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openpathsampling-openpathsampling-2a1bfab
- .coveragerc
  
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- .gitignore
  
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- .project
  
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- .pydevproject
  
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- .travis.yml
  
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- LICENSE
  
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- MANIFEST.in
  
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- README.md
  
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- devtools
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- docs
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  - README.md
    
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  - api_sections.rst
    
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  - collectivevariable.rst
    
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  - conf.py
    
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  - dev_docs
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    - README.md
      
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    - TISAnalysisStructure.graffle
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      - image1.pdf
        
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    - Venn.pxm
      
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  - developers
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    - engines_overview.rst
      
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    - index.rst
      
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    - pathmovers_and_movestrategies.rst
      
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    - pathsimulators.rst
      
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    - storage_need_to_know.rst
      
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  - engines
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    - index.rst
      
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    - openmm.rst
      
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    - toy.rst
      
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  - ensemble.rst
    
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  - examples
    - AD_fixed_len_tps.rst
      
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    - AD_mstis.rst
      
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    - AD_tps.rst
      
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    - AD_tps_advanced_analysis.rst
      
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    - custom_movescheme.rst
      
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    - customizing_visualization.rst
      
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    - index.rst
      
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    - miscellaneous
      - committors.rst
        
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      - committors_alanine_dipeptide.rst
        
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      - fun_with_pathmovers.rst
        
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      - index.rst
        
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      - langevin.rst
        
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      - tutorial_handle_nan.rst
        
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      - tutorial_path_histogram.rst
        
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    - mistis.rst
      
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    - move_schemes_strategies.rst
      
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    - mstis.rst
      
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    - restarting.rst
      
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    - srtis.rst
      
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    - storage.rst
      
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  - faq.rst
    
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  - guides
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  - index.rst
    
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  - install.rst
    
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  - logo
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    - logo.pdf
      
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    - logo.svg
      
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    - logo_highres.png
      
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  - make.bat
    
    6.7 kB
  - movestrategy.rst
    
    1.2 kB
  - netcdfplus
    - base.rst
      
      244 Bytes
    - cache.rst
      
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    - dictify.rst
      
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    - index.rst
      
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    - netcdfplus.rst
      
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    - proxy.rst
      
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    - stores.rst
      
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    - util.rst
      
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  - network.rst
    
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  - pathmover.rst
    
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  - pathsimulator.rst
    
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  - premake.py
    
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  - readme.rst
    
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  - requirements.txt
    
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  - shooting.rst
    
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  - sphinxext
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  - storage.rst
    
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  - tis_analysis.rst
    
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  - topics
    - absolute_beginners.rst
      
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    - common_setups.rst
      
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    - data_objects.rst
      
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    - ensembles_apply_to_trajectories_not_frames.rst
      
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    - ensembles_frames.png
      
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    - index.rst
      
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    - mcstep_structure.png
      
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    - ops_output.rst
      
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    - simulation_setup.rst
      
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    - three_state_tis.png
      
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    - tis_analysis.rst
      
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    - tis_analysis_structure.png
      
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    - transitions_and_networks.rst
      
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    - two_state_tis.png
      
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    - which_network.rst
      
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  - treemixin.rst
    
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  - volume.rst
    
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  - wip
    - README.md
      
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    - sequential_ensembles.ipynb
      
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    - troubleshooting_ops.ipynb
      
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- examples
  - README.md
    
    1.1 kB
  - alanine_dipeptide_mstis
    - AD_mstis_1_setup.ipynb
      
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    - AD_mstis_2_run.ipynb
      
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    - AD_mstis_3_restart.ipynb
      
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    - AD_mstis_4_analysis.ipynb
      
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    - README.md
      
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    - alatools.py
      
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  - alanine_dipeptide_tps
    - AD_tps_1_trajectory.ipynb
      
      310.9 kB
    - AD_tps_1b_trajectory.ipynb
      
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    - AD_tps_2a_run_flex.ipynb
      
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    - AD_tps_2b_run_fixed.ipynb
      
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    - AD_tps_3a_analysis_flex.ipynb
      
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    - AD_tps_3b_analysis_fixed.ipynb
      
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    - AD_tps_4_advanced.ipynb
      
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    - README.md
      
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  - extra_ipynbs.sh
    
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  - ipynbtests.sh
    
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  - misc
    - README.md
      
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    - alanine_dipeptide_committor
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      - 2_committor_simulation.ipynb
        
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      - 3_committor_analysis.ipynb
        
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      - 4_analysis_help.ipynb
        
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      - README.md
        
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    - committors.ipynb
      
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    - custom_strategy_repex_shoot_repex.ipynb
      
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    - fun_with_pathmovers.ipynb
      
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    - move_strategies_and_schemes.ipynb
      
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    - tutorial_handle_nan.ipynb
      
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    - tutorial_movetree_visualization.ipynb
      
