MANIFEST.in
README.md
changes.rst
run_tests.py
setup.cfg
setup.py
contributors/cpptraj.md
contributors/pytraj.rst
examples/README.md
examples/example_Amber_to_CHARMM.py
examples/example_append_traj_and_write.py
examples/example_autocorrelation.py
examples/example_average_structure.py
examples/example_bfactors.py
examples/example_calculate_chi_angle.py
examples/example_center_of_geometry.py
examples/example_center_of_mass.py
examples/example_cpptraj_style.py
examples/example_distance.py
examples/example_distance_matrix.py
examples/example_dssp.py
examples/example_energy_decomposition.py
examples/example_fancy_indexing_traj.py
examples/example_get_atom_mass.py
examples/example_hydrogen_bonding.py
examples/example_kmeans_sklearn.py
examples/example_load_filelist.py
examples/example_load_pdb_as_trajectory.py
examples/example_load_pdb_from_rcsb.py
examples/example_load_trajectory_by_chunk.py
examples/example_mdtraj_to_pytraj.py
examples/example_minimum_distance.py
examples/example_multidihedral.py
examples/example_native_contacts.py
examples/example_nucleic_analysis.py
examples/example_out_of_core_calculation.py
examples/example_pairwise_rmsd.py
examples/example_pandas_DataFrame.py
examples/example_parallelize.py
examples/example_pca.py
examples/example_pca_sklearn_vs_cpptraj.py
examples/example_radgyr.py
examples/example_read_gaussian_output.py
examples/example_rmsd.py
examples/example_rmsd_2trajs.py
examples/example_rmsd_two_pars.py
examples/example_rotate_dihedral_and_energy_calc.py
examples/example_rotate_dihedral_for_movie.py
examples/example_save_traj_with_autoimage_and_rms.py
examples/example_selecting_atoms.py
examples/example_slice_to_get_z_coordinates.py
examples/example_split_and_write_trajectory.py
examples/example_strip_solvent.py
examples/example_superpose.py
examples/example_water_clustering.py
examples/example_write_force_to_trajectory.py
examples/example_write_parm.py
examples/example_write_pdb_options.py
examples/example_write_pdbs_for_movies.py
examples/example_write_traj.py
examples/example_write_traj_with_indices.py
examples/get_py_files.py
examples/progress_bar.gif
examples/pytraj_readme.ipynb
examples/run_examples.py
examples/advanced_users/example_actionlist.py
examples/data/mdfrc
examples/data/mdfrc.prmtop
examples/figures/nglview.png
examples/figures/nglview_pytraj.gif
examples/figures/nglview_pytraj_autoimage.png
examples/figures/progress_bar.gif
examples/figures/pytraj.gif
examples/mpi_examples/cpptraj.py
examples/mpi_examples/mpi_load_batch.py
examples/mpi_examples/mpi_molsurf.py
examples/mpi_examples/mpi_pysander.py
examples/mpi_examples/rmsd_mpi_example.py
examples/mpi_examples/run_mpi_examples.sh
examples/mpi_examples/serial_cal_molsurf_0_for_mpi_test.py
examples/mpi_examples/output/__init__.py
examples/outdated/example_density.py
examples/outdated/example_dihedral.py
examples/outdated/example_randomize_ions.py
examples/outdated/extract_temperature_traj_remd.py
examples/output/README.md
licenses/README
licenses/pytraj.md
licenses/externals/dask.txt
licenses/externals/jupyter-themes.txt
licenses/externals/magic.txt
licenses/externals/mdtraj.txt
licenses/externals/pandas.txt
licenses/externals/six.txt
licenses/externals/toolz.txt
pytraj/__init__.py
pytraj/all_actions.py
pytraj/io.py
pytraj/version.py
pytraj.egg-info/PKG-INFO
pytraj.egg-info/SOURCES.txt
pytraj.egg-info/dependency_links.txt
pytraj.egg-info/requires.txt
pytraj.egg-info/top_level.txt
pytraj/analysis/__init__.py
pytraj/analysis/base_holder.py
pytraj/analysis/dihedral_analysis.py
pytraj/analysis/dssp_analysis.py
pytraj/analysis/energy_analysis.py
pytraj/analysis/hbond_analysis.py
pytraj/analysis/matrix.py
pytraj/analysis/nmr.py
pytraj/analysis/nucleic_acid_analysis.py
pytraj/analysis/rmsd.py
pytraj/analysis/topology_analysis.py
pytraj/analysis/vector.py
