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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 또는 Claude로 설치 이 Prompt를 복사해 Codex, Claude 또는 다른 어시스턴트에 붙여 넣으면 Skill 페이지를 검토하고 설치를 진행할 수 있습니다.
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| 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