├── .clang-format ├── .github └── workflows │ └── netsci_CI.yml ├── .gitignore ├── .gitmodules ├── .readthedocs.yaml ├── CMakeLists.txt ├── README.md ├── cnpy ├── CMakeLists.txt ├── include │ └── cnpy.h └── src │ └── cnpy.cpp ├── cuarray ├── CMakeLists.txt ├── include │ └── cuarray.h ├── python │ ├── cuarray │ │ └── __init__.py │ └── setup.py ├── samples │ ├── cpp │ │ ├── CMakeLists.txt │ │ └── src │ │ │ ├── CuArray_CuArray.cpp │ │ │ ├── CuArray_allocateDevice.cpp │ │ │ ├── CuArray_allocateHost.cpp │ │ │ ├── CuArray_allocatedDevice.cpp │ │ │ ├── CuArray_allocatedHost.cpp │ │ │ ├── CuArray_argsort.cpp │ │ │ ├── CuArray_bytes.cpp │ │ │ ├── CuArray_deallocateHost.cpp │ │ │ ├── CuArray_device.cpp │ │ │ ├── CuArray_fromCuArrayDeepCopy.cpp │ │ │ ├── CuArray_fromCuArrayShallowCopy.cpp │ │ │ ├── CuArray_fromNumpy1.cpp │ │ │ ├── CuArray_fromNumpy2.cpp │ │ │ ├── CuArray_get.cpp │ │ │ ├── CuArray_host.cpp │ │ │ ├── CuArray_init1.cpp │ │ │ ├── CuArray_init2.cpp │ │ │ ├── CuArray_load.cpp │ │ │ ├── CuArray_m.cpp │ │ │ ├── CuArray_n.cpp │ │ │ ├── CuArray_owner.cpp │ │ │ ├── CuArray_save.cpp │ │ │ ├── CuArray_set.cpp │ │ │ ├── CuArray_size.cpp │ │ │ ├── CuArray_sort.cpp │ │ │ ├── CuArray_subscriptOperator.cpp │ │ │ ├── CuArray_toDevice.cpp │ │ │ ├── CuArray_toHost.cpp │ │ │ ├── CuArray_toNumpy1.cpp │ │ │ └── CuArray_toNumpy2.cpp │ └── python │ │ ├── CuArray___getitem__.py │ │ ├── CuArray___init__.py │ │ ├── CuArray_argsort.py │ │ ├── CuArray_fromCuArray.py │ │ ├── CuArray_fromNumpy1D.py │ │ ├── CuArray_fromNumpy2D.py │ │ ├── CuArray_get.py │ │ ├── CuArray_init.py │ │ ├── CuArray_load.py │ │ ├── CuArray_m.py │ │ ├── CuArray_n.py │ │ ├── CuArray_save.py │ │ ├── CuArray_set.py │ │ ├── CuArray_size.py │ │ ├── CuArray_sort.py │ │ ├── CuArray_toNumpy1D.py │ │ └── CuArray_toNumpy2D.py ├── src │ └── cuarray.cu ├── swig │ ├── numpy.i │ ├── numpy_float_array.i │ ├── numpy_int_array.i │ ├── python_cuarray.i │ ├── python_cuarray_docs.i │ ├── python_cuarray_headers.i │ ├── python_cuarray_ignore.i │ ├── python_cuarray_include.i │ ├── python_cuarray_pythoncode.i │ ├── python_cuarray_rename.i │ ├── python_cuarray_template.i │ ├── python_cuarray_typemaps.i │ ├── tcl_cuarray.i │ ├── tcl_cuarray_headers.i │ ├── tcl_cuarray_ignore.i │ ├── tcl_cuarray_include.i │ ├── tcl_cuarray_rename.i │ └── tcl_cuarray_template.i └── tcl │ ├── create_vmd_package.tcl │ └── cuarray.tcl ├── docs ├── Makefile ├── conf.py ├── index.rst ├── installation.rst ├── introduction.rst ├── make.bat ├── media │ ├── protG_short.dcd │ ├── protG_short.pdb │ ├── prot_G_gen_corr_global.png │ ├── prot_G_gen_corr_local.png │ ├── raw_correl_apo.png │ └── serca_correl.png ├── program_options.rst ├── requirements.txt ├── requirements.yaml ├── tutorial.rst ├── tutorial1_simple_gaussian_mi.rst ├── tutorial2_protein_structure_gc.rst └── tutorial3_bootstrapping.rst ├── doxygen └── index.h ├── examples ├── README ├── bootstrap_sample.py ├── find_mutual_inf_sample.py ├── make_two_cols_indep_data.py └── sample.dat ├── install.sh ├── netcalc ├── CMakeLists.txt ├── include │ ├── generalized_correlation.h │ ├── hedetniemi.h │ ├── math_utils.h │ ├── mutual_information.h │ ├── platform.h │ └── psi.h ├── python │ ├── netcalc │ │ └── __init__.py │ └── setup.py ├── samples │ └── python │ │ ├── NetCalc_generalizedCorrelation.py │ │ ├── NetCalc_generalizedCorrelationWithCheckpointing.py │ │ ├── NetCalc_mutualInformation.py │ │ └── NetCalc_mutualInformationWithCheckpointing.py ├── scratch │ ├── checkpointing_scratch.cpp │ └── hedetniemi_scratch.cpp ├── src │ ├── generalized_correlation.cpp │ ├── generalized_correlation_cpu.cpp │ ├── generalized_correlation_gpu.cpp │ ├── hedetniemi.cpp │ ├── hedetniemi_cpu.cpp │ ├── hedetniemi_gpu.cu │ ├── math_utils.cpp │ ├── math_utils_gpu.cu │ ├── mutual_information.cpp │ ├── mutual_information_cpu.cpp │ ├── mutual_information_gpu.cu │ └── psi.cpp └── swig │ ├── numpy.i │ ├── numpy_int_array.i │ ├── python_netcalc.i │ ├── python_netcalc_header.i │ ├── python_netcalc_include.i │ └── python_netcalc_rename.i ├── netchem ├── CMakeLists.txt ├── include │ ├── atom.h │ ├── atoms.h │ ├── chemical_properties.h │ ├── dcd │ │ ├── dcd.h │ │ ├── endianswap.h │ │ ├── fastio.h │ │ ├── largefiles.h │ │ ├── molfile_plugin.h │ │ └── vmdplugin.h │ ├── json │ │ ├── LISCENSE.MIT │ │ ├── include │ │ │ └── nlohmann │ │ │ │ ├── adl_serializer.hpp │ │ │ │ ├── byte_container_with_subtype.hpp │ │ │ │ ├── detail │ │ │ │ ├── abi_macros.hpp │ │ │ │ ├── conversions │ │ │ │ │ ├── from_json.hpp │ │ │ │ │ ├── to_chars.hpp │ │ │ │ │ └── to_json.hpp │ │ │ │ ├── exceptions.hpp │ │ │ │ ├── hash.hpp │ │ │ │ ├── input │ │ │ │ │ ├── binary_reader.hpp │ │ │ │ │ ├── input_adapters.hpp │ │ │ │ │ ├── json_sax.hpp │ │ │ │ │ ├── lexer.hpp │ │ │ │ │ ├── parser.hpp │ │ │ │ │ └── position_t.hpp │ │ │ │ ├── iterators │ │ │ │ │ ├── internal_iterator.hpp │ │ │ │ │ ├── iter_impl.hpp │ │ │ │ │ ├── iteration_proxy.hpp │ │ │ │ │ ├── iterator_traits.hpp │ │ │ │ │ ├── json_reverse_iterator.hpp │ │ │ │ │ └── primitive_iterator.hpp │ │ │ │ ├── json_custom_base_class.hpp │ │ │ │ ├── json_pointer.hpp │ │ │ │ ├── json_ref.hpp │ │ │ │ ├── macro_scope.hpp │ │ │ │ ├── macro_unscope.hpp │ │ │ │ ├── meta │ │ │ │ │ ├── call_std │ │ │ │ │ │ ├── begin.hpp │ │ │ │ │ │ └── end.hpp │ │ │ │ │ ├── cpp_future.hpp │ │ │ │ │ ├── detected.hpp │ │ │ │ │ ├── identity_tag.hpp │ │ │ │ │ ├── is_sax.hpp │ │ │ │ │ ├── std_fs.hpp │ │ │ │ │ ├── type_traits.hpp │ │ │ │ │ └── void_t.hpp │ │ │ │ ├── output │ │ │ │ │ ├── binary_writer.hpp │ │ │ │ │ ├── output_adapters.hpp │ │ │ │ │ └── serializer.hpp │ │ │ │ ├── string_concat.hpp │ │ │ │ ├── string_escape.hpp │ │ │ │ └── value_t.hpp │ │ │ │ ├── json.hpp │ │ │ │ ├── json_fwd.hpp │ │ │ │ ├── ordered_map.hpp │ │ │ │ └── thirdparty │ │ │ │ └── hedley │ │ │ │ ├── hedley.hpp │ │ │ │ └── hedley_undef.hpp │ │ ├── single_include │ │ │ └── nlohmann │ │ │ │ ├── json.hpp │ │ │ │ └── json_fwd.hpp │ │ └── tools │ │ │ ├── amalgamate │ │ │ ├── CHANGES.md │ │ │ ├── README.md │ │ │ ├── amalgamate.py │ │ │ ├── config_json.json │ │ │ └── config_json_fwd.json │ │ │ ├── gdb_pretty_printer │ │ │ ├── README.md │ │ │ └── nlohmann-json.py │ │ │ ├── generate_natvis │ │ │ ├── README.md │ │ │ ├── generate_natvis.py │ │ │ └── nlohmann_json.natvis.j2 │ │ │ ├── macro_builder │ │ │ └── main.cpp │ │ │ └── serve_header │ │ │ ├── README.md │ │ │ ├── demo.png │ │ │ ├── requirements.txt │ │ │ ├── serve_header.py │ │ │ └── serve_header.yml.example │ ├── network.h │ ├── node.h │ ├── serializer.h │ └── utils.h ├── python │ ├── netchem │ │ ├── __init__.py │ │ └── data │ │ │ ├── __init__.py │ │ │ ├── pyro.tar.gz │ │ │ └── test.tar.gz │ └── setup.py ├── samples │ └── python │ │ ├── NetChem_Atom_chainId.py │ │ ├── NetChem_Atom_element.py │ │ ├── NetChem_Atom_index.py │ │ ├── NetChem_Atom_mass.py │ │ ├── NetChem_Atom_name.py │ │ ├── NetChem_Atom_occupancy.py │ │ ├── NetChem_Atom_residueId.py │ │ ├── NetChem_Atom_residueName.py │ │ ├── NetChem_Atom_segmentId.py │ │ ├── NetChem_Atom_serial.py │ │ ├── NetChem_Atom_tag.py │ │ ├── NetChem_Atom_temperatureFactor.py │ │ ├── NetChem_Atoms_at.py │ │ ├── NetChem_Atoms_atoms.py │ │ ├── NetChem_Atoms_numAtoms.py │ │ ├── NetChem_Network_atoms.py │ │ ├── NetChem_Network_init.py │ │ ├── NetChem_Network_load.py │ │ ├── NetChem_Network_nodeCoordinates1.py │ │ ├── NetChem_Network_nodeCoordinates2.py │ │ ├── NetChem_Network_nodeFromAtomIndex.py │ │ ├── NetChem_Network_nodes.py │ │ ├── NetChem_Network_numFrames.py │ │ ├── NetChem_Network_numNodes.py │ │ ├── NetChem_Network_save.py │ │ ├── NetChem_Node_atoms.py │ │ ├── NetChem_Node_index.py │ │ ├── NetChem_Node_numAtoms.py │ │ ├── NetChem_Node_tag.py │ │ └── NetChem_Node_totalMass.py ├── scratch │ └── stride_scratch.cpp ├── src │ ├── atom.cpp │ ├── atoms.cpp │ ├── dcd │ │ └── dcd.cpp │ ├── network.cpp │ ├── node.cpp │ ├── serializer.cpp │ └── utils.cpp └── swig │ ├── python_netchem.i │ ├── python_netchem_headers.i │ ├── python_netchem_include.i │ ├── python_netchem_template.i │ └── python_netchem_typemaps.i ├── netsci.yml ├── pyproject.toml ├── pytest.ini ├── tests ├── CMakeLists.txt ├── cuarray │ ├── cpp │ │ ├── CMakeLists.txt │ │ ├── FloatCuArrayFixture.h │ │ └── FloatCuArray_test.cpp │ └── python │ │ ├── conftest.py │ │ └── test_FloatCuArray.py ├── data │ ├── 2X_1D_1000_4.npy │ └── 2X_1D_2000_4.npy ├── netcalc │ ├── cpp │ │ ├── CMakeLists.txt │ │ ├── GeneralizedCorrelation_test.cpp │ │ ├── MutualInformation_test.cpp │ │ └── data │ │ │ ├── 2X_1D_1000_4.npy │ │ │ └── 2X_1D_2000_4.npy │ └── python │ │ ├── test_GeneralizedCorrelation.py │ │ └── test_MutualInformation.py └── netchem │ ├── cpp │ ├── CMakeLists.txt │ ├── NetworkStride1_test.cpp │ ├── NetworkStride2_test.cpp │ ├── NetworkStride3_test.cpp │ ├── NetworkStrideCoordinateEquality_test.cpp │ └── data │ │ ├── test.dcd │ │ └── test.pdb │ └── python │ └── test_Network.py └── tutorial ├── protG_short.dcd ├── protG_short.pdb ├── 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