AUTHORS
COPYING
MANIFEST.in
setup.cfg
setup.py
Extras/FAHTools/StripWatersFAH.py
Extras/GPURMSD/AUTHORS
Extras/GPURMSD/COPYING
Extras/GPURMSD/README
Extras/GPURMSD/setup.py
Extras/GPURMSD/gpurmsd/.dirstamp
Extras/GPURMSD/gpurmsd/Makefile
Extras/GPURMSD/gpurmsd/RMSD.cu
Extras/GPURMSD/gpurmsd/RMSD.hh
Extras/GPURMSD/gpurmsd/Xrange.py
Extras/GPURMSD/gpurmsd/__init__.py
Extras/GPURMSD/gpurmsd/gpurmsd.py
Extras/GPURMSD/gpurmsd/kernel_rmsd.cu
Extras/GPURMSD/gpurmsd/numpy.i
Extras/GPURMSD/gpurmsd/swig.i
Extras/GPURMSD/gpurmsd/.deps/.dirstamp
Extras/GPURMSD/gpurmsd/.deps/hello.Po
Extras/GPURMSD/gpurmsd/.deps/main.Po
Extras/GPURMSD/tests/test_gpurmsd.py
Extras/GPURMSD/tests/fixtures/README
Extras/GPURMSD/tests/fixtures/trj0.lh5
Extras/GPURMSD/tests/fixtures/ww-aligned.xtc
Extras/GPURMSD/tests/fixtures/ww.pdb
Extras/GPURMSD/tests/fixtures/ww.xtc
Extras/LPRMSD/README
Extras/LPRMSD/lprmsd.py
Extras/LPRMSD/setup.cfg
Extras/LPRMSD/setup.py
Extras/LPRMSD/scripts/CalculateLPRMSD.py
Extras/LPRMSD/scripts/SaveAlignedPDBs.py
Extras/LPRMSD/src/apc.c
Extras/LPRMSD/src/apc.h
Extras/LPRMSD/src/cblas.h
Extras/LPRMSD/src/cblas_dgemm.c
Extras/LPRMSD/src/cblas_f77.h
Extras/LPRMSD/src/cblas_globals.c
Extras/LPRMSD/src/cblas_xerbla.c
Extras/LPRMSD/src/lprmsd.c
Extras/LPRMSD/src/qcprot.c
Extras/LPRMSD/src/qcprot.h
Extras/LPRMSD/src/theobald_rmsd.c
Extras/LPRMSD/src/theobald_rmsd.h
Extras/LPRMSD/src/xerbla.c
Extras/LPRMSD/tests/TestLPRMSD_00.py
Extras/LPRMSD/tests/trj0.lh5
Extras/TPTdiagrams/GenerateTPTgraph.py
Extras/TPTdiagrams/KyleGeneratePNG.py
Extras/TPTdiagrams/README.txt
Extras/TPTdiagrams/RenderStateImages.py
Extras/parallel_assign/README.md
Extras/parallel_assign/assign_pbs_example.sh
Extras/parallel_assign/setup.py
Extras/parallel_assign/lib/__init__.py
Extras/parallel_assign/lib/local.py
Extras/parallel_assign/lib/remote.py
Extras/parallel_assign/lib/vtraj.py
Extras/parallel_assign/scripts/AssignParallel.py
Extras/parallel_assign/scripts/__init__.py
Extras/parallel_assign/tests/__init__.py
Extras/parallel_assign/tests/common.py
Extras/parallel_assign/tests/test_local.py
Extras/parallel_assign/tests/test_remote.py
Extras/parallel_assign/tests/test_script.py
Extras/parallel_assign/tests/fixtures/Assignments.h5
Extras/parallel_assign/tests/fixtures/Assignments.h5.distances
Extras/parallel_assign/tests/fixtures/Gens.lh5
Extras/parallel_assign/tests/fixtures/ProjectInfo.h5
Extras/parallel_assign/tests/fixtures/native.pdb
Extras/parallel_assign/tests/fixtures/trj0.lh5
MSMBuilder/Citation.py
MSMBuilder/License.py
MSMBuilder/MSMLib.py
MSMBuilder/SCRE.py
MSMBuilder/__init__.py
MSMBuilder/arglib.py
MSMBuilder/assigning.py
MSMBuilder/cfep.py
MSMBuilder/clustering.py
MSMBuilder/drift.py
MSMBuilder/fahproject.py
