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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.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
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.
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.
Multiwfn 波函数分析工具。支持轨道分析、光谱绘制、拓扑分析等。
| name | molecular-sampler |
| version | 1.0.0 |
| description | 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. |
| homepage | https://github.com/STOKES-DOT/molecular-sampler |
| metadata | {"category":"chemistry","emoji":"🧪","tags":["chemistry","sampling","molecules","gaussian","oniom"]} |
从 Gaussian ONIOM 或 XYZ 文件中采样分子结构。
python3 molecular_sampler.py <input_file> [options]
input_file: Gaussian GJF 或 XYZ 文件路径--output-dir: 输出目录 (默认: ./molecular_samples)--samples: 每种多聚体的采样数量 (默认: 20)--layer: 选择层 ('H', 'L', 或 'all') (默认: 'L')# 采样 L 层分子
python3 molecular_sampler.py guest_monomer.gjf --layer L --samples 20
# 采样所有层分子
python3 molecular_sampler.py structure.xyz --layer all --output-dir ./my_samples
molecular_samples/
├── monomers/ # 所有单体分子
│ ├── monomer_01.xyz
│ ├── monomer_02.xyz
│ └── ...
├── dimers/ # 二聚体 (20个样本)
├── trimers/ # 三聚体 (20个样本)
├── tetramers/ # 四聚体 (20个样本)
├── pentamers/ # 五聚体 (20个样本)
└── sampling_summary.txt
标准 XYZ 格式：
<atom_count>
<comment>
<element> <x> <y> <z>
...
re, collections, os, argparse