Atom Ops

What it does

When your agent uses it

• The user asks to add an atom
• Remove this atom
• Replace H with Li
• Any single-atom edit — including add a hydrogen on top of atom 12 / delete atoms 5–9 / swap the oxygen at site 3 for fluorine

Example prompts

• “add an atom”
• “delete atoms”
• “remove this atom”
• “/atom-ops”

Workflow steps

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

1. 1If the user just told you the coordinate, use it directly with position.
2. 2Otherwise call mcpcatgocatgo_structure {"action":"get_info"} once, find the site, add [0, 0, height] to its xyz, then issue add_atom. Do…

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

Atom Ops loads about 1.2k tokens when it runs. Until then it costs about 150 tokens; SKILL.md has 600 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~150

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

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). 600 words, ~1,202 tokens.

name

atom-ops

description

One-shot recipes for adding, deleting, moving, and replacing individual atoms in the active CatGo viewer structure. Use whenever the user asks to "add an atom", "delete atoms", "remove this atom", "move atom N", "replace H with Li", or any single-atom edit — including "add a hydrogen on top of atom 12" / "delete atoms 5–9" / "swap the oxygen at site 3 for fluorine". Skips the discovery loop (no need to list structure tools or check adsorption sites first); goes straight to the matching `catgo_structure` action. Triggers in Chinese on 加原子, 删原子, 减原子, 移动原子, 替换原子, 增加氢, 删除氧, 把 ... 换成 ....

{"action":"add_atom","element":"H","position":[1.5,2.0,6.3]}

{"action":"delete_atoms","indices":[5,6,7]}

{"action":"delete_atoms","element":"H"}

{"action":"replace_atom","index":3,"new_element":"F"}

{"action":"move_atom","index":12,"position":[2.0,3.0,5.5]}

© 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 server/catgo/workflow/skills/structure/atom_ops of Hello-QM/catgo-LRG.

Open the folder on GitHubat commit fd6291b