MSMBuilder/msm_analysis.py
MSMBuilder/plot_graph.py
MSMBuilder/testing.py
MSMBuilder/tpt.py
MSMBuilder/utils.py
MSMBuilder/version.py
MSMBuilder/lumping/__init__.py
MSMBuilder/lumping/lumper.py
MSMBuilder/lumping/pcca.py
MSMBuilder/lumping/pcca_plus.py
MSMBuilder/lumping/utils.py
MSMBuilder/metrics/__init__.py
MSMBuilder/metrics/baseclasses.py
MSMBuilder/metrics/contact.py
MSMBuilder/metrics/dihedral.py
MSMBuilder/metrics/hybrid.py
MSMBuilder/metrics/parsers.py
MSMBuilder/metrics/positions.py
MSMBuilder/metrics/projection.py
MSMBuilder/metrics/rmsd.py
MSMBuilder/project/__init__.py
MSMBuilder/project/builder.py
MSMBuilder/project/project.py
MSMBuilder/project/reference_data.py
MSMBuilder/project/utils.py
MSMBuilder/project/validators.py
MSMBuilder/reduce/__init__.py
MSMBuilder/reduce/baseclasses.py
MSMBuilder/reduce/tICA.py
Tutorial/AtomIndices.dat
Tutorial/PlotDihedrals.py
Tutorial/Tutorial.html
Tutorial/native.pdb
Tutorial/XTC/RUN00/frame0.xtc
Tutorial/XTC/RUN01/frame0.xtc
Tutorial/XTC/RUN02/frame0.xtc
Tutorial/XTC/RUN03/frame0.xtc
Tutorial/XTC/RUN04/frame0.xtc
Tutorial/XTC/RUN05/frame0.xtc
Tutorial/XTC/RUN06/frame0.xtc
Tutorial/XTC/RUN07/frame0.xtc
Tutorial/XTC/RUN08/frame0.xtc
Tutorial/XTC/RUN09/frame0.xtc
Tutorial/XTC/RUN10/frame0.xtc
Tutorial/XTC/RUN11/frame0.xtc
Tutorial/XTC/RUN12/frame0.xtc
Tutorial/XTC/RUN13/frame0.xtc
Tutorial/XTC/RUN14/frame0.xtc
Tutorial/XTC/RUN15/frame0.xtc
Tutorial/XTC/RUN16/frame0.xtc
Tutorial/XTC/RUN17/frame0.xtc
Tutorial/XTC/RUN18/frame0.xtc
Tutorial/XTC/RUN19/frame0.xtc
Tutorial/XTC/RUN20/frame0.xtc
Tutorial/XTC/RUN21/frame0.xtc
Tutorial/XTC/RUN22/frame0.xtc
Tutorial/XTC/RUN23/frame0.xtc
Tutorial/XTC/RUN24/frame0.xtc
Tutorial/XTC/RUN25/frame0.xtc
Tutorial/XTC/RUN26/frame0.xtc
Tutorial/XTC/RUN27/frame0.xtc
Tutorial/XTC/RUN28/frame0.xtc
Tutorial/XTC/RUN29/frame0.xtc
Tutorial/XTC/RUN30/frame0.xtc
Tutorial/XTC/RUN31/frame0.xtc
Tutorial/XTC/RUN32/frame0.xtc
Tutorial/XTC/RUN33/frame0.xtc
Tutorial/XTC/RUN34/frame0.xtc
Tutorial/XTC/RUN35/frame0.xtc
Tutorial/XTC/RUN36/frame0.xtc
Tutorial/XTC/RUN37/frame0.xtc
Tutorial/XTC/RUN38/frame0.xtc
Tutorial/XTC/RUN39/frame0.xtc
Tutorial/XTC/RUN40/frame0.xtc
Tutorial/XTC/RUN41/frame0.xtc
Tutorial/XTC/RUN42/frame0.xtc
Tutorial/XTC/RUN43/frame0.xtc
Tutorial/XTC/RUN44/frame0.xtc
Tutorial/XTC/RUN45/frame0.xtc
Tutorial/XTC/RUN46/frame0.xtc
Tutorial/XTC/RUN47/frame0.xtc
Tutorial/XTC/RUN48/frame0.xtc
Tutorial/XTC/RUN49/frame0.xtc
Tutorial/XTC/RUN50/frame0.xtc
Tutorial/XTC/RUN51/frame0.xtc
Tutorial/XTC/RUN52/frame0.xtc
Tutorial/XTC/RUN53/frame0.xtc
Tutorial/XTC/RUN54/frame0.xtc
Tutorial/XTC/RUN55/frame0.xtc
Tutorial/XTC/RUN56/frame0.xtc
Tutorial/XTC/RUN57/frame0.xtc
Tutorial/XTC/RUN58/frame0.xtc
