, mc3d, alexandria, twodmatpedia, omdb)
  • catgo_search_crystals — Search and list multiple matches. Use this first when browsing, then catgo_fetch_crystal with a specific structure_id.
  • catgo_fetch_molecule — Fetch molecules from PubChem by name, formula, or SMILES.

Provider heuristics:

  • General inorganic crystals: mp (largest database)
  • 2D materials: twodmatpedia
  • Organic molecules: use catgo_fetch_molecule, not OPTIMADE
From Current Viewer

Call catgo_structure_info to inspect the loaded structure. All structure-modifying tools auto-fetch the current viewer structure — no need to pass structure dicts.

Atom-Level Operations

ToolUse When
catgo_add_atom / catgo_add_atomsAdding atoms at Cartesian positions (Angstroms)
catgo_delete_atomsRemoving atoms by 0-based index
catgo_replace_atomChanging element at a site
catgo_move_atom / catgo_move_atomsRepositioning atoms

Lattice and Cell Operations

ToolUse When
catgo_supercellExpanding unit cell by [na, nb, nc] or 3x3 matrix
catgo_set_latticeAdding/changing periodic cell (wraps molecules in a box)
catgo_mergeCombining two structures at a given position

Defect Engineering

ToolUse When
catgo_build_defectPoint defects: vacancy, substitution, interstitial
catgo_dopingSubstitutional doping (replace host with dopant)
catgo_substitutionCombinatorial multi-site substitution
catgo_intercalationInsert species (Li, Na) into layered structures
catgo_build_strainApply strain/deformation (Voigt notation or 3x3 matrix)

Nanostructures

ToolUse When
catgo_nanotube_buildCarbon or BN nanotubes from chiral indices (n, m)
catgo_nanotube_infoCompute nanotube geometry before building

Common Recipes

Doped supercell
  1. catgo_fetch_crystal → 2. catgo_supercell → 3. catgo_doping → 4. catgo_structure_info
Defective structure for DFT
  1. Fetch bulk → 2. catgo_supercell (large enough to avoid defect-defect interaction) →
  2. catgo_build_defect → 4. catgo_structure_info
Intercalated battery material
  1. catgo_fetch_crystal (e.g. MoS2) → 2. catgo_intercalation (species="Li") → 3. Verify

© 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 catbot-plugin/skills/structure-builder of Hello-QM/catgo-LRG.

Open the folder on GitHubat commit fd6291b

Compare with similar skills

Structure Builder 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 Builder compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Structure Builder this skillHello-QM/catgo-LRG205—~700Automated safety check: PassAGPL-3.0
LobeHub Data Fetching Layerslobehub/lobehub83k—~1.7kAutomated safety check: PassCustom licence
Team Builderaffaan-m/ECC275k1 repos~1.8kAutomated safety check: PassMIT
Team Builderaffaan-m/ECC275k1 repos~808Automated safety check: PassMIT
Dashboard Builderaffaan-m/ECC275k—~221Automated safety check: PassMIT
Dashboard Builderaffaan-m/ECC275k—~279Automated safety check: PassMIT

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Questions about Structure Builder

What does Structure Builder do?

A skill your agent uses when the user asks to load, fetch, build, modify, or transform crystal/molecular structures. Structure Builder is an agent skill from Hello-QM/catgo-LRG. Use when the user asks to load, fetch, build, modify, or transform crystal/molecular structures.

When should I use Structure Builder?

Structure Builder fits situations like: the user asks to load; transform crystal/molecular structures.

How do I install Structure Builder in Claude Code?

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

How do I install Structure Builder in Codex?

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

Can I use Structure Builder 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-builder -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-builder, .gemini/skills/structure-builder, .github/skills/structure-builder and .opencode/skills/structure-builder in your project.

What does Structure Builder need to run?

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

Does Structure Builder 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 Builder 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 Builder use?

Structure Builder 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 Builder use?

About 700 tokens (SKILL.md is roughly 2.8k 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 Structure Builder?

Skills that share tags, products or a category with Structure Builder: LobeHub Data Fetching Layers (lobehub/lobehub, 83k stars), Team Builder (affaan-m/ECC, 275k stars), Team Builder (affaan-m/ECC, 275k stars) and Dashboard Builder (affaan-m/ECC, 275k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Structure Builder?

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.