IMP  2.3.1
The Integrative Modeling Platform
argument_index.md
1 Argument Index {#argument_index}
2 ==============
3 
4 # Overview #
5 [TOC]
6 Functions that take objects of a given type as arguments:
7 
8 See also [Factory Index](@ref factory_index), [Argument Index](@ref argument_index), [Class Examples](@ref class_example_index), [Function Examples](@ref function_example_index)
9 # IMP.algebra # {#argument_index_algebra}
10 <table><tr>
11 <th>Class</th><th>Users</th></tr>
12 <tr><td>@ref IMP::algebra::BoundingBoxD</td><td><a href="classIMP_1_1algebra_1_1BoundingBoxD.html#ac93f335b7c79748991ec968e7209b28f">IMP::algebra::BoundingBoxD::get_contains()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#a2469d780b50d800679f17bdc0b536541">IMP::algebra::BoundingBoxD::operator+()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#aa8092895377c9aca82b78050456b33c9">IMP::algebra::BoundingBoxD::operator+=()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a75841ace50c634c2ffa23e4e5d458564">IMP::algebra::DefaultEmbeddingD::initialize_from_box()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#aba328c5e51d34efea9057707ac80695c">IMP::algebra::GridD::voxels_begin()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#ad206879a1a9b301229b3034dbe3c87c5">IMP::algebra::GridD::voxels_end()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a17f80a5eac1f7d71b66f49334a8f9d93">IMP::algebra::GridD::voxels_begin()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a63d86b3db27639e5117b86f0964dd7e9">IMP::algebra::GridD::voxels_end()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a0e73f5094989644138b2df7a923e59f5">IMP::algebra::GridD::indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#aa18ee2704ae69eff7db20ca04098fedf">IMP::algebra::GridD::indexes_end()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a91df12851f5e94fb5d1eaa17228b74a6">IMP::algebra::GridD::extended_indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#ab8d1e94d9e10cc7d56abf46cdbb71dd6">IMP::algebra::GridD::extended_indexes_end()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a3e65b1bbbceeb84c5bed65fb4506a2fa">IMP::algebra::GridD::get_indexes()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a7a7210fd159af13e5af33db938498adc">IMP::algebra::GridD::get_extended_indexes()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a97ccb184c448edc82741a0b8126ec750">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#aa575da807c4f8427657289c1725587c2">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#ab96be5a02e7d8a1729e6b47e8f6b93da">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#ab560837a0b4afe66e89bfc0d628deaa8">IMP::algebra::GridD::set_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#aa0ae0da722e8d9f7f7111424309f58f9">IMP::algebra::LogEmbeddingD::initialize_from_box()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a11cfe0991d05693602b83f0a601a9c26">IMP::algebra::LogEmbeddingD::LogEmbeddingD()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a4c822d5e5d8b3895b3f820b6cad91f42">IMP::core::GenericBoundingBox3DSingletonScore::GenericBoundingBox3DSingletonScore()</a>, <a href="classIMP_1_1core_1_1MCCGSampler.html#ad2439bf720e48f108c5250f2ad6fd84c">IMP::core::MCCGSampler::set_bounding_box()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#a09bd7874b00fda0019a13c52054fec6b">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#abffcb4633c7da35860a1a7f3f97f35b0">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#a6f4bacf190fc76a5ecdc2459bfed9891">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#ae5b0e15df553dc00f20635f7f1b3f7fd">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#aac5c637efa72beefcc9cc51b6ca71eb7">IMP::display::BoundingBoxGeometry::set_geometry()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#ae16321e35f3831e87c4dbbaaa26badc9">IMP::example::ExampleSingletonModifier::ExampleSingletonModifier()</a>, <a href="classIMP_1_1statistics_1_1HistogramD.html#a7598b6d1cd28f41e56929ec813bed28d">IMP::statistics::HistogramD::HistogramD()</a>, <a href="namespaceIMP_1_1algebra.html#aa93b951ad9978ca2264245e0178777fc">IMP::algebra::get_random_vector_in()</a>, <a href="namespaceIMP_1_1algebra.html#a1d68a09215054f5656feb5c310a9e9e0">IMP::algebra::get_random_vector_on()</a>, <a href="namespaceIMP_1_1algebra.html#acd7374a5c7f5ae77930afbbf226315f6">IMP::algebra::get_grid_interior_cover_by_spacing()</a>, <a href="namespaceIMP_1_1algebra.html#a17aeb2742e60928cf687ef786530d44c">IMP::algebra::get_edges()</a>, <a href="namespaceIMP_1_1algebra.html#ab00c98290b98833acf41b7cdfaa1a701">IMP::algebra::get_interiors_intersect()</a>, <a href="namespaceIMP_1_1algebra.html#a7d107e54c2f6c82ac6af484a62dba718">IMP::algebra::get_intersection()</a>, <a href="namespaceIMP_1_1algebra.html#a06143c1eada26a19c52b0727f8ab2028">IMP::algebra::get_maximum_length()</a>, <a href="namespaceIMP_1_1algebra.html#aec3bea2d24fbbf621216822517ca1593">IMP::algebra::get_transformed()</a>, <a href="namespaceIMP_1_1algebra.html#a5884c6b32a247dd314db4c33b92508b8">IMP::algebra::get_union()</a>, <a href="namespaceIMP_1_1algebra.html#a8d62bc96f3a84795ae43665423fe9414">IMP::algebra::get_vertices()</a>, <a href="namespaceIMP_1_1algebra.html#a94f280e1b578da3b5875fb157cfc7c68">IMP::algebra::get_volume()</a>, <a href="namespaceIMP_1_1core.html#a2d189bddcf9e654a50e9ce934a9a4ac6">IMP::core::create_bounding_box_3d_singleton_score()</a>, <a href="namespaceIMP_1_1display.html#a788545ff045770aea75e72b5568aba1d">IMP::display::create_geometry()</a>, <a href="namespaceIMP_1_1em.html#a11f40ffc07e7b3d9dde0711015f3e97e">IMP::em::create_density_header()</a></td></tr>
13 <tr><td>@ref IMP::algebra::Cone3D</td><td><a href="classIMP_1_1algebra_1_1Cone3D.html#a42215f5c82c6b41689887aee272d6f29">IMP::algebra::Cone3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Cone3D.html#a9408590e3b4ed9bea9901e0cc53f1039">IMP::algebra::Cone3D::get_cone_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1Cone3D.html#a65a8552f8446684eba1acb5a97edd9c2">IMP::algebra::Cone3D::get_surface_area()</a>, <a href="classIMP_1_1algebra_1_1Cone3D.html#a024adad21c3b01de7558343ad0520532">IMP::algebra::Cone3D::get_volume()</a>, <a href="classIMP_1_1algebra_1_1Cone3D.html#a8ef5b67cbfb8740ffc1efe1d2c28ab9e">IMP::algebra::Cone3D::set_cone_3d_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a87c353d6dce6da5d919b552792b88c46">IMP::algebra::get_uniform_surface_cover()</a></td></tr>
14 <tr><td>@ref IMP::algebra::Cylinder3D</td><td><a href="classIMP_1_1algebra_1_1Cylinder3D.html#a2c0e1a36a0080caf666ff5e8657c44ea">IMP::algebra::Cylinder3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Cylinder3D.html#a1f598fc535a050c3979cd2726732a552">IMP::algebra::Cylinder3D::get_cylinder_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1Cylinder3D.html#a16c33aab2de593af8b93d80f4c76f74e">IMP::algebra::Cylinder3D::get_surface_area()</a>, <a href="classIMP_1_1algebra_1_1Cylinder3D.html#a8a6dda8bdf445ff3c166165eddc7e2e5">IMP::algebra::Cylinder3D::get_volume()</a>, <a href="classIMP_1_1algebra_1_1Cylinder3D.html#a286efcbeac664dac18d23afae3232bb7">IMP::algebra::Cylinder3D::set_cylinder_3d_geometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#ae1b4a1736ef8057c5ce389bc4310e7ef">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#ab08ceebc8704d641be302119db1ebb73">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#af38ad28d6d178422d8db293d14b7d646">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#a31190a41e1a7354c221761274eaf5f34">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#abf3c1eee4096e672e2f5ed468c766e0f">IMP::display::CylinderGeometry::set_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a0c132a833a6f30793378bbed6dfb8f65">IMP::algebra::get_random_vector_in()</a>, <a href="namespaceIMP_1_1algebra.html#a991a576bd3cb05927a2cf4b0089f9d56">IMP::algebra::get_uniform_surface_cover()</a>, <a href="namespaceIMP_1_1algebra.html#af754ef2df6fa5f3ba1a211458399a8b5">IMP::algebra::get_grid_surface_cover()</a>, <a href="namespaceIMP_1_1display.html#a418acde3993b51a25f3ba4311f4c9b74">IMP::display::create_geometry()</a></td></tr>
15 <tr><td>@ref IMP::algebra::DenseGridStorageD</td><td><a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#ab208fed96240a99ad591add590f90ed2">IMP::algebra::DenseGridStorageD::copy_from()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#aae130f31cd621b14e73d06497b671ddb">IMP::algebra::DenseGridStorageD::DenseGridStorageD()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#a5cd0208038b5008c73248047c91f38a7">IMP::algebra::DenseGridStorageD::operator=()</a>, <a href="namespaceIMP_1_1em.html#a325cd7401c937376cfb3504606e4ffd3">IMP::em::create_density_map()</a></td></tr>
16 <tr><td>@ref IMP::algebra::Ellipsoid3D</td><td><a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a51e51989d370ac6d1f72605ea2b55659">IMP::algebra::Ellipsoid3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a2fd68925f46292fc3f90454f7a34bded">IMP::algebra::Ellipsoid3D::get_ellipsoid_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a5cea431932512ba0f6c5e54fd129deba">IMP::algebra::Ellipsoid3D::get_surface_area()</a>, <a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a7a64fb811faa2d387a26960c723bb772">IMP::algebra::Ellipsoid3D::get_volume()</a>, <a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a00d1a28d190859480cc3a8f1c01aef0e">IMP::algebra::Ellipsoid3D::set_ellipsoid_3d_geometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#ac975d8291f2dce584758a7fa4c0ac3e5">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a8b23de125510a349978b1b789743ea33">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a880be80c539c27f6e16c0a38a9fa9c9c">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#ae80469cfe57e39a43311da048a65b785">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a06dbe9b339d4fdb16b7f76b095ff4cf7">IMP::display::EllipsoidGeometry::set_geometry()</a>, <a href="namespaceIMP_1_1display.html#acbb9389b216a0e7f8c4d9794075ccbf8">IMP::display::create_geometry()</a></td></tr>
17 <tr><td>@ref IMP::algebra::ExtendedGridIndexD</td><td><a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a406ec057e7a1bee2dd04eb234e8756fc">IMP::algebra::BoundedGridRangeD::indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a43156c09951cce2f2519378f32681b54">IMP::algebra::BoundedGridRangeD::indexes_end()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a962bbb90a0676e27b1707dbb9b2c0386">IMP::algebra::BoundedGridRangeD::extended_indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#af6ebb547d959a0ef5b0c2f0ec24c8f43">IMP::algebra::BoundedGridRangeD::extended_indexes_end()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a2cc3b3ebbceaf09645e7243039a54743">IMP::algebra::BoundedGridRangeD::get_indexes()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a7daff516adaa890c3d2ce985fcf8c432">IMP::algebra::BoundedGridRangeD::get_extended_indexes()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a4aae88234ef495bca2bfd9baf28b8ce3">IMP::algebra::BoundedGridRangeD::get_has_index()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#acf1f33b1c1d7957330f442f15d656ac9">IMP::algebra::BoundedGridRangeD::get_index()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a42f36edf378dc3cb21d8b8320b2262d9">IMP::algebra::DefaultEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#aa939cc38c61633c05ba8f512671c9922">IMP::algebra::DefaultEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1ExtendedGridIndexD.html#a86a4c3b004691c387e506c2b811e071c">IMP::algebra::ExtendedGridIndexD::compare()</a>, <a href="classIMP_1_1algebra_1_1ExtendedGridIndexD.html#a90a201d5f614a5a06afdad11b40ce16f">IMP::algebra::ExtendedGridIndexD::IMP_COMPARISONS()</a>, <a href="classIMP_1_1algebra_1_1ExtendedGridIndexD.html#a4aba51011654e969e574224831b909be">IMP::algebra::ExtendedGridIndexD::IMP_HASHABLE_INLINE()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a6f4d8f177ef76a4b4f05dbc3e26489f1">IMP::algebra::LogEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#afcefc82a3dc1a028efd0ef7a76ae3f62">IMP::algebra::LogEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a08248411df29a888727eb1fbe06c2538">IMP::algebra::SparseGridStorageD::indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a9ba25e899fa8d084b868bb334e482945">IMP::algebra::SparseGridStorageD::indexes_end()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a1b65e9c70a1684711065212bf2de936e">IMP::algebra::SparseGridStorageD::get_indexes()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#ab3283a6eb40d179b0648b804a95ef499">IMP::algebra::SparseGridStorageD::add_voxel()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a053acf2aeafd935e97726038903032b6">IMP::algebra::SparseGridStorageD::get_has_index()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#abcf4643d745ad8f61ac711026cb9a5cb">IMP::algebra::SparseGridStorageD::get_index()</a>, <a href="classIMP_1_1algebra_1_1UnboundedGridRangeD.html#adfa1746ee9fc9f43027330471032f67d">IMP::algebra::UnboundedGridRangeD::extended_indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1UnboundedGridRangeD.html#a2902667d16ac2e28ebe7b9f7cbb5be27">IMP::algebra::UnboundedGridRangeD::extended_indexes_end()</a>, <a href="classIMP_1_1algebra_1_1UnboundedGridRangeD.html#a8ff58568320c5e193c8111f06a4b54d8">IMP::algebra::UnboundedGridRangeD::get_extended_indexes()</a>, <a href="classIMP_1_1algebra_1_1UnboundedGridRangeD.html#aa2c6004fc6e1985df04a8a4ee3e77c33">IMP::algebra::UnboundedGridRangeD::get_has_index()</a></td></tr>
18 <tr><td>@ref IMP::algebra::Gaussian3D</td><td><a href="classIMP_1_1core_1_1Gaussian.html#a2082e2294d5ce5f87380e4bc3d14b2e2">IMP::core::Gaussian::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#af92ca363ddd615765a0f0fd6240d453c">IMP::core::Gaussian::setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a3604f4f66e86521693d77592bfd6b892">IMP::core::Gaussian::setup_particle()</a>, <a href="namespaceIMP_1_1algebra.html#a93344559ddd68046d06cd644e4bb7192">IMP::algebra::get_covariance()</a></td></tr>
19 <tr><td>@ref IMP::algebra::GridD</td><td><a href="classIMP_1_1display_1_1IsosurfaceGeometry.html#aee4743136bd5d0a62b41fd956ab1d7da">IMP::display::IsosurfaceGeometry::IsosurfaceGeometry()</a>, <a href="namespaceIMP_1_1algebra.html#a9ed792e2cc65d410fdcce57c0850eb92">IMP::algebra::get_bounding_box()</a>, <a href="namespaceIMP_1_1algebra.html#adb4e0a724bc2f1f9c54e3ebc9437c260">IMP::algebra::get_linearly_interpolated()</a>, <a href="namespaceIMP_1_1algebra.html#a32242a25f36a56f9acc877f4841b3c24">IMP::algebra::get_trilinearly_interpolated()</a>, <a href="namespaceIMP_1_1em.html#ae63d1d8a3cfad97be2846c51d1a03203">IMP::em::create_density_map()</a>, <a href="namespaceIMP_1_1em.html#a325cd7401c937376cfb3504606e4ffd3">IMP::em::create_density_map()</a></td></tr>
20 <tr><td>@ref IMP::algebra::GridIndexD</td><td><a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a584a87ad7db962f804e65beb46356e8a">IMP::algebra::DefaultEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a2ef44b764283d6da46c20bfbf17dbff7">IMP::algebra::DefaultEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#a85058347da34147a6b5f84c6426c4186">IMP::algebra::DenseGridStorageD::at()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#a694d33906f3ba67e60e0ea60d8a17a26">IMP::algebra::DenseGridStorageD::at()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#ad933d82953ca758bf6dc392ddfac821b">IMP::algebra::DenseGridStorageD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#a4df3d9da366d98183e66457bc64d14c6">IMP::algebra::DenseGridStorageD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a1f513a99898cd34a8f760b887b4f9220">IMP::algebra::GridD::get_extended_index()</a>, <a href="classIMP_1_1algebra_1_1GridIndexD.html#a7395cf092160a16c034f2463a0d201d2">IMP::algebra::GridIndexD::compare()</a>, <a href="classIMP_1_1algebra_1_1GridIndexD.html#a2bb1616e7c972fb3a4f972cc6f048fdd">IMP::algebra::GridIndexD::IMP_COMPARISONS()</a>, <a href="classIMP_1_1algebra_1_1GridIndexD.html#a415a95740bb325aff1fd8fc142dfec4b">IMP::algebra::GridIndexD::IMP_HASHABLE_INLINE()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a5cb83dd94de983716f6591c717d1b47a">IMP::algebra::LogEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a19437cca74047a689ad5622534007858">IMP::algebra::LogEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#abed2b815720c9ede48da08042f7fc746">IMP::algebra::SparseGridStorageD::at()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a37c00e0b555991fdea311958456f5859">IMP::algebra::SparseGridStorageD::at()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#afcd504ad60ecde44a739a6f87da87c37">IMP::algebra::SparseGridStorageD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#aa3df25129d9c6875e71f1029274be1e4">IMP::algebra::SparseGridStorageD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a6f314f928557c11837214335428533f0">IMP::algebra::SparseGridStorageD::remove_voxel()</a></td></tr>
21 <tr><td>@ref IMP::algebra::Plane3D</td><td><a href="classIMP_1_1algebra_1_1Plane3D.html#a2ce4dc9bc8335a283d1993a24ed1130e">IMP::algebra::Plane3D::get_area()</a>, <a href="classIMP_1_1algebra_1_1Plane3D.html#aedce7034965a145fc52252f640761b26">IMP::algebra::Plane3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Plane3D.html#ade3bebd378b15acf3e134236ccf4a894">IMP::algebra::Plane3D::get_plane_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1Plane3D.html#a6e8806b130e7420d2a33e532c4ecfdcf">IMP::algebra::Plane3D::set_plane_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1Reflection3D.html#a03378aadd6106ab2f6b3bd04db45c605">IMP::algebra::Reflection3D::Reflection3D()</a>, <a href="classIMP_1_1algebra_1_1SpherePatch3D.html#ae2287e153d7407b77aa454e4e838fa65">IMP::algebra::SpherePatch3D::SpherePatch3D()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#a48ddb9438d24ddbc71317779b7010caa">IMP::display::FilterGeometry::FilterGeometry()</a>, <a href="classIMP_1_1display_1_1PlaneGeometry.html#a14117c198d70a7eb81b96e2f336800f8">IMP::display::PlaneGeometry::PlaneGeometry()</a>, <a href="namespaceIMP_1_1algebra.html#a1bcf2debc9b22076e1fb66f9ac3d0991">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#a2ef88c55248b535ca69a39e67fd935bd">IMP::algebra::get_reflected()</a></td></tr>
22 <tr><td>@ref IMP::algebra::PrincipalComponentAnalysisD</td><td><a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a4d8d20acb063e51daa4bc67e3f0ecc68">IMP::algebra::PrincipalComponentAnalysisD::compare()</a>, <a href="namespaceIMP_1_1algebra.html#aea2393b6f73c8eb830dfbe6996cafdc5">IMP::algebra::get_alignments_from_first_to_second()</a>, <a href="namespaceIMP_1_1multifit.html#a2ded6207f6b3f25048701821adf3bea7">IMP::multifit::write_markers()</a></td></tr>
23 <tr><td>@ref IMP::algebra::ReferenceFrame3D</td><td><a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a4e9bc6c671de9b3e82ecd7680e567a28">IMP::algebra::Ellipsoid3D::Ellipsoid3D()</a>, <a href="classIMP_1_1algebra_1_1Gaussian3D.html#a552489afb6a4079a4bfd4dbd17fab338">IMP::algebra::Gaussian3D::Gaussian3D()</a>, <a href="classIMP_1_1algebra_1_1ReferenceFrame3D.html#af4e8c0e2c90dffb8a059a866ada3f7e4">IMP::algebra::ReferenceFrame3D::get_global_reference_frame()</a>, <a href="classIMP_1_1algebra_1_1ReferenceFrame3D.html#ac4adf03ce952d182320a9a99709cb728">IMP::algebra::ReferenceFrame3D::get_local_reference_frame()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a7af0bef69680d9dcf62a249092eb27c2">IMP::core::RigidBody::add_member_internal()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a374fd139b4809108f4052367ed7b9736">IMP::core::RigidBody::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a9f4a8f119d07286c0b233f98c2a5eab8">IMP::core::RigidBody::set_reference_frame()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a16aa0a44a153cc3efe7e7fb54191248e">IMP::core::RigidBody::set_reference_frame_lazy()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a8886b4deabe13472bf227ae012ce2595">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a2d18a7d5d57b5bf9e7d824928c94a88a">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a525a097acac17a27ed993e7142ec35a3">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a431e05df3b0c309759e12b8049948402">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a7525a19a4c0cd13b906ed83124a89a33">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#af3a77034f7e8360e3c5b9c2a32c15ca6">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a754864fc968d2e3ae69d23236d5c4501">IMP::display::ReferenceFrameGeometry::set_geometry()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a879e819eda0a9d2851e6ac8c654b8355">IMP::kinematics::KinematicForest::set_reference_frame_safe()</a>, <a href="namespaceIMP_1_1algebra.html#a2e7851e2cdd810e68bb3235699c0f5ba">IMP::algebra::get_transformation_from_first_to_second()</a>, <a href="namespaceIMP_1_1algebra.html#ad1ae16d9089296d2d7f458c2d667e587">IMP::algebra::get_transformed()</a>, <a href="namespaceIMP_1_1display.html#a7e059bdeb2a7290b1260cab6923bdd29">IMP::display::create_geometry()</a></td></tr>
24 <tr><td>@ref IMP::algebra::Reflection3D</td><td><a href="classIMP_1_1core_1_1TransformationAndReflectionSymmetry.html#a9dabd7d0f4cdaeeed13f806dbe89a09c">IMP::core::TransformationAndReflectionSymmetry::TransformationAndReflectionSymmetry()</a></td></tr>
25 <tr><td>@ref IMP::algebra::Rotation2D</td><td><a href="classIMP_1_1algebra_1_1Transformation2D.html#ae38299503ccbbfc00f6601c73c934524">IMP::algebra::Transformation2D::Transformation2D()</a>, <a href="namespaceIMP_1_1algebra.html#a4ace4e3f3bb2f5d5fd442360945370a3">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#ae3383dcf150f2e7d76498fecbc55dde9">IMP::algebra::get_rotation_about_point()</a></td></tr>
26 <tr><td>@ref IMP::algebra::Rotation3D</td><td><a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a5dad9047d0e92873b41b9153cc768ca9">IMP::algebra::Ellipsoid3D::Ellipsoid3D()</a>, <a href="classIMP_1_1algebra_1_1Rotation3D.html#add6b45584377d72708fa41d93cf0e912">IMP::algebra::Rotation3D::operator*()</a>, <a href="classIMP_1_1algebra_1_1Rotation3D.html#a1f4eed6fc383b00ae8c5430c42190d39">IMP::algebra::Rotation3D::operator/()</a>, <a href="classIMP_1_1algebra_1_1Rotation3D.html#a754ca1baec7553d4487fa6bd532bf372">IMP::algebra::Rotation3D::operator/=()</a>, <a href="classIMP_1_1algebra_1_1Transformation3D.html#a0f2df89b87c067870907e1cf5103e036">IMP::algebra::Transformation3D::Transformation3D()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#a79fdaffbae5ee9fbecf3e457085f5db8">IMP::em2d::ProjectionParameters::set_rotation()</a>, <a href="classIMP_1_1em2d_1_1RegistrationResult.html#ad0d2a9e3362a2e5d70c02d7a9573f0d1">IMP::em2d::RegistrationResult::RegistrationResult()</a>, <a href="classIMP_1_1em2d_1_1RegistrationResult.html#a996ceea30768ec25b24b6c306415039e">IMP::em2d::RegistrationResult::set_rotation()</a>, <a href="namespaceIMP_1_1algebra.html#a9ff9afb5d3b97dc0f5a1af70a0a6dde8">IMP::algebra::get_fixed_xyz_from_rotation()</a>, <a href="namespaceIMP_1_1algebra.html#a216ec1243a72a2c3f9ddf6bd8bc22ece">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#a691fe5fa25816b65206ae26096c72213">IMP::algebra::get_axis_and_angle()</a>, <a href="namespaceIMP_1_1algebra.html#a55e80fed63202bf78ee2234003ddbd0f">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#aad56f25091896ce8e87f8e5f1098bf79">IMP::algebra::get_interpolated()</a>, <a href="namespaceIMP_1_1algebra.html#abd23e8a25dda2d4acf8c00db35e2537f">IMP::algebra::get_random_rotation_3d()</a>, <a href="namespaceIMP_1_1algebra.html#a07063149bf0d6fd24bd5a1116d6b5115">IMP::algebra::get_rotation_about_point()</a>, <a href="namespaceIMP_1_1em2d.html#af3b3894a70e76077900ac8230c59f9ec">IMP::em2d::do_project_particles()</a>, <a href="namespaceIMP_1_1em2d.html#a33ff594b9223f368d44b25a7da4c349e">IMP::em2d::do_project_vectors()</a>, <a href="namespaceIMP_1_1em2d.html#a3cc89c1d22ffa4f91512f49072542be6">IMP::em2d::do_project_vectors()</a>, <a href="namespaceIMP_1_1em2d.html#ad5dd142cfbb44bbea471ab17f9d8ff77">IMP::em2d::get_unique_index()</a></td></tr>
27 <tr><td>@ref IMP::algebra::Segment3D</td><td><a href="classIMP_1_1algebra_1_1Cone3D.html#a54ff89422998af39f072dd3f3723e772">IMP::algebra::Cone3D::Cone3D()</a>, <a href="classIMP_1_1algebra_1_1Cylinder3D.html#ad34db39ba5b3bbfffd6e8dbb5c5f1d60">IMP::algebra::Cylinder3D::Cylinder3D()</a>, <a href="classIMP_1_1algebra_1_1Segment3D.html#abd21d39499ca4acd3616d7a9355b90fd">IMP::algebra::Segment3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Segment3D.html#af5c43b376efc839be7570ffa3ee7825b">IMP::algebra::Segment3D::get_segment_3d_geometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#aacb32ca6ae044acacb1a67263de8ad27">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a0eda17f53f2e8cef8ae21c615f3e1b2b">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a0722985d583856076e2251d4cb85f380">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a2bcd2eb9aa948125500f86b9dbf99344">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a91092ed036516a4474cd0d7143a5cd2a">IMP::display::SegmentGeometry::set_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a242c09659e380bd7d7c1dbc779863023">IMP::algebra::get_shortest_segment()</a>, <a href="namespaceIMP_1_1algebra.html#afacab5ba739f7028d32cd34be05a10c7">IMP::algebra::get_shortest_segment()</a>, <a href="namespaceIMP_1_1algebra.html#a7f7687e40a5b27f12babf9730ff8d80c">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#a27ea6a618c778638a2a0198aeb9fbd7c">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#ac5577591de549991f08c38744447c953">IMP::algebra::get_relative_projection_on_segment()</a>, <a href="namespaceIMP_1_1algebra.html#ad4acc0a53f732829a51ec021d4bb604d">IMP::algebra::set_segment_3d_geometry()</a>, <a href="namespaceIMP_1_1display.html#a071ef8e162f88294b235de620e423d2c">IMP::display::create_geometry()</a></td></tr>
28 <tr><td>@ref IMP::algebra::SphereD</td><td><a href="classIMP_1_1algebra_1_1SphereD.html#a77963d4ae201c1d27518495e9c13275d">IMP::algebra::SphereD::get_contains()</a>, <a href="namespaceIMP_1_1algebra.html#a2d16674563f8d6b2ec19ca4ac4141f35">IMP::algebra::get_random_vector_in()</a>, <a href="namespaceIMP_1_1algebra.html#a13112e2dae882f9c03a368a64986c198">IMP::algebra::get_random_vector_in()</a>, <a href="namespaceIMP_1_1algebra.html#a5cee60da7af2c8bdb9939983e71b4c40">IMP::algebra::get_random_vector_on()</a>, <a href="namespaceIMP_1_1algebra.html#ae70c5237b41e2f094e952fd1298e2e2a">IMP::algebra::get_uniform_surface_cover()</a>, <a href="namespaceIMP_1_1algebra.html#a3d0722a9b5c0e62dbca7cd5f65fbb738">IMP::algebra::get_uniform_upper_hemisphere_cover()</a>, <a href="namespaceIMP_1_1algebra.html#a847f07074743af85946a6b46cd2a296f">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#a9538f0814e3bdb8494ad2083acea5f20">IMP::algebra::get_interiors_intersect()</a>, <a href="namespaceIMP_1_1algebra.html#a79e54ebe8fa9974a1401ba40be75d732">IMP::algebra::get_power_distance()</a>, <a href="namespaceIMP_1_1algebra.html#a707b6892f5273351caf839871b84b04a">IMP::algebra::get_vector_geometry()</a></td></tr>
29 <tr><td>@ref IMP::algebra::SpherePatch3D</td><td><a href="classIMP_1_1algebra_1_1SpherePatch3D.html#a96d364ca0c2621089adcfe22945de30b">IMP::algebra::SpherePatch3D::get_area()</a>, <a href="classIMP_1_1algebra_1_1SpherePatch3D.html#ae5375e21b4c4a14ecf4278d36cab2387">IMP::algebra::SpherePatch3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1SpherePatch3D.html#ab64eeda4f1106781fd57c3635e593b12">IMP::algebra::SpherePatch3D::get_sphere_patch_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1SpherePatch3D.html#a45d61d6b1d79f6f08aaa5e7540b25001">IMP::algebra::SpherePatch3D::set_sphere_patch_3d_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a72ff2a60e8a826fcc1914fba3552f359">IMP::algebra::get_uniform_surface_cover()</a></td></tr>
30 <tr><td>@ref IMP::algebra::Transformation2D</td><td><a href="classIMP_1_1algebra_1_1Transformation2D.html#a522e638b36bb208b63a4cff80481b2fd">IMP::algebra::Transformation2D::operator*()</a>, <a href="classIMP_1_1algebra_1_1Transformation2D.html#afaf5b30d6215c311e8d00ad6f2ae28ab">IMP::algebra::Transformation2D::operator*=()</a>, <a href="classIMP_1_1algebra_1_1Transformation2D.html#aeea8a543dd04a6a6c4eb1b646eee47ed">IMP::algebra::Transformation2D::operator/()</a>, <a href="classIMP_1_1algebra_1_1Transformation2D.html#aa4796bb23d7e3855e14f3603323f8260">IMP::algebra::Transformation2D::operator/=()</a>, <a href="classIMP_1_1em2d_1_1RegistrationResult.html#ae9ab15bdd1f3d4e782063f8b0d7f1923">IMP::em2d::RegistrationResult::add_in_plane_transformation()</a>, <a href="namespaceIMP_1_1algebra.html#a5d83cbee6a0e0af8738adf030f364f6d">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#a95b9c2466fd2ba29cddff88efc887aff">IMP::algebra::get_transformation_3d()</a>, <a href="namespaceIMP_1_1em2d.html#a0701b9da59d031b6bb82fbb493d824b1">IMP::em2d::get_transformed()</a></td></tr>
31 <tr><td>@ref IMP::algebra::Transformation3D</td><td><a href="classIMP_1_1algebra_1_1ReferenceFrame3D.html#a2784d26ef83ccd5b34f1f2752d0940fc">IMP::algebra::ReferenceFrame3D::ReferenceFrame3D()</a>, <a href="classIMP_1_1algebra_1_1Transformation3D.html#a3d4eb9fcd2303c38d71935e133c909ea">IMP::algebra::Transformation3D::operator*()</a>, <a href="classIMP_1_1algebra_1_1Transformation3D.html#a07bc275d62927745a4eb2df457bbaf12">IMP::algebra::Transformation3D::operator*=()</a>, <a href="classIMP_1_1algebra_1_1Transformation3D.html#ad527f26807df0a9fe8a5aca648d91b4c">IMP::algebra::Transformation3D::operator/()</a>, <a href="classIMP_1_1algebra_1_1Transformation3D.html#afe442ff46864a4e9fde422dc62d30047">IMP::algebra::Transformation3D::operator/=()</a>, <a href="classIMP_1_1core_1_1RigidBodyMember.html#a20d2d7d753660ff877180065eacfdad8">IMP::core::RigidBodyMember::set_internal_transformation()</a>, <a href="classIMP_1_1core_1_1Transform.html#a82c43f463be9cd6645ebad7030c7a3a1">IMP::core::Transform::Transform()</a>, <a href="classIMP_1_1core_1_1TransformationAndReflectionSymmetry.html#a9dabd7d0f4cdaeeed13f806dbe89a09c">IMP::core::TransformationAndReflectionSymmetry::TransformationAndReflectionSymmetry()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#a1d253ea2704fc7d13430962c7ae9b90a">IMP::core::TransformationSymmetry::TransformationSymmetry()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#a18d9ea122d7eb647fbd53c3a17cb110c">IMP::core::TransformedDistancePairScore::TransformedDistancePairScore()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#aef34c0fb45006291f5f984f1d4e84669">IMP::core::TransformedDistancePairScore::set_transformation()</a>, <a href="classIMP_1_1em_1_1EnvelopeScore.html#a3cb71c9a620b34666337b83956d3d61a">IMP::em::EnvelopeScore::is_penetrating()</a>, <a href="classIMP_1_1em_1_1EnvelopeScore.html#ae32bb323620155ce5b555bd1f301be1c">IMP::em::EnvelopeScore::score()</a>, <a href="classIMP_1_1em_1_1FittingSolutions.html#a29fe60f4c55c1b2c278382c0a6b91dd5">IMP::em::FittingSolutions::add_solution()</a>, <a href="classIMP_1_1em_1_1FittingSolutions.html#a352dad9206bc06891bf050b04e2c3985">IMP::em::FittingSolutions::multiply()</a>, <a href="classIMP_1_1kinematics_1_1Joint.html#a39e9a4cc8ba86e14a84109bdab62a12a">IMP::kinematics::Joint::set_transformation_child_to_parent_no_checks()</a>, <a href="classIMP_1_1kinematics_1_1TransformationJoint.html#ac2ae8dc832dc667fdf4ed898160c99e5">IMP::kinematics::TransformationJoint::set_transformation_child_to_parent()</a>, <a href="classIMP_1_1multifit_1_1FittingSolutionRecord.html#a630272d692c4a3ca1667619ab555ddb7">IMP::multifit::FittingSolutionRecord::set_dock_transformation()</a>, <a href="classIMP_1_1multifit_1_1FittingSolutionRecord.html#a5691631ad5cb65972c19a04120ded5be">IMP::multifit::FittingSolutionRecord::set_fit_transformation()</a>, <a href="namespaceIMP_1_1algebra.html#af2121b116324f67ee007e4aef258555c">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#a4a5934ef70db58630906eaaf2ff5bae8">IMP::algebra::get_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1algebra.html#ad1ae16d9089296d2d7f458c2d667e587">IMP::algebra::get_transformed()</a>, <a href="namespaceIMP_1_1algebra.html#aec3bea2d24fbbf621216822517ca1593">IMP::algebra::get_transformed()</a>, <a href="namespaceIMP_1_1algebra.html#a6fd63b261e533e6e344228afadfca32f">IMP::algebra::get_weighted_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1atom.html#a45c4dcd0ed6dfa048aba6524c7927e94">IMP::atom::get_rmsd()</a>, <a href="namespaceIMP_1_1atom.html#aca20f445896d46445b8db0ab72bcf238">IMP::atom::get_rmsd()</a>, <a href="namespaceIMP_1_1atom.html#a937e02edf6a236ffac22fbb236800f05">IMP::atom::get_rmsd()</a>, <a href="namespaceIMP_1_1atom.html#acbef157acdeda4f2e6ed0b25398b206c">IMP::atom::get_rmsd()</a>, <a href="namespaceIMP_1_1atom.html#a6548fc0fb1b2329ba9bb38511610953c">IMP::atom::get_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1atom.html#a603f2b73d6e22b3a9128e0398bc6e082">IMP::atom::get_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1atom.html#adf218eed76f556ada452b525acd835ee">IMP::atom::transform()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a3733609ff3265bd070779045acf03fca">IMP::cnmultifit::build_cn_dens_assembly()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a4a6654fa258c0a93903370ff327d4199">IMP::cnmultifit::transform_cn_assembly()</a>, <a href="namespaceIMP_1_1core.html#a556f7cad1de8ed389d05b4d7acbeb4d0">IMP::core::transform()</a>, <a href="namespaceIMP_1_1core.html#a4c5298df54cae6b0e4419852390281be">IMP::core::transform()</a>, <a href="namespaceIMP_1_1em.html#a52260afb0cbcc46e0ad4bdd377095a03">IMP::em::get_number_of_particles_outside_of_the_density()</a>, <a href="namespaceIMP_1_1em.html#a4d80dfedcdc41944135ecde0149e2b25">IMP::em::get_percentage_of_voxels_covered_by_particles()</a>, <a href="namespaceIMP_1_1em.html#a24e9ee45b3f3e2c55bfe9e73971e7737">IMP::em::get_transformed()</a>, <a href="namespaceIMP_1_1em.html#a4a69963f03e3f972639b15a378467798">IMP::em::get_transformed()</a>, <a href="namespaceIMP_1_1em.html#a8bd63b39d8f60348030c5607e83ba6b7">IMP::em::get_transformed_into()</a>, <a href="namespaceIMP_1_1em.html#abd0e642dde82199ac2b181e297526241">IMP::em::get_transformed_into2()</a></td></tr>
