├── .github └── workflows │ ├── ci.yml │ └── publish.yml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── conf.py ├── make.bat ├── requirements-rtd.txt └── source │ ├── _modules │ ├── enspara.apps.rst │ ├── enspara.cards.rst │ ├── enspara.cluster.rst │ ├── enspara.exception.rst │ ├── enspara.geometry.rst │ ├── enspara.info_theory.rst │ ├── enspara.mpi.rst │ ├── enspara.msm.rst │ ├── enspara.rst │ ├── enspara.tpt.rst │ └── enspara.util.rst │ ├── cards.rst │ ├── cli.rst │ ├── clustering.rst │ ├── conf.py │ ├── cookbook.rst │ ├── developing.rst │ ├── exposons.rst │ ├── index.rst │ ├── installation.rst │ ├── pocket-detection.rst │ ├── smFRET.rst │ ├── transition-path-theory.rst │ └── tutorial │ ├── analysis.rst │ ├── clustering-trajectories.rst │ ├── distance-to-cluster-center.svg │ ├── eq-prob-per-state.svg │ ├── fitting.rst │ ├── frames-per-cluster.svg │ ├── frames-per-each-cluster.svg │ ├── hbond-free-energy.svg │ ├── hbond-mi.svg │ ├── mean-hbond-energy.svg │ ├── tprobs-grid.svg │ └── tutorial.rst ├── enspara.sublime-project ├── enspara ├── __init__.py ├── apps │ ├── __init__.py │ ├── cluster.py │ ├── collect_cards.py │ ├── compute-shannon-entropy.py │ ├── implied_timescales.py │ ├── main.py │ ├── reassign.py │ ├── smFRET_dye_MC.py │ ├── smFRET_point_clouds.py │ └── util.py ├── cards │ ├── __init__.py │ ├── cards.py │ ├── disorder.py │ └── featurizers.py ├── citation │ ├── __init__.py │ ├── articles.json │ └── citation.py ├── cluster │ ├── __init__.py │ ├── hybrid.py │ ├── kcenters.py │ ├── kmedoids.py │ ├── save_states.py │ └── util.py ├── data │ └── dyes │ │ ├── R0 │ │ ├── ATTO390.csv │ │ ├── ATTO425.csv │ │ ├── ATTO465.csv │ │ ├── ATTO488.csv │ │ ├── ATTO495.csv │ │ ├── ATTO520.csv │ │ ├── ATTO550.csv │ │ ├── ATTO610.csv │ │ ├── ATTO647N.csv │ │ ├── ATTOThio12.csv │ │ ├── AlexaFluor350.csv │ │ ├── AlexaFluor405.csv │ │ ├── AlexaFluor430.csv │ │ ├── AlexaFluor488.csv │ │ ├── AlexaFluor514.csv │ │ ├── AlexaFluor532.csv │ │ ├── AlexaFluor546.csv │ │ ├── AlexaFluor555.csv │ │ ├── AlexaFluor561.csv │ │ ├── AlexaFluor568.csv │ │ ├── AlexaFluor594.csv │ │ ├── AlexaFluor610.csv │ │ ├── AlexaFluor633.csv │ │ ├── AlexaFluor635.csv │ │ ├── AlexaFluor647.csv │ │ ├── AlexaFluor660.csv │ │ ├── AlexaFluor680.csv │ │ ├── AlexaFluor700.csv │ │ ├── AlexaFluor750.csv │ │ ├── AlexaFluor790.csv │ │ ├── CF660R.csv │ │ ├── Dyes_extinction_QD.csv │ │ ├── LumiprobeCy3.csv │ │ ├── LumiprobeCy3W.csv │ │ ├── LumiprobeCy3b.csv │ │ ├── LumiprobeCy5.csv │ │ ├── LumiprobeCy55.csv │ │ ├── LumiprobeCy5W.csv │ │ ├── LumiprobeCy7.csv │ │ ├── LumiprobeCy75.csv │ │ └── R0_pairs.csv │ │ ├── README.md │ │ ├── interphoton_times.npy │ │ ├── libraries.yml │ │ ├── point-clouds │ │ ├── AF488.pdb │ │ ├── AF594.pdb │ │ ├── README │ │ └── make_point_clouds.py │ │ └── structures │ │ ├── A35_C1R.pdb │ │ ├── A35_L1R.pdb │ │ ├── A48_B1R.pdb │ │ ├── A48_C1R.pdb │ │ ├── A48_L1R.pdb │ │ ├── A53_C1R.pdb │ │ ├── A53_L1R.pdb │ │ ├── A56_C1R.pdb │ │ ├── A56_L1R.pdb │ │ ├── A59_C1R.pdb │ │ ├── A59_L1R.pdb │ │ ├── A64_C2R.pdb │ │ ├── A64_L1R.pdb │ │ ├── C3N_C2R.pdb │ │ ├── C55_C2R.pdb │ │ ├── C55_L1R.pdb │ │ ├── C75_L1R.pdb │ │ ├── README.md │ │ ├── T39_C2R.pdb │ │ ├── T39_L1R.pdb │ │ ├── T42_C2R.pdb │ │ ├── T42_L1R.pdb │ │ ├── T46_C2R.pdb │ │ ├── T46_L1R.pdb │ │ ├── T48_C3R.pdb │ │ ├── T49_C2R.pdb │ │ ├── T49_L1R.pdb │ │ ├── T52_C2R.pdb │ │ ├── T52_L1R.pdb │ │ ├── T61_C2R.pdb │ │ ├── T61_L1R.pdb │ │ └── Tth_C3R.pdb ├── exception.py ├── geometry │ ├── .gitignore │ ├── __init__.py │ ├── dye_lifetimes.py │ ├── dyes_from_expt_dist.py │ ├── explicit_r0_calc.py │ ├── helix.py │ ├── libdist.pyx │ ├── pockets.py │ ├── rmsf.py │ └── rotamer.py ├── info_theory │ ├── .gitignore │ ├── __init__.py │ ├── entropy.py │ ├── exposons.py │ ├── libinfo.pyx │ └── mutual_info.py ├── mpi │ ├── __init__.py │ ├── io.py │ ├── ops.py │ └── util.py ├── msm │ ├── .gitignore │ ├── __init__.py │ ├── bace.py │ ├── bootstrap.py │ ├── builders.py │ ├── libmsm.pyx │ ├── msm.py │ ├── synthetic_data.py │ ├── timescales.py │ └── transition_matrices.py ├── ra │ ├── __init__.py │ └── ra.py ├── test │ ├── __init__.py │ ├── cards_data │ │ ├── PROT_only.pdb │ │ ├── cards_d_s_mi.dat │ │ ├── cards_dis_mi.dat │ │ ├── cards_inds.dat │ │ ├── cards_s_d_mi.dat │ │ ├── cards_ss_mi.dat │ │ ├── dis_n_states.dat │ │ ├── dis_trj0.dat │ │ ├── dis_trj1.dat │ │ ├── disordered_times.dat │ │ ├── mean_disordered_times.dat │ │ ├── mean_ordered_times.dat │ │ ├── n_disordered_times.dat │ │ ├── n_ordered_times.dat │ │ ├── ordered_times.dat │ │ ├── transition_times.dat │ │ └── trj0.xtc │ ├── data │ │ ├── beta-peptide.pdb │ │ ├── beta-peptide.xtc │ │ ├── frame0.h5 │ │ ├── frame0.xtc │ │ └── native.pdb │ ├── fret_data │ │ ├── a48-c1r-mini.xtc │ │ ├── a48-c1r.pdb │ │ ├── a48-tcounts.npy │ │ ├── a59-c1r-mini.xtc │ │ ├── a59-c1r.pdb │ │ ├── a59-tcounts.npy │ │ ├── ab40-tprobs.npy │ │ ├── ab40.pdb │ │ └── ab40.xtc │ ├── geometry_data │ │ ├── PROT_only.pdb │ │ ├── rotamer_trj0.dat │ │ ├── rotamer_trj1.dat │ │ └── trj0.xtc │ ├── msm_data.py │ ├── pytest.ini │ ├── test_apps_cluster.py │ ├── test_apps_cluster_mpi.py │ ├── test_apps_implied_timescales.py │ ├── test_apps_reassign.py │ ├── test_bace.py │ ├── test_cards.py │ ├── test_cluster.py │ ├── test_cluster_util.py │ ├── test_disorder.py │ ├── test_entropy.py │ ├── test_exposons.py │ ├── test_libdist.py │ ├── test_mpi_io.py │ ├── test_mpi_ops.py │ ├── test_msm_bootstrap.py │ ├── test_msm_funcs.py │ ├── test_msm_libmsm.py │ ├── test_msm_obj.py │ ├── test_mutual_info.py │ ├── test_ra.py │ ├── test_rotamer.py │ ├── test_smfret.py │ ├── test_tpt_fluxes.py │ └── util.py ├── tpt │ ├── __init__.py │ ├── core.py │ ├── path.py │ └── tpt.py └── util │ ├── __init__.py │ ├── array.py │ ├── load.py │ ├── log.py │ └── parallel.py ├── environment.yaml ├── gen_meta.py ├── meta.yaml.j2 ├── pyproject.toml └── setup.py /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.github/workflows/publish.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/.github/workflows/publish.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/README.md -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/requirements-rtd.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/requirements-rtd.txt -------------------------------------------------------------------------------- /docs/source/_modules/enspara.apps.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/_modules/enspara.apps.rst -------------------------------------------------------------------------------- /docs/source/_modules/enspara.cards.