Tutorial/XTC/RUN59/frame0.xtc
Tutorial/XTC/RUN60/frame0.xtc
Tutorial/XTC/RUN61/frame0.xtc
Tutorial/XTC/RUN62/frame0.xtc
Tutorial/XTC/RUN63/frame0.xtc
Tutorial/XTC/RUN64/frame0.xtc
Tutorial/XTC/RUN65/frame0.xtc
Tutorial/XTC/RUN66/frame0.xtc
Tutorial/XTC/RUN67/frame0.xtc
Tutorial/XTC/RUN68/frame0.xtc
Tutorial/XTC/RUN69/frame0.xtc
Tutorial/XTC/RUN70/frame0.xtc
Tutorial/XTC/RUN71/frame0.xtc
Tutorial/XTC/RUN72/frame0.xtc
Tutorial/XTC/RUN73/frame0.xtc
Tutorial/XTC/RUN74/frame0.xtc
Tutorial/XTC/RUN75/frame0.xtc
Tutorial/XTC/RUN76/frame0.xtc
Tutorial/XTC/RUN77/frame0.xtc
Tutorial/XTC/RUN78/frame0.xtc
Tutorial/XTC/RUN79/frame0.xtc
Tutorial/XTC/RUN80/frame0.xtc
Tutorial/XTC/RUN81/frame0.xtc
Tutorial/XTC/RUN82/frame0.xtc
Tutorial/XTC/RUN83/frame0.xtc
Tutorial/XTC/RUN84/frame0.xtc
Tutorial/XTC/RUN85/frame0.xtc
Tutorial/XTC/RUN86/frame0.xtc
Tutorial/XTC/RUN87/frame0.xtc
Tutorial/XTC/RUN88/frame0.xtc
Tutorial/XTC/RUN89/frame0.xtc
Tutorial/XTC/RUN90/frame0.xtc
Tutorial/XTC/RUN91/frame0.xtc
Tutorial/XTC/RUN92/frame0.xtc
Tutorial/XTC/RUN93/frame0.xtc
Tutorial/XTC/RUN94/frame0.xtc
Tutorial/XTC/RUN95/frame0.xtc
Tutorial/XTC/RUN96/frame0.xtc
Tutorial/XTC/RUN97/frame0.xtc
Tutorial/XTC/RUN98/frame0.xtc
Tutorial/XTC/RUN99/frame0.xtc
msmbuilder.egg-info/PKG-INFO
msmbuilder.egg-info/SOURCES.txt
msmbuilder.egg-info/dependency_links.txt
msmbuilder.egg-info/entry_points.txt
msmbuilder.egg-info/not-zip-safe
msmbuilder.egg-info/top_level.txt
reference/AllPairs.dat
reference/Assignments.Fixed.h5
reference/Assignments.h5
reference/Assignments.h5.distances
reference/AtomIndices.dat
reference/ClusterRadii.dat
reference/Gens.lh5
reference/HeavyAtomPairs.dat
reference/ImpliedTimescales.dat
reference/Mapping.dat
reference/OldAtomIndices.dat
reference/Populations.dat
reference/ProjectInfo.yaml
reference/RUN00_frame0.dcd
reference/RUN00_frame0.xtc
reference/WardAssignments.h5
reference/XTC.tgz
reference/ZMatrix.h5
reference/g_sas_ref.dat
reference/native.pdb
reference/tCounts.mtx
reference/tICA_phipsi_t10.h5
reference/tICA_ref_mle.h5
reference/tICA_ref_trans.h5
reference/tICA_tutorial.ipynb
reference/tProb.mtx
reference/PCCA_ref/Assignments.Fixed.h5
reference/PCCA_ref/MacroAssignments.h5
reference/PCCA_ref/MacroMapping.dat
reference/PCCA_ref/Mapping.dat
reference/PCCA_ref/Populations.dat
reference/PCCA_ref/tCounts.mtx
reference/PCCA_ref/tProb.mtx
reference/Trajectories/trj0.h5
reference/Trajectories/trj1.h5
reference/Trajectories/trj10.h5
reference/Trajectories/trj11.h5
reference/Trajectories/trj12.h5
reference/Trajectories/trj13.h5
reference/Trajectories/trj14.h5
reference/Trajectories/trj15.h5
reference/Trajectories/trj16.h5
reference/Trajectories/trj17.h5
reference/Trajectories/trj18.h5
reference/Trajectories/trj19.h5