32 <tr><td>@ref IMP::algebra::Triangle3D</td><td><a href="classIMP_1_1display_1_1TriangleGeometry.html#a035a07939f07970172cd8e8349277f90">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a8880501417b489547a254c4c2003cf3d">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a6a039b1098c7111bafe6a715fdbdc6ba">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a33df56da0761fbdde97e8e938c13b96a">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a9c7b1a40aaf76f2d29c5c38be25ce8d4">IMP::display::TriangleGeometry::set_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a40b9b1290fa21102bda8255d8eb3c4d8">IMP::algebra::get_transformation_from_first_triangle_to_second()</a>, <a href="namespaceIMP_1_1display.html#a54a071369efd0709c091051cd6355e67">IMP::display::create_geometry()</a></td></tr>
33 <tr><td>@ref IMP::algebra::VectorBaseD</td><td><a href="classIMP_1_1algebra_1_1VectorBaseD.html#a6d175c10b69919d25d4bf5675a1cdaa1">IMP::algebra::VectorBaseD::check_compatible_vector()</a>, <a href="classIMP_1_1algebra_1_1VectorBaseD.html#a19b24b188ccfe587839d8b422e2bad70">IMP::algebra::VectorBaseD::get_scalar_product()</a></td></tr>
34 <tr><td>@ref IMP::algebra::VectorD</td><td><a href="classIMP_1_1algebra_1_1BoundingBoxD.html#a7850dae79dc4afd896372a3a3156e027">IMP::algebra::BoundingBoxD::BoundingBoxD()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#af4deddc06a6067f120d36d48d8cc5ecd">IMP::algebra::BoundingBoxD::BoundingBoxD()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#aa8e971575487bfbf089febb50526c54c">IMP::algebra::BoundingBoxD::BoundingBoxD()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#a79a46310633b3f17c6ba14b06f25492f">IMP::algebra::BoundingBoxD::get_contains()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#abe7e39f1ee5d58dae32272ee29e51f0b">IMP::algebra::BoundingBoxD::operator+=()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a9b5bbdb991053c94930f1a13f08555df">IMP::algebra::DefaultEmbeddingD::get_elementwise_product()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a8d2e2913eb8be64456c599b7cf91ce2a">IMP::algebra::DefaultEmbeddingD::DefaultEmbeddingD()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a7c5f5633d6495ade19fa00cca4dccff5">IMP::algebra::DefaultEmbeddingD::get_extended_index()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#ae4437a1c4ca95b4abbf58c9531209d02">IMP::algebra::DefaultEmbeddingD::get_index()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a2bac26324f8cff64d5c484aa94d5bde9">IMP::algebra::DefaultEmbeddingD::set_origin()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a0f1379242a9846c0eda7c219fe08b937">IMP::algebra::DefaultEmbeddingD::set_unit_cell()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a81b743c5cc601b32b1eb1b31874afeb6">IMP::algebra::GridD::get_nearest_index()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a0e464be5a75232f1392a54c3bd9711eb">IMP::algebra::GridD::get_nearest_extended_index()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#ab96be5a02e7d8a1729e6b47e8f6b93da">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#adb32bd20c18445dd15609b6d71ab6eff">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a1331afb93fdf474e352ce38076a1dd56">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a24ba706b342d7dc7e3c5cb42ed64fccf">IMP::algebra::GridD::add_voxel()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a6ed148a6870b552c9a0ece4fbade160f">IMP::algebra::GridD::at()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#adb7e2e9c0cb96a26c31683ac51541273">IMP::algebra::GridD::at()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a4253e432b3e29c9717dec9cdc29ba314">IMP::algebra::GridD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#adf5b3de175047e40a340c7acdb47b7d9">IMP::algebra::GridD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a16239837f79a0844a742d9282646b83e">IMP::algebra::LogEmbeddingD::LogEmbeddingD()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a11cfe0991d05693602b83f0a601a9c26">IMP::algebra::LogEmbeddingD::LogEmbeddingD()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a8d697bdd7ff524e64906160bd1cea582">IMP::algebra::LogEmbeddingD::LogEmbeddingD()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a333cca1384be415a4beb6423dc4e6273">IMP::algebra::LogEmbeddingD::get_extended_index()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a09613ab4444befc995178b6b8a416358">IMP::algebra::LogEmbeddingD::get_index()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#ad08277a3eeb3b3e7e1c7e78420efc7ea">IMP::algebra::LogEmbeddingD::set_origin()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a49a414e862bc4b3722e1c4e09bb2ff32">IMP::algebra::LogEmbeddingD::set_unit_cell()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a789d0401da99b97b26b6f1d685a42a1e">IMP::algebra::LogEmbeddingD::set_unit_cell()</a>, <a href="classIMP_1_1algebra_1_1NearestNeighborD.html#a465b01fda7cda63dfda53413c3fe87b6">IMP::algebra::NearestNeighborD::NearestNeighborD()</a>, <a href="classIMP_1_1algebra_1_1NearestNeighborD.html#ae8e3cd61ac7781993d837de4bb875b41">IMP::algebra::NearestNeighborD::get_in_ball()</a>, <a href="classIMP_1_1algebra_1_1NearestNeighborD.html#a4b167c84313976e55534a4324732673e">IMP::algebra::NearestNeighborD::get_nearest_neighbor()</a>, <a href="classIMP_1_1algebra_1_1NearestNeighborD.html#a7beece69ce6579d62acad7e1bb8fed83">IMP::algebra::NearestNeighborD::get_nearest_neighbors()</a>, <a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a2f747f49892c8e8cadd5be8c174467f4">IMP::algebra::PrincipalComponentAnalysisD::PrincipalComponentAnalysisD()</a>, <a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#acda30c2ce2059cbc07177515cafa9397">IMP::algebra::PrincipalComponentAnalysisD::set_centroid()</a>, <a href="classIMP_1_1algebra_1_1Rotation3D.html#a7f9a88f4c31d4d8f2115beeda2a979a8">IMP::algebra::Rotation3D::Rotation3D()</a>, <a href="classIMP_1_1algebra_1_1SphereD.html#abd5763e637b98958069b7ba8806fd209">IMP::algebra::SphereD::SphereD()</a>, <a href="classIMP_1_1algebra_1_1SphereD.html#a9c5b271fe56058daa14d41b4463994e1">IMP::algebra::SphereD::get_contains()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#a6a954f4fa6f2c313b4bb83672fc48f32">IMP::algebra::VectorD::VectorD()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#ac4af6defcf88fe29cefed14a2f3a28cb">IMP::algebra::VectorD::operator*()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#a441606f948618b1faa1372da374647b2">IMP::algebra::VectorD::operator+()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#abf2def3932df79b1c577d4eaba27b5da">IMP::algebra::VectorD::operator+=()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#a35f40a1bd09bdb4cf1c48c7b189be911">IMP::algebra::VectorD::operator-()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#ad2e8dd83e90954e1b9bfa24d2ecff466">IMP::algebra::VectorD::operator-=()</a>, <a href="classIMP_1_1example_1_1ExampleTemplateClassD.html#aa93938fc836a0c96102da8f1530e1e6c">IMP::example::ExampleTemplateClassD::ExampleTemplateClassD()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a8dbc8daec12deaf6fad60f92ed5837e2">IMP::multifit::GeometricHash::GeometricHash()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a55cdc6df5f5b89e3c5f8f42e4a1b749d">IMP::multifit::GeometricHash::add()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a66c9f0b496a518db3e5dcc57a52e0618">IMP::multifit::GeometricHash::bucket()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#afe9af3b97de330452c7586379948501d">IMP::multifit::GeometricHash::neighbors()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a6c2ba8256d11954e48844f26d8a09ff4">IMP::multifit::GeometricHash::neighbors()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a4a243f10f4650280f7873c0e2e5f5d4a">IMP::multifit::GeometricHash::neighbors()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#adb8e5c95a478e0bbe3d809319c83b1b9">IMP::multifit::GeometricHash::neighbors()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#ad836b61873521a48bf1a0211f2d139f2">IMP::multifit::GeometricHash::neighbors_data()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a3846d3f77b57a015b3294005fd1fa6e5">IMP::multifit::GeometricHash::cube_inside_sphere_rec()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#ae094fb3a173684802c426d64a8e88c6d">IMP::multifit::GeometricHash::to_bucket()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#ab715cee46df8e90e95c9981a8b7d6a9e">IMP::multifit::GeometricHash::inf_distance()</a>, <a href="classIMP_1_1statistics_1_1HistogramD.html#a592798e458c9acaded04b9ed7a9a95d7">IMP::statistics::HistogramD::add()</a>, <a href="classIMP_1_1statistics_1_1HistogramD.html#aa8f8a40723844f8f480074771dc3f0d2">IMP::statistics::HistogramD::get_standard_deviation()</a>, <a href="namespaceIMP_1_1algebra.html#a964a6d360e228da939368f3621f6aab9">IMP::algebra::get_l2_norm()</a>, <a href="namespaceIMP_1_1algebra.html#a7574f7e7033de011d30e6c1a22a034f4">IMP::algebra::get_l1_norm()</a>, <a href="namespaceIMP_1_1algebra.html#aab0012e9e00266f181f4ec0ab7f01444">IMP::algebra::get_linf_norm()</a>, <a href="namespaceIMP_1_1algebra.html#aa040b3bcfec950a979371f3e19b14058">IMP::algebra::compare()</a>, <a href="namespaceIMP_1_1algebra.html#a01d00ac6807479bb970254b3e188bcc6">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#af800ee8500d39c126da5897ca6f8ebaa">IMP::algebra::get_elementwise_product()</a>, <a href="namespaceIMP_1_1algebra.html#a019cfab4b720c4002cd8ca3085176778">IMP::algebra::get_elementwise_product()</a>, <a href="namespaceIMP_1_1algebra.html#adb4e0a724bc2f1f9c54e3ebc9437c260">IMP::algebra::get_linearly_interpolated()</a>, <a href="namespaceIMP_1_1algebra.html#ab2ff21c0e217ace29b614ac74089c2e3">IMP::algebra::get_principal_components()</a>, <a href="namespaceIMP_1_1algebra.html#a3003fd1a5254db165a8600f2979e7146">IMP::algebra::get_rotation_from_vector4d()</a>, <a href="namespaceIMP_1_1algebra.html#af6c0ba059d657cbc42dad97dfb6cc490">IMP::algebra::get_squared_distance()</a>, <a href="namespaceIMP_1_1algebra.html#afdc2e1d2d13e716a0d8b2b315187e13e">IMP::algebra::operator*()</a></td></tr>
35 </table>
36 # IMP.atom # {#argument_index_atom}
37 <table><tr>
38 <th>Class</th><th>Users</th></tr>
39 <tr><td>@ref IMP::atom::Atom</td><td><a href="classIMP_1_1atom_1_1Atom.html#a1f02e81ea574a455e5494b4f15e1882e">IMP::atom::Atom::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#abd5014bfa4ce1840322f1b9337966db7">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a27acf841df41fc228ce9dd3c644b531c">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#ac05940015eac5733ba23c5dd1c405cb7">IMP::atom::CHARMMParameters::get_force_field_atom_type()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#a7ab2b4cd229510811991b7e5b72760a0">IMP::atom::ForceFieldParameters::get_epsilon()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#aa18ecbbff837742ea4cf8ae2c1e144f6">IMP::atom::ForceFieldParameters::get_radius()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#a8f1bb071899906abd71171f38b934ba1">IMP::atom::ForceFieldParameters::get_force_field_atom_type()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#ad88beca24508ce2d57b8fae69f8034bb">IMP::score_functor::OrientedSoap::score_doublets()</a>, <a href="namespaceIMP_1_1atom.html#a1b9a562a6a9548c3e85047d8fe53183d">IMP::atom::get_residue()</a></td></tr>
40 <tr><td>@ref IMP::atom::AtomType</td><td><a href="classIMP_1_1atom_1_1Atom.html#af14a86aba6d844bf959566fcd5a5daab">IMP::atom::Atom::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a8dfcc4758811f77db0c3cac0dc0ed992">IMP::atom::Atom::set_atom_type()</a>, <a href="classIMP_1_1atom_1_1Atom.html#acca5fca63715a18614fc64d14ca5d788">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a43d9352c21c8b5827fe20d860cafb82c">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a91fff9329d2a36aa42719d443fb5fc35">IMP::atom::CHARMMResidueTopologyBase::get_atom()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters_1_1Bond.html#a23a3cef96fb2868431d501bb9811df0a">IMP::atom::ForceFieldParameters::Bond::Bond()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a6e55212a17fd8bc1329b9f8481bb6afb">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#aa8af1e705fed866dd406011e8e6b2937">IMP::atom::Selection::set_atom_type()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#ada53a356af89839596eb5148c15de6d8">IMP::rotamer::ResidueRotamer::get_atom_exists()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#aa3b628cc432c926a0a90b6065eeb0592">IMP::rotamer::ResidueRotamer::get_coordinates()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#a4e6c416e3801b8584c2e712a7a397cf5">IMP::rotamer::ResidueRotamer::get_number_of_cases()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#a4303f70f6f7cea1ef5fbbf126b88abeb">IMP::rotamer::ResidueRotamer::add_coordinates()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#aa7af13636acbba99ebef5cca6754265c">IMP::rotamer::ResidueRotamer::get_coordinates()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#ae5a59dd0ebd0d5590db3d2127444204e">IMP::saxs::FormFactorTable::get_carbon_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#adc7d132da89b412ddc3bed43094c29a5">IMP::saxs::FormFactorTable::get_nitrogen_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a01b57170c71bbaa7edc35ce486805ac6">IMP::saxs::FormFactorTable::get_oxygen_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a3453246d72667c72492393cb9e7b00e1">IMP::saxs::FormFactorTable::get_sulfur_atom_type()</a>, <a href="namespaceIMP_1_1atom.html#a899927712a6b9ae00aa8875407f5311a">IMP::atom::get_atom()</a>, <a href="namespaceIMP_1_1atom.html#a75d5d735a5ea9dcfc3289baae0dd51fe">IMP::atom::get_element_for_atom_type()</a></td></tr>
41 <tr><td>@ref IMP::atom::Bond</td><td><a href="classIMP_1_1atom_1_1BondGeometry.html#a02bf784b049c0439f004cbd1a70cd490">IMP::atom::BondGeometry::BondGeometry()</a>, <a href="group__bond.html#ga1c817f9827d6115fe10530ca349098fa">IMP::atom::create_bond()</a>, <a href="group__bond.html#ga53d105256db430c876b1a83c5a2786a4">IMP::atom::destroy_bond()</a></td></tr>
42 <tr><td>@ref IMP::atom::Bonded</td><td><a href="group__bond.html#gad928d4afc3de5646070a1a55499772d3">IMP::atom::create_bond()</a>, <a href="group__bond.html#ga1c817f9827d6115fe10530ca349098fa">IMP::atom::create_bond()</a>, <a href="group__bond.html#ga4434a119a32491177223b0fe0d6f7d6d">IMP::atom::create_custom_bond()</a>, <a href="group__bond.html#gaf75358e1a709b3b9cf2153bf741b5efa">IMP::atom::get_bond()</a></td></tr>
43 <tr><td>@ref IMP::atom::BrownianDynamics</td><td><a href="namespaceIMP_1_1atom.html#a0e5dbe5aa039ab94bb0bdd9cb18bf91e">IMP::atom::get_maximum_time_step_estimate()</a></td></tr>
44 <tr><td>@ref IMP::atom::CHARMMAtomTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMAtomTopology.html#ad1fb27edcbf97c268c4f0db85b45f7b2">IMP::atom::CHARMMAtomTopology::CHARMMAtomTopology()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a010e65c13afaec4e7740704393aca2b1">IMP::atom::CHARMMResidueTopologyBase::add_atom()</a></td></tr>
45 <tr><td>@ref IMP::atom::CHARMMBondEndpoint</td><td><a href="classIMP_1_1atom_1_1CHARMMConnection.html#a22ff0e7ededfb20f89185a650fff7d79">IMP::atom::CHARMMConnection::CHARMMConnection()</a>, <a href="classIMP_1_1atom_1_1CHARMMInternalCoordinate.html#a9d280e5a18153f82f84c5371c43b1764">IMP::atom::CHARMMInternalCoordinate::CHARMMInternalCoordinate()</a></td></tr>
46 <tr><td>@ref IMP::atom::CHARMMConnection</td><td><a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a9347ca0463be92c325e6a102f1a55c91">IMP::atom::CHARMMResidueTopologyBase::add_angle()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#af6451fe6bbacb79b49b9cd547fde5f05">IMP::atom::CHARMMResidueTopologyBase::add_bond()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a736a8348838b728ca24de82ebad1355a">IMP::atom::CHARMMResidueTopologyBase::add_dihedral()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#aad7ed56d6b1421d1ee7fdd526e546533">IMP::atom::CHARMMResidueTopologyBase::add_improper()</a></td></tr>
47 <tr><td>@ref IMP::atom::CHARMMIdealResidueTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#a532d6c3f6529759fccff26616f0f7e27">IMP::atom::CHARMMParameters::add_residue_topology()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopology.html#adf36f0b3ed6504c273e75a78dd024e70">IMP::atom::CHARMMResidueTopology::CHARMMResidueTopology()</a></td></tr>
48 <tr><td>@ref IMP::atom::CHARMMInternalCoordinate</td><td><a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a9142afbbc65ceebb6c471f4ae8825c91">IMP::atom::CHARMMResidueTopologyBase::add_internal_coordinate()</a></td></tr>
49 <tr><td>@ref IMP::atom::CHARMMParameters</td><td><a href="classIMP_1_1atom_1_1CHARMMSegmentTopology.html#a61807dec0e56f4a375bc9e6b6f62d574">IMP::atom::CHARMMSegmentTopology::apply_default_patches()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aa10f457dd2b70f950ea875a3f271ae86">IMP::atom::CHARMMTopology::CHARMMTopology()</a></td></tr>
50 <tr><td>@ref IMP::atom::CHARMMPatch</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#ad47e2ffd1893d14ac6b120b12213b9aa">IMP::atom::CHARMMParameters::add_patch()</a></td></tr>
51 <tr><td>@ref IMP::atom::CHARMMResidueTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMBondEndpoint.html#a78501b3f4e2e1f8f67ac507253244ade">IMP::atom::CHARMMBondEndpoint::CHARMMBondEndpoint()</a>, <a href="classIMP_1_1atom_1_1CHARMMBondEndpoint.html#a5271a836eccdc72f7763d32a0af46573">IMP::atom::CHARMMBondEndpoint::get_atom()</a>, <a href="classIMP_1_1atom_1_1CHARMMConnection.html#adf29f3ca8131dfa961d939a35ce4af60">IMP::atom::CHARMMConnection::get_atoms()</a>, <a href="classIMP_1_1atom_1_1CHARMMPatch.html#a3e11ae77d0d6eade9acbe77caf143b92">IMP::atom::CHARMMPatch::apply()</a>, <a href="classIMP_1_1atom_1_1CHARMMPatch.html#ac0f0e4636e87cb7aa2dc2da9de0fca2d">IMP::atom::CHARMMPatch::apply()</a>, <a href="classIMP_1_1atom_1_1CHARMMSegmentTopology.html#a44a86531107d85bdafc879df3e68c987">IMP::atom::CHARMMSegmentTopology::remove_residue()</a>, <a href="classIMP_1_1atom_1_1CHARMMSegmentTopology.html#ab93a919188ee694d37ed07f146fc5e20">IMP::atom::CHARMMSegmentTopology::add_residue()</a></td></tr>
52 <tr><td>@ref IMP::atom::CHARMMResidueTopologyBase</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#a0e017ab02dc3673cfa7cd48fb6e4686d">IMP::atom::CHARMMParameters::parse_atom_line()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#aa0c19662e8ac391cdce1666af3b810eb">IMP::atom::CHARMMParameters::parse_bond_line()</a></td></tr>
53 <tr><td>@ref IMP::atom::CHARMMSegmentTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMTopology.html#a26bc410f529a0f187d78db52d401a7ad">IMP::atom::CHARMMTopology::remove_segment()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aa24e0702d81ced734eba1ec5533a411f">IMP::atom::CHARMMTopology::add_segment()</a></td></tr>
54 <tr><td>@ref IMP::atom::CHARMMTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#aa053a5423e162bc45edb28ed4777bf57">IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint()</a>, <a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#ae55a4983c41e935a811d933ba32a60c8">IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint()</a></td></tr>
55 <tr><td>@ref IMP::atom::Chain</td><td><a href="classIMP_1_1atom_1_1Chain.html#a99932fe4fe7be6d68fc1e823443f38bb">IMP::atom::Chain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#afb3582455ead3991c70d4c9271c51483">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a97cc8e8cf2ba8e7cef878150a3c4eb8b">IMP::atom::Chain::setup_particle()</a>, <a href="namespaceIMP_1_1atom.html#af12315103e56599289223816dc3b3aeb">IMP::atom::create_simplified_along_backbone()</a></td></tr>
56 <tr><td>@ref IMP::atom::Domain</td><td><a href="classIMP_1_1atom_1_1Domain.html#affc45f2a7390a38ee6a71ea222d2d937">IMP::atom::Domain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#a3fcce9fba7f9ef896343d54170db2594">IMP::atom::Domain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#aa681be58da92a7bcf73c8de91b320d57">IMP::atom::Domain::setup_particle()</a></td></tr>
57 <tr><td>@ref IMP::atom::ForceFieldParameters</td><td><a href="namespaceIMP_1_1atom.html#a0b3af7559bf1bed6ecdfe98701fab423">IMP::atom::add_bonds()</a>, <a href="namespaceIMP_1_1atom.html#ad6e74dd86fdc8480090199a6cdc8bf55">IMP::atom::add_radii()</a></td></tr>
58 <tr><td>@ref IMP::atom::Fragment</td><td><a href="classIMP_1_1atom_1_1Fragment.html#a706b5dd2c1780a6581e9a06c894555df">IMP::atom::Fragment::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#ac1e1a2331511b0daa732d33ae34b3285">IMP::atom::Fragment::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#a7c954667ebbe7a69821a72ed60f6a75b">IMP::atom::Fragment::setup_particle()</a></td></tr>
59 <tr><td>@ref IMP::atom::Hierarchy</td><td><a href="classIMP_1_1atom_1_1BondGraph.html#a93e77475a24d5f08f9568e11befa2224">IMP::atom::BondGraph::BondGraph()</a>, <a href="classIMP_1_1atom_1_1CHARMMBondEndpoint.html#a5271a836eccdc72f7763d32a0af46573">IMP::atom::CHARMMBondEndpoint::get_atom()</a>, <a href="classIMP_1_1atom_1_1CHARMMConnection.html#adf29f3ca8131dfa961d939a35ce4af60">IMP::atom::CHARMMConnection::get_atoms()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#aab56534fc18ba3715778af3f2aea8073">IMP::atom::CHARMMParameters::create_topology()</a>, <a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#aa053a5423e162bc45edb28ed4777bf57">IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint()</a>, <a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#ae55a4983c41e935a811d933ba32a60c8">IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aab1206d77a4f09ece75f44e668185915">IMP::atom::CHARMMTopology::map_residue_topology_to_hierarchy()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aa7c8c6a2a0e48500776a56be1029a7a8">IMP::atom::CHARMMTopology::add_atom_types()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#a27ba1dfd62880570d47a5084af6e9c4c">IMP::atom::CHARMMTopology::add_bonds()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aeba76e2f28c02ab70dc1a4b2148e02e4">IMP::atom::CHARMMTopology::add_charges()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#a4018c73156fe2bdd6257cd861b9acf16">IMP::atom::CHARMMTopology::add_coordinates()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#a18d4cacf0b2baa177f96b02e1c12a50b">IMP::atom::CHARMMTopology::add_dihedrals()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aa081f3c847b273f6a3eeeff75ed85f4f">IMP::atom::CHARMMTopology::add_impropers()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#ae9806eee2eb64e7742e679c0a3217fe3">IMP::atom::CHARMMTopology::add_missing_atoms()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#a1aef3017da939dbaec3a4f88ab5853bd">IMP::atom::CHARMMTopology::setup_hierarchy()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#a8ec3c7e77ae87b988c803bfc2f375772">IMP::atom::ForceFieldParameters::add_bonds()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#ad37b61f76545a6e4e6aa67783bfe7f1b">IMP::atom::ForceFieldParameters::add_radii()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#a797d6ab508017979fb7d5ab6dbeae578">IMP::atom::ForceFieldParameters::add_well_depths()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a6a8c2cba388bf79adef66c28a7c78a57">IMP::atom::Hierarchy::add_child()</a>, <a href="classIMP_1_1atom_1_1ProteinLigandRestraint.html#ae938de2b2aa36558d19a335b0e33787c">IMP::atom::ProteinLigandRestraint::initialize()</a>, <a href="classIMP_1_1atom_1_1ProteinLigandRestraint.html#ae7c1888332ceda6b47560b590cc8dbea">IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint()</a>, <a href="classIMP_1_1atom_1_1ProteinLigandRestraint.html#a84df68054cc57ef9fb71924f9224ee1a">IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a6e55212a17fd8bc1329b9f8481bb6afb">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#ab37f62060b5266fbc0f233534ebf41a8">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a535a8e78f95c6e63610f918361f164b1">IMP::kinematics::KinematicForest::KinematicForest()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#ad154ae9c6644263a3b0f9fc9b743916a">IMP::kinematics::ProteinKinematics::ProteinKinematics()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#ad8658b5d9e343f49810a4e5b67e0a517">IMP::kinematics::ProteinKinematics::ProteinKinematics()</a>, <a href="classIMP_1_1multifit_1_1Ensemble.html#aaccff3f8521198b49310efcaf86f5ea9">IMP::multifit::Ensemble::add_component_and_fits()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#a136cac955ee735ec87b1238b82aa67ac">IMP::multifit::FFTFitting::do_global_fitting()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#ae47864b146f9cf99c92495967e611d01">IMP::multifit::FFTFitting::do_local_fitting()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#ab18f1bb918cf5b1f45d22d800a80fad4">IMP::multifit::FFTFitting::prepare_probe()</a>, <a href="classIMP_1_1multifit_1_1MergeTreeBuilder.html#ae22a43002fc2abd6556fdc73b5c6166a">IMP::multifit::MergeTreeBuilder::increase_edge()</a>, <a href="classIMP_1_1rotamer_1_1RotamerCalculator.html#a7b2c4dcc21cd3cf6cee2430993a1e756">IMP::rotamer::RotamerCalculator::transform()</a>, <a href="namespaceIMP_1_1atom.html#a830fbd488be01d4f14b53cb840ab7ce9">IMP::atom::add_dope_score_data()</a>, <a href="namespaceIMP_1_1atom.html#a1b4c863b0fefde1c1d95cdf6fed794a8">IMP::atom::create_simplified_along_backbone()</a>, <a href="namespaceIMP_1_1atom.html#ab8f5c1d19389bcbe4c5bee4728069bee">IMP::atom::get_residue_indexes()</a>, <a href="namespaceIMP_1_1atom.html#a7bc45846fa709afb3ea73f2e9a3ad923">IMP::atom::get_residue_type()</a>, <a href="namespaceIMP_1_1atom.html#abfb867733e9b44b3d5d03dd3fae18a79">IMP::atom::get_chain_id_char()</a>, <a href="namespaceIMP_1_1atom.html#af4a6c11848aec861d0ef55068cf6261a">IMP::atom::get_atom_type()</a>, <a href="namespaceIMP_1_1atom.html#a4b530a5d405a84e423361b2ba7f93cff">IMP::atom::get_domain_name()</a>, <a href="namespaceIMP_1_1atom.html#a8b76c2984bf4e6625faad378d70e9bf3">IMP::atom::write_mol2()</a>, <a href="namespaceIMP_1_1atom.html#ae1ede2b0bd5e5af085111120d11f149d">IMP::atom::read_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a948fb97a18c5b5d08144b058d2b39ec6">IMP::atom::add_protein_ligand_score_data()</a>, <a href="namespaceIMP_1_1atom.html#aeb911633eea643d7307e2dbe8e7684a5">IMP::atom::show_molecular_hierarchy()</a>, <a href="namespaceIMP_1_1atom.html#a0b3af7559bf1bed6ecdfe98701fab423">IMP::atom::add_bonds()</a>, <a href="namespaceIMP_1_1atom.html#ad6e74dd86fdc8480090199a6cdc8bf55">IMP::atom::add_radii()</a>, <a href="namespaceIMP_1_1atom.html#a7dc65895f7eaeb1eb7c2a60479ada5d1">IMP::atom::create_clone()</a>, <a href="namespaceIMP_1_1atom.html#abeb9fd1491717f57691272fed6ec4ee5">IMP::atom::create_clone_one()</a>, <a href="namespaceIMP_1_1atom.html#a70ac55d293e6851c67b45d7fd55a3163">IMP::atom::create_compatible_rigid_body()</a>, <a href="namespaceIMP_1_1atom.html#a40da5b3553d98acf020078b4e435b12a">IMP::atom::create_rigid_body()</a>, <a href="namespaceIMP_1_1atom.html#a1ec0bdeff49fc6221a7c4e370ba68279">IMP::atom::create_simplified_assembly_from_volume()</a>, <a href="namespaceIMP_1_1atom.html#ad36632c4fe1304975ff1afce38816295">IMP::atom::create_simplified_from_volume()</a>, <a href="namespaceIMP_1_1atom.html#aebd43e49579403cf41067dc8873ca2c8">IMP::atom::destroy()</a>, <a href="namespaceIMP_1_1atom.html#a45b3b96085fb5dbf171f218e95c73f22">IMP::atom::get_bounding_box()</a>, <a href="namespaceIMP_1_1atom.html#a867c05b3b3faa5f272a6370408b28915">IMP::atom::get_bounding_sphere()</a>, <a href="namespaceIMP_1_1atom.html#a3b3f1f1666e2a122bd766f10a9eb84a9">IMP::atom::get_by_type()</a>, <a href="namespaceIMP_1_1atom.html#a13fb268fe2be9e83bbd9a1a2197499ef">IMP::atom::get_chain()</a>, <a href="namespaceIMP_1_1atom.html#a46482205ec4626a8fb4800a6bce46af7">IMP::atom::get_chain_id()</a>, <a href="namespaceIMP_1_1atom.html#a8f2e62640647e36570c22b0328283a9c">IMP::atom::get_charmm_untyped_atoms()</a>, <a href="namespaceIMP_1_1atom.html#aa9d8e71ec12f5e1011ed0f457c70ec3a">IMP::atom::get_copy_index()</a>, <a href="namespaceIMP_1_1atom.html#a3ad3ffc63b7488509170066bcd021c4c">IMP::atom::get_hierarchy_tree()</a>, <a href="namespaceIMP_1_1atom.html#ac90fe977731f00cc049724fdeb3b6532">IMP::atom::get_internal_bonds()</a>, <a href="namespaceIMP_1_1atom.html#a54984a22dcecd2d77bb7ffbe174dd0d6">IMP::atom::get_is_heterogen()</a>, <a href="namespaceIMP_1_1atom.html#ae40f2053c2f95c317a034bdcb0e38478">IMP::atom::get_leaves()</a>, <a href="namespaceIMP_1_1atom.html#a3e2c48e16f6245ccf46936fe4ed5837b">IMP::atom::get_molecule_name()</a>, <a href="namespaceIMP_1_1atom.html#addc26081dbfab30a1c5c74af47bbc93d">IMP::atom::get_residue()</a>, <a href="namespaceIMP_1_1atom.html#a0413486542eba96a7d75081dff43a096">IMP::atom::get_resolution()</a>, <a href="namespaceIMP_1_1atom.html#ae6a2b0d20131a9186cfbea24d9320574">IMP::atom::get_root()</a>, <a href="namespaceIMP_1_1atom.html#a230e74d4b499e3e9ada75e78e93c1af8">IMP::atom::get_state_index()</a>, <a href="namespaceIMP_1_1atom.html#ab986bb0421e989ecdf45675e06e143fd">IMP::atom::remove_charmm_untyped_atoms()</a>, <a href="namespaceIMP_1_1atom.html#a86c2aff722129fb074c5e32484dd31aa">IMP::atom::setup_as_approximation()</a>, <a href="namespaceIMP_1_1atom.html#aa937fd3e26ae660ae1c406781c29bc34">IMP::atom::show()</a>, <a href="namespaceIMP_1_1atom.html#adf218eed76f556ada452b525acd835ee">IMP::atom::transform()</a>, <a href="namespaceIMP_1_1multifit.html#a2fc41bcf60a63d0ecc658c8df0a6e096">IMP::multifit::create_coarse_molecule_from_molecule()</a>, <a href="namespaceIMP_1_1multifit.html#af83b1866a4b7bb6747eea98bd9bb28e1">IMP::multifit::fft_based_rigid_fitting()</a>, <a href="namespaceIMP_1_1multifit.html#a0a9580f83f49e4fb5dd13fc36465448b">IMP::multifit::get_close_to_point()</a>, <a href="namespaceIMP_1_1multifit.html#ad9a90449965866bc3f547eb9e2193399">IMP::multifit::get_points_close_to_molecule()</a>, <a href="namespaceIMP_1_1multifit.html#a602f75b13bf7afebbc5fbfb3ab89e1e9">IMP::multifit::get_points_far_from_molecule()</a>, <a href="namespaceIMP_1_1multifit.html#aedc64c26eefe139ef34e5cce89d13a51">IMP::multifit::molecule2anchors()</a>, <a href="namespaceIMP_1_1rmf.html#afb3c4144b9161813668b971b21295c8e">IMP::rmf::add_hierarchy()</a></td></tr>
60 <tr><td>@ref IMP::atom::LennardJones</td><td><a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#ac927946f510789b92834bc6603dd2f20">IMP::atom::LennardJonesPairScore::get_factors()</a></td></tr>
61 <tr><td>@ref IMP::atom::Mol2Selector</td><td><a href="namespaceIMP_1_1atom.html#a9b13cfbe2f98dd95b8837f10dbb6fdfd">IMP::atom::read_mol2()</a></td></tr>
62 <tr><td>@ref IMP::atom::Molecule</td><td><a href="classIMP_1_1atom_1_1Molecule.html#a9c2ad4affa0f40376e6ad4a8217d8688">IMP::atom::Molecule::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#a7701b4db810cc963ad3ebc3a519e0a99">IMP::atom::Molecule::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#a7ba1ec0b5c5a38cd30156fc42d2d1316">IMP::atom::Molecule::setup_particle()</a></td></tr>
63 <tr><td>@ref IMP::atom::PDBSelector</td><td><a href="classIMP_1_1atom_1_1AndPDBSelector.html#ae53bc29f8e73c1dd5f716f8107d3fb36">IMP::atom::AndPDBSelector::AndPDBSelector()</a>, <a href="classIMP_1_1atom_1_1NotPDBSelector.html#a325e5301ba51b57e4e7f4b04659c4a47">IMP::atom::NotPDBSelector::NotPDBSelector()</a>, <a href="classIMP_1_1atom_1_1OrPDBSelector.html#a796cbfff392c6c35a3632f6da515aa0d">IMP::atom::OrPDBSelector::OrPDBSelector()</a>, <a href="namespaceIMP_1_1atom.html#ac65059962426cd7e45339ff9f3ed70df">IMP::atom::read_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a13159795e7c78f154e98bc20cc4fb8d8">IMP::atom::read_multimodel_pdb()</a></td></tr>