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/_modules/enspara.cards.rst -------------------------------------------------------------------------------- /docs/source/_modules/enspara.cluster.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/_modules/enspara.cluster.rst -------------------------------------------------------------------------------- /docs/source/_modules/enspara.exception.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/_modules/enspara.exception.rst -------------------------------------------------------------------------------- /docs/source/_modules/enspara.geometry.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/_modules/enspara.geometry.rst -------------------------------------------------------------------------------- /docs/source/_modules/enspara.info_theory.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/_modules/enspara.info_theory.rst -------------------------------------------------------------------------------- /docs/source/_modules/enspara.mpi.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/_modules/enspara.mpi.rst -------------------------------------------------------------------------------- /docs/source/_modules/enspara.msm.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/_modules/enspara.msm.rst -------------------------------------------------------------------------------- /docs/source/_modules/enspara.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/_modules/enspara.rst -------------------------------------------------------------------------------- /docs/source/_modules/enspara.tpt.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/_modules/enspara.tpt.rst -------------------------------------------------------------------------------- /docs/source/_modules/enspara.util.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/_modules/enspara.util.rst -------------------------------------------------------------------------------- /docs/source/cards.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/cards.rst -------------------------------------------------------------------------------- /docs/source/cli.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/cli.rst -------------------------------------------------------------------------------- /docs/source/clustering.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/clustering.rst -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/cookbook.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/cookbook.rst -------------------------------------------------------------------------------- /docs/source/developing.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/developing.rst -------------------------------------------------------------------------------- /docs/source/exposons.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/exposons.rst -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/source/installation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/installation.rst -------------------------------------------------------------------------------- /docs/source/pocket-detection.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/pocket-detection.rst -------------------------------------------------------------------------------- /docs/source/smFRET.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/smFRET.rst -------------------------------------------------------------------------------- /docs/source/transition-path-theory.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/transition-path-theory.rst -------------------------------------------------------------------------------- /docs/source/tutorial/analysis.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/analysis.rst -------------------------------------------------------------------------------- /docs/source/tutorial/clustering-trajectories.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/clustering-trajectories.rst -------------------------------------------------------------------------------- /docs/source/tutorial/distance-to-cluster-center.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/distance-to-cluster-center.svg -------------------------------------------------------------------------------- /docs/source/tutorial/eq-prob-per-state.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/eq-prob-per-state.svg -------------------------------------------------------------------------------- /docs/source/tutorial/fitting.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/fitting.rst -------------------------------------------------------------------------------- /docs/source/tutorial/frames-per-cluster.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/frames-per-cluster.svg -------------------------------------------------------------------------------- /docs/source/tutorial/frames-per-each-cluster.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/frames-per-each-cluster.svg -------------------------------------------------------------------------------- /docs/source/tutorial/hbond-free-energy.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/hbond-free-energy.svg -------------------------------------------------------------------------------- /docs/source/tutorial/hbond-mi.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/hbond-mi.svg -------------------------------------------------------------------------------- /docs/source/tutorial/mean-hbond-energy.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/mean-hbond-energy.svg -------------------------------------------------------------------------------- /docs/source/tutorial/tprobs-grid.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/tprobs-grid.svg -------------------------------------------------------------------------------- /docs/source/tutorial/tutorial.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/docs/source/tutorial/tutorial.rst -------------------------------------------------------------------------------- /enspara.sublime-project: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara.sublime-project -------------------------------------------------------------------------------- /enspara/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/__init__.py -------------------------------------------------------------------------------- /enspara/apps/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/apps/__init__.py -------------------------------------------------------------------------------- /enspara/apps/cluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/apps/cluster.py -------------------------------------------------------------------------------- /enspara/apps/collect_cards.