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    - tutorial_path_histogram.ipynb
      
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    - tutorial_pathtree_visualization.ipynb
      
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    - tutorial_storage.ipynb
      
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  - move_to_docs
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    - sliced_sequential_ensembles.ipynb
      
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  - resources
    - AD_initial_frame.pdb
      
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    - README.md
      
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    - debug_logging.conf
      
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    - logging.conf
      
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    - toy_plot_helpers.py
      
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  - simple_tps
    - README.md
      
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    - simple_fixed_length_tps.ipynb
      
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    - simple_tps.ipynb
      
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  - tests
    - README.md
      
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    - langevin_integrator_check.ipynb
      
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    - storage_mem_test.ipynb
      
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    - test_cv.ipynb
      
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    - test_netcdfplus.ipynb
      
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    - test_openmm_integration.ipynb
      
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    - test_pyemma.ipynb
      
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    - test_snapshot.ipynb
      
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    - test_snapshot_modifier.ipynb
      
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  - toy_model_mistis
    - README.md
      
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    - toy_mistis_1_setup_run.ipynb
      
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    - toy_mistis_2_flux.ipynb
      
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    - toy_mistis_3_analysis.ipynb
      
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  - toy_model_mstis
    - README.md
      
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    - toy_mstis_1_setup.ipynb
      
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    - toy_mstis_2_run.ipynb
      
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    - toy_mstis_3_analysis.ipynb
      
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    - toy_mstis_4_repex_analysis.ipynb
      
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    - toy_mstis_5_srtis.ipynb
      
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    - toy_mstis_A1_split.ipynb
      
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    - toy_mstis_A2_split_analysis.ipynb
      
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    - toy_mstis_A3_new_analysis.ipynb
      
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- openpathsampling
  - .gitignore
    
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  - README.md
    
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  - __init__.py
    
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  - analysis
    - __init__.py
      
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    - channel_analysis.py
      
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    - ensemble_representation.py
      
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    - path_histogram.py
      
      12.1 kB
    - replica_network.py
      
      19.7 kB
    - shooting_point_analysis.py
      
      11.1 kB
    - tis
      - __init__.py
        
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      - core.py
        
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      - crossing_probability.py
        