reference/Trajectories/trj2.h5
reference/Trajectories/trj20.h5
reference/Trajectories/trj21.h5
reference/Trajectories/trj22.h5
reference/Trajectories/trj23.h5
reference/Trajectories/trj24.h5
reference/Trajectories/trj25.h5
reference/Trajectories/trj26.h5
reference/Trajectories/trj27.h5
reference/Trajectories/trj28.h5
reference/Trajectories/trj29.h5
reference/Trajectories/trj3.h5
reference/Trajectories/trj30.h5
reference/Trajectories/trj31.h5
reference/Trajectories/trj32.h5
reference/Trajectories/trj33.h5
reference/Trajectories/trj34.h5
reference/Trajectories/trj35.h5
reference/Trajectories/trj36.h5
reference/Trajectories/trj37.h5
reference/Trajectories/trj38.h5
reference/Trajectories/trj39.h5
reference/Trajectories/trj4.h5
reference/Trajectories/trj40.h5
reference/Trajectories/trj41.h5
reference/Trajectories/trj42.h5
reference/Trajectories/trj43.h5
reference/Trajectories/trj44.h5
reference/Trajectories/trj45.h5
reference/Trajectories/trj46.h5
reference/Trajectories/trj47.h5
reference/Trajectories/trj48.h5
reference/Trajectories/trj49.h5
reference/Trajectories/trj5.h5
reference/Trajectories/trj50.h5
reference/Trajectories/trj51.h5
reference/Trajectories/trj52.h5
reference/Trajectories/trj53.h5
reference/Trajectories/trj54.h5
reference/Trajectories/trj55.h5
reference/Trajectories/trj56.h5
reference/Trajectories/trj57.h5
reference/Trajectories/trj58.h5
reference/Trajectories/trj59.h5
reference/Trajectories/trj6.h5
reference/Trajectories/trj60.h5
reference/Trajectories/trj61.h5
reference/Trajectories/trj62.h5
reference/Trajectories/trj63.h5
reference/Trajectories/trj64.h5
reference/Trajectories/trj65.h5
reference/Trajectories/trj66.h5
reference/Trajectories/trj67.h5
reference/Trajectories/trj68.h5
reference/Trajectories/trj69.h5
reference/Trajectories/trj7.h5
reference/Trajectories/trj70.h5
reference/Trajectories/trj71.h5
reference/Trajectories/trj72.h5
reference/Trajectories/trj73.h5
reference/Trajectories/trj74.h5
reference/Trajectories/trj75.h5
reference/Trajectories/trj76.h5
reference/Trajectories/trj77.h5
reference/Trajectories/trj78.h5
reference/Trajectories/trj79.h5
reference/Trajectories/trj8.h5
reference/Trajectories/trj80.h5
reference/Trajectories/trj81.h5
reference/Trajectories/trj82.h5
reference/Trajectories/trj83.h5
reference/Trajectories/trj84.h5
reference/Trajectories/trj85.h5
reference/Trajectories/trj86.h5
reference/Trajectories/trj87.h5
reference/Trajectories/trj88.h5
reference/Trajectories/trj89.h5
reference/Trajectories/trj9.h5
reference/Trajectories/trj90.h5
reference/Trajectories/trj91.h5
reference/Trajectories/trj92.h5
reference/Trajectories/trj93.h5
reference/Trajectories/trj94.h5
reference/Trajectories/trj95.h5
reference/Trajectories/trj96.h5