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/apps/collect_cards.py -------------------------------------------------------------------------------- /enspara/apps/compute-shannon-entropy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/apps/compute-shannon-entropy.py -------------------------------------------------------------------------------- /enspara/apps/implied_timescales.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/apps/implied_timescales.py -------------------------------------------------------------------------------- /enspara/apps/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/apps/main.py -------------------------------------------------------------------------------- /enspara/apps/reassign.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/apps/reassign.py -------------------------------------------------------------------------------- /enspara/apps/smFRET_dye_MC.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/apps/smFRET_dye_MC.py -------------------------------------------------------------------------------- /enspara/apps/smFRET_point_clouds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/apps/smFRET_point_clouds.py -------------------------------------------------------------------------------- /enspara/apps/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/apps/util.py -------------------------------------------------------------------------------- /enspara/cards/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/cards/__init__.py -------------------------------------------------------------------------------- /enspara/cards/cards.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/cards/cards.py -------------------------------------------------------------------------------- /enspara/cards/disorder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/cards/disorder.py -------------------------------------------------------------------------------- /enspara/cards/featurizers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/cards/featurizers.py -------------------------------------------------------------------------------- /enspara/citation/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/citation/__init__.py -------------------------------------------------------------------------------- /enspara/citation/articles.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/citation/articles.json -------------------------------------------------------------------------------- /enspara/citation/citation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/citation/citation.py -------------------------------------------------------------------------------- /enspara/cluster/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/cluster/__init__.py -------------------------------------------------------------------------------- /enspara/cluster/hybrid.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/cluster/hybrid.py -------------------------------------------------------------------------------- /enspara/cluster/kcenters.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/cluster/kcenters.py -------------------------------------------------------------------------------- /enspara/cluster/kmedoids.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/cluster/kmedoids.py -------------------------------------------------------------------------------- /enspara/cluster/save_states.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/cluster/save_states.py -------------------------------------------------------------------------------- /enspara/cluster/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/cluster/util.py -------------------------------------------------------------------------------- /enspara/data/dyes/R0/ATTO390.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/ATTO390.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/ATTO425.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/ATTO425.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/ATTO465.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/ATTO465.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/ATTO488.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/ATTO488.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/ATTO495.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/ATTO495.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/ATTO520.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/ATTO520.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/ATTO550.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/ATTO550.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/ATTO610.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/ATTO610.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/ATTO647N.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/ATTO647N.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/ATTOThio12.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/ATTOThio12.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor350.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor350.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor405.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor405.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor430.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor430.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor488.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor488.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor514.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor514.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor532.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor532.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor546.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor546.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor555.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor555.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor561.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor561.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor568.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor568.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor594.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor594.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor610.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor610.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor633.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor633.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor635.