pytraj/analysis/water.py
pytraj/analysis/c_action/__init__.py
pytraj/analysis/c_action/actionlist.cpp
pytraj/analysis/c_action/actionlist.pxd
pytraj/analysis/c_action/actionlist.pyx
pytraj/analysis/c_action/c_action.cpp
pytraj/analysis/c_action/c_action.pxd
pytraj/analysis/c_action/c_action.pyx
pytraj/analysis/c_analysis/__init__.py
pytraj/analysis/c_analysis/analysis_dict.py
pytraj/analysis/c_analysis/c_analysis.cpp
pytraj/analysis/c_analysis/c_analysis.pxd
pytraj/analysis/c_analysis/c_analysis.pyx
pytraj/builder/__init__.py
pytraj/builder/build.py
pytraj/cluster/__init__.py
pytraj/core/__init__.py
pytraj/core/box.cpp
pytraj/core/box.pxd
pytraj/core/box.pyx
pytraj/core/c_core.cpp
pytraj/core/c_core.pxd
pytraj/core/c_core.pyx
pytraj/core/c_dict.cpp
pytraj/core/c_dict.pxd
pytraj/core/c_dict.pyx
pytraj/core/c_options.cpp
pytraj/core/c_options.pyx
pytraj/core/coordinfo.cpp
pytraj/core/coordinfo.pxd
pytraj/core/coordinfo.pyx
pytraj/core/cpp_vector.pxd
pytraj/core/elements.py
pytraj/core/parameter_types.cpp
pytraj/core/parameter_types.pxd
pytraj/core/parameter_types.pyx
pytraj/core/topology_objects.cpp
pytraj/core/topology_objects.pxd
pytraj/core/topology_objects.pyx
pytraj/cython_extra_header/__init__.py
pytraj/cython_extra_header/cpp_algorithm.pxd
pytraj/cython_extra_header/cpp_vector.pxd
pytraj/datafiles/README
pytraj/datafiles/__init__.py
pytraj/datafiles/datafiles.cpp
pytraj/datafiles/datafiles.pxd
pytraj/datafiles/datafiles.pyx
pytraj/datafiles/load_samples.py
pytraj/datafiles/rna.pdb
pytraj/datafiles/ala3/Ala3.crd
pytraj/datafiles/ala3/Ala3.top
pytraj/datafiles/ala3/__init__.py
pytraj/datafiles/dpdp/DPDP.nc
pytraj/datafiles/dpdp/DPDP.parm7
pytraj/datafiles/dpdp/__init__.py
pytraj/datafiles/remd_ala2/__init__.py
pytraj/datafiles/remd_ala2/ala2.parm7
pytraj/datafiles/remd_ala2/rem.nc.000
pytraj/datafiles/remd_ala2/rem.nc.001
pytraj/datafiles/remd_ala2/rem.nc.002
pytraj/datafiles/remd_ala2/rem.nc.003
pytraj/datafiles/trpcage/__init__.py
pytraj/datafiles/trpcage/trpcage.pdb.gz
pytraj/datafiles/tz2/__init__.py
pytraj/datafiles/tz2/tz2.nc
pytraj/datafiles/tz2/tz2.ortho.nc
pytraj/datafiles/tz2/tz2.ortho.parm7
pytraj/datafiles/tz2/tz2.parm7
pytraj/datasets/__init__.py
pytraj/datasets/array.py
pytraj/datasets/c_datasetlist.cpp
pytraj/datasets/c_datasetlist.pxd
pytraj/datasets/c_datasetlist.pyx
pytraj/datasets/c_datasets.cpp
pytraj/datasets/c_datasets.pxd
pytraj/datasets/c_datasets.pyx
pytraj/datasets/cast_dataset.cpp
pytraj/datasets/cast_dataset.pyx
pytraj/datasets/datasetlist.py
pytraj/externals/README
pytraj/externals/__init__.py
pytraj/externals/load_other_packages.py
pytraj/externals/magic.py
pytraj/externals/six.py
pytraj/externals/wurlitzer.py
pytraj/math/__init__.py
pytraj/math/cpp_math.cpp
pytraj/math/cpp_math.pxd
pytraj/math/cpp_math.pyx
pytraj/parallel/__init__.py
pytraj/parallel/base.py
pytraj/parallel/dataset.py
pytraj/parallel/mpi.py
pytraj/parallel/multiprocess.py
pytraj/sandbox/TrajectoryBaseIterator.py
pytraj/sandbox/__init__.py
pytraj/sandbox/lazy.py
pytraj/sandbox/qm.py
pytraj/sandbox/transform.py
pytraj/serialize/__init__.py
pytraj/serialize/serialize.py
pytraj/testing/__init__.py
pytraj/testing/run_tests.py
pytraj/testing/testing.py
pytraj/topology/__init__.py
pytraj/topology/topology.cpp
pytraj/topology/topology.pxd
pytraj/topology/topology.pyx
pytraj/trajectory/__init__.py
pytraj/trajectory/frame.cpp
pytraj/trajectory/frame.pxd
pytraj/trajectory/frame.pyx
pytraj/trajectory/frameiter.py
pytraj/trajectory/shared_methods.py
pytraj/trajectory/shared_trajectory.py
pytraj/trajectory/stripped_trajectory.py
pytraj/trajectory/trajectory.py
pytraj/trajectory/trajectory_iterator.py
pytraj/trajectory/c_traj/__init__.py
pytraj/trajectory/c_traj/c_trajectory.cpp
pytraj/trajectory/c_traj/c_trajectory.pxd
