Contents Menu Expand Light mode Dark mode Auto light/dark, in light mode Auto light/dark, in dark mode
pdb2reaction
pdb2reaction

Guides

  • Getting Started
  • Installation
  • Quickstart: pdb2reaction all
  • Quickstart: single-structure scan workflow (--scan-lists/-s)
  • Quickstart: pdb2reaction tsopt
  • Frozen Atoms
  • Common Error Recipes
  • Troubleshooting
  • CLI Conventions

Commands

  • all
  • extract
  • fix-altloc
  • add-elem-info
  • opt
  • tsopt
  • path-opt
  • path-search
  • scan
  • scan2d
  • scan3d
  • freq
  • irc
  • dft
  • trj2fig
  • energy-diagram
  • bond-summary

Reference

  • CLI Command Reference
    • pdb2reaction add-elem-info
    • pdb2reaction all
    • pdb2reaction bond-summary
    • pdb2reaction dft
    • pdb2reaction energy-diagram
    • pdb2reaction extract
    • pdb2reaction fix-altloc
    • pdb2reaction freq
    • pdb2reaction irc
    • pdb2reaction opt
    • pdb2reaction path-opt
    • pdb2reaction path-search
    • pdb2reaction scan
    • pdb2reaction scan2d
    • pdb2reaction scan3d
    • pdb2reaction trj2fig
    • pdb2reaction tsopt
  • YAML Reference
  • JSON Output Reference
  • MLIP Calculator
  • HPC example: PBS + Open MPI + Ray
  • Glossary

Language

  • pdb2reaction ドキュメント
    • はじめに
    • インストール
    • クイックスタート: pdb2reaction all
    • クイックスタート: 単一構造スキャンワークフロー(--scan-lists)
    • クイックスタート: pdb2reaction tsopt
    • 凍結原子(Frozen Atoms)
    • 典型エラー別レシピ
    • トラブルシューティング
    • CLI 規約
    • all
    • extract
    • fix-altloc
    • add-elem-info
    • opt
    • tsopt
    • path-opt
    • path-search
    • scan
    • scan2d
    • scan3d
    • freq
    • irc
    • dft
    • trj2fig
    • energy-diagram
    • bond-summary
    • YAML 設定リファレンス
    • JSON 出力リファレンス
    • MLIP 計算機
    • HPC 実行例: PBS + Open MPI + Ray
    • 用語集
Back to top
EN | JA
Copyright © 2025, Takuto Ohmura
Made with Sphinx and @pradyunsg's Furo