64 <tr><td>@ref IMP::atom::Residue</td><td><a href="classIMP_1_1atom_1_1ForceFieldParameters.html#acc61a54cee5f3f8746ee722c8611c357">IMP::atom::ForceFieldParameters::add_bonds()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#a3aad1834ad554e00e510ff9d6229929c">IMP::atom::ForceFieldParameters::add_bonds()</a>, <a href="classIMP_1_1atom_1_1Residue.html#ad2a52bcb7885926fe37afe38c7b435d3">IMP::atom::Residue::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a54f33948b4d60dad09738d4ce504b43a">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a957af7eabce3843c1dc83c4a27eeda92">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#accd45ac766ff32953bafd0ae2cfd8ae3">IMP::kinematics::ProteinKinematics::get_phi()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a85b379c6f7ca0861de3d4800cf946168">IMP::kinematics::ProteinKinematics::get_psi()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a158ecc1761e6b1129cfcce34a7625a03">IMP::kinematics::ProteinKinematics::set_phi()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#addb633aa7568c17093408445e7e6f580">IMP::kinematics::ProteinKinematics::set_psi()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#ad8d6d36cd7f8e7ee0632dbb0eeca1436">IMP::kinematics::ProteinKinematics::add_dihedral_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#aac311bcba110ca759d8da22c9422550a">IMP::kinematics::ProteinKinematics::add_dihedral_joints()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a835aa2388efa9ec612bcfb70bec0b657">IMP::kinematics::ProteinKinematics::get_phi_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a1191debca9d2da9745d40ae719c2d56e">IMP::kinematics::ProteinKinematics::get_psi_joint()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#a07539b639bd491e81d4b86e87405df8c">IMP::rotamer::ResidueRotamer::set_coordinates()</a>, <a href="classIMP_1_1rotamer_1_1RotamerCalculator.html#a87f7878daf288370734d78479eaea929">IMP::rotamer::RotamerCalculator::get_rotamer()</a>, <a href="namespaceIMP_1_1atom.html#a899927712a6b9ae00aa8875407f5311a">IMP::atom::get_atom()</a>, <a href="namespaceIMP_1_1atom.html#a2cadcc607aa4c1f8b1ec4c0c8d493312">IMP::atom::get_next_residue()</a>, <a href="namespaceIMP_1_1atom.html#a6ef3ab3e84fd5ab0e83ce40fdc675455">IMP::atom::get_phi_dihedral_atoms()</a>, <a href="namespaceIMP_1_1atom.html#ad329e5c66a8de2f49304492c5a690d90">IMP::atom::get_previous_residue()</a>, <a href="namespaceIMP_1_1atom.html#a1c15e940e47a1a8f5872029fcb93c601">IMP::atom::get_psi_dihedral_atoms()</a></td></tr>
65 <tr><td>@ref IMP::atom::ResidueType</td><td><a href="classIMP_1_1atom_1_1CHARMMIdealResidueTopology.html#a53ca62b5ccb300cee4346944619ebbba">IMP::atom::CHARMMIdealResidueTopology::CHARMMIdealResidueTopology()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a93c5e6fbf6e839294e91ec2a179f74af">IMP::atom::CHARMMParameters::get_residue_topology()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a0e017ab02dc3673cfa7cd48fb6e4686d">IMP::atom::CHARMMParameters::parse_atom_line()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#aa0c19662e8ac391cdce1666af3b810eb">IMP::atom::CHARMMParameters::parse_bond_line()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopology.html#acd586e0463d6dddd9399956945c4e5cc">IMP::atom::CHARMMResidueTopology::CHARMMResidueTopology()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a7b68e49e0559daa33bc690c125bd13ca">IMP::atom::Residue::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#aa47d3e8ac5a0f07fc67eea29c60b2792">IMP::atom::Residue::set_residue_type()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a854ba587cbc24e74b3eca1e2b5eb3908">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a438d28031569985e208a7fff1e33471a">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#ad4f6159d760e9ae95f2b4c293f7d780e">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#aa4ffa278f6ca0abeac027c259b607afd">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a8d590f34cd5ffeb959672af4bdccd514">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a5afda2b941d117fe773529106da4d30d">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a6e55212a17fd8bc1329b9f8481bb6afb">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a68024499c221b617df3ee27d6460b4d6">IMP::atom::Selection::set_residue_type()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#ad8f9411effe5a159c0619e8135993d9a">IMP::rotamer::ResidueRotamer::ResidueRotamer()</a>, <a href="classIMP_1_1rotamer_1_1RotamerLibrary.html#a917624d3ba6e635f360c999efe4ce0f7">IMP::rotamer::RotamerLibrary::get_rotamers()</a>, <a href="classIMP_1_1rotamer_1_1RotamerLibrary.html#a17b121526a2716bca70671c76dc56fc5">IMP::rotamer::RotamerLibrary::get_rotamers_fast()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#ae5a59dd0ebd0d5590db3d2127444204e">IMP::saxs::FormFactorTable::get_carbon_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#ae157752399dbb8bbac2cf4a7ad84838a">IMP::saxs::FormFactorTable::get_dummy_form_factor()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a0bd345ed1e81cc77e53143b11ec525bb">IMP::saxs::FormFactorTable::get_form_factor()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#adc7d132da89b412ddc3bed43094c29a5">IMP::saxs::FormFactorTable::get_nitrogen_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a01b57170c71bbaa7edc35ce486805ac6">IMP::saxs::FormFactorTable::get_oxygen_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a3453246d72667c72492393cb9e7b00e1">IMP::saxs::FormFactorTable::get_sulfur_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a7ec1b171f8f6022fc79fff4d6e6bef20">IMP::saxs::FormFactorTable::get_vacuum_form_factor()</a>, <a href="namespaceIMP_1_1atom.html#a3982cc0d820dfdeb89abf056f3338754">IMP::atom::get_volume_from_residue_type()</a>, <a href="namespaceIMP_1_1atom.html#a7236ea7f2911d16543c5af18f46f0f5c">IMP::atom::get_mass()</a>, <a href="namespaceIMP_1_1atom.html#a6bf9912d67e4c9d6a134930015a928de">IMP::atom::get_one_letter_code()</a></td></tr>
66 <tr><td>@ref IMP::atom::SecondaryStructureResidue</td><td><a href="namespaceIMP_1_1atom.html#a3164dab692507ddc3602d0a179f642c6">IMP::atom::get_secondary_structure_match_score()</a></td></tr>
67 <tr><td>@ref IMP::atom::Selection</td><td><a href="classIMP_1_1atom_1_1Selection.html#a79306b9477cdce20dc3589eb1b5040bf">IMP::atom::Selection::set_difference()</a>, <a href="classIMP_1_1atom_1_1Selection.html#ab230edcc56bbc2163dcb2d8bb1a822f2">IMP::atom::Selection::set_intersection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#adab4f65a622a2a377c6805ac3341049c">IMP::atom::Selection::set_symmetric_difference()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a63be78e2118e882d1fb047b20b085368">IMP::atom::Selection::set_union()</a>, <a href="classIMP_1_1atom_1_1SelectionGeometry.html#afbe413545c59b4ed65283124b438d359">IMP::atom::SelectionGeometry::SelectionGeometry()</a>, <a href="namespaceIMP_1_1atom.html#a22904e48fa8d027f2b8ca2ab2f40ba04">IMP::atom::write_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a3840b931d1d234dcb59f7c9090e8a847">IMP::atom::write_pdb_of_c_alphas()</a>, <a href="namespaceIMP_1_1atom.html#aed5950befd1610327f1bc9bc737de49f">IMP::atom::create_cover()</a>, <a href="namespaceIMP_1_1atom.html#af6c28249c49b2aa2f4eda4faf0bda484">IMP::atom::create_distance_restraint()</a>, <a href="namespaceIMP_1_1atom.html#a94f17b92edb1887c13d9bd886914b761">IMP::atom::create_internal_connectivity_restraint()</a>, <a href="namespaceIMP_1_1atom.html#ab330fa176a652b7d204ed9ee820e3158">IMP::atom::create_internal_connectivity_restraint()</a>, <a href="namespaceIMP_1_1atom.html#af5b0cc808be9672d3996baeb2f9210fd">IMP::atom::get_leaves()</a>, <a href="namespaceIMP_1_1atom.html#ae122a232c9f291d3f5f4d218c06652e4">IMP::atom::get_mass()</a>, <a href="namespaceIMP_1_1atom.html#a8ac4a06cec8ed51c3f992851dbaf25b8">IMP::atom::get_radius_of_gyration()</a>, <a href="namespaceIMP_1_1atom.html#a9793120929ce62d48d46e06575e19721">IMP::atom::get_rmsd()</a>, <a href="namespaceIMP_1_1atom.html#aca20f445896d46445b8db0ab72bcf238">IMP::atom::get_rmsd()</a>, <a href="namespaceIMP_1_1atom.html#a603f2b73d6e22b3a9128e0398bc6e082">IMP::atom::get_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1atom.html#a1ffa9eaea1cc4ecd2d9e3a10b2dd50b2">IMP::atom::get_surface_area()</a>, <a href="namespaceIMP_1_1atom.html#ada8d754330898011ea1435fa0e693136">IMP::atom::get_volume()</a></td></tr>
68 <tr><td>@ref IMP::atom::Simulator</td><td><a href="classIMP_1_1rmf_1_1SaveOptimizerState.html#aaf387b770701f90b639953345671c103">IMP::rmf::SaveOptimizerState::set_simulator()</a></td></tr>
69 <tr><td>@ref IMP::atom::SmoothingFunction</td><td><a href="classIMP_1_1atom_1_1CoulombPairScore.html#a9fefe76aa6517db64b15098e4a08000e">IMP::atom::CoulombPairScore::CoulombPairScore()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#a125aef6ff287967f6aee1177254bf0e1">IMP::atom::LennardJonesPairScore::LennardJonesPairScore()</a></td></tr>
70 </table>
71 # IMP.base # {#argument_index_base}
72 <table><tr>
73 <th>Class</th><th>Users</th></tr>
74 <tr><td>@ref IMP::base::Array</td><td><a href="classIMP_1_1atom_1_1BondedPairFilter.html#a75c2b2f3aa8c79d4c7169b85e334a4ba">IMP::atom::BondedPairFilter::get_value_index()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#a944c8f13dcd0e5a9f17818267b6df1ad">IMP::atom::CoulombPairScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#a09069403d92ed646a2282ca0769ce3b9">IMP::atom::LennardJonesPairScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1SameResiduePairFilter.html#a88f48e89dec3d57c6f9e37c70ba0d40f">IMP::atom::SameResiduePairFilter::get_value_index()</a>, <a href="classIMP_1_1atom_1_1SoapPairFilter.html#a3a8060397dbfa2955fb0e04767f5bdfd">IMP::atom::SoapPairFilter::get_value_index()</a>, <a href="classIMP_1_1atom_1_1StereochemistryPairFilter.html#adb57965907990fd3b9ef83424574afa2">IMP::atom::StereochemistryPairFilter::get_value_index()</a>, <a href="classIMP_1_1base_1_1Array.html#a57e8bff60ef77ba70c91f2b92845a943">IMP::base::Array::compare()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairContainer.html#a88452f4d3cde210cb6b0100cf639e596">IMP::container::ConsecutivePairContainer::get_contains()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairFilter.html#a3c0f55bd920e1f6cccb8b81f2807d104">IMP::container::ConsecutivePairFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairContainer.html#a18b593dda14f61e7214df42e5b179be1">IMP::container::ExclusiveConsecutivePairContainer::get_contains()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairFilter.html#aee0e8320efee240132247dad46b7bb7b">IMP::container::ExclusiveConsecutivePairFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1InContainerPairFilter.html#a4db9c1be7defcdb7b7a18c667ff79881">IMP::container::InContainerPairFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1InContainerQuadFilter.html#a7fc4d9cda419966ec433d00a8e9aad60">IMP::container::InContainerQuadFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1InContainerTripletFilter.html#a204c9f423c9d11a69ec150aea96953d7">IMP::container::InContainerTripletFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1MinimumPairScore.html#a606874cbdde3983c9c2a4408249db333">IMP::container::MinimumPairScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1container_1_1MinimumPairScore.html#aac4d844f1e584b753cbb39a89f9fb4ab">IMP::container::MinimumPairScore::evaluate_index()</a>, <a href="classIMP_1_1container_1_1MinimumQuadScore.html#a5ba36352ef9bf938a86a176a1a27bfd0">IMP::container::MinimumQuadScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1container_1_1MinimumQuadScore.html#a9cd9bda67413ee67843d6980ae693930">IMP::container::MinimumQuadScore::evaluate_index()</a>, <a href="classIMP_1_1container_1_1MinimumTripletScore.html#abcaf06f492f9ffaba5b6c130a4d9bd03">IMP::container::MinimumTripletScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1container_1_1MinimumTripletScore.html#a1fc19beea8adb484c0624f808ddb0599">IMP::container::MinimumTripletScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1AllSamePairPredicate.html#a67ab4e4394d71776131bf34b231dfb99">IMP::core::AllSamePairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1AllSameQuadPredicate.html#a55b5693e955b7363002af939ba00bddd">IMP::core::AllSameQuadPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1AllSameTripletPredicate.html#a3ebfeb2badaf2e3c186e46bcaa1d59be">IMP::core::AllSameTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1AngleTripletScore.html#aaac2a3b7c18787b682bcd25164258caa">IMP::core::AngleTripletScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#ad4f2643c1a3a43d1b4e90ea27edc26ef">IMP::core::ClosePairsPairScore::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a19f2bcf9067be83e06e0721256119bda">IMP::core::ClosePairsPairScore::create_current_decomposition()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a7f46fea8797b2b839baadca9fe06e692">IMP::core::ClosePairsPairScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#ac784aad0c4d13dd7f3a33360916d2c53">IMP::core::ClosePairsPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1CoinFlipPairPredicate.html#a83ee244fdbd8f9feca1b234e4eb2e550">IMP::core::CoinFlipPairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1CoinFlipQuadPredicate.html#a38eb9e85d3aff19eb5d578cb98b7cd9c">IMP::core::CoinFlipQuadPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1CoinFlipTripletPredicate.html#a115b51a7dff84d546b12b7567646d1f0">IMP::core::CoinFlipTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1ConstantPairPredicate.html#aabbe3a38f2f73bd8428111ebf5b755af">IMP::core::ConstantPairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1ConstantQuadPredicate.html#ab905ecef4fe4bb89b9ac472ca4d0c7f7">IMP::core::ConstantQuadPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1ConstantTripletPredicate.html#ab0a446efcc68498dc8d6c10e81f8fd34">IMP::core::ConstantTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1DistancePairScore.html#aa775e76afb1dbbc7f5c68867c0566c8e">IMP::core::DistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicDistancePairScore.html#af234d80f86f34116a488f25f36e5e854">IMP::core::HarmonicDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicSphereDistancePairScore.html#a8ffa19ac305c4e230e1bd0bb993f4e69">IMP::core::HarmonicSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBoundSphereDiameterPairScore.html#a97b84d88135ee9445f819ea18385006f">IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBoundSphereDistancePairScore.html#ab024358b515f13a13cdeef25d5cd8f2c">IMP::core::HarmonicUpperBoundSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1IsCollisionPairPredicate.html#a83d5764f00d80afabe1a099d2b9725f4">IMP::core::IsCollisionPairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1KClosePairsPairScore.html#abc1df7468a99e683cbb32784dd3ac680">IMP::core::KClosePairsPairScore::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1KClosePairsPairScore.html#a85d19929355c36a8a75b67aee312057a">IMP::core::KClosePairsPairScore::create_current_decomposition()</a>, <a href="classIMP_1_1core_1_1KClosePairsPairScore.html#a534db675b49d128c701c6c0b66700d1f">IMP::core::KClosePairsPairScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1core_1_1KClosePairsPairScore.html#a47e0f36595be4c3998a4c89901a19528">IMP::core::KClosePairsPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#a4ea41ea99f1a2eb565180c1755d02d5e">IMP::core::NormalizedSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1OrderedTypePairPredicate.html#ab0e8e856c9abd9ccbb821af32efbc484">IMP::core::OrderedTypePairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1OrderedTypeQuadPredicate.html#a4dc5ee2f7476af38f63890289a30f2aa">IMP::core::OrderedTypeQuadPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1OrderedTypeTripletPredicate.html#ac34cda6e2b6b6e4f10f49e7b2b9d66e8">IMP::core::OrderedTypeTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1PairConstraint.html#a2054cb2895d90c474fef16856c262ef6">IMP::core::PairConstraint::PairConstraint()</a>, <a href="classIMP_1_1core_1_1PairRestraint.html#a8a2032099b9ca936b285a91981566093">IMP::core::PairRestraint::PairRestraint()</a>, <a href="classIMP_1_1core_1_1QuadConstraint.html#a8cab020f6af1cc18c1b59309a34187ab">IMP::core::QuadConstraint::QuadConstraint()</a>, <a href="classIMP_1_1core_1_1QuadRestraint.html#a5fc2cadbe62cd7f922201e7c06241121">IMP::core::QuadRestraint::QuadRestraint()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#ab6536f0e1fd858ded1239673fab7c53e">IMP::core::RefinedPairsPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SoftSpherePairScore.html#a9f0ff574e4e142cb76a9125b77e124ce">IMP::core::SoftSpherePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SphereDistancePairScore.html#af35d96e28844898402854dbb38d58102">IMP::core::SphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#af31f1dbc1a08962f44060d7e8c0c8862">IMP::core::TransformedDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1TripletConstraint.html#a52c5cff853de9ad26763cd55453a3e29">IMP::core::TripletConstraint::TripletConstraint()</a>, <a href="classIMP_1_1core_1_1TripletRestraint.html#a041a7391fce8254c70be35362b11b703">IMP::core::TripletRestraint::TripletRestraint()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#a1ca72bd80eb4af1c16cb6302a73f4ec9">IMP::core::TypedPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1UnorderedTypePairPredicate.html#a4095a82242be94b6e5069b672c186840">IMP::core::UnorderedTypePairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeQuadPredicate.html#a3ac014caf3e265977337489aa27ae279">IMP::core::UnorderedTypeQuadPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeTripletPredicate.html#a7fadfa3c395a29597f8af137d841ccfb">IMP::core::UnorderedTypeTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1WeightedSphereDistancePairScore.html#a4174eb63688a5a812824f7884b1a139f">IMP::core::WeightedSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#ae6ec7ef81689c35265f57b748a3675c9">IMP::example::ExamplePairScore::evaluate_index()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#a6e106a5d378334a2e16794ada101fd2b">IMP::isd::CrossLinkMSRestraint::add_contribution()</a>, <a href="classIMP_1_1isd_1_1RepulsiveDistancePairScore.html#a7f78921b5eb1d5e120f7fb227d27bd3c">IMP::isd::RepulsiveDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1kernel_1_1PairModifier.html#a5bea4bf225f4d1d9550debeb76c3d106">IMP::kernel::PairModifier::apply_index()</a>, <a href="classIMP_1_1kernel_1_1PairPredicate.html#a6f6aeb965bba69c8d9d457c9b7703586">IMP::kernel::PairPredicate::get_value_index()</a>, <a href="classIMP_1_1kernel_1_1PairPredicate.html#a1d22f338857b21fa9b0a8c00898c1def">IMP::kernel::PairPredicate::operator()()</a>, <a href="classIMP_1_1kernel_1_1PairScore.html#ab0d0fe3d2f6fed57aaa150d1b5e2ace3">IMP::kernel::PairScore::create_current_decomposition()</a>, <a href="classIMP_1_1kernel_1_1PairScore.html#aa6ab389ab63b24f1e32a0e8593f5a8b7">IMP::kernel::PairScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1kernel_1_1PairScore.html#af503989bb181141514e3616babf52305">IMP::kernel::PairScore::evaluate_index()</a>, <a href="classIMP_1_1kernel_1_1PairScore.html#adf15d77e4bbbd87969d19afc9da28501">IMP::kernel::PairScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1kernel_1_1QuadModifier.html#a222d59855f8f0f194c05608649438a01">IMP::kernel::QuadModifier::apply_index()</a>, <a href="classIMP_1_1kernel_1_1QuadPredicate.html#ae72cf8bcdecca010c806a42738a44edb">IMP::kernel::QuadPredicate::get_value_index()</a>, <a href="classIMP_1_1kernel_1_1QuadPredicate.html#accc7dbdc52042d1c2fb40fe1022436f1">IMP::kernel::QuadPredicate::operator()()</a>, <a href="classIMP_1_1kernel_1_1QuadScore.html#afcc962631fe0b7e7c8d3e4314d8cdef0">IMP::kernel::QuadScore::create_current_decomposition()</a>, <a href="classIMP_1_1kernel_1_1QuadScore.html#a85e7f0835df1be9e96dfdecd3e16372e">IMP::kernel::QuadScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1kernel_1_1QuadScore.html#a79c2b432dd52988d5c21bec6d447e8f4">IMP::kernel::QuadScore::evaluate_index()</a>, <a href="classIMP_1_1kernel_1_1QuadScore.html#af854cb469e34c598b9eeea8cb1a87606">IMP::kernel::QuadScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1kernel_1_1TripletModifier.html#a41e051f92947f25747ad1bce64700d8c">IMP::kernel::TripletModifier::apply_index()</a>, <a href="classIMP_1_1kernel_1_1TripletPredicate.html#a51951e33a645d9a3adac638bbcac89fe">IMP::kernel::TripletPredicate::get_value_index()</a>, <a href="classIMP_1_1kernel_1_1TripletPredicate.html#a4ee04d1613caaa908ac4edd9e3119212">IMP::kernel::TripletPredicate::operator()()</a>, <a href="classIMP_1_1kernel_1_1TripletScore.html#a80839b21ddc1c2a92e2070b5fef2e54b">IMP::kernel::TripletScore::create_current_decomposition()</a>, <a href="classIMP_1_1kernel_1_1TripletScore.html#af1ff450c58223ee74dd9795eddf5d8f0">IMP::kernel::TripletScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1kernel_1_1TripletScore.html#a1eeab1dee8f026829f646edb22570364">IMP::kernel::TripletScore::evaluate_index()</a>, <a href="classIMP_1_1kernel_1_1TripletScore.html#ad1674d34fb55bde32fee8b8f390fbd3c">IMP::kernel::TripletScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1misc_1_1CommonEndpointPairFilter.html#a7b593b5a448a54250e318cff4b9145c2">IMP::misc::CommonEndpointPairFilter::get_value_index()</a>, <a href="classIMP_1_1misc_1_1LogPairScore.html#ac63899594d3caebf37b35954b4bd53f1">IMP::misc::LogPairScore::evaluate_index()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#a677ec8f87f21f3b2e5bb99e13d5154a7">IMP::misc::LowestRefinedPairScore::evaluate_index()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#ac93a6cfc558a16532cd9f743a33ca26b">IMP::misc::SoftCylinderPairScore::evaluate_index()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#aee21f4a20638827ddd81294faef862b4">IMP::score_functor::AddScores::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#a322efefec3bd1aff867221582aca8db0">IMP::score_functor::AddScores::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#add1bf87841d6edc68a610c0ac07eed79">IMP::score_functor::AddScores::get_score()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#ac83905ff1ddd74aea476066e18792364">IMP::score_functor::AddScores::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#ad4bcede3ec86019e31b02474a518deff">IMP::score_functor::DistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1score__functor_1_1Harmonic.html#af377b7cbf55e104eccb1581803b2ac67">IMP::score_functor::Harmonic::get_score()</a>, <a href="classIMP_1_1score__functor_1_1Harmonic.html#a2af784c86e739e77abd46b4805c33ed6">IMP::score_functor::Harmonic::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#a29d438dde0771932178078208b1b13fc">IMP::score_functor::HarmonicLowerBound::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#a2d821b402df9dd99ed3a0883bacb4587">IMP::score_functor::HarmonicLowerBound::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#a91e616d213c2137eb0515461fb89a60f">IMP::score_functor::HarmonicLowerBound::get_score()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#a4be1d95e4f0429120de6138e68c07e7c">IMP::score_functor::HarmonicLowerBound::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicUpperBound.html#aa020645b78d825313ad7b51f03671dd2">IMP::score_functor::HarmonicUpperBound::get_score()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicUpperBound.html#a172a58beac89a0fc4121898d29df0e93">IMP::score_functor::HarmonicUpperBound::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#aa387607d984c8699f6702625dcbeb92c">IMP::score_functor::LinearLowerBound::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#a49d48cd27830e2c8d414ab3e1d4a9811">IMP::score_functor::LinearLowerBound::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#a4b72334997737b255f2ef0613a266602">IMP::score_functor::LinearLowerBound::get_score()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#ad8620337b62f86a717db16e5f68e355c">IMP::score_functor::LinearLowerBound::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#af8b6a7b7a999063db7489c121c7a8243">IMP::score_functor::OpenCubicSpline::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#aded05aa3cfec1730a7eb684fb990d581">IMP::score_functor::OpenCubicSpline::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#a2ee2e2dc06741ce79b6215b619cddfe1">IMP::score_functor::OpenCubicSpline::get_score()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#a832cf1b36efc9d16a04c10ac272c67ba">IMP::score_functor::OpenCubicSpline::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#a3a7aeb3363d73facc8d30aa726e950af">IMP::score_functor::OrientedSoap::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#afd81d695cb19ff3faa31ba3539f8d13f">IMP::score_functor::OrientedSoap::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#a6d5c8ba69379e4f51cd4829a1089cc7b">IMP::score_functor::OrientedSoap::get_score()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#ae516bd22a59d95b339f2731d42aa39fc">IMP::score_functor::OrientedSoap::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#af79c80d2b2692580299f1b40574d2e0e">IMP::score_functor::Shift::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#a7bb8bb363d32ecd7ac801ff4f5bf1090">IMP::score_functor::Shift::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#a26d46440841618f9eacec9cda9257716">IMP::score_functor::Shift::get_score()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#a548926aa847e2ea40466dac9b83ccd43">IMP::score_functor::Shift::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a314709d5c92cd0d13a92c0c2c2713a55">IMP::score_functor::SphereDistance::get_rsum()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a2064930f07606d402fa12656bce40fed">IMP::score_functor::SphereDistance::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a9902dc11f6e2cbec8d6db6895afbe938">IMP::score_functor::SphereDistance::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a367f590bcbb5b13bf9effd79f6c46b12">IMP::score_functor::SphereDistance::get_score()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a6b3917980e91a4be251d95f6dcdcaa4e">IMP::score_functor::SphereDistance::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#a07631071763a11077f020605137dafcd">IMP::score_functor::Statistical::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1UnaryFunctionEvaluate.html#a4c031c07ab4e3ff130ba1a1b696e194b">IMP::score_functor::UnaryFunctionEvaluate::get_score()</a>, <a href="classIMP_1_1score__functor_1_1UnaryFunctionEvaluate.html#ab80bfb4ff7e064bc3f760f27a1639a71">IMP::score_functor::UnaryFunctionEvaluate::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1WeightScore.html#aa3c8c81ebfc8ab781fb7a843b70c442c">IMP::score_functor::WeightScore::get_score()</a>, <a href="classIMP_1_1score__functor_1_1WeightScore.html#a6041da95abd500298d10fbd9d6203353">IMP::score_functor::WeightScore::get_score_and_derivative()</a></td></tr>
75 <tr><td>@ref IMP::base::ConstVector</td><td><a href="classIMP_1_1base_1_1ConstVector.html#aaec8760ba273afb6535d65a1e2fa1fbf">IMP::base::ConstVector::compare()</a>, <a href="namespaceIMP_1_1base.html#a978a1e14b7048b32fcfe5aa8f578b41d">IMP::base::swap()</a></td></tr>
76 <tr><td>@ref IMP::base::Index</td><td><a href="classIMP_1_1base_1_1Index.html#a375c5cd87906a1dd728d21d55ed0237c">IMP::base::Index::IMP_COMPARISONS_1()</a>, <a href="classIMP_1_1base_1_1Index.html#aad88b247bef770efe08ffac043f9f6b5">IMP::base::Index::IMP_HASHABLE_INLINE()</a>, <a href="classIMP_1_1base_1_1IndexVector.html#a26471b4ba1070157f37111517420a82b">IMP::base::IndexVector::at()</a>, <a href="classIMP_1_1base_1_1IndexVector.html#a5b798b49ea367cc4512b1d6d6d86ab51">IMP::base::IndexVector::at()</a>, <a href="classIMP_1_1base_1_1IndexVector.html#a4ec826bc4dd325796d6d3ec47be01f33">IMP::base::IndexVector::operator[]()</a>, <a href="classIMP_1_1base_1_1IndexVector.html#ad3f0a6e9e5a6d94150026823454a8db3">IMP::base::IndexVector::operator[]()</a>, <a href="namespaceIMP_1_1base.html#ab3db2cbdecd9c0b17050b0bbafac9a98">IMP::base::get_as_unsigned_int()</a>, <a href="namespaceIMP_1_1base.html#a52bfb50ee044cb0a12de3a15038c0837">IMP::base::resize_to_fit()</a></td></tr>
77 <tr><td>@ref IMP::base::Object</td><td><a href="classIMP_1_1base_1_1CreateLogContext.html#ae76d5bf3a153faf0f6aa3923100d5510">IMP::base::CreateLogContext::CreateLogContext()</a>, <a href="classIMP_1_1base_1_1CreateLogContext.html#a6b504af18defe5872a62f3f2840afe47">IMP::base::CreateLogContext::CreateLogContext()</a>, <a href="classIMP_1_1base_1_1CreateLogContext.html#ae89256e23f6859585d9f505e4d299330">IMP::base::CreateLogContext::set()</a>, <a href="classIMP_1_1base_1_1Object.html#ab2ff8b0453d5ef52790053ba491a899f">IMP::base::Object::add_live_object()</a>, <a href="classIMP_1_1base_1_1Object.html#ace7935f80ed186745796132a7c0b4603">IMP::base::Object::remove_live_object()</a>, <a href="classIMP_1_1base_1_1Object.html#ac2b8271c18f4f209bea7072fdaee5ced">IMP::base::Object::compare()</a>, <a href="classIMP_1_1base_1_1SetCheckState.html#a263e90cadd61ac038c6c55dbbfd81269">IMP::base::SetCheckState::do_set()</a>, <a href="classIMP_1_1base_1_1SetCheckState.html#a02355506e991326e18cbfc94cb4d6f45">IMP::base::SetCheckState::SetCheckState()</a>, <a href="classIMP_1_1base_1_1SetCheckState.html#afb8e9281f4ff14c740ab51dd1718e863">IMP::base::SetCheckState::set()</a>, <a href="classIMP_1_1base_1_1SetLogState.html#a71608ec7ce68aa4d317a2f64c53d44a0">IMP::base::SetLogState::do_set()</a>, <a href="classIMP_1_1base_1_1SetLogState.html#a175a53b0dd151f4669063f7c2cb068b2">IMP::base::SetLogState::SetLogState()</a>, <a href="classIMP_1_1base_1_1SetLogState.html#af97105e47dd93b674c78fa857dd1f8fe">IMP::base::SetLogState::set()</a>, <a href="classIMP_1_1base_1_1Timer.html#aaa14eb2c8620d60b4396c8df4394fbfc">IMP::base::Timer::Timer()</a>, <a href="classIMP_1_1base_1_1Timer.html#a1dd48a8c280d32d3050a16b122e0a2df">IMP::base::Timer::Timer()</a>, <a href="classIMP_1_1kernel_1_1Decorator.html#a1be87eb9be566c989a08323d477ad041">IMP::kernel::Decorator::compare()</a>, <a href="classIMP_1_1kernel_1_1Model.html#af4020ed0f172180c96c3f1d142e11f76">IMP::kernel::Model::add_data()</a>, <a href="namespaceIMP_1_1base.html#aba9c8aeb3d72fc29d404ea9a42ce9d50">IMP::base::object_cast()</a>, <a href="namespaceIMP_1_1rmf.html#ad73cae6f16aee4923011ed98b74fdb68">IMP::rmf::get_node_from_association()</a>, <a href="namespaceIMP_1_1rmf.html#a0ed72dc889bd987bd1abb2ba57c49811">IMP::rmf::get_node_from_association()</a>, <a href="namespaceIMP_1_1rmf.html#ac3997be50139e58a290ad0812ebcb1c8">IMP::rmf::get_has_associated_node()</a>, <a href="namespaceIMP_1_1rmf.html#ada156f068d25ad04eff2d014771d5e95">IMP::rmf::set_association()</a></td></tr>
78 <tr><td>@ref IMP::base::TextInput</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#aa7d9982f2268fc72c8a1efdf11fa0bf5">IMP::atom::CHARMMParameters::read_parameter_file()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a271ee725c077609436c2408c70c36304">IMP::atom::CHARMMParameters::read_topology_file()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a6e2ca976e6be19b62e6481f1552a79ee">IMP::atom::CHARMMParameters::CHARMMParameters()</a>, <a href="classIMP_1_1atom_1_1DopePairScore.html#a0bce52d383c2226477b405fa9ea27276">IMP::atom::DopePairScore::DopePairScore()</a>, <a href="classIMP_1_1atom_1_1ProteinLigandAtomPairScore.html#a6efbb06f6d214ac3c44f3b74220dd36a">IMP::atom::ProteinLigandAtomPairScore::ProteinLigandAtomPairScore()</a>, <a href="classIMP_1_1atom_1_1ProteinLigandRestraint.html#a84df68054cc57ef9fb71924f9224ee1a">IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint()</a>, <a href="classIMP_1_1core_1_1StatisticalPairScore.html#aed8e2be13286b11dbb50908f7d777606">IMP::core::StatisticalPairScore::StatisticalPairScore()</a>, <a href="classIMP_1_1core_1_1StatisticalPairScore.html#a25a58885d56bf4b01dac690a376a055b">IMP::core::StatisticalPairScore::StatisticalPairScore()</a>, <a href="classIMP_1_1score__functor_1_1Dope.html#a3e0adce8c17693b4a900b7b4bc09bee3">IMP::score_functor::Dope::Dope()</a>, <a href="classIMP_1_1score__functor_1_1SingletonStatistical.html#aaaaaa7ff1dcc8ab65e2ff578d0cb582e">IMP::score_functor::SingletonStatistical::SingletonStatistical()</a>, <a href="classIMP_1_1score__functor_1_1Soap.html#a03ff27c9cf3518a4b37665d4b88837b0">IMP::score_functor::Soap::Soap()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#a72c6efb9669977b720e502aee907e7d8">IMP::score_functor::Statistical::Statistical()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#a8d168e9e5a393d7de16d795b18068132">IMP::score_functor::Statistical::Statistical()</a>, <a href="namespaceIMP_1_1algebra.html#a2b99092e2bf90a45ecee7ab1208b4dc8">IMP::algebra::read_pts()</a>, <a href="namespaceIMP_1_1algebra.html#a0511471fbfb34ac96a132d8f181c6ea0">IMP::algebra::read_spheres()</a>, <a href="namespaceIMP_1_1atom.html#a9b13cfbe2f98dd95b8837f10dbb6fdfd">IMP::atom::read_mol2()</a>, <a href="namespaceIMP_1_1atom.html#ac65059962426cd7e45339ff9f3ed70df">IMP::atom::read_pdb()</a>, <a href="namespaceIMP_1_1atom.html#ae1ede2b0bd5e5af085111120d11f149d">IMP::atom::read_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a13159795e7c78f154e98bc20cc4fb8d8">IMP::atom::read_multimodel_pdb()</a>, <a href="namespaceIMP_1_1atom.html#ac376e29826164bc29ba340b438507a35">IMP::atom::read_psipred()</a>, <a href="namespaceIMP_1_1atom.html#a3b8e395cdf044456ec136c147761b0f9">IMP::atom::read_psipred()</a></td></tr>