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      - flux.py
        
        13.9 kB
      - misc.py
        
        3.2 kB
      - standard_analysis.py
        
        14.0 kB
    - tools.py
      
      2.9 kB
    - trajectory_transition_analysis.py
      
      15.5 kB
  - bias_function.py
    
    12.9 kB
  - collectivevariable.py
    
    24.2 kB
  - engines
    - __init__.py
      
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    - delayedinterrupt.py
      
      1.2 kB
    - dynamics_engine.py
      
      26.2 kB
    - features
      - __init__.py
        
        200 Bytes
      - base.py
        
        22.0 kB
      - box_vectors.py
        
        337 Bytes
      - coordinates.py
        
        874 Bytes
      - engine.py
        
        490 Bytes
      - kinetics.py
        
        1.6 kB
      - numpydoctools.py
        
        6.3 kB
      - shared.py
        
        9.5 kB
      - statics.py
        
        2.6 kB
      - topology.py
        
        371 Bytes
      - velocities.py
        
        544 Bytes
    - openmm
      - __init__.py
        
        371 Bytes
      - engine.py
        
        16.1 kB
      - features
        
        __init__.py
        
        196 Bytes
        
        instantaneous_temperature.py
        
        1.8 kB
        
        masses.py
        
        1.4 kB
      - snapshot.py
        
        3.0 kB
      - tools.py
        
        9.8 kB
      - topology.py
        
        3.3 kB
    - snapshot.py
      
      6.2 kB
    - topology.py
      
      525 Bytes
    - toy
      - __init__.py
        
        458 Bytes
      - engine.py
        
        3.6 kB
      - features
        
        __init__.py
        
        145 Bytes
        
        instantaneous_temperature.py
        
        802 Bytes
      - integrators.py
        
        3.5 kB
      - pes.py
        
        8.8 kB
      - snapshot.py
        
        973 Bytes
      - topology.py
        
        609 Bytes
    - trajectory.py
      
      19.1 kB
  - ensemble.py
    
    115.0 kB
  - high_level
    - __init__.py
      
      115 Bytes
    - interface_set.py
      
      14.0 kB
    - move_scheme.py
      
      35.3 kB
    - move_strategy.py
      
      42.9 kB
    - ms_outer_interface.py
      
      6.6 kB
    - network.py
      
      34.6 kB
    - transition.py
      
      20.4 kB
  - logging.conf
    
    663 Bytes
  - movechange.py
    
    17.6 kB
  - netcdfplus
    - __init__.py
      
      819 Bytes
    - attribute.py
      
      15.3 kB
    - base.py
      
      12.0 kB
    - cache.py
      
      13.8 kB
    - chaindict.py
      
      13.2 kB
    - dictify.py
      
      26.4 kB
    - netcdfplus.py
      
      42.7 kB
    - proxy.py
      
      5.0 kB
    - stores
      - __init__.py
        
        290 Bytes
      - attribute.py
        
        5.9 kB
      - dict.py
        
        6.1 kB
      - indexed.py
        
        3.3 kB
      - named.py
        
        18.1 kB
      - object.py
        
        39.5 kB
      - value.py
        
        4.1 kB
      - variable.py
        
        3.6 kB
    - util.py
      
      437 Bytes
    - version.py
      
      110 Bytes
  - numerics
    - __init__.py
      
      342 Bytes
    - histogram.py
      
      26.8 kB
    - lookup_function.py
      
      8.2 kB
    - resampling_statistics.py
      
      6.1 kB
    - wham.py
      
      20.3 kB
  - ops_logging.py
    
    732 Bytes
  - pathmover.py
    
    83.6 kB
  - pathmover_inout.py
    
    16.6 kB
  - pathsimulator.py
    
    41.9 kB
  - range_logic.py
    
    10.4 kB
  - resources
    - debug_logging.conf
      
      756 Bytes
    - logging.conf
      
      759 Bytes
    - vis.css
      
      2.7 kB
  - sample.py
    
    33.2 kB
  - shooting.py
    
    5.5 kB
  - snapshot_modifier.py
    
    17.3 kB
  - step_visualizer_2D.py
    
    3.8 kB
  - storage
    - __init__.py
      
      329 Bytes
    - distributed.py
      
      3.7 kB
    - storage.py
      
      17.8 kB
    - stores
      - __init__.py
        
        397 Bytes
      - collectivevariable.py
        
        988 Bytes
      - mcstep.py
        
        715 Bytes
      - movechange.py
        
        5.2 kB
      - pathsimulator.py
        
        492 Bytes
      - sample.py
        
        2.1 kB
      - snapshot_base.py
        
        5.7 kB
      - snapshot_feature.py
        
        1.2 kB
      - snapshot_value.py
        
        2.8 kB
      - snapshot_wrapper.py
        
        25.1 kB
      - trajectory.py
        
        3.5 kB
    - util.py
      
      2.7 kB
  - tests
    - .gitignore
      
      16 Bytes
    - __init__.py
      
      862 Bytes
    - test_attribute.py
      
      6.4 kB
    - test_bias_function.py
      
      15.4 kB
    - test_channel_analysis.py
      
      16.1 kB
    - test_collectivevariable.py
      
      12.4 kB
    - test_data
      - ala_small_traj.pdb
        
        1.3 MB
    - test_dynamicsengine.py
      
      2.7 kB
    - test_ensemble.py
      
      110.3 kB
    - test_features.py
      
      2.5 kB
    - test_helpers.py
      
      10.0 kB
    - test_histogram.py
      
      10.0 kB
    - test_interface_set.py
      
      9.1 kB
    - test_lookup_function.py
      
      5.1 kB
    - test_mdtraj_support.py
      
      3.0 kB
    - test_movescheme.py
      
      34.4 kB
    - test_movestrategy.py
      
      58.4 kB
    - test_ms_outer_interface.py
      
      6.9 kB
    - test_network.py
      
      23.7 kB
    - test_openmm_engine.py
      
      9.8 kB
    - test_openmm_snapshot.py
      
      3.4 kB
    - test_path_histogram.py
      
      10.1 kB
    - test_pathmover.py
      
      61.0 kB
    - test_pathsimulator.py
      
      29.6 kB
    - test_range_logic.py
      
      4.1 kB
    - test_resampling_statistics.py
      
      7.5 kB
    - test_sample.py
      
      8.0 kB
    - test_shooting.py
      
      2.8 kB
    - test_shooting_point_analysis.py
      
      12.0 kB
    - test_snapshot.py
      
      2.7 kB
    - test_snapshot_modifier.py
      
      27.0 kB
    - test_storage.py
      
      13.6 kB
    - test_tis_analysis.py
      
      47.7 kB
    - test_tools.py
      
      2.0 kB
    - test_toy_dynamics.py
      
      12.2 kB
    - test_toy_features.py
      
      2.4 kB
    - test_trajectory.py
      
      5.9 kB
    - test_trajectory_transition_analysis.py
      
      11.7 kB
    - test_transitions.py
      
      6.0 kB
    - test_volume.py
      
      17.0 kB
    - test_wham.py
      
      9.1 kB
  - tools.py
    
    6.8 kB
  - treelogic.py
    
    14.6 kB
  - visualize.py
    
    92.8 kB
  - volume.py
    
    20.5 kB
- setup.py
  
  6.9 kB
- setup.yaml
  
  1.9 kB

openpathsampling/openpathsampling-v0.9.4.zip