├── .devcontainer ├── Dockerfile ├── Dockerfile_20250125 └── devcontainer.json ├── .github └── workflows │ └── unittest.yml ├── .gitignore ├── .vscode ├── extensions.json └── settings.json ├── LICENSE ├── Makefile ├── README.md ├── README_JP.md ├── docs ├── en │ ├── impl │ │ ├── msmd.md │ │ └── pmap.md │ └── user_guide │ │ ├── advanced.md │ │ ├── basic.md │ │ └── probe_preparation.md └── ja │ ├── impl │ ├── msmd.md │ └── pmap.md │ └── user_guide │ ├── advanced.md │ ├── basic.md │ └── probe_preparation.md ├── environment.yaml ├── example ├── 1F47B.pdb ├── A11.mol2 ├── A11.pdb ├── A11_elec.gjf ├── A11_opt.gjf ├── README_JP.md ├── debug_protocol.yaml ├── example_protocol.yaml └── yanagisawa2022_protocol.yaml ├── exprorer_msmd ├── invmap_matching実装メモ.md ├── probe_profile ├── protein_hotspot ├── scheduler_wrapper.py ├── script ├── __init__.py ├── add_posredefine2top.py ├── addvirtatom2gro.py ├── addvirtatom2top.py ├── alignresenv.py ├── bash_functions.sh ├── generate_msmd_system.py ├── genpmap.py ├── maxpmap.py ├── mdrun.py ├── profile.py ├── resenv.py ├── setting.py ├── template │ ├── equilibration.mdp │ ├── heating.mdp │ ├── mdrun.sh │ ├── minimization.mdp │ ├── position_restraints │ └── production.mdp ├── test_add_posredefine2top.py ├── test_addvirtatom2gro.py ├── test_addvirtatom2top.py ├── test_alignresenv.py ├── test_data │ ├── A11.frcmod │ ├── A11.mol2 │ ├── A11.pdb │ ├── maxpmap_for_resenv.dx │ ├── noatom.pdb │ ├── pmap1.dx │ ├── pmap2.dx │ ├── resenv_expected.pdb │ ├── setting.yaml │ ├── singleatom.pdb │ ├── small_grid.dx │ ├── trajectory_for_resenv.pdb │ ├── tripeptide.pdb │ ├── tripeptide.rst7 │ ├── tripeptide_A11.parm7 │ ├── tripeptide_A11.rst7 │ ├── twoatoms.pdb │ └── twomodels.pdb ├── test_generate_msmd_system.py ├── test_genpmap.py ├── test_maxpmap.py ├── test_mdrun.py ├── test_mdrun_integration.py ├── test_profile.py ├── test_resenv.py └── utilities │ ├── Bio │ ├── PDB.py │ ├── __init__.py │ ├── sklearn_interface.py │ ├── test_PDB.py │ └── test_data │ │ └── PDB │ │ ├── 7m67.pdb │ │ └── 7m67.pdb.gz │ ├── GPUtil.py │ ├── GridUtil.py │ ├── __init__.py │ ├── const.py │ ├── executable │ ├── __init__.py │ ├── cpptraj.py │ ├── execute.py │ ├── packmol.py │ ├── parmchk.py │ ├── template │ │ ├── cpptraj_pmap.in │ │ ├── leap.in │ │ └── packmol.in │ ├── test_cpptraj.py │ ├── test_data │ │ ├── A11.frcmod │ │ ├── A11.mol2 │ │ ├── A11.pdb │ │ ├── cpptraj │ │ │ ├── inputprotein.pdb │ │ │ ├── topology.top │ │ │ └── trajectory.xtc │ │ └── tripeptide.pdb │ ├── test_execute.py │ ├── test_packmol.py │ ├── test_parmchk.py │ ├── test_tleap.py │ └── tleap.py │ ├── gromacs.py │ ├── logger.py │ ├── pmd.py │ ├── scipy │ ├── __init__.py │ └── spatial_func.py │ ├── test_GPUtil.py │ ├── test_data │ ├── empty.yaml │ ├── empty_sequence.yaml │ ├── normal_setting.json │ ├── normal_setting.yaml │ ├── pmd │ │ ├── system.gro │ │ ├── system.parm7 │ │ ├── system.rst7 │ │ └── system.top │ ├── small_grid.dx │ └── tripeptide.pdb │ ├── test_grid_util.py │ ├── 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