├── .gitattributes ├── LICENSE.md ├── README.md ├── environment.yml ├── install_miniconda_MSMbuilder.sh └── notebook ├── .ipynb_checkpoints ├── APLoD-checkpoint.ipynb ├── Analysis-checkpoint.ipynb ├── Clustering-checkpoint.ipynb ├── Featurization-checkpoint.ipynb ├── Gmrq-checkpoint.ipynb ├── SpectraloASIS-Parallel-checkpoint.ipynb ├── TICA-checkpoint.ipynb ├── micorstate_MSM&PCCA-checkpoint.ipynb └── qMSM-checkpoint.ipynb ├── Analysis.ipynb ├── Clustering.ipynb ├── Featurization.ipynb ├── Featurization ├── AtomIndices.dat └── ala2.pdb ├── Gmrq.ipynb ├── SpectraloASIS-Parallel.ipynb ├── TICA.ipynb ├── micorstate_MSM&PCCA.ipynb ├── qMSM.ipynb └── qMSM ├── LICENSE.md ├── QuasiMSM_ModuleBuilder.py ├── README.md └── __pycache__ ├── QuasiMSM.cpython-36.pyc ├── QuasiMSM_ModuleBuild_version1.cpython-36.pyc ├── QuasiMSM_ModuleBuilder.cpython-36.pyc ├── QuasiMSM_ModuleBuilder_Graph.cpython-36.pyc ├── QuasiMSM_ModuleBuilder_version2.cpython-36.pyc └── qMSM_module.cpython-36.pyc /.gitattributes: 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