79 <tr><td>@ref IMP::base::TextOutput</td><td><a href="classIMP_1_1base_1_1SetLogTarget.html#aaac659e4191f85760409f7e8992ce97d">IMP::base::SetLogTarget::SetLogTarget()</a>, <a href="classIMP_1_1base_1_1SetLogTarget.html#af433fee846ea1732db99a55ffd8f7d87">IMP::base::SetLogTarget::set()</a>, <a href="classIMP_1_1core_1_1WriteRestraintScoresOptimizerState.html#a2ee9271e696071b83357e8d10b9df058">IMP::core::WriteRestraintScoresOptimizerState::WriteRestraintScoresOptimizerState()</a>, <a href="classIMP_1_1display_1_1ChimeraWriter.html#ad92c0bd95da3f001d1d92e9adcfd9bcc">IMP::display::ChimeraWriter::ChimeraWriter()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#aa6a9512cf3c50315f47c65bec91f01de">IMP::display::PymolWriter::PymolWriter()</a>, <a href="classIMP_1_1display_1_1TextWriter.html#af929d06ead2298291d5b3240d9f72365">IMP::display::TextWriter::TextWriter()</a>, <a href="namespaceIMP_1_1algebra.html#a3f9082844e652ee26c3a52edaf8f6213">IMP::algebra::write_pts()</a>, <a href="namespaceIMP_1_1algebra.html#a6244e1d73eac38d5507ae0d530b74b58">IMP::algebra::write_spheres()</a>, <a href="namespaceIMP_1_1atom.html#a8b76c2984bf4e6625faad378d70e9bf3">IMP::atom::write_mol2()</a>, <a href="namespaceIMP_1_1atom.html#a22904e48fa8d027f2b8ca2ab2f40ba04">IMP::atom::write_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a3840b931d1d234dcb59f7c9090e8a847">IMP::atom::write_pdb_of_c_alphas()</a>, <a href="namespaceIMP_1_1atom.html#a94a390f980c6b8b2c64499b0f0efb6a5">IMP::atom::write_multimodel_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a8b4cd32a2cc9e7487803d25b89e41f22">IMP::atom::show_as_graphviz()</a>, <a href="namespaceIMP_1_1base.html#a31dd68ecb46a1f62296c7ab532542a3e">IMP::base::set_log_target()</a>, <a href="namespaceIMP_1_1base.html#a1320b55833e66769be1d3e5a7705f871">IMP::base::show_timings()</a>, <a href="namespaceIMP_1_1core.html#a2abc47490c92e47767b9fe3b6771efa0">IMP::core::show_rigid_body_hierarchy()</a>, <a href="namespaceIMP_1_1domino.html#a2d55685583d92caff0965072f3eabb37">IMP::domino::show_as_graphviz()</a>, <a href="namespaceIMP_1_1kernel.html#a8963d9f8d3757f130f4824de9e3eb113">IMP::kernel::show_as_graphviz()</a>, <a href="namespaceIMP_1_1multifit.html#a51ea4bd63c8eaf2b9a3173b2bbe15870">IMP::multifit::write_connolly_surface()</a></td></tr>
80 <tr><td>@ref IMP::base::Vector</td><td><a href="classIMP_1_1algebra_1_1BoundingBoxD.html#aa8e971575487bfbf089febb50526c54c">IMP::algebra::BoundingBoxD::BoundingBoxD()</a>, <a href="classIMP_1_1algebra_1_1NearestNeighborD.html#a465b01fda7cda63dfda53413c3fe87b6">IMP::algebra::NearestNeighborD::NearestNeighborD()</a>, <a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a2f747f49892c8e8cadd5be8c174467f4">IMP::algebra::PrincipalComponentAnalysisD::PrincipalComponentAnalysisD()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#ab2447a656e1c29da465f3f88ffc2cc69">IMP::atom::AngleSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#abff2c9cc18193705300fe190a466aff8">IMP::atom::AngleSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a0a406eac77fe3e277b814639d947942a">IMP::atom::AngleSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1BerendsenThermostatOptimizerState.html#adece6f2562d157cafd4acb53f57e49a3">IMP::atom::BerendsenThermostatOptimizerState::BerendsenThermostatOptimizerState()</a>, <a href="classIMP_1_1atom_1_1BerendsenThermostatOptimizerState.html#a9c32a70ae3a204ed0f8a4283439fe05f">IMP::atom::BerendsenThermostatOptimizerState::set_particles()</a>, <a href="classIMP_1_1atom_1_1BondEndpointsRefiner.html#ad94833a1f040145775968a914b0f28f6">IMP::atom::BondEndpointsRefiner::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#aabc0f99a8709f132433132ae74954eea">IMP::atom::BondSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#ad6089666d6fa114e3f6554cb3eb38760">IMP::atom::BondSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#afb15c9170d376019812460f41ea56f2f">IMP::atom::BondSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1BondedPairFilter.html#ae019b8756c90df8c2d2cb4fe19cb7f45">IMP::atom::BondedPairFilter::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamics.html#a8ebadaa294b87ba1ec3e3a28e023d26f">IMP::atom::BrownianDynamics::advance_chunk()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamics.html#aab9915cb1b32d23a85091359ae340189">IMP::atom::BrownianDynamics::do_step()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamics.html#a4339df1cf0f25eb722209075e09d4039">IMP::atom::BrownianDynamics::setup()</a>, <a href="classIMP_1_1atom_1_1CHARMMConnection.html#a22ff0e7ededfb20f89185a650fff7d79">IMP::atom::CHARMMConnection::CHARMMConnection()</a>, <a href="classIMP_1_1atom_1_1CHARMMInternalCoordinate.html#a9d280e5a18153f82f84c5371c43b1764">IMP::atom::CHARMMInternalCoordinate::CHARMMInternalCoordinate()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#ab9e89e0e6448c516389a46b7b3e31971">IMP::atom::CHARMMParameters::add_angle()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a7493e32f1b5534c11661f4ae1d283e8b">IMP::atom::CHARMMParameters::add_dihedral()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a629d4fad7858d635635acc80d38c1474">IMP::atom::CHARMMParameters::parse_dihedrals_parameters_line()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a94b0d8be48111e039b031c0ec97dd132">IMP::atom::CHARMMParameters::create_angles()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a946bbc8aa744593740f19de3ddc67c4a">IMP::atom::CHARMMParameters::create_dihedrals()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#a70af866b212ce09b410de004b9631058">IMP::atom::CoulombPairScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1CoverBond.html#ad42e67780c818b8bdef31406910f5e04">IMP::atom::CoverBond::apply_indexes()</a>, <a href="classIMP_1_1atom_1_1CoverBond.html#a2c4edb0d15faceaa62203407c236c364">IMP::atom::CoverBond::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1CoverBond.html#a4bf334420d46bd96c527e3db0c5b3a20">IMP::atom::CoverBond::do_get_outputs()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#afc173df050df65fd630e90c8c3e44e10">IMP::atom::DihedralSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a471df902ea7b72e0bb70fa39496e1f0c">IMP::atom::DihedralSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a9b036c3cab6fd2b9b74be27d6bbb62dc">IMP::atom::DihedralSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1EzRestraint.html#a1d22717abc46f61c9cc68e8e725bd938">IMP::atom::EzRestraint::EzRestraint()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#ac70520f9545a764064407d22d2e1a330">IMP::atom::ImproperSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#a432083c036c2efafb46cf647b5e67f7d">IMP::atom::ImproperSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#a09fa9d1dae33b1c0d19f25f538139d9d">IMP::atom::ImproperSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1LangevinThermostatOptimizerState.html#a1df32cd8c92cbec18153981882f91b53">IMP::atom::LangevinThermostatOptimizerState::set_particles()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#a7e13fbe176a0cee6386ce1e2fb1e94af">IMP::atom::LennardJonesPairScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1MolecularDynamics.html#a04cd7bf73f21b5a68c84d63daeeaade6">IMP::atom::MolecularDynamics::do_step()</a>, <a href="classIMP_1_1atom_1_1MolecularDynamics.html#aef38c67ecafccb22603aee9acaa7d54f">IMP::atom::MolecularDynamics::setup()</a>, <a href="classIMP_1_1atom_1_1MolecularDynamics.html#a043e0a3a9a1ee5f5f6633f730ddc81f0">IMP::atom::MolecularDynamics::propagate_coordinates()</a>, <a href="classIMP_1_1atom_1_1MolecularDynamics.html#af5af84d583c00c26288cbb1d388c2dd3">IMP::atom::MolecularDynamics::propagate_velocities()</a>, <a href="classIMP_1_1atom_1_1MolecularDynamics.html#acb0a009c821c1521c5515faef5f0d4a7">IMP::atom::MolecularDynamics::setup_degrees_of_freedom()</a>, <a href="classIMP_1_1atom_1_1RemoveRigidMotionOptimizerState.html#a15f2d100906ff7a648829447370c9e50">IMP::atom::RemoveRigidMotionOptimizerState::set_particles()</a>, <a href="classIMP_1_1atom_1_1RemoveTranslationOptimizerState.html#a319867d177dbd4b67b8aa10de76dc1b2">IMP::atom::RemoveTranslationOptimizerState::set_particles()</a>, <a href="classIMP_1_1atom_1_1SameResiduePairFilter.html#a16f3e7a76fa9a027ce19becb67897276">IMP::atom::SameResiduePairFilter::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a8fa90b4762c312a29c0776d029adfb80">IMP::atom::Selection::set_hierarchies()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a6e55212a17fd8bc1329b9f8481bb6afb">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#ad1607c56d5b295206039732b6c5d620b">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#aa382f78f97cb063e198413d0bc25bce9">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a215267c1208e2b3cdfc150f2faa86dfe">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#a38f0e6730058941b361251d46709acff">IMP::atom::Simulator::remove_particles()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#a3297690fa16bfaccb93623d79c5bdb03">IMP::atom::Simulator::set_particles()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#aac02f06c52fce78b31213e12cbcca18f">IMP::atom::Simulator::set_particles_order()</a>, <a 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href="classIMP_1_1core_1_1SoftSpherePairScore.html#a1dbe4c8959c01ad2fd9710cbbe013a67">IMP::core::SoftSpherePairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1SphereDistancePairScore.html#ae8221b52afc000cf46adbb93f980fd90">IMP::core::SphereDistancePairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1SphereDistanceToSingletonScore.html#a1931fc0bc595f571b227ae94585961fa">IMP::core::SphereDistanceToSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1SphereDistanceToSingletonScore.html#ade44d143a4514cdf794a5d515ea14465">IMP::core::SphereDistanceToSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1SphereDistanceToSingletonScore.html#aefaf01c6035a84dd050d2a4a71640986">IMP::core::SphereDistanceToSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a7615780047e92e9962c3ccdb70a6cab0">IMP::core::TableRefiner::add_particle()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#aa2a81f54e9fa0c35421a2b8002a6ef08">IMP::core::TableRefiner::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a359aebec2be2b5f56e477e62424e6700">IMP::core::TableRefiner::set_particle()</a>, <a href="classIMP_1_1core_1_1Transform.html#a08a4cad5d8bf101f6769f01112d66473">IMP::core::Transform::apply_indexes()</a>, <a href="classIMP_1_1core_1_1Transform.html#a527c6b87602f00474444c96a0f83fde7">IMP::core::Transform::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1Transform.html#a5cded5294cb1f566b66fa3cabda9f7d9">IMP::core::Transform::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1TransformationAndReflectionSymmetry.html#ac9546947cd25117917c956c60e046eca">IMP::core::TransformationAndReflectionSymmetry::apply_indexes()</a>, <a href="classIMP_1_1core_1_1TransformationAndReflectionSymmetry.html#a18eaca2e513baf0b0620b13ca5548111">IMP::core::TransformationAndReflectionSymmetry::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1TransformationAndReflectionSymmetry.html#a3aa758f7f317cc5d408b2049e48f313f">IMP::core::TransformationAndReflectionSymmetry::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#ad5330642b6fbd562724711a41ef6f79a">IMP::core::TransformationSymmetry::apply_indexes()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#aaa0f5022b6739d039db1d9e91e61c736">IMP::core::TransformationSymmetry::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#a756a33cd5e283d6256be552d7b8b8df9">IMP::core::TransformationSymmetry::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#aa331664d4f990db58c9f5a5fe2f792d0">IMP::core::TransformedDistancePairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#acc1893f538a00817b3ad7ae525f4b436">IMP::core::TypedPairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1UnorderedTypePairPredicate.html#a847d694721c195a04b360b52ad1dc819">IMP::core::UnorderedTypePairPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeQuadPredicate.html#ae93960af923279ce2bfa8f670a1f69bf">IMP::core::UnorderedTypeQuadPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeSingletonPredicate.html#a766e8f517a169a754de6d6447631877e">IMP::core::UnorderedTypeSingletonPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeSingletonPredicate.html#af025fb71522bf985c638fce3429203bb">IMP::core::UnorderedTypeSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeSingletonPredicate.html#a10689a449bfbbb67c69539afef657115">IMP::core::UnorderedTypeSingletonPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeTripletPredicate.html#ab97a7dcfdc24aba8d597e3c44f8e96f4">IMP::core::UnorderedTypeTripletPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1WeightedDerivativesToRefined.html#ab508efa3e3e4eee693176aac6b71420a">IMP::core::WeightedDerivativesToRefined::apply_indexes()</a>, <a href="classIMP_1_1core_1_1WeightedDerivativesToRefined.html#ac65dd93e535195a26438e4b00bdc325f">IMP::core::WeightedDerivativesToRefined::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1WeightedDerivativesToRefined.html#a16ce595c17ce70459d3612687de11116">IMP::core::WeightedDerivativesToRefined::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1WeightedSphereDistancePairScore.html#a928ece55a50d0976b8e79d4f84eb2471">IMP::core::WeightedSphereDistancePairScore::do_get_inputs()</a>, <a href="classIMP_1_1domino_1_1DependencyScoreState.html#ad98074d99c5e28a96dfbb5c00ce2d717">IMP::domino::DependencyScoreState::set_input_particles()</a>, <a href="classIMP_1_1domino_1_1DependencyScoreState.html#ad784ed3c29023290bee30c5bd5750f94">IMP::domino::DependencyScoreState::set_output_particles()</a>, <a href="classIMP_1_1domino_1_1DisjointSetsSubsetFilterTable.html#a5f9690cf65d0e57971aaaa3fe5f48d74">IMP::domino::DisjointSetsSubsetFilterTable::add_set()</a>, <a href="classIMP_1_1domino_1_1Order.html#a78fe2c73f2df449f321066ad106f9d20">IMP::domino::Order::Order()</a>, <a href="classIMP_1_1domino_1_1PairListSubsetFilterTable.html#aad0f9d8bac17f64a00ee99b2fa8ab856">IMP::domino::PairListSubsetFilterTable::fill()</a>, <a href="classIMP_1_1domino_1_1ParticlesAdaptor.html#a04ffc186ecb90e83ca1c916d55a907f2">IMP::domino::ParticlesAdaptor::ParticlesAdaptor()</a>, <a href="classIMP_1_1domino_1_1ReadAssignmentContainer.html#a578c47d5474bbb32d29bcaad8f6cf388">IMP::domino::ReadAssignmentContainer::ReadAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1ReadHDF5AssignmentContainer.html#a1d5717bb895dc7f7e7ca3af4ccd7a351">IMP::domino::ReadHDF5AssignmentContainer::ReadHDF5AssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a6257822105ec410478841f77578b0ae0">IMP::domino::RestraintCache::load_cache()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a53c075b008f0fb41239383459f40438a">IMP::domino::RestraintCache::save_cache()</a>, <a href="classIMP_1_1domino_1_1Subset.html#ad7e9718aca30793514b4a6c7e6a39738">IMP::domino::Subset::get_sorted()</a>, <a href="classIMP_1_1domino_1_1Subset.html#aa9eb350f78281c7dd16da093ca71a465">IMP::domino::Subset::Subset()</a>, <a href="classIMP_1_1domino_1_1WriteAssignmentContainer.html#a0e3927e5d8e69e9d233fa025913dfa2a">IMP::domino::WriteAssignmentContainer::WriteAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1WriteHDF5AssignmentContainer.html#a93bf947f7a3edad64d045b6e3214362b">IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1WriteHDF5AssignmentContainer.html#abe70878e668dbb8aff5e71c1f9afcedc">IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer()</a>, <a href="classIMP_1_1em2d_1_1CollisionCrossSection.html#aff6ade34d263d74f6fa28e27dab4c02b">IMP::em2d::CollisionCrossSection::set_model_particles()</a>, <a href="classIMP_1_1em2d_1_1Fine2DRegistrationRestraint.html#a67370df5b0c459a94053130e8a6a07ae">IMP::em2d::Fine2DRegistrationRestraint::setup()</a>, <a href="classIMP_1_1em2d_1_1MasksManager.html#aa3d1166fd6a4c05ee0b6f99934d82b9e">IMP::em2d::MasksManager::create_masks()</a>, <a href="classIMP_1_1em2d_1_1PCAFitRestraint.html#a638ac14a1c1cb6c82ba9866be4ea00d5">IMP::em2d::PCAFitRestraint::PCAFitRestraint()</a>, <a href="classIMP_1_1em2d_1_1ProjectionFinder.html#a1027494f847acdb8302fa6314ad5a02c">IMP::em2d::ProjectionFinder::set_model_particles()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#af061f3bf53dde9fec3da4b4432220b84">IMP::em2d::RigidBodiesImageFitRestraint::RigidBodiesImageFitRestraint()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#a7e10193f89c1bae88669bcba6f821afd">IMP::em::DensityFillingRestraint::DensityFillingRestraint()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#a240bc7e6da3e5a5c925ab8eaf7e9babb">IMP::em::DensityFillingRestraint::add_particles()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#a40eb0eea2dc1a89c4abbc81078e2680d">IMP::em::DensityFillingRestraint::remove_particles()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#a3dbe984ad41b75f4e205a912409d4bab">IMP::em::DensityFillingRestraint::set_particles()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#a06cce12f32a3b2cad17c94689649dc99">IMP::em::DensityFillingRestraint::set_particles_order()</a>, <a href="classIMP_1_1em_1_1EnvelopeFitRestraint.html#a8f10c532152aa55376e42a1121c98d1d">IMP::em::EnvelopeFitRestraint::EnvelopeFitRestraint()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#acdc0d23301996c084c90fccddc2f7478">IMP::em::EnvelopePenetrationRestraint::EnvelopePenetrationRestraint()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#a76c2acc6f22adf240f070282ca6ce75d">IMP::em::EnvelopePenetrationRestraint::add_particles()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#a94fbc7653d15907ad278c25dfc72acf8">IMP::em::EnvelopePenetrationRestraint::remove_particles()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#a89786db5a2aa1d7aab6cdf28c6af09c0">IMP::em::EnvelopePenetrationRestraint::set_particles()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#af42ebdd1fd46f21ce6d506669715d014">IMP::em::EnvelopePenetrationRestraint::set_particles_order()</a>, <a 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href="classIMP_1_1symmetry_1_1RigidBodyMover.html#a5569015e9d07f620ba5cb39921844cdc">IMP::symmetry::RigidBodyMover::get_rigid_bodies()</a>, <a href="namespaceIMP_1_1algebra.html#ab2ff21c0e217ace29b614ac74089c2e3">IMP::algebra::get_principal_components()</a>, <a href="namespaceIMP_1_1atom.html#a94a390f980c6b8b2c64499b0f0efb6a5">IMP::atom::write_multimodel_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a3b8e395cdf044456ec136c147761b0f9">IMP::atom::read_psipred()</a>, <a href="namespaceIMP_1_1atom.html#afd2757eb3f37160c3288198c7e647e44">IMP::atom::create_excluded_volume_restraint()</a>, <a href="namespaceIMP_1_1atom.html#aaccceee6a56745c2892b75ad9a0ca456">IMP::atom::create_fragment()</a>, <a href="namespaceIMP_1_1atom.html#a1b72819ad85249bfe290fe31b4084e9e">IMP::atom::create_rigid_body()</a>, <a href="namespaceIMP_1_1atom.html#acf2a8c9e18db10d978cbdb97c654eaf4">IMP::atom::get_component_placement_score()</a>, <a href="namespaceIMP_1_1atom.html#acb0e2875f7d5b8fd8b51b89dbdc0cf3a">IMP::atom::get_leaves()</a>, <a href="namespaceIMP_1_1atom.html#ac1ac30470fc07d7436876b1e1f7accab">IMP::atom::get_pairwise_rmsd_score()</a>, <a href="namespaceIMP_1_1atom.html#ad664639ebfb7a53a52704685bbe1a803">IMP::atom::get_placement_score()</a>, <a href="namespaceIMP_1_1atom.html#a93f3e64bb36c2e744695df66fbd039fe">IMP::atom::get_radius_of_gyration()</a>, <a href="namespaceIMP_1_1atom.html#aa8c6ee981db76d88d7661bb4dd6fb63b">IMP::atom::get_rmsd()</a>, <a href="namespaceIMP_1_1atom.html#acbef157acdeda4f2e6ed0b25398b206c">IMP::atom::get_rmsd()</a>, <a href="namespaceIMP_1_1atom.html#a6548fc0fb1b2329ba9bb38511610953c">IMP::atom::get_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1atom.html#a990dcd12c2cfff8656227b9e059090f4">IMP::atom::setup_as_approximation()</a>, <a href="namespaceIMP_1_1atom.html#ae4a0d2d12be0e63c5def48217feea082">IMP::atom::setup_coarse_secondary_structure_residue()</a>, <a href="namespaceIMP_1_1atom.html#acff5cafee785a8eca3f4e923bba2ef03">IMP::atom::setup_coarse_secondary_structure_residues()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a957e7710eb8a161975d25f3549824df8">IMP::cnmultifit::cn_symm_score()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a6067aedfd378547038d133f84bb820e3">IMP::cnmultifit::fit_cn_assembly()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a4438e6a4266c8a34503f504f861e890a">IMP::cnmultifit::generate_cn_transformations()</a>, <a href="namespaceIMP_1_1cnmultifit.html#ae902a3b7629959005fa3c503903dc95d">IMP::cnmultifit::generate_translations_along_symm_axis()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a6955cc359b815de543af54b62dcaf87d">IMP::cnmultifit::get_cn_rmsd()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a326d661ede67dfeb87070ee6447ad678">IMP::cnmultifit::symmetry_local_fitting()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a4a6654fa258c0a93903370ff327d4199">IMP::cnmultifit::transform_cn_assembly()</a>, <a href="namespaceIMP_1_1container.html#ad108abbf3fe6bae316927d253f03ac63">IMP::container::get_slack_estimate()</a>, <a href="namespaceIMP_1_1core.html#a155534ed7f804d5a1b5da51c0c1d148f">IMP::core::assign_blame()</a>, <a href="namespaceIMP_1_1core.html#af0517d5191fdf1aa3c01b9115537c6ad">IMP::core::create_blame_geometries()</a>, <a href="namespaceIMP_1_1core.html#a0ba3b6f5fba01f4ecf8a3b8f18a311f2">IMP::core::get_bounding_box()</a>, <a href="namespaceIMP_1_1core.html#a46250a46a10465f03487ad0670586394">IMP::core::get_centroid()</a>, <a href="namespaceIMP_1_1core.html#ac28cbff46cedec4186ab8e63a3c3b41b">IMP::core::get_enclosing_sphere()</a>, <a href="namespaceIMP_1_1core.html#a4a6d455367f3db8a6b6d9cbc3302e185">IMP::core::get_initial_reference_frame()</a>, <a href="namespaceIMP_1_1core.html#a6c72c4715dfbfd21c4dd054113be7c1c">IMP::core::get_initial_reference_frame()</a>, <a href="namespaceIMP_1_1core.html#a25735ab61a19f9813d051462afd24b2f">IMP::core::set_enclosing_radius()</a>, <a href="namespaceIMP_1_1core.html#a9f00e88e92a88b5ef349978fe737df7d">IMP::core::set_enclosing_sphere()</a>, <a href="namespaceIMP_1_1domino.html#a7b7d1d626ea1749a1254a51733a383c6">IMP::domino::get_interaction_graph()</a>, <a href="namespaceIMP_1_1domino.html#a3d42584059960c107bf93955fa624a20">IMP::domino::write_merge_tree()</a>, <a href="namespaceIMP_1_1domino.html#a5d4df06cb4d6065adacaabb353bbbdd2">IMP::domino::read_merge_tree()</a>, <a href="namespaceIMP_1_1domino.html#abae30b608c6edfba57967c5e14d4fead">IMP::domino::get_index()</a>, <a href="namespaceIMP_1_1domino.html#af2a5221a0befe7a9847b1fe9946429cf">IMP::domino::get_partial_index()</a>, <a href="namespaceIMP_1_1domino.html#a77f217ed83f57ed3d3155baa13efc22b">IMP::domino::get_possible_interactions()</a>, <a href="namespaceIMP_1_1em.html#a46c20ecb2df0e49d8d1872bcdfa6ddab">IMP::em::add_to_map()</a>, <a href="namespaceIMP_1_1em.html#a820c75d52b5f2b63a8b9c67a883bda15">IMP::em::compute_fitting_score()</a>, <a href="namespaceIMP_1_1em.html#aa99a3856b86b49aad83e79c255f360db">IMP::em::compute_fitting_scores()</a>, <a href="namespaceIMP_1_1em.html#a52260afb0cbcc46e0ad4bdd377095a03">IMP::em::get_number_of_particles_outside_of_the_density()</a>, <a href="namespaceIMP_1_1em.html#a3b0328cacfc463600b955c3f0c93b3be">IMP::em::get_numbers_of_particles_outside_of_the_density()</a>, <a href="namespaceIMP_1_1em.html#a4d80dfedcdc41944135ecde0149e2b25">IMP::em::get_percentage_of_voxels_covered_by_particles()</a>, <a href="namespaceIMP_1_1em.html#a6521ac8778500885341c924cc7b4b027">IMP::em::local_rigid_fitting_grid_search()</a>, <a href="namespaceIMP_1_1em.html#a75a97c569a7443bfd742238d9366294f">IMP::em::particles2binarized_density()</a>, <a href="namespaceIMP_1_1em.html#a8096ce5628c41c09a9dbba6fa2a960ed">IMP::em::particles2density()</a>, <a href="namespaceIMP_1_1em.html#a349475f169be4c7b03a820f1873471fc">IMP::em::particles2surface()</a>, <a href="namespaceIMP_1_1em2d.html#ade0e4f389263022c17983259431ba87a">IMP::em2d::create_evenly_distributed_projections()</a>, <a href="namespaceIMP_1_1em2d.html#af3b3894a70e76077900ac8230c59f9ec">IMP::em2d::do_project_particles()</a>, <a href="namespaceIMP_1_1em2d.html#a19744bfebeacb0146a1e16ce00115210">IMP::em2d::get_enclosing_image_size()</a>, <a href="namespaceIMP_1_1em2d.html#a3cfb06b6362604cfeafa6ab79b5a5769">IMP::em2d::get_projection()</a>, <a href="namespaceIMP_1_1em2d.html#a87fb708668f8c56200d34b3c09edabc3">IMP::em2d::get_projections()</a>, <a href="namespaceIMP_1_1em2d.html#ad67f1f21b56148b8ab04291845ca7083">IMP::em2d::get_projections()</a>, <a href="namespaceIMP_1_1example.html#ab77a6d1a8b6ce3666ab2b28c607c053b">IMP::example::create_chain_restraint()</a>, <a href="namespaceIMP_1_1example.html#a5fb0266ce6ed660deb76c589a3bed8fa">IMP::example::create_excluded_volume()</a>, <a href="namespaceIMP_1_1example.html#ab2432bf59a54498b4485a0f6eaa92ae6">IMP::example::create_serial_mover()</a>, <a href="namespaceIMP_1_1example.html#aeb921c9172705d1165e189f047f8ca98">IMP::example::get_number_of_incidences()</a>, <a href="namespaceIMP_1_1example.html#a40b8d52cacc198cdbd93d89217d94fdf">IMP::example::optimize_assembly()</a>, <a href="namespaceIMP_1_1example.html#a9901de5c502a7c881b8f48676c26a26f">IMP::example::optimize_balls()</a>, <a href="namespaceIMP_1_1kernel.html#a1efb3ada8f4005237b39e4f0efd605c6">IMP::kernel::write_particles_to_buffer()</a>, <a href="namespaceIMP_1_1kernel.html#ab97593ae3a6f18b085c45f9bf4cdf967">IMP::kernel::read_particles_from_buffer()</a>, <a href="namespaceIMP_1_1kernel.html#aee6f77349c0038477a4565d8462066bf">IMP::kernel::get_indexes()</a>, <a href="namespaceIMP_1_1kernel.html#a832b34207ebf86a3a4c0ec65d6cda191">IMP::kernel::get_particles()</a>, <a href="namespaceIMP_1_1multifit.html#a4c8cc2536fde9f27a2ee3cfda1915030">IMP::multifit::create_coarse_molecules_from_molecules()</a>, <a href="namespaceIMP_1_1multifit.html#a7bac7b0f86c7064a13d331e9f60d3e2f">IMP::multifit::get_actual_radius_of_gyration()</a>, <a href="namespaceIMP_1_1multifit.html#a173eff7add1e1652a69ce9c1365ddf2f">IMP::multifit::get_anchor_indices_matching_secondary_structure()</a>, <a href="namespaceIMP_1_1multifit.html#aae3c93b62256b393e1ac553cce6a19e3">IMP::multifit::pca_based_rigid_fitting()</a>, <a href="namespaceIMP_1_1multifit.html#a51ea4bd63c8eaf2b9a3173b2bbe15870">IMP::multifit::write_connolly_surface()</a>, <a href="namespaceIMP_1_1rmf.html#adbc5eb9278e61f0a4449eb181cbd2a74">IMP::rmf::add_hierarchies()</a>, <a href="namespaceIMP_1_1rmf.html#a9f63044bfe82f715e14e819e1ae3a2f4">IMP::rmf::add_hierarchies()</a>, <a href="namespaceIMP_1_1rmf.html#a5bc1f4e588466260be12aba4bac30255">IMP::rmf::link_hierarchies()</a>, <a href="namespaceIMP_1_1rmf.html#a291836c7032c342403624af06b23a6ad">IMP::rmf::add_particles()</a>, <a href="namespaceIMP_1_1rmf.html#a17937bb384622cefe820c6b488e905fa">IMP::rmf::add_particles()</a>, <a href="namespaceIMP_1_1rmf.html#a5fae5bf9a3af9aa21ff8a00bf73f0e12">IMP::rmf::link_particles()</a>, <a href="namespaceIMP_1_1saxs.html#ab483217a045ebcad39252cb545ec0d07">IMP::saxs::compute_max_distance()</a>, <a href="namespaceIMP_1_1saxs.html#ac167d04ded08efe608fb2b0fb0f77d5f">IMP::saxs::compute_max_distance()</a>, <a href="namespaceIMP_1_1saxs.html#a22b0c7ea0b5f4f9d34870ce78131518a">IMP::saxs::compute_profile()</a>, <a href="namespaceIMP_1_1saxs.html#a4ad6ed5c4f12520063a29be80cf726a0">IMP::saxs::get_coordinates()</a>, <a href="namespaceIMP_1_1saxs.html#a480827857014751342a217cf2fcc91e8">IMP::saxs::get_form_factors()</a>, <a href="namespaceIMP_1_1saxs.html#a86db9d84ce75b1a295987e9931e6f6fa">IMP::saxs::radius_of_gyration()</a></td></tr>
81 </table>
82 # IMP.cnmultifit # {#argument_index_cnmultifit}
83 <table><tr>
84 <th>Class</th><th>Users</th></tr>
85 <tr><td>@ref IMP::cnmultifit::AlignSymmetric</td><td><a href="namespaceIMP_1_1cnmultifit.html#a6067aedfd378547038d133f84bb820e3">IMP::cnmultifit::fit_cn_assembly()</a></td></tr>
86 <tr><td>@ref IMP::cnmultifit::CnSymmAxisDetector</td><td><a href="namespaceIMP_1_1cnmultifit.html#a1b5327db66abe2f5bc1712f1013a4436">IMP::cnmultifit::fit_cn_assembly()</a></td></tr>
87 <tr><td>@ref IMP::cnmultifit::MolCnSymmAxisDetector</td><td><a href="namespaceIMP_1_1cnmultifit.html#a1b5327db66abe2f5bc1712f1013a4436">IMP::cnmultifit::fit_cn_assembly()</a></td></tr>
88 </table>
89 # IMP.container # {#argument_index_container}
90 <table><tr>
91 <th>Class</th><th>Users</th></tr>
92 <tr><td>@ref IMP::container::ClosePairContainer</td><td><a href="namespaceIMP_1_1container.html#ad108abbf3fe6bae316927d253f03ac63">IMP::container::get_slack_estimate()</a></td></tr>
93 <tr><td>@ref IMP::container::ConsecutivePairContainer</td><td><a href="classIMP_1_1container_1_1ConsecutivePairFilter.html#a2e0d4f04b8080a9c0d77a9a0e1a68ba5">IMP::container::ConsecutivePairFilter::ConsecutivePairFilter()</a></td></tr>
94 </table>
95 # IMP.core # {#argument_index_core}
96 <table><tr>
97 <th>Class</th><th>Users</th></tr>
98 <tr><td>@ref IMP::core::ClosePairsFinder</td><td><a href="classIMP_1_1container_1_1ClosePairContainer.html#a19f52fd2b6c1f34261b304f5870ac9ca">IMP::container::ClosePairContainer::ClosePairContainer()</a>, <a href="classIMP_1_1core_1_1RigidClosePairsFinder.html#a7b77f4659d0ba5ebf6656168aaad0af9">IMP::core::RigidClosePairsFinder::RigidClosePairsFinder()</a></td></tr>
99 <tr><td>@ref IMP::core::DataObject</td><td><a href="classIMP_1_1core_1_1DataObject.html#a21902b043155f25d342ab159bcbd55bd">IMP::core::DataObject::IMP_OBJECT_METHODS()</a></td></tr>
100 <tr><td>@ref IMP::core::Hierarchy</td><td><a href="classIMP_1_1atom_1_1Hierarchy.html#a776a2d762c4245a3aa0da74e0b51cf09">IMP::atom::Hierarchy::Hierarchy()</a>, <a href="classIMP_1_1atom_1_1HierarchyGeometry.html#ad9ff1e203d46f1a116dc32de72f50acf">IMP::atom::HierarchyGeometry::HierarchyGeometry()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#adc79064f4b0e3857aa00c9416bcf7d48">IMP::core::Hierarchy::add_child()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#af755f5483b8fdab8c227d07220e96cc7">IMP::core::Hierarchy::add_child_at()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#ad99b4f19345b28138ee910b6af438426">IMP::core::Hierarchy::remove_child()</a>, <a href="classIMP_1_1core_1_1HierarchyVisitor.html#aa45442c4bff64f5fea3fcc547783f412">IMP::core::HierarchyVisitor::operator()()</a>, <a href="classIMP_1_1core_1_1ModifierVisitor.html#ae7529eda6952ce1e036e8e018cf3fa84">IMP::core::ModifierVisitor::operator()()</a>, <a href="namespaceIMP_1_1core.html#a24d4c4b06793bcadc5962885098ed400">IMP::core::get_all_descendants()</a>, <a href="namespaceIMP_1_1core.html#a65ebb1067e86f517214ff78f111ad622">IMP::core::get_internal()</a>, <a href="namespaceIMP_1_1core.html#a8743287de001c73866a23377c8bd466f">IMP::core::get_leaves()</a>, <a href="namespaceIMP_1_1core.html#a4c078026c66398b7ae77eeb6f13ddcd0">IMP::core::get_root()</a>, <a href="group__hierarchy.html#ga346251f63e1305b2bd2b0599f1d8d761">IMP::core::show()</a>, <a href="namespaceIMP_1_1multifit.html#a3e058408a3879546f50897a4e8f9253b">IMP::multifit::add_surface_index()</a></td></tr>
101 <tr><td>@ref IMP::core::HierarchyTraits</td><td><a href="classIMP_1_1core_1_1ChildrenRefiner.html#ac93f559610e5324ee059430e86e4b7c0">IMP::core::ChildrenRefiner::ChildrenRefiner()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#ae9981d084948a463335f9f5cee9f4c5f">IMP::core::Hierarchy::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#ac8c4830b3c0ece985b7e13de048546e3">IMP::core::Hierarchy::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#ae475cf1a3b9caa7337112c6dd43f8f5c">IMP::core::Hierarchy::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#aff9b158507f67597bca45f4d9cf12443">IMP::core::Hierarchy::Hierarchy()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#aafeb2bd93edb8664fabef879c81160f9">IMP::core::Hierarchy::Hierarchy()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#aff10f327112a0edbcf34bc8c58f85b91">IMP::core::Hierarchy::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#af71bbb61965ee7747bec578320f694ca">IMP::core::Hierarchy::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a071bdca8bec3e0429efc652d79883372">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#afa445d9465c192c43ade1df6a4871b02">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a422624be7426817c54942fdff1ce4d77">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a603057a8541c1768f5bc917ac204ad1f">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a83a803677b4aa43ad2016e00a1963179">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a7a6c4632c606e31bd882b536ac517e36">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1HierarchyTraits.html#a963da285babd3bf204ce3d25c632dd15">IMP::core::HierarchyTraits::operator==()</a>, <a href="classIMP_1_1core_1_1LeavesRefiner.html#ab054bc5b90fd5c7a2906d93f39e7b412">IMP::core::LeavesRefiner::LeavesRefiner()</a></td></tr>
102 <tr><td>@ref IMP::core::IncrementalScoringFunction</td><td><a href="classIMP_1_1core_1_1MonteCarlo.html#ad373e9c68d7c1b64424f454a9f6755a2">IMP::core::MonteCarlo::set_incremental_scoring_function()</a></td></tr>
103 <tr><td>@ref IMP::core::IsCollisionPairPredicate</td><td><a href="classIMP_1_1core_1_1IsCollisionPairPredicate.html#a996b7777db7f4b01ca37f2586d2fc0c5">IMP::core::IsCollisionPairPredicate::IMP_PAIR_PREDICATE_METHODS()</a></td></tr>
104 <tr><td>@ref IMP::core::MonteCarlo</td><td><a href="classIMP_1_1core_1_1MCCGSampler.html#a3bbeae34bab083c8ae1aaf5a636a4c90">IMP::core::MCCGSampler::set_up_movers()</a></td></tr>