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor635.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor647.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor647.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor660.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor660.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor680.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor680.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor700.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor700.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor750.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor750.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/AlexaFluor790.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/AlexaFluor790.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/CF660R.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/CF660R.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/Dyes_extinction_QD.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/Dyes_extinction_QD.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/LumiprobeCy3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/LumiprobeCy3.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/LumiprobeCy3W.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/LumiprobeCy3W.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/LumiprobeCy3b.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/LumiprobeCy3b.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/LumiprobeCy5.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/LumiprobeCy5.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/LumiprobeCy55.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/LumiprobeCy55.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/LumiprobeCy5W.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/LumiprobeCy5W.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/LumiprobeCy7.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/LumiprobeCy7.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/LumiprobeCy75.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/LumiprobeCy75.csv -------------------------------------------------------------------------------- /enspara/data/dyes/R0/R0_pairs.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/R0/R0_pairs.csv -------------------------------------------------------------------------------- /enspara/data/dyes/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/README.md -------------------------------------------------------------------------------- /enspara/data/dyes/interphoton_times.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/interphoton_times.npy -------------------------------------------------------------------------------- /enspara/data/dyes/libraries.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/libraries.yml -------------------------------------------------------------------------------- /enspara/data/dyes/point-clouds/AF488.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/point-clouds/AF488.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/point-clouds/AF594.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/point-clouds/AF594.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/point-clouds/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/point-clouds/README -------------------------------------------------------------------------------- /enspara/data/dyes/point-clouds/make_point_clouds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/point-clouds/make_point_clouds.py -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A35_C1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A35_C1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A35_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A35_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A48_B1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A48_B1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A48_C1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A48_C1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A48_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A48_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A53_C1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A53_C1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A53_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A53_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A56_C1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A56_C1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A56_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A56_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A59_C1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A59_C1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A59_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A59_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A64_C2R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A64_C2R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/A64_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/A64_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/C3N_C2R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/C3N_C2R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/C55_C2R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/C55_C2R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/C55_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/C55_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/C75_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/C75_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/README.md -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T39_C2R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T39_C2R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T39_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T39_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T42_C2R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T42_C2R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T42_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T42_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T46_C2R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T46_C2R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T46_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T46_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T48_C3R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T48_C3R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T49_C2R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T49_C2R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T49_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T49_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T52_C2R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T52_C2R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T52_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T52_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T61_C2R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T61_C2R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/T61_L1R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/T61_L1R.pdb -------------------------------------------------------------------------------- /enspara/data/dyes/structures/Tth_C3R.