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…
Prepare and convert atomistic structures before calculations.
Install Structure Prep
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill structure-prep -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist structure-prep --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/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .claude/skills && cp -r skills-src/tools/structure-prep .claude/skills/structure-prep && 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 "structure-prep" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/structure-prep into .claude/skills/structure-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-prep", 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/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/structure-prepType 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 JCLiuGroup/AI-Computational-Chemist --skill structure-prep -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist structure-prep --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .agents/skills && cp -r skills-src/tools/structure-prep .agents/skills/structure-prep && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "structure-prep" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/structure-prep into .agents/skills/structure-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-prep", 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 JCLiuGroup/AI-Computational-Chemist --skill structure-prep -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist structure-prep --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/tools/structure-prep .cursor/skills/structure-prep && 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 "structure-prep" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/structure-prep into .cursor/skills/structure-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-prep", 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/JCLiuGroup/AI-Computational-Chemist.git --path tools/structure-prep--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 JCLiuGroup/AI-Computational-Chemist --skill structure-prep -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist structure-prep --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/tools/structure-prep .gemini/skills/structure-prep && 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 "structure-prep" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/structure-prep into .gemini/skills/structure-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-prep", 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 JCLiuGroup/AI-Computational-Chemist structure-prepInstalls 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 JCLiuGroup/AI-Computational-Chemist --skill structure-prep -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .github/skills && cp -r skills-src/tools/structure-prep .github/skills/structure-prep && 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 "structure-prep" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/structure-prep into .github/skills/structure-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-prep", 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 JCLiuGroup/AI-Computational-Chemist --skill structure-prep -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist structure-prep --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/tools/structure-prep .opencode/skills/structure-prep && 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 "structure-prep" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/structure-prep into .opencode/skills/structure-prep/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-prep", 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
structure-prep- GitHub stars
- 145
- Used in
- 1 other repo
- Token cost
- ~856 tokens
- SKILL.md length
- 324 words
- Files
- 13 (incl. scripts, references)
- Skills in repo
- 21
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Prepare and convert atomistic structures before calculations.
- Works in 4 steps: Search only the project root/current… → Enumerate scientifically distinct… → Validate after each operation. For… → …
- CIF/POSCAR/CONTCAR/XYZ/PDB/MOL/SDF/SMILES handling
- SKILL.md covers Required inputs, Route map, Workflow and Hard guardrails, plus 1 more section
- Runs Python scripts from its folder
What it does
Structure Prep is an agent skill from JCLiuGroup/AI-Computational-Chemist. Prepare and convert atomistic structures before calculations. Use for CIF/POSCAR/CONTCAR/XYZ/PDB/MOL/SDF/SMILES handling, supercells, slabs, surface terminations, defects, substitutions, adsorbate placement, symmetry analysis, conformer generation, and charge/multiplicity determination for molecules.
Its SKILL.md is about 860 tokens, which your agent loads only when the skill is triggered. The skill folder holds 15 other files, including scripts and reference files (for example `examples/README.md`, `references/errors.md` and `references/resources.md`).
It sits in Research & Science, covering Drug discovery and cheminformatics.
When your agent uses it
- CIF/POSCAR/CONTCAR/XYZ/PDB/MOL/SDF/SMILES handling
- Surface terminations
- Adsorbate placement
- Symmetry analysis
Example prompts
- “/structure-prep”
Requirements
- Python 3
Workflow steps
4 steps, taken from the first numbered list in SKILL.md.
- Search only the project root/current working directory and user-explicit paths for
- Enumerate scientifically distinct candidates where termination, site, defect, or
- Validate after each operation. For surface/defect/adsorbate models, run
- Release only accepted candidates to the engine skill. Report paths, formula, atom
What it can do on your machine
Read from SKILL.md and the folder at commit e27b555. 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
Ships 7 files in scripts/ (Python), which the agent can run.
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 Prep loads about 856 tokens when it runs, and up to ~7.7k if it reads all its reference files. Until then it costs about 79 tokens; SKILL.md has 324 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); the scripts in this folder are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 324 words (~856 tokens).
“Use pymatgen for periodic crystals/slabs/defects and RDKit for finite molecules and conformers.”
- name
- structure-prep
Files
SKILL.md and 12 other files (scripts, references) in tools/structure-prep of JCLiuGroup/AI-Computational-Chemist.