105 <tr><td>@ref IMP::core::MonteCarloMover</td><td><a href="classIMP_1_1core_1_1MonteCarlo.html#aef0c0e787d5720c79b492b7418da7ecd">IMP::core::MonteCarlo::remove_mover()</a>, <a href="classIMP_1_1core_1_1MonteCarlo.html#a4da70b551db763688cf1e25a42a6bca3">IMP::core::MonteCarlo::add_mover()</a></td></tr>
106 <tr><td>@ref IMP::core::RigidBody</td><td><a href="classIMP_1_1core_1_1RigidBody.html#a31cf63db783589db090984512e76bc09">IMP::core::RigidBody::teardown_particle()</a>, <a href="classIMP_1_1core_1_1RigidBodyDerivativeGeometry.html#aedb8aae145938a6e43f5d1704ae8d538">IMP::core::RigidBodyDerivativeGeometry::RigidBodyDerivativeGeometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyFrameGeometry.html#aad20ba7053ff132800b3aae9c59ddfc9">IMP::core::RigidBodyFrameGeometry::RigidBodyFrameGeometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyHierarchyGeometry.html#a0eb4572df723d1db871b82a409628f08">IMP::core::RigidBodyHierarchyGeometry::RigidBodyHierarchyGeometry()</a>, <a href="classIMP_1_1em2d_1_1RelativePositionMover.html#af7912452d781bfdc25f904b717101676">IMP::em2d::RelativePositionMover::RelativePositionMover()</a>, <a href="classIMP_1_1em2d_1_1RelativePositionMover.html#a2045622f5bc5c6c61b42f5f27748c4f9">IMP::em2d::RelativePositionMover::add_internal_transformations()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#adc029e547932f000de091deb35097fe4">IMP::em2d::RigidBodiesImageFitRestraint::get_number_of_masks()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#a9ecd59712114458c5d440bb7e01870f1">IMP::em2d::RigidBodiesImageFitRestraint::set_orientations()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#ad421603f6b2c67d918d5262140c50095">IMP::em2d::RigidBodiesImageFitRestraint::get_rigid_body_index()</a>, <a href="classIMP_1_1kinematics_1_1BondAngleRevoluteJoint.html#a16ba2ca9dff457daf656a6336e46f56a">IMP::kinematics::BondAngleRevoluteJoint::BondAngleRevoluteJoint()</a>, <a href="classIMP_1_1kinematics_1_1CompositeJoint.html#a06ea6091af7ff36c08a5d5eb5dfd780e">IMP::kinematics::CompositeJoint::CompositeJoint()</a>, <a href="classIMP_1_1kinematics_1_1DihedralAngleRevoluteJoint.html#a518c71ba70ed25ad87aae3cb9dbab4ff">IMP::kinematics::DihedralAngleRevoluteJoint::DihedralAngleRevoluteJoint()</a>, <a href="classIMP_1_1kinematics_1_1Joint.html#a7e1a407b470b3ee5e785583430b0a5e6">IMP::kinematics::Joint::Joint()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a4f4f75ae4464f9238edbd4f9f53da211">IMP::kinematics::KinematicForest::add_edge()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#ab7e7b80fe79c36af1bca159df73f7f97">IMP::kinematics::KinematicForest::get_coordinates_safe()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a35103e7f5bb31a571e30965ec39e3ae3">IMP::kinematics::KinematicForest::get_is_member()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#ae9aea73c759c2ceeb7c88c46553fdc47">IMP::kinematics::KinematicForest::get_reference_frame_safe()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#ab9ffe60cb86e0edc2ee54cbd36c98199">IMP::kinematics::KinematicForest::set_coordinates_safe()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a879e819eda0a9d2851e6ac8c654b8355">IMP::kinematics::KinematicForest::set_reference_frame_safe()</a>, <a href="classIMP_1_1kinematics_1_1PrismaticJoint.html#a69b32641f0207229ec1fd26b6d399546">IMP::kinematics::PrismaticJoint::PrismaticJoint()</a>, <a href="classIMP_1_1kinematics_1_1PrismaticJoint.html#ae1c2a772c0581223f7a8ed3dc5fdfd8a">IMP::kinematics::PrismaticJoint::PrismaticJoint()</a>, <a href="classIMP_1_1kinematics_1_1RevoluteJoint.html#a531e935921d67d59df7b1b09f6c258fe">IMP::kinematics::RevoluteJoint::RevoluteJoint()</a>, <a href="classIMP_1_1kinematics_1_1TransformationJoint.html#af215277d41c031829b1fae9c7e5ba73b">IMP::kinematics::TransformationJoint::TransformationJoint()</a>, <a href="classIMP_1_1multifit_1_1ComplementarityRestraint.html#a1c372e35090c02f005c21761512c986c">IMP::multifit::ComplementarityRestraint::get_grid_object()</a>, <a href="classIMP_1_1symmetry_1_1RigidBodyMover.html#ae34857696890574b896e795367dd8e08">IMP::symmetry::RigidBodyMover::RigidBodyMover()</a>, <a href="namespaceIMP_1_1core.html#a2abc47490c92e47767b9fe3b6771efa0">IMP::core::show_rigid_body_hierarchy()</a>, <a href="namespaceIMP_1_1core.html#a4c5298df54cae6b0e4419852390281be">IMP::core::transform()</a>, <a href="namespaceIMP_1_1em.html#ab8beedad8915dcd1aa22b5ba75a61439">IMP::em::compute_fitting_scores()</a>, <a href="namespaceIMP_1_1multifit.html#a3359231b0601df5803958afcd8d93184">IMP::multifit::create_hit_map()</a>, <a href="namespaceIMP_1_1multifit.html#a8273d850c0ab1cd53983c9f169af3cd6">IMP::multifit::create_weighted_excluded_volume_restraint()</a>, <a href="namespaceIMP_1_1multifit.html#a45c8385d6183240ec7216ae97374c7a9">IMP::multifit::pca_based_rigid_fitting()</a></td></tr>
107 <tr><td>@ref IMP::core::RigidMember</td><td><a href="classIMP_1_1core_1_1RigidBody.html#aba355d51adad0c18053680d1b0b20fa1">IMP::core::RigidBody::get_coordinates()</a>, <a href="namespaceIMP_1_1core.html#af9636f52f818df052141f98a829e1eeb">IMP::core::get_root_rigid_body()</a></td></tr>
108 <tr><td>@ref IMP::core::SoftSpherePairScore</td><td><a href="classIMP_1_1core_1_1ExcludedVolumeRestraint.html#a3901b13b7a361386dfe813d43384b05e">IMP::core::ExcludedVolumeRestraint::ExcludedVolumeRestraint()</a></td></tr>
109 <tr><td>@ref IMP::core::XYZ</td><td><a href="classIMP_1_1atom_1_1Angle.html#a0c2bec3db873b3b4d2b0b9eb29d42e49">IMP::atom::Angle::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a63d9c956874f958f360d0f35e517a087">IMP::atom::Angle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a12c690f31dfbd13226378ef50ef215ce">IMP::atom::Angle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a358de23aff9901f1e49cefdd0967e9a3">IMP::atom::Dihedral::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#af6ed0a2d5ba3c1ea3ce31a4362abb845">IMP::atom::Dihedral::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a3cb4c03e2291bd27f55d33cf85f3b886">IMP::atom::Dihedral::setup_particle()</a>, <a href="classIMP_1_1core_1_1AngleRestraint.html#aa1965071bcfd1d7a08f6453d431d9fed">IMP::core::AngleRestraint::AngleRestraint()</a>, <a href="classIMP_1_1core_1_1XYZ.html#abdf4dcafcd415cddf90e0b7565f89f62">IMP::core::XYZ::get_vector_to()</a>, <a href="classIMP_1_1core_1_1XYZDerivativeGeometry.html#a348f6ac949c5a28e305b377e86d78d70">IMP::core::XYZDerivativeGeometry::XYZDerivativeGeometry()</a>, <a href="classIMP_1_1kinematics_1_1BondAngleRevoluteJoint.html#a16ba2ca9dff457daf656a6336e46f56a">IMP::kinematics::BondAngleRevoluteJoint::BondAngleRevoluteJoint()</a>, <a href="classIMP_1_1kinematics_1_1BondAngleRevoluteJoint.html#a879f42c6e5b39ca8e849f6283deb98e5">IMP::kinematics::BondAngleRevoluteJoint::get_perpendicular_vector()</a>, <a href="classIMP_1_1kinematics_1_1DihedralAngleRevoluteJoint.html#a518c71ba70ed25ad87aae3cb9dbab4ff">IMP::kinematics::DihedralAngleRevoluteJoint::DihedralAngleRevoluteJoint()</a>, <a href="classIMP_1_1kinematics_1_1PrismaticJoint.html#a69b32641f0207229ec1fd26b6d399546">IMP::kinematics::PrismaticJoint::PrismaticJoint()</a>, <a href="namespaceIMP_1_1core.html#a8586c04d2d9396490dc9cc71f7899141">IMP::core::get_dihedral()</a>, <a href="namespaceIMP_1_1core.html#af2049fdca8aae38e86549cfdeff1d1fc">IMP::core::get_distance()</a>, <a href="namespaceIMP_1_1core.html#ae738399c12616c3b84686ccf3582e632">IMP::core::get_vector_geometry()</a>, <a href="namespaceIMP_1_1core.html#aa284a594e40d97aa3e915a3da70a4d3d">IMP::core::set_vector_geometry()</a>, <a href="namespaceIMP_1_1core.html#a556f7cad1de8ed389d05b4d7acbeb4d0">IMP::core::transform()</a></td></tr>
110 <tr><td>@ref IMP::core::XYZR</td><td><a href="classIMP_1_1core_1_1XYZRGeometry.html#a7e4091e42fc2eea3a7a2e4098037f845">IMP::core::XYZRGeometry::XYZRGeometry()</a>, <a href="namespaceIMP_1_1core.html#ad65d79ddb3c6e1db815d57f73c8f18ea">IMP::core::get_distance()</a>, <a href="namespaceIMP_1_1core.html#a25735ab61a19f9813d051462afd24b2f">IMP::core::set_enclosing_radius()</a>, <a href="namespaceIMP_1_1core.html#a9f00e88e92a88b5ef349978fe737df7d">IMP::core::set_enclosing_sphere()</a></td></tr>
111 </table>
112 # IMP.display # {#argument_index_display}
113 <table><tr>
114 <th>Class</th><th>Users</th></tr>
115 <tr><td>@ref IMP::display::BoundingBoxGeometry</td><td><a href="classIMP_1_1display_1_1GeometryProcessor.html#a5f2b7edfdeef5ca64a4000c048e5e45d">IMP::display::GeometryProcessor::handle_bounding_box()</a></td></tr>
116 <tr><td>@ref IMP::display::Color</td><td><a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#abffcb4633c7da35860a1a7f3f97f35b0">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#a6f4bacf190fc76a5ecdc2459bfed9891">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1ChimeraWriter.html#a636713e4fad818f5ef1fda95d77df8c4">IMP::display::ChimeraWriter::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1ChimeraWriter.html#acf4ab76c430cc89c5438d09744755683">IMP::display::ChimeraWriter::handle_ellipsoid()</a>, <a href="classIMP_1_1display_1_1ChimeraWriter.html#a2f82dfd1c236a39fd95c5803784f0070">IMP::display::ChimeraWriter::handle_point()</a>, <a href="classIMP_1_1display_1_1ChimeraWriter.html#a65a1d6f98ee933ed6690ed6bd44deda6">IMP::display::ChimeraWriter::handle_polygon()</a>, <a href="classIMP_1_1display_1_1ChimeraWriter.html#a249c78387b7694744f39bd7ba3699a44">IMP::display::ChimeraWriter::handle_segment()</a>, <a href="classIMP_1_1display_1_1ChimeraWriter.html#a8439024bc95a24c0856efc9b8d6c864a">IMP::display::ChimeraWriter::handle_sphere()</a>, <a href="classIMP_1_1display_1_1ChimeraWriter.html#ad03fe8578cd5bff2a1d8eb90171f427f">IMP::display::ChimeraWriter::handle_triangle()</a>, <a href="classIMP_1_1display_1_1Color.html#a2ac3767f2e1dfdd2d5168a5ff34388c5">IMP::display::Color::compare()</a>, <a href="classIMP_1_1display_1_1Colored.html#aed4375669ca927e91b06b4ef4b30ad4f">IMP::display::Colored::do_setup_particle()</a>, <a href="classIMP_1_1display_1_1Colored.html#a496c82c2b609ba9e97936aa5c1ca1423">IMP::display::Colored::set_color()</a>, <a href="classIMP_1_1display_1_1Colored.html#ae61a8919949f06a3aa4847d7fb8d9e8e">IMP::display::Colored::setup_particle()</a>, <a href="classIMP_1_1display_1_1Colored.html#a9ed326bb7aab6bf5263d51e007f7e30b">IMP::display::Colored::setup_particle()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#ab08ceebc8704d641be302119db1ebb73">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#af38ad28d6d178422d8db293d14b7d646">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a8b23de125510a349978b1b789743ea33">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a880be80c539c27f6e16c0a38a9fa9c9c">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#ace71488df43cbc6136b3e4805fb86256">IMP::display::FilterGeometry::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#a385bb7f540f28e4be780764ec4dbbac3">IMP::display::FilterGeometry::handle_point()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#a43fffd6a9d69c4ce15e6f1290772ec5d">IMP::display::FilterGeometry::handle_segment()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#ac60a266887c09160d1949ddbb8cb17c4">IMP::display::FilterGeometry::handle_sphere()</a>, <a href="classIMP_1_1display_1_1Geometry.html#ab56604ac628c5536a5277797a3f586e5">IMP::display::Geometry::Geometry()</a>, <a href="classIMP_1_1display_1_1Geometry.html#a5e68da46ed42586463a05eaa006c9533">IMP::display::Geometry::set_color()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a5cb9e1aa859508c2b54013ee5bdcadfd">IMP::display::GeometryProcessor::handle_anything()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a5f2b7edfdeef5ca64a4000c048e5e45d">IMP::display::GeometryProcessor::handle_bounding_box()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#adfa4f37b2300fd8c0443515ad00c8416">IMP::display::GeometryProcessor::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#aeb1a54db3c67211bbe8c32922354d7af">IMP::display::GeometryProcessor::handle_ellipsoid()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a354c0c4086663725556733b3aeecd7e0">IMP::display::GeometryProcessor::handle_label()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a89102436eae74971a1a982d63cfc5b4e">IMP::display::GeometryProcessor::handle_point()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#acc01161a988e1c3ced6c32c6b500f16b">IMP::display::GeometryProcessor::handle_polygon()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a14360b2b0fc05eb9ae45018f30d5ca5e">IMP::display::GeometryProcessor::handle_segment()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#acbee35eb67b6659899f44b2218127ef1">IMP::display::GeometryProcessor::handle_sphere()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a53e8793ca9ccb036c3f234967a492fd6">IMP::display::GeometryProcessor::handle_surface_mesh()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a835b0ea8d9b35735917b0eb9efd9afba">IMP::display::GeometryProcessor::handle_triangle()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a883ab2186aa243200cee7ce65b7c92c4">IMP::display::GeometryProcessor::handle_geometry_internal()</a>, <a href="classIMP_1_1display_1_1GeometrySet.html#abc566fc8470c8cc0059a8fe9fd78baf2">IMP::display::GeometrySet::GeometrySet()</a>, <a href="classIMP_1_1display_1_1GeometrySet.html#a3f808d88d9832770e804ce07813806fa">IMP::display::GeometrySet::GeometrySet()</a>, <a href="classIMP_1_1display_1_1PairsGeometry.html#a1a82af0664dd2d3206b5e4f4aeb0ca5d">IMP::display::PairsGeometry::PairsGeometry()</a>, <a href="classIMP_1_1display_1_1PointGeometry.html#a6fded29c99e011a7d7735e845f745ad7">IMP::display::PointGeometry::PointGeometry()</a>, <a href="classIMP_1_1display_1_1PointGeometry.html#affe821e4562c888981f6cc674f6f6144">IMP::display::PointGeometry::PointGeometry()</a>, <a href="classIMP_1_1display_1_1PolygonGeometry.html#acd5cc1ee58451042ac360b2302916b6a">IMP::display::PolygonGeometry::PolygonGeometry()</a>, <a href="classIMP_1_1display_1_1PolygonGeometry.html#ac357ffc56fb03894e549a5e5d9a20b7e">IMP::display::PolygonGeometry::PolygonGeometry()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#adf65270d7a6288b6bb1207ffac5af062">IMP::display::PymolWriter::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a37b5143f0b5ae311db1fe45bb88384f9">IMP::display::PymolWriter::handle_label()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#adc29c2e61c29bc42a26c0f2b5f097b0c">IMP::display::PymolWriter::handle_point()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a2e7061f9395e31948fd871ebf750bd5c">IMP::display::PymolWriter::handle_polygon()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a4993e607662088fb6667987a24714db4">IMP::display::PymolWriter::handle_segment()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a35b2b860e0325a6beb3ac0d49e83c490">IMP::display::PymolWriter::handle_sphere()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a9e0e77ab73c48a55efac2081eb4b710e">IMP::display::PymolWriter::handle_surface()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a3a6fd19e9d1e8b25ee0de69b99dd769a">IMP::display::PymolWriter::handle_triangle()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a431e05df3b0c309759e12b8049948402">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a7525a19a4c0cd13b906ed83124a89a33">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a0eda17f53f2e8cef8ae21c615f3e1b2b">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a0722985d583856076e2251d4cb85f380">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SingletonsGeometry.html#a6bfeea07e40dfd0843f9174ed55189a4">IMP::display::SingletonsGeometry::SingletonsGeometry()</a>, <a href="classIMP_1_1display_1_1SphereGeometry.html#ad3f60723035bcb75f0b0fa499678c5de">IMP::display::SphereGeometry::SphereGeometry()</a>, <a href="classIMP_1_1display_1_1SphereGeometry.html#a4667a4de9e70e142a3b0d3bb7a102996">IMP::display::SphereGeometry::SphereGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a8880501417b489547a254c4c2003cf3d">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a6a039b1098c7111bafe6a715fdbdc6ba">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="namespaceIMP_1_1display.html#ada2a3156a15dd0217840bfc8675724d8">IMP::display::get_interpolated_rgb()</a></td></tr>
117 <tr><td>@ref IMP::display::CylinderGeometry</td><td><a href="classIMP_1_1display_1_1ChimeraWriter.html#a636713e4fad818f5ef1fda95d77df8c4">IMP::display::ChimeraWriter::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#ace71488df43cbc6136b3e4805fb86256">IMP::display::FilterGeometry::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#adfa4f37b2300fd8c0443515ad00c8416">IMP::display::GeometryProcessor::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#adf65270d7a6288b6bb1207ffac5af062">IMP::display::PymolWriter::handle_cylinder()</a></td></tr>
118 <tr><td>@ref IMP::display::EllipsoidGeometry</td><td><a href="classIMP_1_1display_1_1ChimeraWriter.html#acf4ab76c430cc89c5438d09744755683">IMP::display::ChimeraWriter::handle_ellipsoid()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#aeb1a54db3c67211bbe8c32922354d7af">IMP::display::GeometryProcessor::handle_ellipsoid()</a></td></tr>
119 <tr><td>@ref IMP::display::Geometry</td><td><a href="classIMP_1_1display_1_1FilterGeometry.html#ae62eb73dfa5a06f67362a8753ec3238a">IMP::display::FilterGeometry::add_geometry()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a5cb9e1aa859508c2b54013ee5bdcadfd">IMP::display::GeometryProcessor::handle_anything()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a2ec53ebfd26f0e83e5260de90a16e0de">IMP::display::GeometryProcessor::handle_geometry()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a883ab2186aa243200cee7ce65b7c92c4">IMP::display::GeometryProcessor::handle_geometry_internal()</a>, <a href="classIMP_1_1display_1_1WriteOptimizerState.html#a585eefb24f1e1b12baf0ddc9daa7728f">IMP::display::WriteOptimizerState::add_geometry()</a>, <a href="classIMP_1_1display_1_1WriteOptimizerState.html#a7ebf99fba15e4baccdcd33931c76519a">IMP::display::WriteOptimizerState::remove_geometry()</a>, <a href="classIMP_1_1display_1_1Writer.html#ad844e55168736fe8a629eeef6a7ccb40">IMP::display::Writer::add_geometry()</a></td></tr>
120 <tr><td>@ref IMP::display::LabelGeometry</td><td><a href="classIMP_1_1display_1_1GeometryProcessor.html#a354c0c4086663725556733b3aeecd7e0">IMP::display::GeometryProcessor::handle_label()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a37b5143f0b5ae311db1fe45bb88384f9">IMP::display::PymolWriter::handle_label()</a></td></tr>
121 <tr><td>@ref IMP::display::PointGeometry</td><td><a href="classIMP_1_1display_1_1ChimeraWriter.html#a2f82dfd1c236a39fd95c5803784f0070">IMP::display::ChimeraWriter::handle_point()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#a385bb7f540f28e4be780764ec4dbbac3">IMP::display::FilterGeometry::handle_point()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a89102436eae74971a1a982d63cfc5b4e">IMP::display::GeometryProcessor::handle_point()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#adc29c2e61c29bc42a26c0f2b5f097b0c">IMP::display::PymolWriter::handle_point()</a></td></tr>
122 <tr><td>@ref IMP::display::PolygonGeometry</td><td><a href="classIMP_1_1display_1_1ChimeraWriter.html#a65a1d6f98ee933ed6690ed6bd44deda6">IMP::display::ChimeraWriter::handle_polygon()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#acc01161a988e1c3ced6c32c6b500f16b">IMP::display::GeometryProcessor::handle_polygon()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a2e7061f9395e31948fd871ebf750bd5c">IMP::display::PymolWriter::handle_polygon()</a></td></tr>
123 <tr><td>@ref IMP::display::SegmentGeometry</td><td><a href="classIMP_1_1display_1_1ChimeraWriter.html#a249c78387b7694744f39bd7ba3699a44">IMP::display::ChimeraWriter::handle_segment()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#a43fffd6a9d69c4ce15e6f1290772ec5d">IMP::display::FilterGeometry::handle_segment()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a14360b2b0fc05eb9ae45018f30d5ca5e">IMP::display::GeometryProcessor::handle_segment()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a4993e607662088fb6667987a24714db4">IMP::display::PymolWriter::handle_segment()</a></td></tr>
124 <tr><td>@ref IMP::display::SphereGeometry</td><td><a href="classIMP_1_1display_1_1ChimeraWriter.html#a8439024bc95a24c0856efc9b8d6c864a">IMP::display::ChimeraWriter::handle_sphere()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#ac60a266887c09160d1949ddbb8cb17c4">IMP::display::FilterGeometry::handle_sphere()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#acbee35eb67b6659899f44b2218127ef1">IMP::display::GeometryProcessor::handle_sphere()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a35b2b860e0325a6beb3ac0d49e83c490">IMP::display::PymolWriter::handle_sphere()</a></td></tr>
125 <tr><td>@ref IMP::display::SurfaceMeshGeometry</td><td><a href="classIMP_1_1display_1_1GeometryProcessor.html#a53e8793ca9ccb036c3f234967a492fd6">IMP::display::GeometryProcessor::handle_surface_mesh()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a9e0e77ab73c48a55efac2081eb4b710e">IMP::display::PymolWriter::handle_surface()</a></td></tr>
126 <tr><td>@ref IMP::display::TriangleGeometry</td><td><a href="classIMP_1_1display_1_1ChimeraWriter.html#ad03fe8578cd5bff2a1d8eb90171f427f">IMP::display::ChimeraWriter::handle_triangle()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a835b0ea8d9b35735917b0eb9efd9afba">IMP::display::GeometryProcessor::handle_triangle()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a3a6fd19e9d1e8b25ee0de69b99dd769a">IMP::display::PymolWriter::handle_triangle()</a></td></tr>
127 <tr><td>@ref IMP::display::Writer</td><td><a href="classIMP_1_1display_1_1WriterAdaptor.html#a5c8ef5befd08eefeb081e6bb41204bb3">IMP::display::WriterAdaptor::WriterAdaptor()</a></td></tr>
128 <tr><td>@ref IMP::display::WriterAdaptor</td><td><a href="classIMP_1_1display_1_1WriteOptimizerState.html#ae6c732748702a5ddfe3729c9f0389d33">IMP::display::WriteOptimizerState::WriteOptimizerState()</a>, <a href="classIMP_1_1display_1_1WriteOptimizerState.html#a6b064de0f80556707f5c7626de74a26f">IMP::display::WriteOptimizerState::write()</a></td></tr>
129 </table>
130 # IMP.domino # {#argument_index_domino}
131 <table><tr>
132 <th>Class</th><th>Users</th></tr>
133 <tr><td>@ref IMP::domino::Assignment</td><td><a href="classIMP_1_1domino_1_1AssignmentContainer.html#a205dd896cae1e38d153254a34cf57b5d">IMP::domino::AssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1CappedAssignmentContainer.html#a5ed14b8e7c62b1c853891c15d817dfcf">IMP::domino::CappedAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1HeapAssignmentContainer.html#a2b659623be5f37ba9f2290d6a4045b2d">IMP::domino::HeapAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentContainer.html#ad8fd70ea8e018c656dd47a130fd711cf">IMP::domino::ListAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1Order.html#acebb05321bf90fe7e6d4bc27b37902df">IMP::domino::Order::get_list_ordered()</a>, <a href="classIMP_1_1domino_1_1PackedAssignmentContainer.html#ab4ce677fc222f2284de6a49fa901f0a7">IMP::domino::PackedAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1RangeViewAssignmentContainer.html#a24c95a9c8decf80d6d9daa9b0e6116a3">IMP::domino::RangeViewAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1ReadAssignmentContainer.html#a123c10790ce5474a09ccd4c89b1aba1d">IMP::domino::ReadAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1ReadHDF5AssignmentContainer.html#abb640818153942e00d0e9740f31c5d9f">IMP::domino::ReadHDF5AssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#ad0fd79f89825f4a73b169de2bcf1aaeb">IMP::domino::RestraintCache::get_score()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#aeacabf8b40ea4789ca165cd4773a0acb">IMP::domino::RestraintCache::get_score()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a7cde8be9e50ebe392c39f47c24316a42">IMP::domino::RestraintCache::load_last_score()</a>, <a href="classIMP_1_1domino_1_1SampleAssignmentContainer.html#ab9dfb0061d501d144f0fac3d16cbb908">IMP::domino::SampleAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1Slice.html#ab3c699a06268f2fa405c296149c4515b">IMP::domino::Slice::get_sliced()</a>, <a href="classIMP_1_1domino_1_1SubsetFilter.html#ae6ac39cf0c88e5f67f47ab75a255252d">IMP::domino::SubsetFilter::get_is_ok()</a>, <a href="classIMP_1_1domino_1_1SubsetFilter.html#a98bb346a18334bae9a8028d7f99851a2">IMP::domino::SubsetFilter::get_next_state()</a>, <a href="classIMP_1_1domino_1_1WriteAssignmentContainer.html#a9823c664b05000244a86680fdfce4393">IMP::domino::WriteAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1WriteHDF5AssignmentContainer.html#a2bc4307eff9201b71e24bd6c3c376b57">IMP::domino::WriteHDF5AssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilter.html#a862db6bdd0cccc956f3a1c5e186d6594">IMP::em2d::DistanceFilter::get_is_ok()</a>, <a href="namespaceIMP_1_1domino.html#a0c08cfa3955a23464c5f59c15f95a4ae">IMP::domino::load_particle_states()</a>, <a href="namespaceIMP_1_1domino.html#a3a112fd41a97e8e93dbff8be3dfb8bb6">IMP::domino::get_distance_if_smaller_than()</a>, <a href="namespaceIMP_1_1domino.html#a3247d32b900c4633e5c58cd7032d043b">IMP::domino::get_embedding()</a>, <a href="namespaceIMP_1_1domino.html#a419db1b5a46dd7eefe31fd0279087c94">IMP::domino::swap()</a></td></tr>
134 <tr><td>@ref IMP::domino::AssignmentContainer</td><td><a href="classIMP_1_1domino_1_1AssignmentsTable.html#a82165fe3c39a0a5bd1005826f5121c26">IMP::domino::AssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundAssignmentsTable.html#a9165b72d63a07e7e68728a8017628e6e">IMP::domino::BranchAndBoundAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1CappedAssignmentContainer.html#a981ac5833c29ad4c1a881b3a89a84710">IMP::domino::CappedAssignmentContainer::CappedAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1DominoSampler.html#a317227a05c7903a41070a939a8ee079b">IMP::domino::DominoSampler::load_vertex_assignments()</a>, <a href="classIMP_1_1domino_1_1DominoSampler.html#a32961043b9b12602d60b6a50a1014aa8">IMP::domino::DominoSampler::load_vertex_assignments()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentsTable.html#aa0422fdbb973a84ae9dfd12c08b3979d">IMP::domino::ListAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentsTable.html#a15fa28a76023dd8fa328b452d2245908">IMP::domino::ListAssignmentsTable::set_assignments()</a>, <a href="classIMP_1_1domino_1_1RangeViewAssignmentContainer.html#a7de21afe06173ad8218f45a82cf21e15">IMP::domino::RangeViewAssignmentContainer::RangeViewAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1RecursiveAssignmentsTable.html#a90514e1adc6368f99d345b59668a803a">IMP::domino::RecursiveAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1SimpleAssignmentsTable.html#a23b9149da5312b4e120a36f3d4949bc9">IMP::domino::SimpleAssignmentsTable::load_assignments()</a>, <a href="namespaceIMP_1_1domino.html#a4570cce69f194985e23b710c3b5e18b4">IMP::domino::load_leaf_assignments()</a>, <a href="namespaceIMP_1_1domino.html#a200c71a273844cc32fd32f6a5eafa0aa">IMP::domino::load_merged_assignments()</a>, <a href="namespaceIMP_1_1domino.html#a3305fe8f61d81cba57e9f6896024b263">IMP::domino::load_merged_assignments_random_order()</a></td></tr>
135 <tr><td>@ref IMP::domino::AssignmentsTable</td><td><a href="classIMP_1_1domino_1_1DiscreteSampler.html#aad5f8f5ee7e3e9b17f247917235ab62b">IMP::domino::DiscreteSampler::set_assignments_table()</a>, <a href="namespaceIMP_1_1domino.html#a4570cce69f194985e23b710c3b5e18b4">IMP::domino::load_leaf_assignments()</a></td></tr>
136 <tr><td>@ref IMP::domino::Order</td><td><a href="namespaceIMP_1_1domino.html#adf25d025631b32526e9e794ae0be804a">IMP::domino::swap()</a></td></tr>
137 <tr><td>@ref IMP::domino::ParticleStates</td><td><a href="classIMP_1_1domino_1_1CompoundStates.html#a43d16cc20bd7c0c107341a1395319ca7">IMP::domino::CompoundStates::CompoundStates()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#afc500a620288204808f5fb15e0e9cff9">IMP::domino::DiscreteSampler::set_particle_states()</a>, <a href="classIMP_1_1domino_1_1ParticleStatesTable.html#a2f3ecc856aa1e60fcbd0d213f0f45dfb">IMP::domino::ParticleStatesTable::set_particle_states()</a>, <a href="classIMP_1_1domino_1_1PermutationStates.html#a95308fa6fbdd565f52c7d58d4fdbaee8">IMP::domino::PermutationStates::PermutationStates()</a></td></tr>
138 <tr><td>@ref IMP::domino::ParticleStatesTable</td><td><a href="classIMP_1_1domino_1_1BranchAndBoundAssignmentsTable.html#a4c39de9b95b22e5efe0804df01b95ee7">IMP::domino::BranchAndBoundAssignmentsTable::BranchAndBoundAssignmentsTable()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundSampler.html#a7b20b50a372ea47e176ac7d3ab2fec0b">IMP::domino::BranchAndBoundSampler::BranchAndBoundSampler()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#ae87fc3c189ff87dbc93ba9959da79e4f">IMP::domino::DiscreteSampler::set_particle_states_table()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#ad06105a5e882bf48ac9a013e8a3e1d2c">IMP::domino::DiscreteSampler::get_subset_filter_tables_to_use()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#ac9a3dc57af62432767395067b932cce3">IMP::domino::DiscreteSampler::DiscreteSampler()</a>, <a href="classIMP_1_1domino_1_1DisjointSetsSubsetFilterTable.html#a6d219703856338684fecf5d96cdd599c">IMP::domino::DisjointSetsSubsetFilterTable::DisjointSetsSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1DominoSampler.html#abce5488102b6313b9edd39c2ccdef0b8">IMP::domino::DominoSampler::DominoSampler()</a>, <a href="classIMP_1_1domino_1_1EqualitySubsetFilterTable.html#a4e777dc82d3cac03bffe26eddb42e129">IMP::domino::EqualitySubsetFilterTable::EqualitySubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1EquivalenceAndExclusionSubsetFilterTable.html#a2354750aa4ca41885dd8726639902dc4">IMP::domino::EquivalenceAndExclusionSubsetFilterTable::EquivalenceAndExclusionSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1EquivalenceSubsetFilterTable.html#a90d1efcd9ae9d2bbc3d14662893a8d28">IMP::domino::EquivalenceSubsetFilterTable::EquivalenceSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1ExclusionSubsetFilterTable.html#a7a840667473246f7a134eba28011636e">IMP::domino::ExclusionSubsetFilterTable::ExclusionSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#a43f47a195717a826c88ad066c1553656">IMP::domino::ListSubsetFilterTable::ListSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1ParticlesAdaptor.html#a7de81f47fe87067fd633f6d442055117">IMP::domino::ParticlesAdaptor::ParticlesAdaptor()</a>, <a href="classIMP_1_1domino_1_1RecursiveAssignmentsTable.html#a0809f8c142a88c80dbd62f57197e795d">IMP::domino::RecursiveAssignmentsTable::RecursiveAssignmentsTable()</a>, <a href="classIMP_1_1domino_1_1RecursiveStates.html#aab5b5225450b5ce8ff2ffbdb5f15f517">IMP::domino::RecursiveStates::RecursiveStates()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#aa442ea37df1d8b970993d4ce57c6e68a">IMP::domino::RestraintCache::RestraintCache()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#a7f12cfb50a6614eeed2d4ecc0f968d2c">IMP::domino::RestraintScoreSubsetFilterTable::RestraintScoreSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1SimpleAssignmentsTable.html#a327026ad51858f3eb8800617576fea85">IMP::domino::SimpleAssignmentsTable::SimpleAssignmentsTable()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilter.html#a0fdd72792f673c8b7d590b5abe80b3fa">IMP::em2d::DistanceFilter::DistanceFilter()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilterTable.html#a8edc09e71c701c228c5a37783130a2de">IMP::em2d::DistanceFilterTable::DistanceFilterTable()</a>, <a href="namespaceIMP_1_1domino.html#a7745ea629841a6a4475211ba0a134b44">IMP::domino::get_interaction_graph()</a>, <a href="namespaceIMP_1_1domino.html#a52b8de54766ce0eeaece21adff2c9bd1">IMP::domino::get_merge_tree()</a>, <a href="namespaceIMP_1_1domino.html#a0c08cfa3955a23464c5f59c15f95a4ae">IMP::domino::load_particle_states()</a>, <a href="namespaceIMP_1_1domino.html#a54f68c619a127b816e0cadcf94638b7d">IMP::domino::get_restraints()</a>, <a href="namespaceIMP_1_1domino.html#a3a112fd41a97e8e93dbff8be3dfb8bb6">IMP::domino::get_distance_if_smaller_than()</a>, <a href="namespaceIMP_1_1domino.html#a3247d32b900c4633e5c58cd7032d043b">IMP::domino::get_embedding()</a>, <a href="namespaceIMP_1_1domino.html#abd8a69ba2cc2b8fea2f49c99189d8711">IMP::domino::get_nearest_assignment()</a>, <a href="namespaceIMP_1_1domino.html#a77f217ed83f57ed3d3155baa13efc22b">IMP::domino::get_possible_interactions()</a>, <a href="namespaceIMP_1_1domino.html#ab0eb2c05d5eb0c9e64fba8c85011ad01">IMP::domino::get_restraint_graph()</a>, <a href="namespaceIMP_1_1domino.html#a7b094ee7dac304dfc212772818a9ba04">IMP::domino::get_state_clusters()</a></td></tr>
139 <tr><td>@ref IMP::domino::RestraintCache</td><td><a href="classIMP_1_1domino_1_1HeapAssignmentContainer.html#ae441675fd3cc83cc810db7fcfc9928e9">IMP::domino::HeapAssignmentContainer::HeapAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1MinimumRestraintScoreSubsetFilterTable.html#a49f8cc9a2111bcce7776062e8cde21fb">IMP::domino::MinimumRestraintScoreSubsetFilterTable::MinimumRestraintScoreSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#afea31f7827234768b9e719e4db0545d2">IMP::domino::RestraintScoreSubsetFilterTable::RestraintScoreSubsetFilterTable()</a></td></tr>