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/data/dyes/structures/Tth_C3R.pdb -------------------------------------------------------------------------------- /enspara/exception.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/exception.py -------------------------------------------------------------------------------- /enspara/geometry/.gitignore: -------------------------------------------------------------------------------- 1 | libdist.c -------------------------------------------------------------------------------- /enspara/geometry/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/geometry/__init__.py -------------------------------------------------------------------------------- /enspara/geometry/dye_lifetimes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/geometry/dye_lifetimes.py -------------------------------------------------------------------------------- /enspara/geometry/dyes_from_expt_dist.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/geometry/dyes_from_expt_dist.py -------------------------------------------------------------------------------- /enspara/geometry/explicit_r0_calc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/geometry/explicit_r0_calc.py -------------------------------------------------------------------------------- /enspara/geometry/helix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/geometry/helix.py -------------------------------------------------------------------------------- /enspara/geometry/libdist.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/geometry/libdist.pyx -------------------------------------------------------------------------------- /enspara/geometry/pockets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/geometry/pockets.py -------------------------------------------------------------------------------- /enspara/geometry/rmsf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/geometry/rmsf.py -------------------------------------------------------------------------------- /enspara/geometry/rotamer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/geometry/rotamer.py -------------------------------------------------------------------------------- /enspara/info_theory/.gitignore: -------------------------------------------------------------------------------- 1 | libinfo.c -------------------------------------------------------------------------------- /enspara/info_theory/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/info_theory/__init__.py -------------------------------------------------------------------------------- /enspara/info_theory/entropy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/info_theory/entropy.py -------------------------------------------------------------------------------- /enspara/info_theory/exposons.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/info_theory/exposons.py -------------------------------------------------------------------------------- /enspara/info_theory/libinfo.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/info_theory/libinfo.pyx -------------------------------------------------------------------------------- /enspara/info_theory/mutual_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/info_theory/mutual_info.py -------------------------------------------------------------------------------- /enspara/mpi/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/mpi/__init__.py -------------------------------------------------------------------------------- /enspara/mpi/io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/mpi/io.py -------------------------------------------------------------------------------- /enspara/mpi/ops.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/mpi/ops.py -------------------------------------------------------------------------------- /enspara/mpi/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/mpi/util.py -------------------------------------------------------------------------------- /enspara/msm/.gitignore: -------------------------------------------------------------------------------- 1 | libmsm.c 2 | -------------------------------------------------------------------------------- /enspara/msm/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/msm/__init__.py -------------------------------------------------------------------------------- /enspara/msm/bace.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/msm/bace.py -------------------------------------------------------------------------------- /enspara/msm/bootstrap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/msm/bootstrap.py -------------------------------------------------------------------------------- /enspara/msm/builders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/msm/builders.py -------------------------------------------------------------------------------- /enspara/msm/libmsm.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/msm/libmsm.pyx -------------------------------------------------------------------------------- /enspara/msm/msm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/msm/msm.py -------------------------------------------------------------------------------- /enspara/msm/synthetic_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/msm/synthetic_data.py -------------------------------------------------------------------------------- /enspara/msm/timescales.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/msm/timescales.py -------------------------------------------------------------------------------- /enspara/msm/transition_matrices.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/msm/transition_matrices.py -------------------------------------------------------------------------------- /enspara/ra/__init__.py: -------------------------------------------------------------------------------- 1 | from .ra import * 2 | -------------------------------------------------------------------------------- /enspara/ra/ra.