reference/Trajectories/trj97.h5
reference/Trajectories/trj98.h5
reference/Trajectories/trj99.h5
reference/assign/Assignments.h5
reference/assign/Assignments.h5.distances
reference/cfep_reference/Gens.lh5
reference/cfep_reference/tCounts.mtx
reference/points_on_cube/AtomIndices.dat
reference/points_on_cube/ProjectInfo.yaml
reference/points_on_cube/native.pdb
reference/points_on_cube/Trajectories/trj0.lh5
reference/project_reference/project.builder/ProjectInfo.yaml
reference/project_reference/project.builder/ProjectInfo_final.yaml
reference/project_reference/project.builder/test.py
reference/project_reference/project.builder/Trajectories/trj0.lh5
reference/project_reference/project.builder/Trajectories/trj1.lh5
reference/project_reference/project.builder/Trajectories/trj2.lh5
reference/project_reference/project.builder/fah_style_data/native.pdb
reference/project_reference/project.builder/fah_style_data/RUN0/CLONE0/frame0.xtc
reference/project_reference/project.builder/fah_style_data/RUN0/CLONE0/frame1.xtc
reference/project_reference/project.builder/fah_style_data/RUN0/CLONE1/frame0.xtc
reference/project_reference/project.builder/fah_style_data/RUN0/CLONE1/frame1.xtc
reference/project_reference/project.builder/fah_style_data/RUN1/CLONE0/frame0.xtc
reference/project_reference/project.builder/fah_style_data/RUN1/CLONE0/frame1.xtc
reference/project_reference/project.builder/fah_style_data/RUN1/CLONE0/frame_1_should_not_work
reference/project_reference/project.builder/fah_style_data/RUN1/CLONE1/frame0.xtc
reference/project_reference/project.builder/fah_style_data/RUN1/CLONE1/frame1.xtc
reference/project_reference/project.builder/fah_style_data/RUN1/CLONE1/frame2.xtc
reference/project_reference/project.builder/fah_style_data/RUN1/CLONE1/frame3.xtc
reference/project_reference/project.builder/fah_style_data/RUN2/CLONE0/frame0.xtc
reference/project_reference/project.builder/fah_style_data/RUN2/CLONE0/frame2.xtc
reference/save_structures/State0-0.lh5
reference/save_structures/State0-1.lh5
reference/save_structures/State0.lh5
reference/save_structures/State1-0.lh5
reference/save_structures/State1-1.lh5
reference/save_structures/State1.lh5
reference/save_structures/State2-0.lh5
reference/save_structures/State2-1.lh5
reference/save_structures/State2.lh5
reference/transition_path_theory_reference/all_to_all_mfpt.h5
reference/transition_path_theory_reference/committors.h5
reference/transition_path_theory_reference/dijkstra_bottlenecks.h5
reference/transition_path_theory_reference/dijkstra_fluxes.h5
reference/transition_path_theory_reference/dijkstra_paths.h5
reference/transition_path_theory_reference/ensemble_mfpt.h5
reference/transition_path_theory_reference/flux.h5