- SKILL.md
- examples/README.md
- references/errors.md
- references/resources.md
- references/running.md
- references/validation.md
- scripts/audit_structure.py
- scripts/convert_structure.py
- scripts/covalent_radii.py
- scripts/dope_structure.py
- scripts/make_slab.py
- scripts/place_adsorbate.py
- scripts/smiles_to_xyz.py
Open the folder on GitHubat commit e27b555
Used in 1 other repository
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in JCLiuGroup/AI-Computational-Chemist, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Structure Prep 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 |
|---|---|---|---|---|---|---|
| Structure Prep this skillJCLiuGroup/AI-Computational-Chemist | 145 | 1 repos | ~856 | Automated safety check: Pass | Custom licence | |
| MolecodeAtomFlow-AI/MoleCode | 305 | — | ~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 | |
| Edu Chem Reactionwy51ai/edulab | 1.4k | — | ~1.2k | Automated safety check: Pass | Apache-2.0 |
Similar skills
Drug Discovery
Tommy-yw/RunbookHermes
Pharmaceutical research assistant for drug discovery workflows.
DiffDock Molecular Docking
K-Dense-AI/scientific-agent-skills
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.
Edu Chem Reaction
wy51ai/edulab
把一个化学反应做成自包含的微观 3D 交互演示网页：左/上为 Three.js 可交互分子动画 （拖滑块看断键·成键·原子重组，分步高亮），右为 KaTeX 反应方程 + 分步讲解 + 原子守恒计数 + 可选能量-反应进程曲线。支持三入口——给定文字反应/方程、随机出题、上传图片识别后演示。
Biopipelines
locbp-uzh/biopipelines
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…
More from JCLiuGroup/AI-Computational-Chemist
All 21 skills in this repoResearch Orchestrator
JCLiuGroup/AI-Computational-Chemist
Define and maintain machine-readable research project state for multi-stage computational chemistry work.
Comp Chem Workflow
JCLiuGroup/AI-Computational-Chemist
Entry point and controller for computational chemistry and materials workflows.
Cp2k
JCLiuGroup/AI-Computational-Chemist
Prepare, validate, run, and troubleshoot CP2K calculations for periodic and large molecular systems.
Deepmd
JCLiuGroup/AI-Computational-Chemist
DeePMD-kit and Deep Potential Molecular Dynamics workflows. An agent skill from JCLiuGroup/AI-Computational-Chemist.
Gaussian
JCLiuGroup/AI-Computational-Chemist
Prepare, validate, and troubleshoot Gaussian molecular quantum chemistry jobs.
Gromacs
JCLiuGroup/AI-Computational-Chemist
Prepare, validate, run, resume, troubleshoot, and analyze GROMACS molecular dynamics.
Related
Categories
Questions about Structure Prep
What does Structure Prep do?
Prepare and convert atomistic structures before calculations. Structure Prep is an agent skill from JCLiuGroup/AI-Computational-Chemist. Prepare and convert atomistic structures before calculations.
When should I use Structure Prep?
Structure Prep fits situations like: CIF/POSCAR/CONTCAR/XYZ/PDB/MOL/SDF/SMILES handling; surface terminations; adsorbate placement; symmetry analysis.
How do I install Structure Prep in Claude Code?
Run `npx skills add JCLiuGroup/AI-Computational-Chemist --skill structure-prep -a claude-code`. Or copy the skill folder (tools/structure-prep in JCLiuGroup/AI-Computational-Chemist) into .claude/skills/structure-prep in your project. Claude Code loads it when a task matches its description.
How do I install Structure Prep in Codex?
Run `npx skills add JCLiuGroup/AI-Computational-Chemist --skill structure-prep -a codex`. Or copy the skill folder (tools/structure-prep in JCLiuGroup/AI-Computational-Chemist) into .agents/skills/structure-prep in your project. Codex loads it when a task matches its description.
Can I use Structure Prep 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 JCLiuGroup/AI-Computational-Chemist --skill structure-prep -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-prep, .gemini/skills/structure-prep, .github/skills/structure-prep and .opencode/skills/structure-prep in your project.
What does Structure Prep need to run?
Going by SKILL.md and its folder, Structure Prep needs Python for the scripts in its folder. Our summary lists: Python 3.
Does Structure Prep 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 Prep 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Structure Prep use?
Structure Prep has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Structure Prep use?
About 856 tokens (SKILL.md is roughly 3.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 6.9k tokens, read only when the agent opens those files.
What are the alternatives to Structure Prep?
Skills that share tags, products or a category with Structure Prep: Molecode (AtomFlow-AI/MoleCode, 305 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 Structure Prep?
JCLiuGroup (a GitHub organization) maintains it in JCLiuGroup/AI-Computational-Chemist, which has 145 GitHub stars. The repository holds 21 skills in this directory. The repository was last updated on September 27, 2026.
Source: JCLiuGroup/AI-Computational-Chemist on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.