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/ra/ra.py -------------------------------------------------------------------------------- /enspara/test/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /enspara/test/cards_data/PROT_only.pdb: -------------------------------------------------------------------------------- 1 | ../data/beta-peptide.pdb -------------------------------------------------------------------------------- /enspara/test/cards_data/cards_d_s_mi.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/cards_d_s_mi.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/cards_dis_mi.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/cards_dis_mi.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/cards_inds.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/cards_inds.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/cards_s_d_mi.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/cards_s_d_mi.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/cards_ss_mi.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/cards_ss_mi.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/dis_n_states.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/dis_n_states.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/dis_trj0.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/dis_trj0.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/dis_trj1.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/dis_trj1.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/disordered_times.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/disordered_times.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/mean_disordered_times.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/mean_disordered_times.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/mean_ordered_times.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/mean_ordered_times.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/n_disordered_times.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/n_disordered_times.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/n_ordered_times.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/n_ordered_times.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/ordered_times.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/ordered_times.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/transition_times.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/cards_data/transition_times.dat -------------------------------------------------------------------------------- /enspara/test/cards_data/trj0.xtc: -------------------------------------------------------------------------------- 1 | ../data/beta-peptide.xtc -------------------------------------------------------------------------------- /enspara/test/data/beta-peptide.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/data/beta-peptide.pdb -------------------------------------------------------------------------------- /enspara/test/data/beta-peptide.xtc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/data/beta-peptide.xtc -------------------------------------------------------------------------------- /enspara/test/data/frame0.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/data/frame0.h5 -------------------------------------------------------------------------------- /enspara/test/data/frame0.xtc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/data/frame0.xtc -------------------------------------------------------------------------------- /enspara/test/data/native.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/data/native.pdb -------------------------------------------------------------------------------- /enspara/test/fret_data/a48-c1r-mini.xtc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/fret_data/a48-c1r-mini.xtc -------------------------------------------------------------------------------- /enspara/test/fret_data/a48-c1r.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/fret_data/a48-c1r.pdb -------------------------------------------------------------------------------- /enspara/test/fret_data/a48-tcounts.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/fret_data/a48-tcounts.npy -------------------------------------------------------------------------------- /enspara/test/fret_data/a59-c1r-mini.xtc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/fret_data/a59-c1r-mini.xtc -------------------------------------------------------------------------------- /enspara/test/fret_data/a59-c1r.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/fret_data/a59-c1r.pdb -------------------------------------------------------------------------------- /enspara/test/fret_data/a59-tcounts.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/fret_data/a59-tcounts.npy -------------------------------------------------------------------------------- /enspara/test/fret_data/ab40-tprobs.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/fret_data/ab40-tprobs.npy -------------------------------------------------------------------------------- /enspara/test/fret_data/ab40.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/fret_data/ab40.pdb -------------------------------------------------------------------------------- /enspara/test/fret_data/ab40.xtc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/fret_data/ab40.xtc -------------------------------------------------------------------------------- /enspara/test/geometry_data/PROT_only.pdb: -------------------------------------------------------------------------------- 1 | ../cards_data/PROT_only.pdb -------------------------------------------------------------------------------- /enspara/test/geometry_data/rotamer_trj0.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/geometry_data/rotamer_trj0.dat -------------------------------------------------------------------------------- /enspara/test/geometry_data/rotamer_trj1.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/geometry_data/rotamer_trj1.dat -------------------------------------------------------------------------------- /enspara/test/geometry_data/trj0.xtc: -------------------------------------------------------------------------------- 1 | ../cards_data/trj0.xtc -------------------------------------------------------------------------------- /enspara/test/msm_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/msm_data.py -------------------------------------------------------------------------------- /enspara/test/pytest.