AUTHORS
CMakeLists.txt
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
ecell4/CMakeLists.txt
ecell4/bd/BDFactory.hpp
ecell4/bd/BDPropagator.cpp
ecell4/bd/BDPropagator.hpp
ecell4/bd/BDSimulator.cpp
ecell4/bd/BDSimulator.hpp
ecell4/bd/BDWorld.hpp
ecell4/bd/CMakeLists.txt
ecell4/bd/functions3d.cpp
ecell4/bd/functions3d.hpp
ecell4/bd/samples/CMakeLists.txt
ecell4/bd/samples/hardbody.cpp
ecell4/bd/tests/BDSimulator_test.cpp
ecell4/bd/tests/BDWorld_test.cpp
ecell4/bd/tests/CMakeLists.txt
ecell4/core/AABB.cpp
ecell4/core/AABB.hpp
ecell4/core/AABBSurface.cpp
ecell4/core/AABBSurface.hpp
ecell4/core/Attribute.cpp
ecell4/core/Attribute.hpp
ecell4/core/BDMLWriter.hpp
ecell4/core/Barycentric.cpp
ecell4/core/Barycentric.hpp
ecell4/core/BoundaryCondition.hpp
ecell4/core/CMakeLists.txt
ecell4/core/Circle.hpp
ecell4/core/CompartmentSpace.cpp
ecell4/core/CompartmentSpace.hpp
ecell4/core/CompartmentSpaceHDF5Writer.hpp
ecell4/core/Cone.hpp
ecell4/core/Context.cpp
ecell4/core/Context.hpp
ecell4/core/Cylinder.cpp
ecell4/core/Cylinder.hpp
ecell4/core/Doxyfile
ecell4/core/DynamicPriorityQueue.hpp
ecell4/core/EventScheduler.hpp
ecell4/core/HCPLatticeSpace.cpp
ecell4/core/HCPLatticeSpace.hpp
ecell4/core/Identifier.hpp
ecell4/core/Integer3.cpp
ecell4/core/Integer3.hpp
ecell4/core/Journal.cpp
ecell4/core/Journal.hpp
ecell4/core/LatticeSpaceCellListImpl.cpp
ecell4/core/LatticeSpaceCellListImpl.hpp
ecell4/core/LatticeSpaceHDF5Writer.hpp
ecell4/core/LatticeSpaceVectorImpl.cpp
ecell4/core/LatticeSpaceVectorImpl.hpp
ecell4/core/Mesh.cpp
ecell4/core/Mesh.hpp
ecell4/core/Model.cpp
ecell4/core/Model.hpp
ecell4/core/ModelWrapper.hpp
ecell4/core/MoleculePool.hpp
ecell4/core/NetfreeModel.cpp
ecell4/core/NetfreeModel.hpp
ecell4/core/NetworkModel.cpp
ecell4/core/NetworkModel.hpp
ecell4/core/ObjectIDContainer.hpp
ecell4/core/OffLatticeSpace.cpp
ecell4/core/OffLatticeSpace.hpp
ecell4/core/Particle.hpp
ecell4/core/ParticleSpace.cpp
ecell4/core/ParticleSpace.hpp
ecell4/core/ParticleSpaceCellListImpl.cpp
ecell4/core/ParticleSpaceCellListImpl.hpp
ecell4/core/ParticleSpaceHDF5Writer.hpp
ecell4/core/ParticleSpaceRTreeImpl.cpp
ecell4/core/ParticleSpaceRTreeImpl.hpp
ecell4/core/PeriodicRTree.hpp
ecell4/core/PlanarSurface.cpp
ecell4/core/PlanarSurface.hpp
ecell4/core/Polygon.cpp
ecell4/core/Polygon.hpp
ecell4/core/PolygonHDF5Writer.cpp
ecell4/core/PolygonHDF5Writer.hpp
ecell4/core/Quantity.hpp
ecell4/core/RandomNumberGenerator.cpp
ecell4/core/RandomNumberGenerator.hpp
ecell4/core/ReactionRule.cpp
ecell4/core/ReactionRule.hpp
ecell4/core/ReactionRuleDescriptor.hpp
ecell4/core/Real3.hpp
ecell4/core/Rod.cpp
ecell4/core/Rod.hpp
ecell4/core/STLFileIO.cpp
ecell4/core/STLFileIO.hpp