140 <tr><td>@ref IMP::domino::Slice</td><td><a href="namespaceIMP_1_1domino.html#a52a530f6cadbd362b3c42b9210ef5dae">IMP::domino::swap()</a></td></tr>
141 <tr><td>@ref IMP::domino::Subset</td><td><a href="classIMP_1_1domino_1_1AssignmentsTable.html#a82165fe3c39a0a5bd1005826f5121c26">IMP::domino::AssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundAssignmentsTable.html#a9165b72d63a07e7e68728a8017628e6e">IMP::domino::BranchAndBoundAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundSampler.html#ae6043ff455cc1079a594cb25d74f117b">IMP::domino::BranchAndBoundSampler::do_get_sample_assignments()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#a127213eff7a87b103e692c4f2d82d133">IMP::domino::DiscreteSampler::do_get_sample_assignments()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#a4174eb43930468fea7d113da69c51656">IMP::domino::DiscreteSampler::get_sample_assignments()</a>, <a href="classIMP_1_1domino_1_1DominoSampler.html#a342ed03b6bd9bb5818c747921d86abb0">IMP::domino::DominoSampler::do_get_sample_assignments()</a>, <a href="classIMP_1_1domino_1_1EqualitySubsetFilterTable.html#a006a9c15d84fd63aa3ec114ce4652823">IMP::domino::EqualitySubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1EqualitySubsetFilterTable.html#a0e41d167243f8bb91c8ebdf1e68fa66b">IMP::domino::EqualitySubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1EquivalenceAndExclusionSubsetFilterTable.html#afe157522e3913cddcd3977c40d458018">IMP::domino::EquivalenceAndExclusionSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1EquivalenceAndExclusionSubsetFilterTable.html#a313e21c2ac19d8a2520391cc7a728692">IMP::domino::EquivalenceAndExclusionSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1EquivalenceSubsetFilterTable.html#afd7e5705543d7ac7071d4222578de781">IMP::domino::EquivalenceSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1EquivalenceSubsetFilterTable.html#a88463fb614a2dcb2b155e62b77d64a23">IMP::domino::EquivalenceSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1ExclusionSubsetFilterTable.html#a2afbe186f5948675dd1c217efe8a4dbd">IMP::domino::ExclusionSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1ExclusionSubsetFilterTable.html#ab21a7dbe5fd65a957b80d37cecb05e10">IMP::domino::ExclusionSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1HeapAssignmentContainer.html#ae441675fd3cc83cc810db7fcfc9928e9">IMP::domino::HeapAssignmentContainer::HeapAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentsTable.html#aa0422fdbb973a84ae9dfd12c08b3979d">IMP::domino::ListAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentsTable.html#a15fa28a76023dd8fa328b452d2245908">IMP::domino::ListAssignmentsTable::set_assignments()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#a9c1103c9929bdfc78a2b084bf1c1ef47">IMP::domino::ListSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#a324e1729565ebd6513a5357b3f8ca424">IMP::domino::ListSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1MinimumRestraintScoreSubsetFilterTable.html#a8d2bbf239dfc3d30c10baff5545ccd0d">IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_restraints()</a>, <a href="classIMP_1_1domino_1_1MinimumRestraintScoreSubsetFilterTable.html#a952953b0b75eec4bdbace3a90ad0ff6b">IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1MinimumRestraintScoreSubsetFilterTable.html#a04cfce4e5e82589e9a958780ec276853">IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1Order.html#a78fe2c73f2df449f321066ad106f9d20">IMP::domino::Order::Order()</a>, <a href="classIMP_1_1domino_1_1PairListSubsetFilterTable.html#aad0f9d8bac17f64a00ee99b2fa8ab856">IMP::domino::PairListSubsetFilterTable::fill()</a>, <a href="classIMP_1_1domino_1_1PairListSubsetFilterTable.html#af8a8fefbfe5e695a47eecd0865b1240d">IMP::domino::PairListSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1PairListSubsetFilterTable.html#abca0f6c8d5df498eed912ef7ccfa1268">IMP::domino::PairListSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1ProbabilisticSubsetFilterTable.html#ab41b77ad7948c43f0d47996997c445fa">IMP::domino::ProbabilisticSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1ProbabilisticSubsetFilterTable.html#ad96b79309670a8ed32b79f69c2ac15de">IMP::domino::ProbabilisticSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1ReadAssignmentContainer.html#a578c47d5474bbb32d29bcaad8f6cf388">IMP::domino::ReadAssignmentContainer::ReadAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1ReadHDF5AssignmentContainer.html#a1d5717bb895dc7f7e7ca3af4ccd7a351">IMP::domino::ReadHDF5AssignmentContainer::ReadHDF5AssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1RecursiveAssignmentsTable.html#a90514e1adc6368f99d345b59668a803a">IMP::domino::RecursiveAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1RecursiveStates.html#aab5b5225450b5ce8ff2ffbdb5f15f517">IMP::domino::RecursiveStates::RecursiveStates()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#adb2fa9c11b8890d5fb8c45e0bb6ddf32">IMP::domino::RestraintCache::add_restraint_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a1912bee15e6361f9c9bb37fc566d0ddb">IMP::domino::RestraintCache::add_restraint_set_child_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a56bb538e2a59268eb5de499e909b2a2e">IMP::domino::RestraintCache::add_restraint_set_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a6097051c55653accc6ec0bfae75c887a">IMP::domino::RestraintCache::get_restraints()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#aeacabf8b40ea4789ca165cd4773a0acb">IMP::domino::RestraintCache::get_score()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a8e10e0f3973fe941986e8cbf1674582d">IMP::domino::RestraintCache::get_slice()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a7cde8be9e50ebe392c39f47c24316a42">IMP::domino::RestraintCache::load_last_score()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#a6270ec3bab499836ff25bd78049318cf">IMP::domino::RestraintScoreSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#afe6c067399f81400198864d011a90efb">IMP::domino::RestraintScoreSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1SimpleAssignmentsTable.html#a23b9149da5312b4e120a36f3d4949bc9">IMP::domino::SimpleAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1Slice.html#aea927878d3695d75c661a75968659d17">IMP::domino::Slice::get_slice()</a>, <a href="classIMP_1_1domino_1_1Slice.html#a70118528acacd6664939fe4131de82e7">IMP::domino::Slice::Slice()</a>, <a href="classIMP_1_1domino_1_1Slice.html#a2f4e028d276be06d17293141b9a472c1">IMP::domino::Slice::get_sliced()</a>, <a href="classIMP_1_1domino_1_1Subset.html#ae3aa0ebb6ac23b03606b5c5156ea6b12">IMP::domino::Subset::get_contains()</a>, <a href="classIMP_1_1domino_1_1SubsetFilterTable.html#abaa42cb0bed9f3c8fcfa4c3ac3e0162b">IMP::domino::SubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1SubsetFilterTable.html#ac455bb060804addf2274c8304a2aa5fd">IMP::domino::SubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1WriteAssignmentContainer.html#a0e3927e5d8e69e9d233fa025913dfa2a">IMP::domino::WriteAssignmentContainer::WriteAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1WriteHDF5AssignmentContainer.html#a93bf947f7a3edad64d045b6e3214362b">IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1WriteHDF5AssignmentContainer.html#abe70878e668dbb8aff5e71c1f9afcedc">IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilter.html#a0fdd72792f673c8b7d590b5abe80b3fa">IMP::em2d::DistanceFilter::DistanceFilter()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilterTable.html#a8edc09e71c701c228c5a37783130a2de">IMP::em2d::DistanceFilterTable::DistanceFilterTable()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilterTable.html#ab98d30cb579fdd0e2c5be13f5d73b2f8">IMP::em2d::DistanceFilterTable::get_strength()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilterTable.html#adca029b4278e5e58f6e1142ba85cc2bc">IMP::em2d::DistanceFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1example_1_1ExampleSubsetFilterTable.html#a0853fa5682f067893c15062765eed42c">IMP::example::ExampleSubsetFilterTable::get_indexes()</a>, <a href="classIMP_1_1example_1_1ExampleSubsetFilterTable.html#ab89d74a7a5ae94bce6c6d0301b0482ef">IMP::example::ExampleSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1example_1_1ExampleSubsetFilterTable.html#a8fe7c10211739dd503ff88579ad18434">IMP::example::ExampleSubsetFilterTable::get_subset_filter()</a>, <a href="namespaceIMP_1_1domino.html#a36895b9e0319ed81ff55feca2b07d596">IMP::domino::get_is_merge_tree()</a>, <a href="namespaceIMP_1_1domino.html#a0c08cfa3955a23464c5f59c15f95a4ae">IMP::domino::load_particle_states()</a>, <a href="namespaceIMP_1_1domino.html#a54f68c619a127b816e0cadcf94638b7d">IMP::domino::get_restraints()</a>, <a href="namespaceIMP_1_1domino.html#a1e91ca287b91fd6144aeeff14960c14a">IMP::domino::get_difference()</a>, <a href="namespaceIMP_1_1domino.html#a3a112fd41a97e8e93dbff8be3dfb8bb6">IMP::domino::get_distance_if_smaller_than()</a>, <a href="namespaceIMP_1_1domino.html#a3247d32b900c4633e5c58cd7032d043b">IMP::domino::get_embedding()</a>, <a href="namespaceIMP_1_1domino.html#abae30b608c6edfba57967c5e14d4fead">IMP::domino::get_index()</a>, <a href="namespaceIMP_1_1domino.html#a399d7344a0696fbab4a6ca6c2796157b">IMP::domino::get_intersection()</a>, <a href="namespaceIMP_1_1domino.html#abd8a69ba2cc2b8fea2f49c99189d8711">IMP::domino::get_nearest_assignment()</a>, <a href="namespaceIMP_1_1domino.html#ad555f4012dda95f5e23001941b79c735">IMP::domino::get_order()</a>, <a href="namespaceIMP_1_1domino.html#af2a5221a0befe7a9847b1fe9946429cf">IMP::domino::get_partial_index()</a>, <a href="namespaceIMP_1_1domino.html#a619c0aea6816fda8b69b08cf5e57876d">IMP::domino::get_slice()</a>, <a href="namespaceIMP_1_1domino.html#a7b094ee7dac304dfc212772818a9ba04">IMP::domino::get_state_clusters()</a>, <a href="namespaceIMP_1_1domino.html#adc940e96eb944fe259a8fba40830a251">IMP::domino::get_union()</a>, <a href="namespaceIMP_1_1domino.html#a4570cce69f194985e23b710c3b5e18b4">IMP::domino::load_leaf_assignments()</a>, <a href="namespaceIMP_1_1domino.html#a200c71a273844cc32fd32f6a5eafa0aa">IMP::domino::load_merged_assignments()</a>, <a href="namespaceIMP_1_1domino.html#a3305fe8f61d81cba57e9f6896024b263">IMP::domino::load_merged_assignments_random_order()</a>, <a href="namespaceIMP_1_1domino.html#a517fc7420fdb629c2f09280f36e898d3">IMP::domino::swap()</a></td></tr>
142 <tr><td>@ref IMP::domino::SubsetFilterTable</td><td><a href="classIMP_1_1domino_1_1DiscreteSampler.html#aea4629b51fe360838144aa20d647c9c4">IMP::domino::DiscreteSampler::remove_subset_filter_table()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#a69a5fd252f550161d778f1a3c0654fa7">IMP::domino::DiscreteSampler::add_subset_filter_table()</a></td></tr>
143 </table>
144 # IMP.em # {#argument_index_em}
145 <table><tr>
146 <th>Class</th><th>Users</th></tr>
147 <tr><td>@ref IMP::em::DensityHeader</td><td><a href="classIMP_1_1em_1_1DensityMap.html#abf9a162f4619e31c0a3cbc021d7cb7b0">IMP::em::DensityMap::DensityMap()</a>, <a href="classIMP_1_1em_1_1DistanceMask.html#aae2e7c52f4bf9bc869986b8eda1f8bb6">IMP::em::DistanceMask::DistanceMask()</a>, <a href="classIMP_1_1em_1_1EMReaderWriter.html#a2adec96c33055a0eab6a8b6e5ec157f5">IMP::em::EMReaderWriter::read()</a>, <a href="classIMP_1_1em_1_1EMReaderWriter.html#a7cd4eef722dc6cbfbc353e19e1f3aaa3">IMP::em::EMReaderWriter::write()</a>, <a href="classIMP_1_1em_1_1MRCReaderWriter.html#addccce7ae3fd97389d0b055c2c142117">IMP::em::MRCReaderWriter::read()</a>, <a href="classIMP_1_1em_1_1MRCReaderWriter.html#af313f416ceca587f7d6d0b3ae510adfc">IMP::em::MRCReaderWriter::write()</a>, <a href="classIMP_1_1em_1_1MapReaderWriter.html#a4e5943c96cad40f104d1076dc05ad197">IMP::em::MapReaderWriter::read()</a>, <a href="classIMP_1_1em_1_1MapReaderWriter.html#af7410c2a895560c6bdcae982f28e5655">IMP::em::MapReaderWriter::write()</a>, <a href="classIMP_1_1em_1_1RadiusDependentDistanceMask.html#af3e62f683eda2980a136e62790edfbe8">IMP::em::RadiusDependentDistanceMask::RadiusDependentDistanceMask()</a>, <a href="classIMP_1_1em_1_1SampledDensityMap.html#a99c7f42f73230ec27c4ab0f664b3dc95">IMP::em::SampledDensityMap::SampledDensityMap()</a>, <a href="classIMP_1_1em_1_1SpiderMapReaderWriter.html#aa73bc0929bf35db8b546d109f7e8d0c1">IMP::em::SpiderMapReaderWriter::read()</a>, <a href="classIMP_1_1em_1_1SpiderMapReaderWriter.html#a6a4605a4c76247437791dc46e4ab2d41">IMP::em::SpiderMapReaderWriter::write()</a>, <a href="classIMP_1_1em_1_1SurfaceShellDensityMap.html#a906367559e2670491fe3f54dca3ced4d">IMP::em::SurfaceShellDensityMap::SurfaceShellDensityMap()</a>, <a href="classIMP_1_1em_1_1XplorReaderWriter.html#a22433b0ad5ba114ffd892fac4544e437">IMP::em::XplorReaderWriter::read()</a>, <a href="classIMP_1_1em_1_1XplorReaderWriter.html#ab65670ab3e1fea1f9d6a36903cb5e33b">IMP::em::XplorReaderWriter::write()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a3733609ff3265bd070779045acf03fca">IMP::cnmultifit::build_cn_dens_assembly()</a>, <a href="namespaceIMP_1_1em.html#a59459b7c51d60c2f2a3c9b6491cb1455">IMP::em::DensityHeader_to_ImageHeader()</a>, <a href="namespaceIMP_1_1em.html#ab7f8287dfcc5d61b20445c3c683c3e12">IMP::em::ImageHeader_to_DensityHeader()</a></td></tr>
148 <tr><td>@ref IMP::em::DensityMap</td><td><a href="classIMP_1_1cnmultifit_1_1AlignSymmetric.html#afcbb4fa0d636862512fb346809db119a">IMP::cnmultifit::AlignSymmetric::AlignSymmetric()</a>, <a href="classIMP_1_1cnmultifit_1_1CnSymmAxisDetector.html#a0dbacc4bb1c3edd576f297c1616e32ef">IMP::cnmultifit::CnSymmAxisDetector::CnSymmAxisDetector()</a>, <a href="classIMP_1_1em_1_1CoarseCC.html#af20504f32c33f8f6261b004a8e9db8dd">IMP::em::CoarseCC::calc_score()</a>, <a href="classIMP_1_1em_1_1CoarseCC.html#a8a788b503910e0ea75300da9089887e3">IMP::em::CoarseCC::cross_correlation_coefficient()</a>, <a href="classIMP_1_1em_1_1CoarseCC.html#abc28b2cd26b083a5b172fb330d2bd246">IMP::em::CoarseCC::local_cross_correlation_coefficient()</a>, <a href="classIMP_1_1em_1_1CoarseCCatIntervals.html#a4d120a2d38fe2f32674507fada921712">IMP::em::CoarseCCatIntervals::evaluate()</a>, <a href="classIMP_1_1em_1_1CoarseConvolution.html#af95d23ee56098360e25659d575c7aca3">IMP::em::CoarseConvolution::convolution()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#a7e10193f89c1bae88669bcba6f821afd">IMP::em::DensityFillingRestraint::DensityFillingRestraint()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a0f672a08c4e0c77954f1a4aef2b01538">IMP::em::DensityMap::add()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a8fdd76efff4b4d2fe640f05fc66a3749">IMP::em::DensityMap::copy_map()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#ad8b6d7f1edcab290e04d6056faf2434c">IMP::em::DensityMap::pick_max()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#aa1bf0fe2dd98afc7cd94e0f441ff38f2">IMP::em::DensityMap::same_dimensions()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#ab6f89d974d50aadf45b16f1879a01326">IMP::em::DensityMap::same_origin()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#afeca80ac2ffc08fc0769e037cca55a31">IMP::em::DensityMap::same_voxel_size()</a>, <a href="classIMP_1_1em_1_1EnvelopeFitRestraint.html#a8f10c532152aa55376e42a1121c98d1d">IMP::em::EnvelopeFitRestraint::EnvelopeFitRestraint()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#acdc0d23301996c084c90fccddc2f7478">IMP::em::EnvelopePenetrationRestraint::EnvelopePenetrationRestraint()</a>, <a href="classIMP_1_1em_1_1FitRestraint.html#a5e15febe4a62218a76ee5b18abd58092">IMP::em::FitRestraint::FitRestraint()</a>, <a href="classIMP_1_1em_1_1HighDensityEmbedding.html#a15ad76f739395c5555e9ade9bbed66ed">IMP::em::HighDensityEmbedding::HighDensityEmbedding()</a>, <a href="classIMP_1_1em_1_1MapDistanceTransform.html#a3e85e6e9693a3b1047ff17f40e906d05">IMP::em::MapDistanceTransform::MapDistanceTransform()</a>, <a href="classIMP_1_1em_1_1PCAAligner.html#a983b2f7a93a890f6103b18c7cf725e00">IMP::em::PCAAligner::PCAAligner()</a>, <a href="classIMP_1_1em_1_1PCAFitRestraint.html#a32ed8a1e66215fb35807084411ed4a90">IMP::em::PCAFitRestraint::PCAFitRestraint()</a>, <a href="classIMP_1_1multifit_1_1DensityDataPoints.html#a51782d49c5e98b159037c274f4e0e99c">IMP::multifit::DensityDataPoints::DensityDataPoints()</a>, <a href="classIMP_1_1multifit_1_1DensityDataPoints.html#ab0e076ff29e061cafed9b70b181b089c">IMP::multifit::DensityDataPoints::set_density()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#a136cac955ee735ec87b1238b82aa67ac">IMP::multifit::FFTFitting::do_global_fitting()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#ae47864b146f9cf99c92495967e611d01">IMP::multifit::FFTFitting::do_local_fitting()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#aaeb4a52a506bcee42b2cacb393fbaa43">IMP::multifit::FFTFitting::copy_density_data()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#a37d65339d5125709922ec82eba2ce9ed">IMP::multifit::FFTFitting::crop_margin()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#ab063459cb69df88446f638fded7d95da">IMP::multifit::FFTFitting::prepare_lowres_map()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#aced49e5f2dae277cdcc74732c76c4aca">IMP::multifit::FFTFitting::prepare_poslist()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#a91969e61ffab79ed9b4f9cd5d222ef37">IMP::multifit::FFTFitting::prepare_poslist_flipped()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a88d1ed53c74d930ee8bd5d6d07a95112">IMP::multifit::ProteomicsEMAlignmentAtomic::set_density_map()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a3733609ff3265bd070779045acf03fca">IMP::cnmultifit::build_cn_dens_assembly()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a6067aedfd378547038d133f84bb820e3">IMP::cnmultifit::fit_cn_assembly()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a1b5327db66abe2f5bc1712f1013a4436">IMP::cnmultifit::fit_cn_assembly()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a326d661ede67dfeb87070ee6447ad678">IMP::cnmultifit::symmetry_local_fitting()</a>, <a href="namespaceIMP_1_1em.html#a46c20ecb2df0e49d8d1872bcdfa6ddab">IMP::em::add_to_map()</a>, <a href="namespaceIMP_1_1em.html#a6e4fd1709fe2bbb486a3e70d4dfe0f27">IMP::em::approximate_molecular_mass()</a>, <a href="namespaceIMP_1_1em.html#a1c88424c8b24a5802ef048175e22787b">IMP::em::binarize()</a>, <a href="namespaceIMP_1_1em.html#a820c75d52b5f2b63a8b9c67a883bda15">IMP::em::compute_fitting_score()</a>, <a href="namespaceIMP_1_1em.html#aa99a3856b86b49aad83e79c255f360db">IMP::em::compute_fitting_scores()</a>, <a href="namespaceIMP_1_1em.html#ab8beedad8915dcd1aa22b5ba75a61439">IMP::em::compute_fitting_scores()</a>, <a href="namespaceIMP_1_1em.html#a8505c0c435a33d043c98f29ade4fc2ee">IMP::em::convolute()</a>, <a href="namespaceIMP_1_1em.html#aa873c569e58e5c5d66dac1c0420f3e6c">IMP::em::create_density_map()</a>, <a href="namespaceIMP_1_1em.html#a97bf357f626dfeaa62507d51614db63d">IMP::em::density2particles()</a>, <a href="namespaceIMP_1_1em.html#a5cbea21ee3c92fa5008bea0e8a6fc612">IMP::em::density2vectors()</a>, <a href="namespaceIMP_1_1em.html#a6cde45849d9d1b0fbdc1ed54b6dd74b6">IMP::em::get_binarized_interior()</a>, <a href="namespaceIMP_1_1em.html#a820db29914536321043260f19e89fca1">IMP::em::get_bounding_box()</a>, <a href="namespaceIMP_1_1em.html#a58f523ec7b9df988f0c9ef3caae1b6a0">IMP::em::get_bounding_box()</a>, <a href="namespaceIMP_1_1em.html#a760df3beba0bbbfffcb79ac1be87bed6">IMP::em::get_density()</a>, <a href="namespaceIMP_1_1em.html#a9c72b01f6d6bbe0c84a0779fc08b809c">IMP::em::get_grid()</a>, <a href="namespaceIMP_1_1em.html#a65ce4b02f4593b0de63eb19d4441e56e">IMP::em::get_interiors_intersect()</a>, <a href="namespaceIMP_1_1em.html#a1a9e2f7c4a8e6a32405eca965626d554">IMP::em::get_molecular_mass_at_threshold()</a>, <a href="namespaceIMP_1_1em.html#a52260afb0cbcc46e0ad4bdd377095a03">IMP::em::get_number_of_particles_outside_of_the_density()</a>, <a href="namespaceIMP_1_1em.html#a3b0328cacfc463600b955c3f0c93b3be">IMP::em::get_numbers_of_particles_outside_of_the_density()</a>, <a href="namespaceIMP_1_1em.html#a4d80dfedcdc41944135ecde0149e2b25">IMP::em::get_percentage_of_voxels_covered_by_particles()</a>, <a href="namespaceIMP_1_1em.html#a61ba13263cb5aa1f440975aae4480d48">IMP::em::get_resampled()</a>, <a href="namespaceIMP_1_1em.html#a8dfa355f085d452c5636987d4f8ab956">IMP::em::get_segment()</a>, <a href="namespaceIMP_1_1em.html#aa92d0be9d42aa9d9b7a20796baacbf3b">IMP::em::get_segment()</a>, <a href="namespaceIMP_1_1em.html#a94fc09c5491718e3e0e61b2c4ff04f8f">IMP::em::get_segment_by_masking()</a>, <a href="namespaceIMP_1_1em.html#a0b1f187c3b53af89037d40912cc10aef">IMP::em::get_sum()</a>, <a href="namespaceIMP_1_1em.html#a7be03879088ecc74f54b40e68ba7a99c">IMP::em::get_threshold_for_approximate_mass()</a>, <a href="namespaceIMP_1_1em.html#ac70c499fce515b0328e43e6084fe92dc">IMP::em::get_threshold_for_approximate_volume()</a>, <a href="namespaceIMP_1_1em.html#a3078e4c77b9e81fa61b8222934185d1e">IMP::em::get_threshold_map()</a>, <a href="namespaceIMP_1_1em.html#a24e9ee45b3f3e2c55bfe9e73971e7737">IMP::em::get_transformed()</a>, <a href="namespaceIMP_1_1em.html#a4a69963f03e3f972639b15a378467798">IMP::em::get_transformed()</a>, <a href="namespaceIMP_1_1em.html#a8bd63b39d8f60348030c5607e83ba6b7">IMP::em::get_transformed_into()</a>, <a href="namespaceIMP_1_1em.html#abd0e642dde82199ac2b181e297526241">IMP::em::get_transformed_into2()</a>, <a href="namespaceIMP_1_1em.html#a402ab2b7809cc5ce708092b3c2c1a297">IMP::em::get_volume_at_threshold()</a>, <a href="namespaceIMP_1_1em.html#a7ca59d2a3aa688060c280efa250d80a7">IMP::em::interpolate_map()</a>, <a href="namespaceIMP_1_1em.html#af2e9693e484be616d4b490bc7e0ceafc">IMP::em::local_rigid_fitting()</a>, <a href="namespaceIMP_1_1em.html#a2d77c6d77688fed98290030953698a82">IMP::em::local_rigid_fitting_around_point()</a>, <a href="namespaceIMP_1_1em.html#a79ed07d59b449e5f31b1479b73b4b054">IMP::em::local_rigid_fitting_around_points()</a>, <a href="namespaceIMP_1_1em.html#a6521ac8778500885341c924cc7b4b027">IMP::em::local_rigid_fitting_grid_search()</a>, <a href="namespaceIMP_1_1em.html#ae6c068669daa6977fb4a6e9800d79b44">IMP::em::mask_and_norm()</a>, <a href="namespaceIMP_1_1em.html#a0337abc873be82054e0b4061912cf0dc">IMP::em::multiply()</a>, <a href="namespaceIMP_1_1em.html#a15d507816249ea57830e0b20f63af937">IMP::em::write_map()</a>, <a href="namespaceIMP_1_1em.html#ab6a3d7f80c70e8db6c86cb5ba1e66e60">IMP::em::write_map()</a>, <a href="namespaceIMP_1_1multifit.html#a6d23b5accff1c34001a8ca97d0241167">IMP::multifit::create_coarse_molecule_from_density()</a>, <a href="namespaceIMP_1_1multifit.html#a3359231b0601df5803958afcd8d93184">IMP::multifit::create_hit_map()</a>, <a href="namespaceIMP_1_1multifit.html#af83b1866a4b7bb6747eea98bd9bb28e1">IMP::multifit::fft_based_rigid_fitting()</a>, <a href="namespaceIMP_1_1multifit.html#af5cfce601c0bc38d4fd668dec337b3f4">IMP::multifit::get_anchors_for_density()</a>, <a href="namespaceIMP_1_1multifit.html#aebdba0d523d4730ee0031629b70b8ea1">IMP::multifit::get_connected_components()</a>, <a href="namespaceIMP_1_1multifit.html#a6945fa68efec8cd7f189ebd51b7af727">IMP::multifit::get_segment_maximum()</a>, <a href="namespaceIMP_1_1multifit.html#aeb628c3804ee3d8aa7df59051b0ad1d2">IMP::multifit::get_segmentation()</a>, <a href="namespaceIMP_1_1multifit.html#a45c8385d6183240ec7216ae97374c7a9">IMP::multifit::pca_based_rigid_fitting()</a>, <a href="namespaceIMP_1_1multifit.html#aae3c93b62256b393e1ac553cce6a19e3">IMP::multifit::pca_based_rigid_fitting()</a>, <a href="namespaceIMP_1_1multifit.html#a8528245410468cfc40ab674d0ef64d70">IMP::multifit::remove_background()</a>, <a href="namespaceIMP_1_1multifit.html#a8009ecb4c53812a36bf544ed7e9fe9a0">IMP::multifit::write_segment_as_mrc()</a>, <a href="namespaceIMP_1_1multifit.html#ac66c9128b0009595989bc520e3e6dcd3">IMP::multifit::write_segments_as_mrc()</a></td></tr>
149 <tr><td>@ref IMP::em::FittingSolutions</td><td><a href="namespaceIMP_1_1multifit.html#a04303e2e87f1a25c6e4fdf2ca2e73453">IMP::multifit::convert_em_to_multifit_format()</a></td></tr>
150 <tr><td>@ref IMP::em::ImageHeader</td><td><a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#a5e44ebd2e762bc482741d31eb2f61ae5">IMP::em2d::ImageReaderWriter::read()</a>, <a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#adbd764fa1dacf7cf79ec44670f49b6a4">IMP::em2d::ImageReaderWriter::read_from_floats()</a>, <a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#ad5d892bb53865c0995d9226d3d7dadfe">IMP::em2d::ImageReaderWriter::read_from_ints()</a>, <a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#aae799f91ac40249ea85441d1154ad0f1">IMP::em2d::ImageReaderWriter::write()</a>, <a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#a59263b05b2204f8a045cadb975604e72">IMP::em2d::ImageReaderWriter::write_to_floats()</a>, <a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#acdc118dbb9ccf187f29072010f4e71d6">IMP::em2d::ImageReaderWriter::write_to_ints()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#ada85593d93e916c209685881c7a4fcd5">IMP::em2d::JPGImageReaderWriter::read()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#abe4ea8ee65e316e0642cfd0dadd2aaaa">IMP::em2d::JPGImageReaderWriter::read_from_floats()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#a3dd656c0f71e7189264c6d57aad86aab">IMP::em2d::JPGImageReaderWriter::read_from_ints()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#a0cf20b7c7d484849803dd81af78b3070">IMP::em2d::JPGImageReaderWriter::write()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#a5a9cd9610c937d6f353c5340ffb557e3">IMP::em2d::JPGImageReaderWriter::write_to_floats()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#a87bc26efc426f5621fb1b703e50289ca">IMP::em2d::JPGImageReaderWriter::write_to_ints()</a>, <a href="classIMP_1_1em2d_1_1RegistrationResult.html#afd9d889f9b8de4e3a3d7d42fa965f41d">IMP::em2d::RegistrationResult::read_from_image()</a>, <a href="classIMP_1_1em2d_1_1RegistrationResult.html#a51e23a3b0f9c050a741b597e2e4448ab">IMP::em2d::RegistrationResult::set_in_image()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#a7d98a6bb47da11f23cf28541af4d3840">IMP::em2d::SpiderImageReaderWriter::read()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#a8f6626f64c73a13c6205432c79396e55">IMP::em2d::SpiderImageReaderWriter::read_from_floats()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#a53e49da7099624ced8586b8aed6a10e0">IMP::em2d::SpiderImageReaderWriter::read_from_ints()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#a111a790b326496d7c87883071043cb09">IMP::em2d::SpiderImageReaderWriter::write()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#a82c2bce1a8a4751a51ca44470733ca03">IMP::em2d::SpiderImageReaderWriter::write_to_floats()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#aaf4a3d2aa39b23806bf5ac24fce657c2">IMP::em2d::SpiderImageReaderWriter::write_to_ints()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#a78eff1cda352c26b9e0155ac080866f1">IMP::em2d::TIFFImageReaderWriter::read()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#a4b60fcfe1dfa744e1b5f468ceae86cd4">IMP::em2d::TIFFImageReaderWriter::read_from_floats()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#a13d4d4bfbd95cff976ef099e68f6ddf6">IMP::em2d::TIFFImageReaderWriter::read_from_ints()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#aea18b2d98bb9115f1cbdef6101bb3b7d">IMP::em2d::TIFFImageReaderWriter::write()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#a819d72ed5ecdbf153adda9421be6314d">IMP::em2d::TIFFImageReaderWriter::write_to_floats()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#a9c3bf9fbc299b23e4f09b5dca61eb458">IMP::em2d::TIFFImageReaderWriter::write_to_ints()</a>, <a href="namespaceIMP_1_1em.html#a59459b7c51d60c2f2a3c9b6491cb1455">IMP::em::DensityHeader_to_ImageHeader()</a>, <a href="namespaceIMP_1_1em.html#ab7f8287dfcc5d61b20445c3c683c3e12">IMP::em::ImageHeader_to_DensityHeader()</a></td></tr>
151 <tr><td>@ref IMP::em::KernelParameters</td><td><a href="classIMP_1_1em2d_1_1ProjectionMask.html#aac6d45633ad47220e1f18e29d6a67eab">IMP::em2d::ProjectionMask::ProjectionMask()</a>, <a href="classIMP_1_1em2d_1_1ProjectionMask.html#a5c50ecc74ac2f8fc0e2bafc1e8116ef7">IMP::em2d::ProjectionMask::create()</a></td></tr>
152 <tr><td>@ref IMP::em::MapDistanceTransform</td><td><a href="classIMP_1_1em_1_1EnvelopeScore.html#afeceacd6778085f40838b7fe1758907e">IMP::em::EnvelopeScore::EnvelopeScore()</a></td></tr>
153 <tr><td>@ref IMP::em::MapReaderWriter</td><td><a href="namespaceIMP_1_1em.html#ac570c6b6325f74c8a4ffa8df6ba6c4c9">IMP::em::read_map()</a>, <a href="namespaceIMP_1_1em.html#a15d507816249ea57830e0b20f63af937">IMP::em::write_map()</a></td></tr>
154 <tr><td>@ref IMP::em::RadiusDependentKernelParameters</td><td><a href="classIMP_1_1em2d_1_1ProjectionMask.html#aac6d45633ad47220e1f18e29d6a67eab">IMP::em2d::ProjectionMask::ProjectionMask()</a>, <a href="classIMP_1_1em2d_1_1ProjectionMask.html#a5c50ecc74ac2f8fc0e2bafc1e8116ef7">IMP::em2d::ProjectionMask::create()</a></td></tr>
155 <tr><td>@ref IMP::em::SampledDensityMap</td><td><a href="classIMP_1_1em_1_1CoarseCC.html#af20504f32c33f8f6261b004a8e9db8dd">IMP::em::CoarseCC::calc_score()</a>, <a href="classIMP_1_1em_1_1CoarseCCatIntervals.html#a4d120a2d38fe2f32674507fada921712">IMP::em::CoarseCCatIntervals::evaluate()</a></td></tr>
156 <tr><td>@ref IMP::em::SurfaceShellDensityMap</td><td><a href="namespaceIMP_1_1em.html#a84a15c16174944d980061dc91958793b">IMP::em::calculate_intersection_score()</a></td></tr>
157 </table>
158 # IMP.em2d # {#argument_index_em2d}
159 <table><tr>
160 <th>Class</th><th>Users</th></tr>
161 <tr><td>@ref IMP::em2d::ClusterSet</td><td><a href="classIMP_1_1em2d_1_1AverageDistanceLinkage.html#a9e4a72284ae366295907143152ca8cb1">IMP::em2d::AverageDistanceLinkage::operator()()</a>, <a href="classIMP_1_1em2d_1_1CompleteLinkage.html#a63235ad1a6acdcb8e7c0b76e42279fd9">IMP::em2d::CompleteLinkage::operator()()</a>, <a href="classIMP_1_1em2d_1_1SingleLinkage.html#a49ba34ff3b564943003feb4950656f1c">IMP::em2d::SingleLinkage::operator()()</a></td></tr>
162 <tr><td>@ref IMP::em2d::Em2DRestraintParameters</td><td><a href="classIMP_1_1em2d_1_1Em2DRestraint.html#a3351edb9bbe8eab5297df9396542effd">IMP::em2d::Em2DRestraint::setup()</a>, <a href="classIMP_1_1em2d_1_1ProjectionFinder.html#aff42f0cb55360eba23aca76e71cc25fd">IMP::em2d::ProjectionFinder::setup()</a></td></tr>
163 <tr><td>@ref IMP::em2d::Image</td><td><a href="classIMP_1_1em2d_1_1ChiSquaredScore.html#a347b3892b7bd2c64baa1cd6b96cf62b7">IMP::em2d::ChiSquaredScore::get_private_score()</a>, <a href="classIMP_1_1em2d_1_1ChiSquaredScore.html#a1fe1b42f7da351ead5b18ac99200940b">IMP::em2d::ChiSquaredScore::set_variance_imag_private()</a>, <a href="classIMP_1_1em2d_1_1EM2DScore.html#a45ecaef07f5671a0f22ba92d60af757d">IMP::em2d::EM2DScore::get_private_score()</a>, <a href="classIMP_1_1em2d_1_1Fine2DRegistrationRestraint.html#a04ddb2aa50708a968d1f2064831afdfe">IMP::em2d::Fine2DRegistrationRestraint::set_subject_image()</a>, <a href="classIMP_1_1em2d_1_1Image.html#a8f60a2fc69d0e0ea1502ed2448b42376">IMP::em2d::Image::set_size()</a>, <a href="classIMP_1_1em2d_1_1MeanAbsoluteDifference.html#a1a8d2ddf225f88452205035cbfc010c4">IMP::em2d::MeanAbsoluteDifference::get_private_score()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#af061f3bf53dde9fec3da4b4432220b84">IMP::em2d::RigidBodiesImageFitRestraint::RigidBodiesImageFitRestraint()</a>, <a href="classIMP_1_1em2d_1_1ScoreFunction.html#a7111cef1cdadc7b3245e8621b7b46fb0">IMP::em2d::ScoreFunction::get_score()</a>, <a href="classIMP_1_1em2d_1_1ScoreFunction.html#afb6049939c1645c590a5b4e0911578ac">IMP::em2d::ScoreFunction::set_variance_image()</a>, <a href="classIMP_1_1em2d_1_1ScoreFunction.html#a936827b9594e03838640cf7f0fc04155">IMP::em2d::ScoreFunction::get_private_score()</a>, <a href="classIMP_1_1em2d_1_1ScoreFunction.html#a75e086aa82705e1efa5501d2b264f200">IMP::em2d::ScoreFunction::set_variance_image_private()</a>, <a href="namespaceIMP_1_1em2d.html#a06c274b3934ad8569f1ed6f97248dc2a">IMP::em2d::add_noise()</a>, <a href="namespaceIMP_1_1em2d.html#a6fbd3f388210a4942c4ac54c95b88fd8">IMP::em2d::apply_diffusion_filter()</a>, <a href="namespaceIMP_1_1em2d.html#a90402327da81d37eb865301ff37fbb19">IMP::em2d::apply_mean_outside_mask()</a>, <a href="namespaceIMP_1_1em2d.html#a258020f16ff0205998ee972aa2656499">IMP::em2d::apply_variance_filter()</a>, <a href="namespaceIMP_1_1em2d.html#af9e50eaa31332e8e42eb3ee0d2b8872e">IMP::em2d::crop()</a>, <a href="namespaceIMP_1_1em2d.html#aec931bf7254087acda23ffca83c40d2b">IMP::em2d::do_combined_fill_holes_and_threshold()</a>, <a href="namespaceIMP_1_1em2d.html#ac225b565975f40a59970616e9b25cc7f">IMP::em2d::do_extend_borders()</a>, <a href="namespaceIMP_1_1em2d.html#a8dbdd9fda0c62746f8d306f171e72939">IMP::em2d::do_fill_holes()</a>, <a href="namespaceIMP_1_1em2d.html#a8ca0f5601724287c85b00fb71ddecc44">IMP::em2d::do_normalize()</a>, <a href="namespaceIMP_1_1em2d.html#aac8b25edf0a90e063935009e934ff14a">IMP::em2d::do_remove_small_objects()</a>, <a href="namespaceIMP_1_1em2d.html#a1d4044443138ae1ad3c60ba33afd6e5e">IMP::em2d::do_resample_polar()</a>, <a href="namespaceIMP_1_1em2d.html#a64eb9b75ba5371ca0b73ad4bb455b6f7">IMP::em2d::do_segmentation()</a>, <a href="namespaceIMP_1_1em2d.html#a5fa6302882e4cc2ddc39262f434058e6">IMP::em2d::do_subtract_images()</a>, <a href="namespaceIMP_1_1em2d.html#a185b28584381f8d779db94c0f91f9db0">IMP::em2d::get_autocorrelation2d()</a>, <a href="namespaceIMP_1_1em2d.html#a47326ad3deacabc6aa0fc68818c453ea">IMP::em2d::get_correlation2d()</a>, <a href="namespaceIMP_1_1em2d.html#af22f5cc59992f1a392b914e6b57a0ecc">IMP::em2d::get_cross_correlation_coefficient()</a>, <a href="namespaceIMP_1_1em2d.html#a4f87a85f1ee35aa0a6dc6f0c859df0b0">IMP::em2d::get_histogram()</a>, <a href="namespaceIMP_1_1em2d.html#a3cfb06b6362604cfeafa6ab79b5a5769">IMP::em2d::get_projection()</a></td></tr>