pytraj/trajectory/c_traj/c_trajectory.pyx
pytraj/trajectory/c_traj/c_trajout.cpp
pytraj/trajectory/c_traj/c_trajout.pxd
pytraj/trajectory/c_traj/c_trajout.pyx
pytraj/utils/Timer.py
pytraj/utils/__init__.py
pytraj/utils/c_commands.py
pytraj/utils/check_and_assert.py
pytraj/utils/context.py
pytraj/utils/convert.py
pytraj/utils/cyutils.cpp
pytraj/utils/cyutils.pyx
pytraj/utils/decorators.py
pytraj/utils/get_common_objects.py
pytraj/utils/log
pytraj/utils/misc.py
pytraj/utils/progress.py
pytraj/utils/tools.py
pytraj/utils/css/oceans16.css
pytraj/utils/progress-circle/README.md
pytraj/utils/progress-circle/progress-circle.js
pytraj/utils/progress-circle/css/circle.css
pytraj/visualization/__init__.py
pytraj/visualization/view.py
scripts/__init__.py
scripts/acsii_art.py
scripts/base_setup.py
scripts/build_wheel.py
scripts/check_openmp.py
scripts/cythonize.py
scripts/find_lib.py
scripts/install_libcpptraj.py
scripts/install_message.py
scripts/six.py
scripts/utils.py
scripts/3rd_party/unistd.h
scripts/__pycache__/__init__.cpython-38.pyc
scripts/__pycache__/base_setup.cpython-38.pyc
scripts/__pycache__/check_openmp.cpython-38.pyc
scripts/__pycache__/find_lib.cpython-38.pyc
scripts/__pycache__/install_libcpptraj.cpython-38.pyc
scripts/__pycache__/install_message.cpython-38.pyc
scripts/ambertools_git/git_diff_amber_git_pytraj_github.sh
scripts/ambertools_git/git_fetch_pytraj_github.sh
scripts/ambertools_git/pull_from_pytraj_github.sh
scripts/ambertools_git/push_to_pytraj_github.sh
scripts/ambertools_git/push_to_pytraj_github_numpy_api.sh
scripts/libcpptraj_tools/PXD_template.dat
scripts/libcpptraj_tools/PYX_template.dat
scripts/libcpptraj_tools/_fix_action.py
scripts/libcpptraj_tools/check_list_headers.py
scripts/libcpptraj_tools/codegen_all_enums.py
scripts/libcpptraj_tools/codegen_enum.py
scripts/libcpptraj_tools/codegen_pxd.py
scripts/libcpptraj_tools/codegen_pyx.py
scripts/libcpptraj_tools/codegen_typedef.py
scripts/libcpptraj_tools/compare_files.py
scripts/libcpptraj_tools/convert_property_to_old_style.py
scripts/libcpptraj_tools/correct_method_names.py
scripts/libcpptraj_tools/enum_to_dict.py
scripts/libcpptraj_tools/find_action_and_analysis_commands.py
scripts/libcpptraj_tools/find_class_name.py
scripts/libcpptraj_tools/find_missing_cpptraj_action_names.py
scripts/libcpptraj_tools/find_then_delete_files_having_keys.py
scripts/libcpptraj_tools/fix_double_colons_for_Analysis.sh
scripts/libcpptraj_tools/grep_class.sh
scripts/libcpptraj_tools/grep_wrap.sh
scripts/libcpptraj_tools/make_new_action_file.py
scripts/libcpptraj_tools/rename_func_c_to_py.py
scripts/libcpptraj_tools/util.py
scripts/libcpptraj_tools/write_action_pxd.py
scripts/libcpptraj_tools/write_action_pyx.py
scripts/libcpptraj_tools/write_allanalyses.py
scripts/libcpptraj_tools/write_analysis_pxd.py
scripts/libcpptraj_tools/write_analysis_pyx.py
scripts/memory/cluster_.py
scripts/memory/mean_structure_.py
scripts/memory/pairwise_rmsd_.py
scripts/memory/rmsd_2trajs.py
scripts/memory/superpose_traj_on_disk.py
scripts/memory/write_traj.py
scripts/misc/change_name.py
scripts/misc/clean_cythonize_files.py
scripts/misc/clean_cythonize_files_git.py
scripts/misc/count_non_blank_lines.sh
scripts/misc/find_libcpptraj.py
scripts/misc/fix_rpath_pip_osx.py
scripts/misc/plot_dihedral.py
scripts/misc/replace_keyword.py
scripts/timing/README.md
scripts/timing/pmap_speed.py
scripts/timing/speed_get_coordinates.py
scripts/timing/timing_distance_actionlist.py
scripts/timing/timing_f_c_orders.py
scripts/timing/timing_iter.py
scripts/timing/timing_load_netcdf.py
scripts/timing/timing_molsurf.py
scripts/timing/timing_netcdf4_vs_pytraj_slicing.py
scripts/timing/timing_pickle_topology.py
scripts/timing/timing_pmap_.py
scripts/timing/timing_pmap_ired_vector_and_matrix.py
scripts/timing/timing_pmap_vs_mdtraj.py