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refactor: モジュール再編成とCLIディスパッチのargs.func方式への移行 - src/utils/ 配下を build/, analysis/, trajectory/ サブパッケージに整理 - cli.py の長大な if-elif チェーンを args.func(args) 方式に置き換え - 全サブコマンドに parser.set_defaults(func=run) を追加 - CLAUDE.md をリポジトリに追加 - .claude/skills/new-subcmd/ スキルを追加（サブコマンド追加テンプレート） - example/mbar/ スクリプトを argparse ベースに整理・関数化 - example/wham/ のコメントアウトコードを削除 - densmap の MDtraj バックエンドを実装 - pca.py の atom_indices/ref_atom_indices の引数順序バグを修正 - extract_ave_str.py の mdtraj 平均構造計算を修正 - calc_ion_conc.py に optimize メソッドの実装を追加 - gen_resp.py の obabel フォーマット指定を修正 (gout) - setup_reus_dist.sh を各レプリカディレクトリのファイルを参照するよう修正 Co-authored-by: Claude <noreply@anthropic.com> ```
test: テストスイート追加とドキュメント更新 - pytest を依存関係に追加し pixi run test / test-fast コマンドを追加 - tests/ ディレクトリを新設: conftest.py, fixtures, 各モジュールのユニットテスト - test_utils: mod_mdp, parse_top, rmfile, atom_selection_parser - test_build: calc_ion_conc, gen_temperatures - test_trajectory: fit - test_analysis: extract_str - test_cv: comdist, rmsd - test_cli: 全サブコマンドの登録確認 - CLAUDE.md にテスト構造・コマンド・サブコマンド登録パターンを追記 - new-subcmd スキルにテスト作成ステップ(ステップ4)を追加し全カテゴリを明示 Co-authored-by: Claude <noreply@anthropic.com> ```
cv/xyz, comvec, mindist, rmsf, pca, densmap, analysis/extract_ave_str, trajectory/print_perf, build/gen_posres, build/add_ndx, utils/partial_tempering, utils/shell_hook, utils/show_npy をカバー。 236テストが全てパス、ruff lint/format エラーなし。 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ings List all subcommands and utilities in each directory, and note unregistered modules that still need to be added to cli.py. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Implement new build subcommands: - addh: Add hydrogen atoms to structures (reduce or PyMOL) - build_vacuum: Build vacuum systems without water/ions/box - place_solvent: Place solvent molecules using 3D-RISM Enhance existing subcommands: - find_bond: Add --output-pdb option to rename CYS→CYM for disulfide bonds Register subcommands in CLI: - Import and register addh, build_vacuum, place_solvent Implement all-atom example scripts: - protein.sh: Vacuum system construction - protein_water.sh: Protein+water system with ion concentration - protein_water_membrane.sh: Protein+water+membrane system - protein_water_membrane_glycan.sh: Protein+water+membrane+glycan system - protein_water_ligand_membrane_glycan.sh: With ligand parameters Add SS-bond detection and handling in all workflows. Update TODO.md with detailed specifications and completion status. Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>
… extraction - Add support for automatic 1D-RISM xvv file generation via _run_rism1d() - Implement both rism3d.snglpnt and sander 3D-RISM interfaces - Implement Placevent-style greedy peak extraction algorithm - Add parameters: --xvv, --solvent-model, --closure, --grdspc, --tolerance, --buffer, --solvcut, --exclusion-radius, --max-sites, --use-sander - Improve DX file parsing with validation and error handling - Use temporary working directory for safer file management - Store g(r) values in PDB output for post-analysis - Organize code into logical sections with clear comments Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>
- Add 8 CV calculation example scripts (comdist, comvec, densmap, mindist, pca, rmsd, rmsf, xyz) - Add distance restraint generation example (gen_distres) - Add 3D-RISM water placement example (place_solvent) - Add REMD temperature generation example (gen_temperatures) Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>
Clear completed task list from version control and add TODO.md to .gitignore to simplify project maintenance. Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>
Add reference links to AMBER tutorials 34 and 40 (3D-RISM and 1D-RISM solvation methods) at the top of place_solvent.py for better documentation. Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>
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