164 <tr><td>@ref IMP::em2d::ImageReaderWriter</td><td><a href="classIMP_1_1em2d_1_1Image.html#a051c8ca01c41487d6d638a3867854283">IMP::em2d::Image::Image()</a>, <a href="classIMP_1_1em2d_1_1Image.html#a3711206f3d3632ed50f56194528574d5">IMP::em2d::Image::read()</a>, <a href="classIMP_1_1em2d_1_1Image.html#a0d4c7013411e8712825ea2bf38188bc5">IMP::em2d::Image::write()</a>, <a href="classIMP_1_1em2d_1_1ProjectingOptions.html#a02c2425aa3903fa5ec263dd65320101b">IMP::em2d::ProjectingOptions::ProjectingOptions()</a>, <a href="namespaceIMP_1_1em2d.html#a9b93ce77266955bd99874dbb269fc87c">IMP::em2d::read_images()</a>, <a href="namespaceIMP_1_1em2d.html#a3c4762ec4e3272cd645d012e24b464b3">IMP::em2d::save_images()</a></td></tr>
165 <tr><td>@ref IMP::em2d::PolarResamplingParameters</td><td><a href="namespaceIMP_1_1em2d.html#aad3c7e6514aadaa236e5e354ceff8856">IMP::em2d::do_resample_polar()</a>, <a href="namespaceIMP_1_1em2d.html#a1d4044443138ae1ad3c60ba33afd6e5e">IMP::em2d::do_resample_polar()</a></td></tr>
166 <tr><td>@ref IMP::em2d::ProjectingOptions</td><td><a href="namespaceIMP_1_1em2d.html#ade0e4f389263022c17983259431ba87a">IMP::em2d::create_evenly_distributed_projections()</a>, <a href="namespaceIMP_1_1em2d.html#af3b3894a70e76077900ac8230c59f9ec">IMP::em2d::do_project_particles()</a>, <a href="namespaceIMP_1_1em2d.html#a3cfb06b6362604cfeafa6ab79b5a5769">IMP::em2d::get_projection()</a>, <a href="namespaceIMP_1_1em2d.html#a87fb708668f8c56200d34b3c09edabc3">IMP::em2d::get_projections()</a>, <a href="namespaceIMP_1_1em2d.html#ad67f1f21b56148b8ab04291845ca7083">IMP::em2d::get_projections()</a></td></tr>
167 <tr><td>@ref IMP::em2d::ProjectingParameters</td><td><a href="classIMP_1_1em2d_1_1Fine2DRegistrationRestraint.html#a67370df5b0c459a94053130e8a6a07ae">IMP::em2d::Fine2DRegistrationRestraint::setup()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#a477b51eb69d95e8a70cc7d42d392327c">IMP::em2d::RigidBodiesImageFitRestraint::set_projecting_parameters()</a></td></tr>
168 <tr><td>@ref IMP::em2d::RegistrationResult</td><td><a href="namespaceIMP_1_1em2d.html#a3cfb06b6362604cfeafa6ab79b5a5769">IMP::em2d::get_projection()</a>, <a href="namespaceIMP_1_1em2d.html#a57a725bb5e94995d20b75abe96d9cfbd">IMP::em2d::get_rotation_error()</a>, <a href="namespaceIMP_1_1em2d.html#ad612906ea96b2c6f162c97b654309c7f">IMP::em2d::get_shift_error()</a></td></tr>
169 <tr><td>@ref IMP::em2d::ScoreFunction</td><td><a href="classIMP_1_1em2d_1_1Em2DRestraint.html#a3351edb9bbe8eab5297df9396542effd">IMP::em2d::Em2DRestraint::setup()</a>, <a href="classIMP_1_1em2d_1_1Fine2DRegistrationRestraint.html#a67370df5b0c459a94053130e8a6a07ae">IMP::em2d::Fine2DRegistrationRestraint::setup()</a>, <a href="classIMP_1_1em2d_1_1ProjectionFinder.html#aff42f0cb55360eba23aca76e71cc25fd">IMP::em2d::ProjectionFinder::setup()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#af061f3bf53dde9fec3da4b4432220b84">IMP::em2d::RigidBodiesImageFitRestraint::RigidBodiesImageFitRestraint()</a></td></tr>
170 <tr><td>@ref IMP::em2d::SegmentationParameters</td><td><a href="namespaceIMP_1_1em2d.html#a90292cd68858d8e90c4e99c2826739bb">IMP::em2d::do_segmentation()</a>, <a href="namespaceIMP_1_1em2d.html#a64eb9b75ba5371ca0b73ad4bb455b6f7">IMP::em2d::do_segmentation()</a></td></tr>
171 </table>
172 # IMP.isd # {#argument_index_isd}
173 <table><tr>
174 <th>Class</th><th>Users</th></tr>
175 <tr><td>@ref IMP::isd::BivariateFunction</td><td><a href="classIMP_1_1isd_1_1GaussianProcessInterpolation.html#ab41bc7acf66cea95ad3b8be03f8015b9">IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation()</a></td></tr>
176 <tr><td>@ref IMP::isd::CrossLinkData</td><td><a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#a33e047d45e77e1b6e5c71bba1ed7d6f0">IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#afc6082000216caa2d5a22f9813a317a2">IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()</a></td></tr>
177 <tr><td>@ref IMP::isd::CysteineCrossLinkData</td><td><a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#afc6082000216caa2d5a22f9813a317a2">IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()</a></td></tr>
178 <tr><td>@ref IMP::isd::FretData</td><td><a href="classIMP_1_1isd_1_1FretRestraint.html#a8b6683ce3a6ec845b6b4a0b22e4861b5">IMP::isd::FretRestraint::FretRestraint()</a></td></tr>
179 <tr><td>@ref IMP::isd::GaussianProcessInterpolation</td><td><a href="classIMP_1_1isd_1_1GaussianProcessInterpolationRestraint.html#a9111f94a0df18602d5d31ea8de9df14e">IMP::isd::GaussianProcessInterpolationRestraint::GaussianProcessInterpolationRestraint()</a></td></tr>
180 <tr><td>@ref IMP::isd::LogWrapper</td><td><a href="classIMP_1_1isd_1_1LogWrapper.html#a8be5cce773725d72e4887c21d807d4d6">IMP::isd::LogWrapper::on_remove()</a></td></tr>
181 <tr><td>@ref IMP::isd::UnivariateFunction</td><td><a href="classIMP_1_1isd_1_1GaussianProcessInterpolation.html#ab41bc7acf66cea95ad3b8be03f8015b9">IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation()</a></td></tr>
182 </table>
183 # IMP.kernel # {#argument_index_kernel}
184 <table><tr>
185 <th>Class</th><th>Users</th></tr>
186 <tr><td>@ref IMP::kernel::Configuration</td><td><a href="classIMP_1_1kernel_1_1Configuration.html#ad4903589e673fe8a3d98fe30de48c1b9">IMP::kernel::Configuration::Configuration()</a></td></tr>
187 <tr><td>@ref IMP::kernel::ConfigurationSet</td><td><a href="classIMP_1_1kernel_1_1SaveToConfigurationSetOptimizerState.html#ac1329f60ad15656fc82e04b8574c154e">IMP::kernel::SaveToConfigurationSetOptimizerState::SaveToConfigurationSetOptimizerState()</a></td></tr>
188 <tr><td>@ref IMP::kernel::Container</td><td><a href="namespaceIMP_1_1kernel.html#abbbf9ad258613cf409a88d2b01529190">IMP::kernel::create_restraint()</a></td></tr>
189 <tr><td>@ref IMP::kernel::Decorator</td><td><a href="classIMP_1_1kernel_1_1ParticleAdaptor.html#ad967db5f6617022ebc2992d59b299341">IMP::kernel::ParticleAdaptor::ParticleAdaptor()</a>, <a href="classIMP_1_1kernel_1_1ParticleIndexAdaptor.html#aaddebac1d5f1745e7fd1fece86ec7df7">IMP::kernel::ParticleIndexAdaptor::ParticleIndexAdaptor()</a>, <a href="namespaceIMP_1_1kernel.html#aca3628b2e46538d5f1c0cb2207911928">IMP::kernel::get_vector_geometry()</a>, <a href="namespaceIMP_1_1kernel.html#a615b4ba42235870a5b3c0dc358442df2">IMP::kernel::set_vector_geometry()</a></td></tr>
190 <tr><td>@ref IMP::kernel::DerivativeAccumulator</td><td><a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#a8998a04e9ba8d376555d6d141595e3c1">IMP::atom::CHARMMStereochemistryRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1PairsRestraint.html#ac9af1971fb689142f3d2c96706053cd0">IMP::container::PairsRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1QuadsRestraint.html#a7435f350d07f81931fd3236b21068a81">IMP::container::QuadsRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1SingletonsRestraint.html#a9842a498b03c84a415d388e925a433d1">IMP::container::SingletonsRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1TripletsRestraint.html#a80d7e10552f9532e5c96989925a15065">IMP::container::TripletsRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1ConstantRestraint.html#a054bb9ba35df5fd8e492fd5f0a2656fb">IMP::core::ConstantRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1DiameterRestraint.html#ada657e344e11d29b4b994aa56eb81f03">IMP::core::DiameterRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1DihedralRestraint.html#a94e311f7607ccecce3ba3507a4b20748">IMP::core::DihedralRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1MSConnectivityRestraint.html#acbbb248c2357046bf7a5f97daf755368">IMP::core::MSConnectivityRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1VolumeRestraint.html#a83e44d5881c8109ea66d6cc07f58eb67">IMP::core::VolumeRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em2d_1_1DummyRestraint.html#a9dccfd33111a3065fb98aed40cadeaaa">IMP::em2d::DummyRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em2d_1_1Em2DRestraint.html#a9fa81bec49a718814361505ff8b0cf38">IMP::em2d::Em2DRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em2d_1_1Fine2DRegistrationRestraint.html#a07fd5bfb207d11a625a9ef50a0583f72">IMP::em2d::Fine2DRegistrationRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em2d_1_1ParticlesDummyRestraint.html#adbeaef004de4728f3b8d163e59d970de">IMP::em2d::ParticlesDummyRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#a114d4a2d523ecfa32121d0bf0ee91066">IMP::em2d::RigidBodiesImageFitRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#ab976bc8d4f449ac7be2b9da85c431b46">IMP::em::DensityFillingRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#a73bcd18c899decbe79668687052339f2">IMP::em::EnvelopePenetrationRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em_1_1FitRestraint.html#a1f22a295ac075717ba8141e40d69caf2">IMP::em::FitRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em_1_1PCAFitRestraint.html#abb9e777688b24e4231ba952faa73f09c">IMP::em::PCAFitRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1example_1_1ExampleComplexRestraint.html#a1627fd71ef808be7ae8224cc13b4c300">IMP::example::ExampleComplexRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1AmbiguousNOERestraint.html#a4fcdd62cde67e4da0f2eab0fcc1a8d52">IMP::isd::AmbiguousNOERestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1AmbiguousRestraint.html#a3ae6263ec9e197dfc497dfeab62dc156">IMP::isd::AmbiguousRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#a2b26b1cd953d147879ae5e2397db6a8d">IMP::isd::CrossLinkMSRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#a34c6399f3b84e4d355a03b0e36057129">IMP::isd::CysteineCrossLinkRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1FretRestraint.html#ae7056b516fe4ac5d0d6121a970f202d8">IMP::isd::FretRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1GaussianEMRestraint.html#a779abe0fa903675e74a8addd4ee4f290">IMP::isd::GaussianEMRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1GaussianRestraint.html#a98d42542228704c22b1abeebbc70366d">IMP::isd::GaussianRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1JeffreysRestraint.html#a8e2e3f135c0996fe1cd0f2e0a93d314f">IMP::isd::JeffreysRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1LogWrapper.html#ad5b2dcd25ed83e00aefae2fb6ef25c15">IMP::isd::LogWrapper::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1LognormalRestraint.html#aa42c0025df75ff30a8a8a2d5ffeb65dd">IMP::isd::LognormalRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1MarginalHBondRestraint.html#a9a5897a72877e30870ed486f56189958">IMP::isd::MarginalHBondRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1MarginalNOERestraint.html#a7ec4bd1d3f89e990ef7b574ebe8aeac1">IMP::isd::MarginalNOERestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1NOERestraint.html#af0fb131a65f91ed4c13e8813f2efa160">IMP::isd::NOERestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1TALOSRestraint.html#ad1f172b6c70d1f7f7ae6bdb65338161a">IMP::isd::TALOSRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1UniformPrior.html#a622a3dfdb20d899ae1e3f7beb48a3744">IMP::isd::UniformPrior::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1WeightRestraint.html#a283e1ac525721241431132c20d9142d6">IMP::isd::WeightRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1vonMisesKappaConjugateRestraint.html#aa2a5f596aab6102ef9539094561bb9aa">IMP::isd::vonMisesKappaConjugateRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1vonMisesKappaJeffreysRestraint.html#a935a6da05c9775905a371f07a95ee0fe">IMP::isd::vonMisesKappaJeffreysRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1kernel_1_1Constraint.html#a0acb448044e0bf9c5c40c5599953b236">IMP::kernel::Constraint::do_after_evaluate()</a>, <a href="classIMP_1_1kernel_1_1Constraint.html#a39c87321918cf43c3c87fa7fd4363ee3">IMP::kernel::Constraint::do_update_derivatives()</a>, <a href="classIMP_1_1kernel_1_1DerivativeAccumulator.html#a87b3bca33ac29d4bae64490347682a91">IMP::kernel::DerivativeAccumulator::DerivativeAccumulator()</a>, <a href="classIMP_1_1kernel_1_1PairScore.html#a630ce1d924b8b2f728bde740b22d2fee">IMP::kernel::PairScore::evaluate()</a>, <a href="classIMP_1_1kernel_1_1PairScore.html#aa6ab389ab63b24f1e32a0e8593f5a8b7">IMP::kernel::PairScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1kernel_1_1PairScore.html#a6cd7e1cdda29f1482c7a72e87d9099b6">IMP::kernel::PairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1kernel_1_1PairScore.html#af503989bb181141514e3616babf52305">IMP::kernel::PairScore::evaluate_index()</a>, <a href="classIMP_1_1kernel_1_1PairScore.html#acc6b26d851fd495b37963ffb16aa6a1e">IMP::kernel::PairScore::evaluate_indexes()</a>, <a href="classIMP_1_1kernel_1_1QuadScore.html#a715a8de980d21da1dc31b861fe746356">IMP::kernel::QuadScore::evaluate()</a>, <a href="classIMP_1_1kernel_1_1QuadScore.html#a85e7f0835df1be9e96dfdecd3e16372e">IMP::kernel::QuadScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1kernel_1_1QuadScore.html#aa5a173fc4feb57961c67b114f9775963">IMP::kernel::QuadScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1kernel_1_1QuadScore.html#a79c2b432dd52988d5c21bec6d447e8f4">IMP::kernel::QuadScore::evaluate_index()</a>, <a href="classIMP_1_1kernel_1_1QuadScore.html#a0c2aba753ba5eff9f9373aebe3d64d41">IMP::kernel::QuadScore::evaluate_indexes()</a>, <a href="classIMP_1_1kernel_1_1RestraintSet.html#a2e2a86e1328f2e04ccc401c5ca483fea">IMP::kernel::RestraintSet::unprotected_evaluate()</a>, <a href="classIMP_1_1kernel_1_1ScoreState.html#a826c68d2659a732178a508fbfbc18299">IMP::kernel::ScoreState::after_evaluate()</a>, <a href="classIMP_1_1kernel_1_1ScoreState.html#a488073a947b38c80f0ce7f1549de0087">IMP::kernel::ScoreState::do_after_evaluate()</a>, <a href="classIMP_1_1kernel_1_1SingletonScore.html#a5e6728362848f96275e177442406bebf">IMP::kernel::SingletonScore::evaluate()</a>, <a href="classIMP_1_1kernel_1_1SingletonScore.html#a99ebabc3681b08affe9ec6f4402055e9">IMP::kernel::SingletonScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1kernel_1_1SingletonScore.html#a8e3e2ca582be01d5d3d30ab1a881dd8c">IMP::kernel::SingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1kernel_1_1SingletonScore.html#af2b0b0cac7755bf5dc0193119643ba22">IMP::kernel::SingletonScore::evaluate_index()</a>, <a href="classIMP_1_1kernel_1_1SingletonScore.html#affc270c25a3c38afd958076775dc11d9">IMP::kernel::SingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1kernel_1_1TripletScore.html#a3df19c76c11bb16f07ea4eba16ca5a7e">IMP::kernel::TripletScore::evaluate()</a>, <a href="classIMP_1_1kernel_1_1TripletScore.html#af1ff450c58223ee74dd9795eddf5d8f0">IMP::kernel::TripletScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1kernel_1_1TripletScore.html#a29a84e5b90522c0e0d020e18600d320f">IMP::kernel::TripletScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1kernel_1_1TripletScore.html#a1eeab1dee8f026829f646edb22570364">IMP::kernel::TripletScore::evaluate_index()</a>, <a href="classIMP_1_1kernel_1_1TripletScore.html#ac095d3780e7302304a4afd07bbd987a1">IMP::kernel::TripletScore::evaluate_indexes()</a>, <a href="classIMP_1_1modeller_1_1MultipleBinormalRestraint.html#ae9b755b31c8706c89159cd5f5c1c7d46">IMP::modeller::MultipleBinormalRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1multifit_1_1ComplementarityRestraint.html#a45e971c271abf590164c0abcfe4a49b1">IMP::multifit::ComplementarityRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1multifit_1_1DummyRestraint.html#affa16e2ba9d9d5b915a75556dc35f0bc">IMP::multifit::DummyRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1multifit_1_1RadiusOfGyrationRestraint.html#ad0c7d950074ecb7fdd3ed35878945f3e">IMP::multifit::RadiusOfGyrationRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1multifit_1_1WeightedExcludedVolumeRestraint.html#a65e794477f6b861c20211dd12b8dccc5">IMP::multifit::WeightedExcludedVolumeRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1pmi_1_1CompositeRestraint.html#a028cd8e0a29bf72e5410c6bfa8670df7">IMP::pmi::CompositeRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1pmi_1_1SigmoidRestraintSphere.html#a6a487487ed4abe3ad43f2cefccebdfd9">IMP::pmi::SigmoidRestraintSphere::unprotected_evaluate()</a>, <a href="classIMP_1_1saxs_1_1RadiusOfGyrationRestraint.html#ac797818869c4a4f92b4c51f4f35aad4d">IMP::saxs::RadiusOfGyrationRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1saxs_1_1Restraint.html#a69e3a140dfb935359f83262e10956555">IMP::saxs::Restraint::unprotected_evaluate()</a></td></tr>
191 <tr><td>@ref IMP::kernel::Key</td><td><a href="classIMP_1_1kernel_1_1Key.html#aac9bb4e342b6ce2213d6ec348911443a">IMP::kernel::Key::add_alias()</a>, <a href="classIMP_1_1kernel_1_1ScopedAddCacheAttribute.html#a1db5f418c0098f0e6dc69e2798ec5e2f">IMP::kernel::ScopedAddCacheAttribute::ScopedAddCacheAttribute()</a>, <a href="classIMP_1_1kernel_1_1ScopedAddCacheAttribute.html#ab25b8a051593ef26d399b58c7f1db660">IMP::kernel::ScopedAddCacheAttribute::set()</a>, <a href="classIMP_1_1kernel_1_1ScopedSetAttribute.html#a7331eb389d48ee743e093960a6730c45">IMP::kernel::ScopedSetAttribute::ScopedSetAttribute()</a>, <a href="classIMP_1_1kernel_1_1ScopedSetAttribute.html#af608ed2c60f0aafa29889b115520c9af">IMP::kernel::ScopedSetAttribute::set()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a5536f1effbec7e595f7aaacf1a076eea">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#ae4ad2edfa41d6afb0a60fb129c8a3e70">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a265d5a103e828613bc86a3ae49bd8dbb">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a01fb1f7ade9751fb227788a9710d20e9">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a3c29f8066699269d333aee62e7f37c61">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a58153db897cba0a15653f29dcdb7065c">IMP::misc::CustomXYZR::setup_particle()</a></td></tr>
192 <tr><td>@ref IMP::kernel::Model</td><td><a href="classIMP_1_1atom_1_1Angle.html#a0c2bec3db873b3b4d2b0b9eb29d42e49">IMP::atom::Angle::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a9abe29f726459ba47f4aac0cd45a6422">IMP::atom::Angle::Angle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a6f17e897198250498f3c731e547ca99c">IMP::atom::Angle::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a63d9c956874f958f360d0f35e517a087">IMP::atom::Angle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#ab2447a656e1c29da465f3f88ffc2cc69">IMP::atom::AngleSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#abff2c9cc18193705300fe190a466aff8">IMP::atom::AngleSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a650571025343dacfefda104d10ed00c1">IMP::atom::AngleSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a0a406eac77fe3e277b814639d947942a">IMP::atom::AngleSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a1f02e81ea574a455e5494b4f15e1882e">IMP::atom::Atom::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#af14a86aba6d844bf959566fcd5a5daab">IMP::atom::Atom::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#ac189b1c9e2ce08293a123a3acad75728">IMP::atom::Atom::Atom()</a>, <a href="classIMP_1_1atom_1_1Atom.html#abdece52df81b9e5285f8330cc8f40efe">IMP::atom::Atom::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Atom.html#abd5014bfa4ce1840322f1b9337966db7">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#acca5fca63715a18614fc64d14ca5d788">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Bond.html#a2b7610c3e690f9aecadc2f7212216897">IMP::atom::Bond::Bond()</a>, <a href="classIMP_1_1atom_1_1Bond.html#ad2ec3bd1bcc7ad283c360f7c58658bca">IMP::atom::Bond::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1BondEndpointsRefiner.html#ad94833a1f040145775968a914b0f28f6">IMP::atom::BondEndpointsRefiner::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#aabc0f99a8709f132433132ae74954eea">IMP::atom::BondSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#ad6089666d6fa114e3f6554cb3eb38760">IMP::atom::BondSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#ade1e43a036f076d638c1050d2412cf27">IMP::atom::BondSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#afb15c9170d376019812460f41ea56f2f">IMP::atom::BondSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#a70e934db89624dd4b412db0374947402">IMP::atom::Bonded::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#a5e5b8519ff950cb38d5fd8541a963e81">IMP::atom::Bonded::Bonded()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#a533a86e427de469baa8ffdbce22a5d69">IMP::atom::Bonded::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#a00f95654c5ef950a9a3e70cbd8c36cdd">IMP::atom::Bonded::setup_particle()</a>, <a href="classIMP_1_1atom_1_1BondedPairFilter.html#ae019b8756c90df8c2d2cb4fe19cb7f45">IMP::atom::BondedPairFilter::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BondedPairFilter.html#a75c2b2f3aa8c79d4c7169b85e334a4ba">IMP::atom::BondedPairFilter::get_value_index()</a>, <a href="classIMP_1_1atom_1_1BondedPairFilter.html#ab7d76b03e6d1072a54870128777f789a">IMP::atom::BondedPairFilter::get_value_index()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamics.html#af7912612ba11288f840e297d988ce098">IMP::atom::BrownianDynamics::BrownianDynamics()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#a7e5b5d04292a324489e749e1e7712070">IMP::atom::CHARMMAtom::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#a1f776cde8d2a468e032d2e19138b2e8c">IMP::atom::CHARMMAtom::CHARMMAtom()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#a26e844e4461fa1dbb2fe1997564cb8c8">IMP::atom::CHARMMAtom::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#a518cb224c569c5ea896c4a8f37725875">IMP::atom::CHARMMAtom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aa146bec02d74a3610fcb85b2087c6bc5">IMP::atom::CHARMMTopology::create_hierarchy()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a817763ee5bfe3cc2b66e3f231c63e0a8">IMP::atom::CenterOfMass::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a75dc2128ae8fad6e556a6b4042a77ad6">IMP::atom::CenterOfMass::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a5d69154caa825ff93e1a7a972b4c44d4">IMP::atom::CenterOfMass::CenterOfMass()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a06c15e0236d6c1689f60339a651ab384">IMP::atom::CenterOfMass::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a07498f969c3bd3ca8bcbf95ca3163b4f">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#aa06c2dc77563750d00144f58c25fed30">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a01652eadb5bfdc9ca7c7b8f31124b156">IMP::atom::Chain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a7d755e8f3428fa52cdd19e6383b05280">IMP::atom::Chain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a99932fe4fe7be6d68fc1e823443f38bb">IMP::atom::Chain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a2c34e8e1a3ba8cee01684232f851c79b">IMP::atom::Chain::Chain()</a>, <a href="classIMP_1_1atom_1_1Chain.html#afd235f4c0252530dfdfd39ab48729cf4">IMP::atom::Chain::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Chain.html#af9bc5e16a6e3716eda480db82bac872c">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a2b95569c0d50a680066ac4c931139144">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#afb3582455ead3991c70d4c9271c51483">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Charged.html#a78567f6cf570c78ddef3d67ad9ec1ba3">IMP::atom::Charged::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Charged.html#a1e4bbedcbc52efe9d44895c2bca9859c">IMP::atom::Charged::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Charged.html#a6e5a15c7368ab94f1185397a8393736c">IMP::atom::Charged::Charged()</a>, <a href="classIMP_1_1atom_1_1Charged.html#aa066c9118112290f19b669feb57657ac">IMP::atom::Charged::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Charged.html#ac9e00ae20d9dfa373e3cc95987b8a298">IMP::atom::Charged::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Charged.html#aea59db6193f503dfbf84d52025ab63af">IMP::atom::Charged::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Copy.html#a038aff5df94e44ee64172a775539caa3">IMP::atom::Copy::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Copy.html#a7f76e9cc2136310b196d071ef8126426">IMP::atom::Copy::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Copy.html#ae9f21916126276b071e6fa186ccb1a9f">IMP::atom::Copy::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Copy.html#a6b2aa055de3a6dad3c54b227ce419017">IMP::atom::Copy::Copy()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#a70af866b212ce09b410de004b9631058">IMP::atom::CoulombPairScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#a51f1439e186cb2e07b67256364bbffbd">IMP::atom::CoulombPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#a944c8f13dcd0e5a9f17818267b6df1ad">IMP::atom::CoulombPairScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#a1671a9200ee76d8d79fd3d30bc29ff3b">IMP::atom::CoulombPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1CoverBond.html#a71d64d5366e006c57bf5a90fa32e932b">IMP::atom::CoverBond::apply_index()</a>, <a href="classIMP_1_1atom_1_1CoverBond.html#ad42e67780c818b8bdef31406910f5e04">IMP::atom::CoverBond::apply_indexes()</a>, <a href="classIMP_1_1atom_1_1CoverBond.html#a2c4edb0d15faceaa62203407c236c364">IMP::atom::CoverBond::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1CoverBond.html#a4bf334420d46bd96c527e3db0c5b3a20">IMP::atom::CoverBond::do_get_outputs()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#a8915c88150afffe3179d11b783e5ae74">IMP::atom::Diffusion::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#aa1e30e4e1796ded48d324690afc727a9">IMP::atom::Diffusion::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#a05bd17e29274fe373f7a86278c253b21">IMP::atom::Diffusion::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#aa807ebebbf64f7c0c62e400be3a7b964">IMP::atom::Diffusion::Diffusion()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#a00a1838715250ef7ee14ae94cafe091a">IMP::atom::Diffusion::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#a0f9946e5a9414bd6b2bb1d61833627b8">IMP::atom::Diffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#aaea5351188277c7df4e53261741efa03">IMP::atom::Diffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#a83010834e7ff4443b97e11ccfc9255f6">IMP::atom::Diffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a358de23aff9901f1e49cefdd0967e9a3">IMP::atom::Dihedral::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a90071f4e6c19ea7ba5597eb497b3e11d">IMP::atom::Dihedral::Dihedral()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a58f0f9a44207b57d38d91e67538f0764">IMP::atom::Dihedral::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a3cb4c03e2291bd27f55d33cf85f3b886">IMP::atom::Dihedral::setup_particle()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#afc173df050df65fd630e90c8c3e44e10">IMP::atom::DihedralSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a471df902ea7b72e0bb70fa39496e1f0c">IMP::atom::DihedralSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a8fe8861782ed3ad50a780e947b6a6055">IMP::atom::DihedralSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a9b036c3cab6fd2b9b74be27d6bbb62dc">IMP::atom::DihedralSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1Domain.html#aa7b8eab8f4422e95f5e8d68e2bb9eaa2">IMP::atom::Domain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#affc45f2a7390a38ee6a71ea222d2d937">IMP::atom::Domain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#a8673ff4cc4f8226c9a72788a2a09721a">IMP::atom::Domain::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Domain.html#aa681be58da92a7bcf73c8de91b320d57">IMP::atom::Domain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#a44da187d7acbcac3cdf82df296961f34">IMP::atom::Domain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#a60ade3ef83522140c9ab69551a2c11c5">IMP::atom::Domain::Domain()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#afcf187e7d86c88bbd17648807ff3668d">IMP::atom::Fragment::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#a706b5dd2c1780a6581e9a06c894555df">IMP::atom::Fragment::do_setup_particle()</a>, <a 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href="classIMP_1_1core_1_1DerivativesFromRefined.html#aa646b4d393ec09369eb76adef64fec43">IMP::core::DerivativesFromRefined::apply_indexes()</a>, <a href="classIMP_1_1core_1_1DerivativesFromRefined.html#a6606728e38866fe9b9d25d567038be53">IMP::core::DerivativesFromRefined::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1DerivativesFromRefined.html#a01284d4386b7a8c57c566830c2713bab">IMP::core::DerivativesFromRefined::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#ab733fdf9860005fbc19d9d9eb2868004">IMP::core::DerivativesToRefined::apply_index()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#a4352ecb0288b7aeb10b78f65b53bec9a">IMP::core::DerivativesToRefined::apply_indexes()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#a82fa3d37977f6eacbbf02b4bf81a280c">IMP::core::DerivativesToRefined::do_get_inputs()</a>, <a 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href="classIMP_1_1core_1_1LeavesRefiner.html#a3deb0cba5c2cd09d55c58a77e8a701e5">IMP::core::LeavesRefiner::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1MCCGSampler.html#a7f376da66e5aa594cf0903b977fdf312">IMP::core::MCCGSampler::MCCGSampler()</a>, <a href="classIMP_1_1core_1_1MonteCarlo.html#a38f12c2f5740273ae7041939a2a2bfb6">IMP::core::MonteCarlo::MonteCarlo()</a>, <a href="classIMP_1_1core_1_1MonteCarloMover.html#a178a1c2d62fcd260da76dc7afdf1c7b7">IMP::core::MonteCarloMover::MonteCarloMover()</a>, <a href="classIMP_1_1core_1_1NearestNeighborsClosePairsFinder.html#a8d9ccccc2c6a737e54c00b4b36897250">IMP::core::NearestNeighborsClosePairsFinder::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1NearestNeighborsClosePairsFinder.html#a851d2b55e35b43fe5d7c18b60dddc68c">IMP::core::NearestNeighborsClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1NearestNeighborsClosePairsFinder.html#a5459615a2b411230bb3962819dc6c9b4">IMP::core::NearestNeighborsClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1NonRigidMember.html#aa6e3228c6c3b22073511f78e0e8609d3">IMP::core::NonRigidMember::NonRigidMember()</a>, <a href="classIMP_1_1core_1_1NonRigidMember.html#a650a002ec77d21c253949b10c5c416e9">IMP::core::NonRigidMember::get_is_setup()</a>, <a href="classIMP_1_1core_1_1NormalMover.html#ab6477aee65a6f52171e7295e06278adc">IMP::core::NormalMover::NormalMover()</a>, <a href="classIMP_1_1core_1_1NormalMover.html#a07b6ab88f640e38c20390307d441c405">IMP::core::NormalMover::NormalMover()</a>, <a href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#a5c9c43de73666eba80eea2a6983be9b0">IMP::core::NormalizedSphereDistancePairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#a1fcbdbdadec33f569f316215bdabfeb0">IMP::core::NormalizedSphereDistancePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#a4ea41ea99f1a2eb565180c1755d02d5e">IMP::core::NormalizedSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#ad8dc68d9202326742a6ef900acd79e9e">IMP::core::NormalizedSphereDistancePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1OrderedTypePairPredicate.html#abc3bf5c976057efdd3a306ff653a921f">IMP::core::OrderedTypePairPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1OrderedTypePairPredicate.html#ab0e8e856c9abd9ccbb821af32efbc484">IMP::core::OrderedTypePairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1OrderedTypePairPredicate.html#a39de8c3649be2575c66902681a936704">IMP::core::OrderedTypePairPredicate::get_value_index()</a>, <a 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href="classIMP_1_1core_1_1OrderedTypeTripletPredicate.html#ace8147de34ba07dbf2033f1227668177">IMP::core::OrderedTypeTripletPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1OrderedTypeTripletPredicate.html#ac34cda6e2b6b6e4f10f49e7b2b9d66e8">IMP::core::OrderedTypeTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1OrderedTypeTripletPredicate.html#ab3558de3e3eeec65bd940ab5ba43d5ba">IMP::core::OrderedTypeTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1PairConstraint.html#a2054cb2895d90c474fef16856c262ef6">IMP::core::PairConstraint::PairConstraint()</a>, <a href="classIMP_1_1core_1_1PairRestraint.html#a8a2032099b9ca936b285a91981566093">IMP::core::PairRestraint::PairRestraint()</a>, <a