reference/transition_path_theory_reference/generate_tpt_ref.py
reference/transition_path_theory_reference/mfpt.h5
reference/transition_path_theory_reference/net_flux.h5
reference/transition_path_theory_reference/tProb.mtx
reference/transition_path_theory_reference/tp_time.h5
reference/transition_path_theory_reference/hub_ref/README
reference/transition_path_theory_reference/hub_ref/edge_1.csv
reference/transition_path_theory_reference/hub_ref/fraction_visited.dat
reference/transition_path_theory_reference/hub_ref/hub_scores.dat
reference/transition_path_theory_reference/hub_ref/hub_simulator.py
reference/transition_path_theory_reference/hub_ref/mat_1.dat
reference/transition_path_theory_reference/hub_ref/node_1.csv
reference/transition_path_theory_reference/hub_ref/ratemat_1.dat
reference/transition_path_theory_reference/many_state/Paths.h5
reference/transition_path_theory_reference/many_state/sinks.dat
reference/transition_path_theory_reference/many_state/sources.dat
reference/transition_path_theory_reference/tpt_ref_9.10.2012/all_to_all_mfpt.h5
reference/transition_path_theory_reference/tpt_ref_9.10.2012/committors.h5
reference/transition_path_theory_reference/tpt_ref_9.10.2012/dijkstra_bottlenecks.h5
reference/transition_path_theory_reference/tpt_ref_9.10.2012/dijkstra_fluxes.h5
reference/transition_path_theory_reference/tpt_ref_9.10.2012/dijkstra_paths.h5
reference/transition_path_theory_reference/tpt_ref_9.10.2012/ensemble_mfpt.h5
reference/transition_path_theory_reference/tpt_ref_9.10.2012/flux.h5
reference/transition_path_theory_reference/tpt_ref_9.10.2012/mfpt.h5
reference/transition_path_theory_reference/tpt_ref_9.10.2012/net_flux.h5
reference/transition_path_theory_reference/tpt_ref_9.10.2012/tp_time.h5
scripts/Assign.py
scripts/AssignHierarchical.py
scripts/BACE_Coarse_Graining.py
scripts/BuildMSM.py
scripts/CalculateClusterRadii.py
scripts/CalculateImpliedTimescales.py
scripts/CalculateMFPTs.py
scripts/CalculateProjectDistance.py
scripts/CalculateProjectSASA.py
scripts/CalculateTPT.py
scripts/Cluster.py
scripts/ConvertDataToHDF.py
scripts/CreateAtomIndices.py
scripts/FindPaths.py
scripts/InteractiveSCRE.py
scripts/PCCA.py
scripts/PlotImpliedTimescales.py
scripts/RebuildProject.py
scripts/SampleTrajectory.py
scripts/SaveStructures.py
scripts/TrimAssignments.py
scripts/__init__.py
scripts/msmb.py
scripts/tICA_train.py
tests/common.py
tests/test_arglib.py
tests/test_cfep.py
tests/test_eigensolvers.py
tests/test_msm_analysis.py
tests/test_msmlib.py
tests/test_project.py
tests/test_rmsd.py
tests/test_tpt.py
tests/test_wrappers.py
tests/reference_generation_scripts/gen_ref_dat.py
tests/reference_generation_scripts/generate_3D_points.py
tests/reference_generation_scripts/generate_tpt_ref.py