ecell4/core/Segment.hpp
ecell4/core/SerialIDGenerator.hpp
ecell4/core/Shape.hpp
ecell4/core/Simulator.hpp
ecell4/core/SimulatorBase.hpp
ecell4/core/SimulatorFactory.hpp
ecell4/core/Space.hpp
ecell4/core/Species.cpp
ecell4/core/Species.hpp
ecell4/core/Sphere.cpp
ecell4/core/Sphere.hpp
ecell4/core/StructureType.hpp
ecell4/core/SubvolumeSpace.cpp
ecell4/core/SubvolumeSpace.hpp
ecell4/core/SubvolumeSpaceHDF5Writer.hpp
ecell4/core/Triangle.cpp
ecell4/core/Triangle.hpp
ecell4/core/TriangleView.hpp
ecell4/core/UnitSpecies.cpp
ecell4/core/UnitSpecies.hpp
ecell4/core/VacantType.hpp
ecell4/core/VoxelPool.hpp
ecell4/core/VoxelSpaceBase.cpp
ecell4/core/VoxelSpaceBase.hpp
ecell4/core/VoxelView.hpp
ecell4/core/WorldInterface.hpp
ecell4/core/collision.cpp
ecell4/core/collision.hpp
ecell4/core/comparators.hpp
ecell4/core/config.h.in
ecell4/core/converter.hpp
ecell4/core/exceptions.hpp
ecell4/core/extras.cpp
ecell4/core/extras.hpp
ecell4/core/functions.hpp
ecell4/core/geometry.cpp
ecell4/core/geometry.hpp
ecell4/core/observers.cpp
ecell4/core/observers.hpp
ecell4/core/shape_operators.hpp
ecell4/core/triangle_geometry.cpp
ecell4/core/triangle_geometry.hpp
ecell4/core/type_name_of.hpp
ecell4/core/types.hpp
ecell4/core/tests/Barycentric_test.cpp
ecell4/core/tests/CMakeLists.txt
ecell4/core/tests/CompartmentSpace_test.cpp
ecell4/core/tests/EventScheduler_test.cpp
ecell4/core/tests/LatticeSpace_test.cpp
ecell4/core/tests/NetfreeModel_test.cpp
ecell4/core/tests/NetworkModel_test.cpp
ecell4/core/tests/ObjectIDContainer_test.cpp
ecell4/core/tests/OffLatticeSpace_test.cpp
ecell4/core/tests/ParticleSpaceRTreeImpl_test.cpp
ecell4/core/tests/ParticleSpace_test.cpp
ecell4/core/tests/PeriodicRTree_test.cpp
ecell4/core/tests/Polygon_test.cpp
ecell4/core/tests/RandomNumberGenerator_test.cpp
ecell4/core/tests/ReactionRule_test.cpp
ecell4/core/tests/Real3_test.cpp
ecell4/core/tests/STLIO_test.cpp
ecell4/core/tests/Shape_test.cpp
ecell4/core/tests/Species_test.cpp
ecell4/core/tests/SubvolumeSpace_test.cpp
ecell4/core/tests/Triangle_test.cpp
ecell4/core/tests/extras_test.cpp
ecell4/core/tests/geometry_test.cpp
ecell4/egfrd/.gitignore
ecell4/egfrd/.hgignore
ecell4/egfrd/AUTHORS
ecell4/egfrd/AnalyticalPair.hpp
ecell4/egfrd/AnalyticalSingle.hpp
ecell4/egfrd/BDPropagator.hpp
ecell4/egfrd/BDSimulator.hpp
ecell4/egfrd/CMakeLists.txt
ecell4/egfrd/COPYING
ecell4/egfrd/ChangeLog
ecell4/egfrd/ConsoleAppender.hpp
ecell4/egfrd/Domain.hpp
ecell4/egfrd/DomainID.hpp
ecell4/egfrd/EGFRDSimulator.hpp
ecell4/egfrd/INSTALL
ecell4/egfrd/Logger.cpp
ecell4/egfrd/Logger.hpp
ecell4/egfrd/MatrixSpace.hpp
ecell4/egfrd/Multi.hpp
ecell4/egfrd/NEWS
ecell4/egfrd/NetworkRulesAdapter.hpp
ecell4/egfrd/Pair.hpp