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/pytest.ini -------------------------------------------------------------------------------- /enspara/test/test_apps_cluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_apps_cluster.py -------------------------------------------------------------------------------- /enspara/test/test_apps_cluster_mpi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_apps_cluster_mpi.py -------------------------------------------------------------------------------- /enspara/test/test_apps_implied_timescales.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_apps_implied_timescales.py -------------------------------------------------------------------------------- /enspara/test/test_apps_reassign.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_apps_reassign.py -------------------------------------------------------------------------------- /enspara/test/test_bace.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_bace.py -------------------------------------------------------------------------------- /enspara/test/test_cards.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_cards.py -------------------------------------------------------------------------------- /enspara/test/test_cluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_cluster.py -------------------------------------------------------------------------------- /enspara/test/test_cluster_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_cluster_util.py -------------------------------------------------------------------------------- /enspara/test/test_disorder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_disorder.py -------------------------------------------------------------------------------- /enspara/test/test_entropy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_entropy.py -------------------------------------------------------------------------------- /enspara/test/test_exposons.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_exposons.py -------------------------------------------------------------------------------- /enspara/test/test_libdist.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_libdist.py -------------------------------------------------------------------------------- /enspara/test/test_mpi_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_mpi_io.py -------------------------------------------------------------------------------- /enspara/test/test_mpi_ops.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_mpi_ops.py -------------------------------------------------------------------------------- /enspara/test/test_msm_bootstrap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_msm_bootstrap.py -------------------------------------------------------------------------------- /enspara/test/test_msm_funcs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_msm_funcs.py -------------------------------------------------------------------------------- /enspara/test/test_msm_libmsm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_msm_libmsm.py -------------------------------------------------------------------------------- /enspara/test/test_msm_obj.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_msm_obj.py -------------------------------------------------------------------------------- /enspara/test/test_mutual_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_mutual_info.py -------------------------------------------------------------------------------- /enspara/test/test_ra.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_ra.py -------------------------------------------------------------------------------- /enspara/test/test_rotamer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_rotamer.py -------------------------------------------------------------------------------- /enspara/test/test_smfret.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_smfret.py -------------------------------------------------------------------------------- /enspara/test/test_tpt_fluxes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/test_tpt_fluxes.py -------------------------------------------------------------------------------- /enspara/test/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/test/util.py -------------------------------------------------------------------------------- /enspara/tpt/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/tpt/__init__.py -------------------------------------------------------------------------------- /enspara/tpt/core.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/tpt/core.py -------------------------------------------------------------------------------- /enspara/tpt/path.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/tpt/path.py -------------------------------------------------------------------------------- /enspara/tpt/tpt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/tpt/tpt.py -------------------------------------------------------------------------------- /enspara/util/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/util/__init__.py -------------------------------------------------------------------------------- /enspara/util/array.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/util/array.py -------------------------------------------------------------------------------- /enspara/util/load.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/util/load.py -------------------------------------------------------------------------------- /enspara/util/log.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/util/log.py -------------------------------------------------------------------------------- /enspara/util/parallel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/enspara/util/parallel.py -------------------------------------------------------------------------------- /environment.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/environment.yaml -------------------------------------------------------------------------------- /gen_meta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/gen_meta.py -------------------------------------------------------------------------------- /meta.yaml.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/meta.yaml.j2 -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/pyproject.toml -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowman-lab/enspara/HEAD/setup.py --------------------------------------------------------------------------------