菜单
Publication-quality molecular graphics. Render molecular structures as SVG, PNG, PDF, and animated GIF from XYZ, mol/SDF, MOL2, PDB, SMILES, CIF, cube files, or quantum chemistry output.
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
PySCF (Python-based Simulations of Chemistry Framework) — modular pure-Python quantum chemistry library. Supports HF, DFT, MP2, CCSD, CCSD(T), CASSCF, TDDFT, geometry optimization, PES scanning, and spectroscopy. Based on pyscf.org documentation.
Gaussian 16 quantum chemistry software. Electronic structure calculations, geometry optimization, frequency analysis, TDDFT excited states, and more. Based on official Gaussian.com documentation.
RDKit molecular analysis and visualization. Use for molecular conformer generation, force field optimization, charge calculation, molecular descriptors, and non-covalent interaction analysis.
Run xTB (GFN-FF / GFN2-xTB) molecular dynamics for organic molecular clusters (e.g., anthracene/benzene), starting from random packed geometries; then generate animated GIFs (full trajectory, COM view, local clustered subset, bond-emphasized). Use when asked to simulate many-molecule stacking/aggregation dynamics, low-temperature “freezing/condensation” behavior, or to visualize xTB MD trajectories as animations.
Sample monomers and multi-molecule complexes from Gaussian ONIOM or XYZ files. Extract all monomers, then sample dimers/trimers/tetramers/pentamers using distance-sorted nearest neighbors.
Multiwfn 波函数分析工具。支持轨道分析、光谱绘制、拓扑分析等。
| name | xyzrender |
| version | 1.0.0 |
| description | Publication-quality molecular graphics. Render molecular structures as SVG, PNG, PDF, and animated GIF from XYZ, mol/SDF, MOL2, PDB, SMILES, CIF, cube files, or quantum chemistry output. |
| homepage | https://github.com/aligfellow/xyzrender |
| metadata | {"category":"visualization","tags":["chemistry","molecular-graphics","svg","gif","xyz","quantum-chemistry","分子可视化","molecule visualization","渲染分子","render molecule","xyz渲染","xyz render","分子出图","molecular graphics"]} |
Render molecular structures as publication-quality SVG, PNG, PDF, and animated GIF from XYZ files and quantum chemistry input/output.
# Using uv (recommended)
uv tool install xyzrender
# Using pip
pip install xyzrender
# Basic rendering (outputs SVG by default)
xyzrender molecule.xyz
# Specify output format
xyzrender molecule.xyz -o molecule.png
# Rotation GIF
xyzrender molecule.xyz --gif-rot -o movie.gif
from xyzrender import load, render, render_gif
mol = load("molecule.xyz")
render(mol, output="output.svg")
render_gif("molecule.xyz", gif_rot="y", output="movie.gif")
# Publication figure
xyzrender molecule.xyz --config paton -o paper.svg
# Rotating molecule
xyzrender molecule.xyz --gif-rot -o rotating.gif
# Transition state
xyzrender ts.out --ts --gif-ts -o ts_animation.gif
# With vdW surface
xyzrender molecule.xyz --vdw --gif-rot -o vdw.gif
A.S. Goodfellow* and B.N. Nguyen, J. Chem. Theory Comput., 2026, DOI: 10.1021/acs.jctc.5c02073