ecell4/egfrd/ParticleContainer.hpp
ecell4/egfrd/ParticleSimulator.hpp
ecell4/egfrd/ParticleTraits.hpp
ecell4/egfrd/Polygon.hpp
ecell4/egfrd/PotentialField.hpp
ecell4/egfrd/README
ecell4/egfrd/ReactionRecord.hpp
ecell4/egfrd/ReactionRecorder.hpp
ecell4/egfrd/ReactionRecorderWrapper.hpp
ecell4/egfrd/ReactionRuleInfo.hpp
ecell4/egfrd/Real3Type.hpp
ecell4/egfrd/ShapedDomain.hpp
ecell4/egfrd/Shell.hpp
ecell4/egfrd/ShellID.hpp
ecell4/egfrd/Single.hpp
ecell4/egfrd/VolumeClearer.hpp
ecell4/egfrd/World.hpp
ecell4/egfrd/egfrd.hpp
ecell4/egfrd/exceptions.hpp
ecell4/egfrd/generator.hpp
ecell4/egfrd/geometry.hpp
ecell4/egfrd/linear_algebra.hpp
ecell4/egfrd/pyport.patch
ecell4/egfrd/sorted_list.hpp
ecell4/egfrd/structures.hpp
ecell4/egfrd/twofold_container.hpp
ecell4/egfrd/samples/CMakeLists.txt
ecell4/egfrd/samples/mymapk.cpp
ecell4/egfrd/samples/polygon.cpp
ecell4/egfrd/samples/wscript
ecell4/egfrd/tests/GreensFunction3DRadInf_test.cpp
ecell4/egfrd/utils/array_helper.hpp
ecell4/egfrd/utils/array_traits.hpp
ecell4/egfrd/utils/collection_contains.hpp
ecell4/egfrd/utils/fun_composition.hpp
ecell4/egfrd/utils/math.hpp
ecell4/egfrd/utils/memberwise_compare.hpp
ecell4/egfrd/utils/pair.hpp
ecell4/egfrd/utils/pointer_as_ref.hpp
ecell4/egfrd/utils/random.hpp
ecell4/egfrd/utils/range.hpp
ecell4/egfrd/utils/stringizer.hpp
ecell4/gillespie/CMakeLists.txt
ecell4/gillespie/GillespieFactory.hpp
ecell4/gillespie/GillespieSimulator.cpp
ecell4/gillespie/GillespieSimulator.hpp
ecell4/gillespie/GillespieWorld.cpp
ecell4/gillespie/GillespieWorld.hpp
ecell4/gillespie/samples/CMakeLists.txt
ecell4/gillespie/samples/simple.cpp
ecell4/gillespie/tests/CMakeLists.txt
ecell4/gillespie/tests/GillespieSimulator_test.cpp
ecell4/gillespie/tests/GillespieWorld_test.cpp
ecell4/meso/CMakeLists.txt
ecell4/meso/MesoscopicFactory.hpp
ecell4/meso/MesoscopicSimulator.cpp
ecell4/meso/MesoscopicSimulator.hpp
ecell4/meso/MesoscopicWorld.cpp
ecell4/meso/MesoscopicWorld.hpp
ecell4/meso/samples/CMakeLists.txt
ecell4/meso/samples/simple-meso.cpp
ecell4/meso/tests/CMakeLists.txt
ecell4/meso/tests/MesoscopicSimulator_test.cpp
ecell4/ode/CMakeLists.txt
ecell4/ode/ODEFactory.hpp
ecell4/ode/ODESimulator.cpp
ecell4/ode/ODESimulator.hpp
ecell4/ode/ODEWorld.cpp
ecell4/ode/ODEWorld.hpp
ecell4/ode/samples/CMakeLists.txt
ecell4/ode/samples/dissociation.cpp
ecell4/ode/samples/equilibrium.cpp
ecell4/ode/samples/equilibrium2.cpp
ecell4/ode/samples/equilibrium_new.cpp
ecell4/ode/samples/odesimulator2.cpp
ecell4/ode/samples/run_test.cpp
ecell4/ode/tests/CMakeLists.txt
ecell4/ode/tests/ODESimulator_new_test.cpp
ecell4/ode/tests/ODESimulator_test.cpp
ecell4/python_api/CMakeLists.txt
ecell4/python_api/bd.cpp
