├── .gitignore ├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── README.rst ├── binder ├── environment.yml └── postBuild ├── pydhamed ├── __init__.py ├── ala5 │ ├── ala5_2ff_1.ipynb │ ├── bl1 │ │ ├── list_bias_ar │ │ └── list_transition_counts │ ├── bl2 │ │ ├── list_bias_ar │ │ └── list_transition_counts │ ├── bl3 │ │ ├── list_bias_ar │ │ └── list_transition_counts │ ├── bl4 │ │ ├── list_bias_ar │ │ └── list_transition_counts │ ├── bl5 │ │ ├── list_bias_ar │ │ └── list_transition_counts │ ├── blall │ │ ├── list_bias_ar │ │ └── list_transition_counts │ └── ref_unbiased_md │ │ ├── notes.txt │ │ ├── r1_5ala_1us_tba.npy │ │ ├── r2_5ala_1us_tba.npy │ │ └── r3_5ala_1us_tba.npy ├── analyze_eq_md.py ├── cg-rna │ ├── 1 │ ├── cg_RNA_duplex_formation.ipynb │ ├── count_matrix_1.txt │ ├── us_step-e4.npy │ └── wfile.txt ├── determine_transition_counts.py ├── glic-ion-channel │ ├── bias.npy │ ├── glic_ion_channel_permeation.ipynb │ └── transition_count_list ├── optimize_dhamed.py ├── prepare_dhamed.py ├── tests │ ├── data │ │ ├── count_matrix_1.txt │ │ ├── us_dt-e4_2_p1.out │ │ └── wfile.txt │ ├── test_dhamed.py │ └── test_rna │ │ ├── .ipynb_checkpoints │ │ ├── RNA_test-checkpoint.ipynb │ │ └── cg_RNA_stab_1-checkpoint.ipynb │ │ ├── RNA_test.ipynb │ │ ├── cg_RNA_stab_1.ipynb │ │ ├── count_matrix_1.txt │ │ ├── notes.txt │ │ ├── rna_pmf.png │ │ ├── us_dt-e4_2_p1.out │ │ └── wfile.txt └── util │ ├── __init__.py │ ├── testing.py │ └── tests │ └── test_testing.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/PyDHAMed/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/PyDHAMed/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE: 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