ecell4/python_api/core.cpp
ecell4/python_api/egfrd.cpp
ecell4/python_api/gillespie.cpp
ecell4/python_api/main.cpp
ecell4/python_api/meso.cpp
ecell4/python_api/model.hpp
ecell4/python_api/observers.hpp
ecell4/python_api/ode.cpp
ecell4/python_api/python_api.hpp
ecell4/python_api/random_number_generator.hpp
ecell4/python_api/reaction_rule_descriptor.hpp
ecell4/python_api/sgfrd.cpp
ecell4/python_api/shape.hpp
ecell4/python_api/simulator.hpp
ecell4/python_api/simulator_factory.hpp
ecell4/python_api/spatiocyte.cpp
ecell4/python_api/type_caster.hpp
ecell4/python_api/world_interface.hpp
ecell4/sgfrd/BDPropagator.hpp
ecell4/sgfrd/BDSimulator.hpp
ecell4/sgfrd/Birth.hpp
ecell4/sgfrd/CMakeLists.txt
ecell4/sgfrd/Multi.hpp
ecell4/sgfrd/MultiContainer.hpp
ecell4/sgfrd/Pair.hpp
ecell4/sgfrd/ReactionInfo.hpp
ecell4/sgfrd/SGFRDEvent.hpp
ecell4/sgfrd/SGFRDFactory.hpp
ecell4/sgfrd/SGFRDSimulator.cpp
ecell4/sgfrd/SGFRDSimulator.hpp
ecell4/sgfrd/SGFRDWorld.cpp
ecell4/sgfrd/SGFRDWorld.hpp
ecell4/sgfrd/Shell.hpp
ecell4/sgfrd/ShellContainer.hpp
ecell4/sgfrd/ShellID.hpp
ecell4/sgfrd/ShellVisitorApplier.hpp
ecell4/sgfrd/ShellVisitors.hpp
ecell4/sgfrd/Single.hpp
ecell4/sgfrd/StructureRegistrator.hpp
ecell4/sgfrd/distance.hpp
ecell4/sgfrd/distance_calculator.hpp
ecell4/sgfrd/expected.hpp
ecell4/sgfrd/statistics.hpp
ecell4/sgfrd/tracer.hpp
ecell4/sgfrd/samples/CMakeLists.txt
ecell4/sgfrd/samples/bdonly.cpp
ecell4/sgfrd/samples/diffusion.cpp
ecell4/sgfrd/samples/plane10x10.stl
ecell4/sgfrd/samples/reaction.cpp
ecell4/sgfrd/samples/reaction.inp
ecell4/sgfrd/samples/rebinding_bd.cpp
ecell4/sgfrd/samples/sphere.stl
ecell4/spatiocyte/CMakeLists.txt
ecell4/spatiocyte/OffLattice.hpp
ecell4/spatiocyte/OneToManyMap.hpp
ecell4/spatiocyte/ReactionEvent.cpp
ecell4/spatiocyte/SpatiocyteEvent.hpp
ecell4/spatiocyte/SpatiocyteFactory.hpp
ecell4/spatiocyte/SpatiocyteReactions.cpp
ecell4/spatiocyte/SpatiocyteReactions.hpp
ecell4/spatiocyte/SpatiocyteSimulator.cpp
ecell4/spatiocyte/SpatiocyteSimulator.hpp
ecell4/spatiocyte/SpatiocyteWorld.cpp
ecell4/spatiocyte/SpatiocyteWorld.hpp
ecell4/spatiocyte/StepEvent.cpp
ecell4/spatiocyte/Voxel.hpp
ecell4/spatiocyte/utils.cpp
ecell4/spatiocyte/utils.hpp
ecell4/spatiocyte/samples/CMakeLists.txt
ecell4/spatiocyte/samples/diffusion.cpp
ecell4/spatiocyte/samples/simple_lattice.cpp
ecell4/spatiocyte/tests/CMakeLists.txt
ecell4/spatiocyte/tests/OneToManyMap_test.cpp
ecell4/spatiocyte/tests/SpatiocyteSimulator_test.cpp
ecell4/spatiocyte/tests/SpatiocyteWorld_test.cpp
ecell4_base.egg-info/PKG-INFO
ecell4_base.egg-info/SOURCES.txt
ecell4_base.egg-info/dependency_links.txt
ecell4_base.egg-info/not-zip-safe
ecell4_base.egg-info/top_level.txt