href="classIMP_1_1core_1_1PredicateSingletonScore.html#a041f8317f8d3ef0e6627f21de2733c19">IMP::core::PredicateSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1PredicateSingletonScore.html#aa348cb8e44ff457612b8d5a89e325cc6">IMP::core::PredicateSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1PredicateSingletonScore.html#a51d87a31d9b4ba406ba83e43eeb55f66">IMP::core::PredicateSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1PredicateSingletonScore.html#aab090db9c45b65ffaeae83ec6894e2b3">IMP::core::PredicateSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1QuadConstraint.html#a8cab020f6af1cc18c1b59309a34187ab">IMP::core::QuadConstraint::QuadConstraint()</a>, <a href="classIMP_1_1core_1_1QuadRestraint.html#a5fc2cadbe62cd7f922201e7c06241121">IMP::core::QuadRestraint::QuadRestraint()</a>, <a href="classIMP_1_1core_1_1QuadraticClosePairsFinder.html#a55a8ae581d31c15682618fd9d064f710">IMP::core::QuadraticClosePairsFinder::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1QuadraticClosePairsFinder.html#a8720470a219eec8548c9207db937afbc">IMP::core::QuadraticClosePairsFinder::get_are_close()</a>, <a href="classIMP_1_1core_1_1QuadraticClosePairsFinder.html#aacaca748df8a5f3f9a9f1dc46469315d">IMP::core::QuadraticClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1QuadraticClosePairsFinder.html#a60cc49be86e21ca4b5dc0b3d1dd391bb">IMP::core::QuadraticClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1Reference.html#a6c473bb38d3ff346656e8cf603b6d0b0">IMP::core::Reference::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Reference.html#a11b9d8f512e31db3309083bc3e2fb0ec">IMP::core::Reference::Reference()</a>, <a href="classIMP_1_1core_1_1Reference.html#a341c312c259a461bd742452247570780">IMP::core::Reference::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Reference.html#ad9a2510e4cbd4392393e15cf43f48950">IMP::core::Reference::setup_particle()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#aba05db702083b7e4c41853c211958186">IMP::core::RefinedPairsPairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#ac3d6bce210396605193004f034156240">IMP::core::RefinedPairsPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#ab6536f0e1fd858ded1239673fab7c53e">IMP::core::RefinedPairsPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#a51d49f4a4b47882bf20a778030d0a52f">IMP::core::RefinedPairsPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a6d174083c79ddd582cc07c2ef8954a32">IMP::core::RigidBody::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a374fd139b4809108f4052367ed7b9736">IMP::core::RigidBody::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a5cbc3824279e37c40fbc65b037e0424c">IMP::core::RigidBody::RigidBody()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ad4024d8ac40d4c14b480f0d2bbf5c341">IMP::core::RigidBody::get_is_setup()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ae678bfb4d66a2934b449f3079989d65e">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a8886b4deabe13472bf227ae012ce2595">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBodyMember.html#a885b1599a86dc2751423c102738e372b">IMP::core::RigidBodyMember::RigidBodyMember()</a>, <a href="classIMP_1_1core_1_1RigidBodyMember.html#a3cc86dc6aa5d02aad989100bce5aa30a">IMP::core::RigidBodyMember::get_is_setup()</a>, <a href="classIMP_1_1core_1_1RigidBodyMover.html#a24ed7b4536fb525039b85ed6f718c927">IMP::core::RigidBodyMover::RigidBodyMover()</a>, <a href="classIMP_1_1core_1_1RigidBodyTunneler.html#af24ca26b450dca88d2b53c698e768582">IMP::core::RigidBodyTunneler::RigidBodyTunneler()</a>, <a 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href="classIMP_1_1core_1_1WeightedDerivativesToRefined.html#ac65dd93e535195a26438e4b00bdc325f">IMP::core::WeightedDerivativesToRefined::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1WeightedDerivativesToRefined.html#a16ce595c17ce70459d3612687de11116">IMP::core::WeightedDerivativesToRefined::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1WeightedSphereDistancePairScore.html#a928ece55a50d0976b8e79d4f84eb2471">IMP::core::WeightedSphereDistancePairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1WeightedSphereDistancePairScore.html#a3bf749f59bdb7db67c66fa8b1540760d">IMP::core::WeightedSphereDistancePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1WeightedSphereDistancePairScore.html#a4174eb63688a5a812824f7884b1a139f">IMP::core::WeightedSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1WeightedSphereDistancePairScore.html#a0c330412519fe6609254531a13e6cc7f">IMP::core::WeightedSphereDistancePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1XYZ.html#ab29d91cf7a7ee189ec0a1ee0ddbfb3c6">IMP::core::XYZ::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZ.html#ab56828846a1a12bf56985637e8246927">IMP::core::XYZ::get_is_setup()</a>, <a href="classIMP_1_1core_1_1XYZ.html#a330a6bb6ec6126cae1b4e0fb5bf73101">IMP::core::XYZ::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZ.html#a01a20d5f64e90ac6e4d640596e7ea7da">IMP::core::XYZ::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZ.html#ab2970a56a626d63de50fb37644e5efd8">IMP::core::XYZ::XYZ()</a>, <a href="classIMP_1_1core_1_1XYZR.html#ae725e6af277a5ced81808e0ed0cef3b7">IMP::core::XYZR::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#ab579ffda147dc94341eba333e491f92e">IMP::core::XYZR::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a0175e29dffd8377f7e34dd3cfe999087">IMP::core::XYZR::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a5267c4d8d2ddcbad1f11866b71143e89">IMP::core::XYZR::XYZR()</a>, <a href="classIMP_1_1core_1_1XYZR.html#abdbf34096e3d265bae65a305e71c3ca6">IMP::core::XYZR::get_is_setup()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a3e2e4782309fa9f88ea528990a2d4f3d">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a73655826f4e1f9158b004b00b3090537">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#adedc98cf7f73a7f29887d37f83066afe">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1display_1_1Colored.html#aed4375669ca927e91b06b4ef4b30ad4f">IMP::display::Colored::do_setup_particle()</a>, <a href="classIMP_1_1display_1_1Colored.html#aeca6bee5f8426f10112ac3b31e7c0c53">IMP::display::Colored::Colored()</a>, <a href="classIMP_1_1display_1_1Colored.html#a07710cfeb3e805d324bb01e396d597bd">IMP::display::Colored::get_is_setup()</a>, <a href="classIMP_1_1display_1_1Colored.html#ae61a8919949f06a3aa4847d7fb8d9e8e">IMP::display::Colored::setup_particle()</a>, <a href="classIMP_1_1display_1_1RestraintGeometry.html#a8d29dbc06176c8b4e3234bdd7b9a744d">IMP::display::RestraintGeometry::RestraintGeometry()</a>, <a href="classIMP_1_1display_1_1WriteOptimizerState.html#ae6c732748702a5ddfe3729c9f0389d33">IMP::display::WriteOptimizerState::WriteOptimizerState()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundSampler.html#ad3b7e6b5335f75d56fcd1e8989166f9d">IMP::domino::BranchAndBoundSampler::BranchAndBoundSampler()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundSampler.html#a7b20b50a372ea47e176ac7d3ab2fec0b">IMP::domino::BranchAndBoundSampler::BranchAndBoundSampler()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#ac9a3dc57af62432767395067b932cce3">IMP::domino::DiscreteSampler::DiscreteSampler()</a>, <a href="classIMP_1_1domino_1_1DominoSampler.html#acebd71a5066ae81da34fb120443f8357">IMP::domino::DominoSampler::DominoSampler()</a>, <a href="classIMP_1_1domino_1_1DominoSampler.html#abce5488102b6313b9edd39c2ccdef0b8">IMP::domino::DominoSampler::DominoSampler()</a>, <a href="classIMP_1_1em2d_1_1Em2DRestraint.html#afa25f2d0c9d7ea93a8adff957bcf51a7">IMP::em2d::Em2DRestraint::Em2DRestraint()</a>, <a href="classIMP_1_1em2d_1_1Fine2DRegistrationRestraint.html#ae9e202aa133302b645199d134da360c3">IMP::em2d::Fine2DRegistrationRestraint::Fine2DRegistrationRestraint()</a>, <a href="classIMP_1_1em2d_1_1Fine2DRegistrationRestraint.html#a67370df5b0c459a94053130e8a6a07ae">IMP::em2d::Fine2DRegistrationRestraint::setup()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#ae8c357f7a85ce6f0eab81cb233ae38f8">IMP::em2d::ProjectionParameters::do_setup_particle()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#a4189e6aa3e725ff10ddb08e0b4a6e230">IMP::em2d::ProjectionParameters::ProjectionParameters()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#aae304202bb8cf7233def4b9f8f62e014">IMP::em2d::ProjectionParameters::set_proper_ranges_for_keys()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#af387417efadeb278cc9ca29aca7332e4">IMP::em2d::ProjectionParameters::get_is_setup()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#ac34926d55261f24dbcb6303fa586abc4">IMP::em2d::ProjectionParameters::setup_particle()</a>, <a href="classIMP_1_1em_1_1Voxel.html#a4c2eafc1cd9a9cab47465b0f6df688cb">IMP::em::Voxel::do_setup_particle()</a>, <a href="classIMP_1_1em_1_1Voxel.html#acc9efb02c225bd7fc8db0116bafb2c6c">IMP::em::Voxel::get_is_setup()</a>, <a href="classIMP_1_1em_1_1Voxel.html#af5bd059cbf3e64ee2867ba3362086523">IMP::em::Voxel::setup_particle()</a>, <a href="classIMP_1_1em_1_1Voxel.html#a0674ecb8bee6bbf165e35b4e5588c949">IMP::em::Voxel::Voxel()</a>, <a href="classIMP_1_1example_1_1ExampleDecorator.html#a2d03967727875cf623604fec5ea930c2">IMP::example::ExampleDecorator::do_setup_particle()</a>, <a href="classIMP_1_1example_1_1ExampleDecorator.html#a34a371466a0cd1fc232ca326b5dbcd42">IMP::example::ExampleDecorator::get_is_setup()</a>, <a href="classIMP_1_1example_1_1ExampleDecorator.html#a06bb1fd227c9297b841d3c5e279d5b49">IMP::example::ExampleDecorator::setup_particle()</a>, <a href="classIMP_1_1example_1_1ExampleDecorator.html#add3828f673d3ac89bdd837d5750bf977">IMP::example::ExampleDecorator::ExampleDecorator()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#a2a5e881dc3bf40e8016e84a412b2c129">IMP::example::ExamplePairScore::do_get_inputs()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#acd1cdd0aeeed842ec2799a51bf9430a9">IMP::example::ExamplePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#ae6ec7ef81689c35265f57b748a3675c9">IMP::example::ExamplePairScore::evaluate_index()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#a9070605d3048da001bc7a37fd8a5a775">IMP::example::ExamplePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1example_1_1ExampleRestraint.html#a49a82c11d1d5e3341dd694f350a3fbd6">IMP::example::ExampleRestraint::ExampleRestraint()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#a7f4fcc9b706074383d96fb8dd000b2d7">IMP::example::ExampleSingletonModifier::apply_index()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#abfa723a033aee6dee0124650228c8a95">IMP::example::ExampleSingletonModifier::apply_indexes()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#a00f6c233aac8f0f5ae2fc93631206329">IMP::example::ExampleSingletonModifier::do_get_inputs()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#a0348f8030e88df1443a9352af2c016a3">IMP::example::ExampleSingletonModifier::do_get_outputs()</a>, <a href="classIMP_1_1gsl_1_1ConjugateGradients.html#a450a66908b2144a086843df01db24e95">IMP::gsl::ConjugateGradients::ConjugateGradients()</a>, <a href="classIMP_1_1gsl_1_1GSLOptimizer.html#a217dc5ae983b5a3812cdce6f5a958175">IMP::gsl::GSLOptimizer::GSLOptimizer()</a>, <a href="classIMP_1_1gsl_1_1QuasiNewton.html#a5db583f97a00be6ecbea53fc6e5b499d">IMP::gsl::QuasiNewton::QuasiNewton()</a>, <a href="classIMP_1_1gsl_1_1Simplex.html#ab4f87f49b063ef3c2a0e9f8a4abe0b0e">IMP::gsl::Simplex::Simplex()</a>, <a href="classIMP_1_1isd_1_1AmbiguousNOERestraint.html#ac4ba7253a939b4a86978febfab4a7ce4">IMP::isd::AmbiguousNOERestraint::AmbiguousNOERestraint()</a>, <a href="classIMP_1_1isd_1_1AmbiguousRestraint.html#a938caaca683e045e9bbf97269112a72b">IMP::isd::AmbiguousRestraint::AmbiguousRestraint()</a>, <a href="classIMP_1_1isd_1_1AmbiguousRestraint.html#aa5643e9c855f323b7f2182a86bd7b44f">IMP::isd::AmbiguousRestraint::AmbiguousRestraint()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#ae1e98163ffed0dca74cf7579318768d2">IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#a26757b4c5f6c39ea35a39d2d6f16f69f">IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#a5540f754155a16a03747d90f69b0b528">IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint()</a>, <a href="classIMP_1_1isd_1_1GaussianProcessInterpolationRestraint.html#a9111f94a0df18602d5d31ea8de9df14e">IMP::isd::GaussianProcessInterpolationRestraint::GaussianProcessInterpolationRestraint()</a>, <a href="classIMP_1_1isd_1_1HybridMonteCarlo.html#ab986acecb52ae1a27a096b2b51128a0e">IMP::isd::HybridMonteCarlo::HybridMonteCarlo()</a>, <a href="classIMP_1_1isd_1_1LogWrapper.html#a68610d564b0c03d3d45a58d085a85773">IMP::isd::LogWrapper::LogWrapper()</a>, <a href="classIMP_1_1isd_1_1LogWrapper.html#a5c144b2354e44e3e4474081c1bcb5363">IMP::isd::LogWrapper::LogWrapper()</a>, <a href="classIMP_1_1isd_1_1MarginalHBondRestraint.html#a7fc09aebc39ac6751d44b4fa7f2997d2">IMP::isd::MarginalHBondRestraint::MarginalHBondRestraint()</a>, <a href="classIMP_1_1isd_1_1MarginalNOERestraint.html#a58a73a53500acfe28777ac061fb8f632">IMP::isd::MarginalNOERestraint::MarginalNOERestraint()</a>, <a href="classIMP_1_1isd_1_1MolecularDynamics.html#ac26748466f25fc232da831b15a4358e4">IMP::isd::MolecularDynamics::MolecularDynamics()</a>, <a href="classIMP_1_1isd_1_1MolecularDynamicsMover.html#a560e26cfed1692342f59a47e5b42f670">IMP::isd::MolecularDynamicsMover::MolecularDynamicsMover()</a>, <a href="classIMP_1_1isd_1_1NOERestraint.html#acfade8076c22cb61d90614b182d5da44">IMP::isd::NOERestraint::NOERestraint()</a>, <a 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href="classIMP_1_1misc_1_1CustomXYZR.html#a265d5a103e828613bc86a3ae49bd8dbb">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a58153db897cba0a15653f29dcdb7065c">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1LogPairScore.html#ac2d8a61583e1a741d0bfcd692d8cfdd2">IMP::misc::LogPairScore::do_get_inputs()</a>, <a href="classIMP_1_1misc_1_1LogPairScore.html#ac63899594d3caebf37b35954b4bd53f1">IMP::misc::LogPairScore::evaluate_index()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#a3af3b60a4b11ce687e517610b4fa1d4c">IMP::misc::LowestRefinedPairScore::do_get_inputs()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#abebae85896653903db475c215ccbe371">IMP::misc::LowestRefinedPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#a677ec8f87f21f3b2e5bb99e13d5154a7">IMP::misc::LowestRefinedPairScore::evaluate_index()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#af8f429385834a2b18cdb68c98d0f7130">IMP::misc::LowestRefinedPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1misc_1_1MetricClosePairsFinder.html#a2f22372fc9f67a93bb77478af1617254">IMP::misc::MetricClosePairsFinder::get_close_pairs_internal()</a>, <a href="classIMP_1_1misc_1_1MetricClosePairsFinder.html#abdf2fbd29c10c6305cd30ff8a4a99153">IMP::misc::MetricClosePairsFinder::get_close_pairs_internal()</a>, <a href="classIMP_1_1misc_1_1MetricClosePairsFinder.html#a60ef4837a84e0a08b796f06c9cd74906">IMP::misc::MetricClosePairsFinder::get_close_pairs_internal()</a>, <a href="classIMP_1_1misc_1_1MetricClosePairsFinder.html#aaeb39a15ad6645bf03473122857d5c86">IMP::misc::MetricClosePairsFinder::get_index()</a>, <a href="classIMP_1_1misc_1_1MetricClosePairsFinder.html#aaedf80409d2b2db5fdacc4433ab65ae4">IMP::misc::MetricClosePairsFinder::do_get_inputs()</a>, <a href="classIMP_1_1misc_1_1MetricClosePairsFinder.html#a70c40a97c2fa1b16ffadbfb61b5aff89">IMP::misc::MetricClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1misc_1_1MetricClosePairsFinder.html#ab3e084ff82b90bcad2c0f6fccfe7662b">IMP::misc::MetricClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#a07170a099da8a669e6eb59e1bc941404">IMP::misc::SoftCylinderPairScore::do_get_inputs()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#ae8c3da39efbfc7d02074427c79af4ace">IMP::misc::SoftCylinderPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#ac93a6cfc558a16532cd9f743a33ca26b">IMP::misc::SoftCylinderPairScore::evaluate_index()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#a99937d7eae78aededee1aec71777e5df">IMP::misc::SoftCylinderPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1misc_1_1StateAdaptor.html#a50a63740e10cacb49378b50312ab5ff8">IMP::misc::StateAdaptor::StateAdaptor()</a>, <a href="classIMP_1_1multifit_1_1AnchorsData.html#a622384f53f11d518a32054e23c62a00c">IMP::multifit::AnchorsData::setup_secondary_structure()</a>, <a href="classIMP_1_1pmi_1_1CompositeRestraint.html#a55c398ef529347aa33425d3fbf55dbb2">IMP::pmi::CompositeRestraint::CompositeRestraint()</a>, <a href="classIMP_1_1pmi_1_1Resolution.html#a43a16d56c78530b261c3a005f690f4b3">IMP::pmi::Resolution::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Resolution.html#a53d017260792799bdf2c60253e1a686f">IMP::pmi::Resolution::Resolution()</a>, <a href="classIMP_1_1pmi_1_1SigmoidRestraintSphere.html#a07bf22f2814d86f43e0e71a662fd346b">IMP::pmi::SigmoidRestraintSphere::SigmoidRestraintSphere()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#ad525fd60aa8680a457e23397c2476eb1">IMP::pmi::Symmetric::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#a5953f9bf4ad5f01b8906a33211494ce8">IMP::pmi::Symmetric::Symmetric()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#ab9f5951296553084c4b54fb89f5b32da">IMP::pmi::TransformMover::TransformMover()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#a395bb1b7e141ecc8d857a9b4ce734e00">IMP::pmi::TransformMover::TransformMover()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#ab9139b4882cf1867b9759f068512e843">IMP::pmi::Uncertainty::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#ad7bd7fd5c725f6102b50900eef8bbb57">IMP::pmi::Uncertainty::Uncertainty()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#a8eeeb2e723c086791b59e65b34e36d80">IMP::rmf::HierarchyLoadLink::add_link_recursive()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#abe0d6ce9bbee510bfc29c0ce9a1f6d8e">IMP::rmf::HierarchyLoadLink::create_recursive()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#add7114279d7ee3371b052d7b2ad3e99a">IMP::rmf::HierarchyLoadLink::do_create()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#a4e40546986b0dc63b8467f282919e5e8">IMP::rmf::HierarchyLoadLink::do_link_particle()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#a84b0c66b5fff2807cb70c3c36c9f7379">IMP::rmf::HierarchyLoadLink::do_load_hierarchy()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#afe965c995507e717123a7ef2ab4038fe">IMP::rmf::HierarchyLoadLink::do_setup_particle()</a>, <a href="classIMP_1_1rmf_1_1SaveOptimizerState.html#a33fb072e426905196b216c175d8046cc">IMP::rmf::SaveOptimizerState::SaveOptimizerState()</a>, <a href="classIMP_1_1rmf_1_1SimpleLoadLink.html#af31b2104ac1e3e3862ff03020b850288">IMP::rmf::SimpleLoadLink::do_create()</a>, <a href="classIMP_1_1rmf_1_1SimpleLoadLink.html#a5fdf2b7e30282dddb88de9ee4cb47af6">IMP::rmf::SimpleLoadLink::create()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#a11ae5dc29fbe5170be160f3dd24cf95a">IMP::score_functor::AddScores::get_inputs()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#aee21f4a20638827ddd81294faef862b4">IMP::score_functor::AddScores::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#a322efefec3bd1aff867221582aca8db0">IMP::score_functor::AddScores::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#add1bf87841d6edc68a610c0ac07eed79">IMP::score_functor::AddScores::get_score()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#ac83905ff1ddd74aea476066e18792364">IMP::score_functor::AddScores::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#ab42c905aef5f15f3dc84c6d494aeea99">IMP::score_functor::DistancePairScore::do_get_inputs()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#ad98e4cd326267c1481f0b18f318079ed">IMP::score_functor::DistancePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#ad4bcede3ec86019e31b02474a518deff">IMP::score_functor::DistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#a2147cc54fd619086e37d22c317ba59d4">IMP::score_functor::DistancePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1score__functor_1_1Harmonic.html#af377b7cbf55e104eccb1581803b2ac67">IMP::score_functor::Harmonic::get_score()</a>, <a href="classIMP_1_1score__functor_1_1Harmonic.html#a2af784c86e739e77abd46b4805c33ed6">IMP::score_functor::Harmonic::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#a29d438dde0771932178078208b1b13fc">IMP::score_functor::HarmonicLowerBound::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#a2d821b402df9dd99ed3a0883bacb4587">IMP::score_functor::HarmonicLowerBound::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#a91e616d213c2137eb0515461fb89a60f">IMP::score_functor::HarmonicLowerBound::get_score()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#a4be1d95e4f0429120de6138e68c07e7c">IMP::score_functor::HarmonicLowerBound::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicUpperBound.html#aa020645b78d825313ad7b51f03671dd2">IMP::score_functor::HarmonicUpperBound::get_score()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicUpperBound.html#a172a58beac89a0fc4121898d29df0e93">IMP::score_functor::HarmonicUpperBound::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#aa387607d984c8699f6702625dcbeb92c">IMP::score_functor::LinearLowerBound::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#a49d48cd27830e2c8d414ab3e1d4a9811">IMP::score_functor::LinearLowerBound::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#a4b72334997737b255f2ef0613a266602">IMP::score_functor::LinearLowerBound::get_score()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#ad8620337b62f86a717db16e5f68e355c">IMP::score_functor::LinearLowerBound::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#af8b6a7b7a999063db7489c121c7a8243">IMP::score_functor::OpenCubicSpline::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#aded05aa3cfec1730a7eb684fb990d581">IMP::score_functor::OpenCubicSpline::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#a2ee2e2dc06741ce79b6215b619cddfe1">IMP::score_functor::OpenCubicSpline::get_score()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#a832cf1b36efc9d16a04c10ac272c67ba">IMP::score_functor::OpenCubicSpline::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#a3d239599ee034854f5d3d2a5c7eb8f0c">IMP::score_functor::OrientedSoap::get_inputs()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#a3a7aeb3363d73facc8d30aa726e950af">IMP::score_functor::OrientedSoap::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#afd81d695cb19ff3faa31ba3539f8d13f">IMP::score_functor::OrientedSoap::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#a6d5c8ba69379e4f51cd4829a1089cc7b">IMP::score_functor::OrientedSoap::get_score()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#ae516bd22a59d95b339f2731d42aa39fc">IMP::score_functor::OrientedSoap::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#af79c80d2b2692580299f1b40574d2e0e">IMP::score_functor::Shift::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#a7bb8bb363d32ecd7ac801ff4f5bf1090">IMP::score_functor::Shift::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#a26d46440841618f9eacec9cda9257716">IMP::score_functor::Shift::get_score()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#a548926aa847e2ea40466dac9b83ccd43">IMP::score_functor::Shift::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1SingletonStatistical.html#aa279b3485846f4f41637d6b50213d3c5">IMP::score_functor::SingletonStatistical::get_score()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a314709d5c92cd0d13a92c0c2c2713a55">IMP::score_functor::SphereDistance::get_rsum()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a2064930f07606d402fa12656bce40fed">IMP::score_functor::SphereDistance::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a9902dc11f6e2cbec8d6db6895afbe938">IMP::score_functor::SphereDistance::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a367f590bcbb5b13bf9effd79f6c46b12">IMP::score_functor::SphereDistance::get_score()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a6b3917980e91a4be251d95f6dcdcaa4e">IMP::score_functor::SphereDistance::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#a4942e336c36130e9bc483dcd3e2bc8d0">IMP::score_functor::Statistical::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#aa83789401cafc81c8e7d811dc42fa462">IMP::score_functor::Statistical::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#ae4e90c260beea02b6d9880a20477176e">IMP::score_functor::Statistical::get_score()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#a07631071763a11077f020605137dafcd">IMP::score_functor::Statistical::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1UnaryFunctionEvaluate.html#a4c031c07ab4e3ff130ba1a1b696e194b">IMP::score_functor::UnaryFunctionEvaluate::get_score()</a>, <a href="classIMP_1_1score__functor_1_1UnaryFunctionEvaluate.html#ab80bfb4ff7e064bc3f760f27a1639a71">IMP::score_functor::UnaryFunctionEvaluate::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1WeightScore.html#aa3c8c81ebfc8ab781fb7a843b70c442c">IMP::score_functor::WeightScore::get_score()</a>, <a href="classIMP_1_1score__functor_1_1WeightScore.html#a6041da95abd500298d10fbd9d6203353">IMP::score_functor::WeightScore::get_score_and_derivative()</a>, <a href="namespaceIMP_1_1atom.html#a9b13cfbe2f98dd95b8837f10dbb6fdfd">IMP::atom::read_mol2()</a>, <a href="namespaceIMP_1_1atom.html#ac65059962426cd7e45339ff9f3ed70df">IMP::atom::read_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a13159795e7c78f154e98bc20cc4fb8d8">IMP::atom::read_multimodel_pdb()</a>, <a href="namespaceIMP_1_1atom.html#ac376e29826164bc29ba340b438507a35">IMP::atom::read_psipred()</a>, <a href="namespaceIMP_1_1atom.html#acff3db79eba55378dcbfd90a142e1221">IMP::atom::create_protein()</a>, <a href="namespaceIMP_1_1atom.html#a0017c87971f647fb5c54bfb3282c3e47">IMP::atom::create_protein()</a>, <a href="namespaceIMP_1_1atom.html#a69572512ee172f8a9660e26db7aacf7d">IMP::atom::get_resolution()</a>, <a href="namespaceIMP_1_1atom.html#ae4a0d2d12be0e63c5def48217feea082">IMP::atom::setup_coarse_secondary_structure_residue()</a>, <a href="namespaceIMP_1_1atom.html#acff5cafee785a8eca3f4e923bba2ef03">IMP::atom::setup_coarse_secondary_structure_residues()</a>, <a href="namespaceIMP_1_1core.html#a142080670d025ed3bcba01dddab39549">IMP::core::create_rigid_bodies()</a>, <a href="namespaceIMP_1_1core.html#ab187aead985c4fb93d7c4c8741fb00c8">IMP::core::create_xyzr_particles()</a>, <a href="namespaceIMP_1_1core.html#a4a6d455367f3db8a6b6d9cbc3302e185">IMP::core::get_initial_reference_frame()</a>, <a href="namespaceIMP_1_1em.html#a97bf357f626dfeaa62507d51614db63d">IMP::em::density2particles()</a>, <a href="namespaceIMP_1_1example.html#a40b8d52cacc198cdbd93d89217d94fdf">IMP::example::optimize_assembly()</a>, <a href="namespaceIMP_1_1kernel.html#ab9c790efc40e09a7b10548c347c9cfd9">IMP::kernel::get_dependency_graph()</a>, <a href="namespaceIMP_1_1kernel.html#a832b34207ebf86a3a4c0ec65d6cda191">IMP::kernel::get_particles()</a>, <a href="namespaceIMP_1_1kernel.html#a1cee9eb14c41b31c6ec65c8612b35ffc">IMP::kernel::get_pruned_dependency_graph()</a>, <a href="namespaceIMP_1_1kernel.html#a1d82a88b0c18c8b55e66c9d2437010da">IMP::kernel::make_predicate_equal()</a>, <a href="namespaceIMP_1_1kernel.html#a1bdaf9123d8d2d5dcbe7dec269ddbbd3">IMP::kernel::make_predicate_not_equal()</a>, <a href="namespaceIMP_1_1multifit.html#a6d23b5accff1c34001a8ca97d0241167">IMP::multifit::create_coarse_molecule_from_density()</a>, <a href="namespaceIMP_1_1multifit.html#a2fc41bcf60a63d0ecc658c8df0a6e096">IMP::multifit::create_coarse_molecule_from_molecule()</a>, <a href="namespaceIMP_1_1multifit.html#a4c8cc2536fde9f27a2ee3cfda1915030">IMP::multifit::create_coarse_molecules_from_molecules()</a>, <a href="namespaceIMP_1_1rmf.html#a31eaf33429ccc15ba6662fae46b59c6a">IMP::rmf::create_hierarchies()</a>, <a href="namespaceIMP_1_1rmf.html#a2375a307294df39c42545c028c25f2cc">IMP::rmf::create_particles()</a>, <a href="namespaceIMP_1_1rmf.html#a8623b5a4db00674a07d7437f7bbef865">IMP::rmf::create_restraints()</a></td></tr>
193 <tr><td>@ref IMP::kernel::ModelObject</td><td><a href="classIMP_1_1kernel_1_1Model.html#a41e98a4e01df95b8c4575d83f04134b8">IMP::kernel::Model::check_dependency_invariants()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a4c0d3da34528c6a616fa21fe773a24be">IMP::kernel::Model::do_add_dependencies()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a45b18e87379f42e7d624eeb014a22cae">IMP::kernel::Model::do_add_model_object()</a>, <a href="classIMP_1_1kernel_1_1Model.html#ab2aeac59cee33029c733a4a7bfb55bcf">IMP::kernel::Model::do_check_inputs_and_outputs()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a7301cb941cf7d0e5d57d50c22ec76d1b">IMP::kernel::Model::do_check_not_in_readers_and_writers()</a>, <a href="classIMP_1_1kernel_1_1Model.html#ae7892b12fb5b31f182f6211b0f566a0f">IMP::kernel::Model::do_check_readers_and_writers()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a8574e0cf0f627059b394708125832341">IMP::kernel::Model::do_check_required_score_states()</a>, <a href="classIMP_1_1kernel_1_1Model.html#aaecc222533f8856b2bff5368904be231">IMP::kernel::Model::do_clear_dependencies()</a>, <a href="classIMP_1_1kernel_1_1Model.html#ad210e6ae0fa604c58cd42164a22c232c">IMP::kernel::Model::do_clear_required_score_states()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a50cabbb4157c02332b50f55dd0ddd3a3">IMP::kernel::Model::do_get_has_dependencies()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a6e5f4466edd3a0fb9d50375617702928">IMP::kernel::Model::do_get_has_required_score_states()</a>, <a href="classIMP_1_1kernel_1_1Model.html#ac370d10fe206c1c9dea1498e8ddaabff">IMP::kernel::Model::do_get_required_score_states()</a>, <a href="classIMP_1_1kernel_1_1Model.html#ad446309d2b0398ebea430480f2075a0e">IMP::kernel::Model::do_remove_model_object()</a>, <a href="classIMP_1_1kernel_1_1Model.html#ac529b7a61217bb36005181020b5f9427">IMP::kernel::Model::do_set_has_dependencies()</a>, <a href="classIMP_1_1kernel_1_1Model.html#ae859b1aea9697b48f40dd4cc9b598ea1">IMP::kernel::Model::do_set_has_required_score_states()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a7b9b35bbe3fcd1f09fe56b99230c4abd">IMP::kernel::Model::get_ancestor_score_states()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a222d429acb2c162403cf31c0d7014221">IMP::kernel::Model::get_dependency_graph_inputs()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a78b14baecff555c3068b268b37cc4e3f">IMP::kernel::Model::get_dependency_graph_outputs()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a7e17fc6cad43e02a79dcdb329a06a917">IMP::kernel::Model::get_descendent_score_states()</a>, <a href="namespaceIMP_1_1kernel.html#a59562be47760e4ee3424b80f4ca2a5ba">IMP::kernel::get_dependent_particles()</a>, <a href="namespaceIMP_1_1kernel.html#a4fad2b9b58de140842bc1eb20789081d">IMP::kernel::get_dependent_restraints()</a>, <a href="namespaceIMP_1_1kernel.html#ae2717e7b6f627a7528153be91cc06ed0">IMP::kernel::get_dependent_score_states()</a>, <a href="namespaceIMP_1_1kernel.html#a802a796f7b46db5afa4673012afebca8">IMP::kernel::get_required_score_states()</a></td></tr>
194 <tr><td>@ref IMP::kernel::Optimizer</td><td><a href="classIMP_1_1kernel_1_1Optimizer.html#a1f7de9517d05f619a1dbb0cce5965fcf">IMP::kernel::Optimizer::set_optimizer_state_optimizer()</a>, <a href="classIMP_1_1kernel_1_1OptimizerState.html#aebbc0023d497f1420375270a1fd1b60b">IMP::kernel::OptimizerState::set_optimizer()</a></td></tr>
195 <tr><td>@ref IMP::kernel::OptimizerState</td><td><a href="classIMP_1_1kernel_1_1Optimizer.html#afc9d922c98d5cf0711aefb436ea637a7">IMP::kernel::Optimizer::remove_optimizer_state()</a>, <a href="classIMP_1_1kernel_1_1Optimizer.html#a1171e9d19ed52aa7d84526b9aeeb4c94">IMP::kernel::Optimizer::add_optimizer_state()</a>, <a href="classIMP_1_1kernel_1_1Optimizer.html#a1f7de9517d05f619a1dbb0cce5965fcf">IMP::kernel::Optimizer::set_optimizer_state_optimizer()</a></td></tr>
196 <tr><td>@ref IMP::kernel::PairContainer</td><td><a href="classIMP_1_1core_1_1NeighborsTable.html#ab2eb07fc46a5cec71ce54a75a35d01e5">IMP::core::NeighborsTable::NeighborsTable()</a>, <a href="classIMP_1_1kernel_1_1PairContainerAdaptor.html#a25c549c30ce171cee0b4650fdd8ec196">IMP::kernel::PairContainerAdaptor::PairContainerAdaptor()</a></td></tr>
197 <tr><td>@ref IMP::kernel::PairContainerAdaptor</td><td><a href="classIMP_1_1container_1_1PairsRestraint.html#a2a1a8a97a961682ae4d4ad541de73a5f">IMP::container::PairsRestraint::PairsRestraint()</a></td></tr>
198 <tr><td>@ref IMP::kernel::PairModifier</td><td><a href="classIMP_1_1kernel_1_1PairContainer.html#aa38a376736ce94a7cc128cc8e418aa0c">IMP::kernel::PairContainer::apply()</a>, <a href="classIMP_1_1kernel_1_1PairContainer.html#af9d8683a1d61dad90bff741577db1830">IMP::kernel::PairContainer::apply_generic()</a>, <a href="classIMP_1_1kernel_1_1PairContainer.html#a648a4d01d7e80ece019cda5aebd19dd3">IMP::kernel::PairContainer::do_apply()</a></td></tr>
199 <tr><td>@ref IMP::kernel::PairScore</td><td><a href="classIMP_1_1container_1_1PairsRestraint.html#a2a1a8a97a961682ae4d4ad541de73a5f">IMP::container::PairsRestraint::PairsRestraint()</a>, <a href="classIMP_1_1container_1_1PredicatePairsRestraint.html#a63bdf9ccfb756be25285e473c2c7839c">IMP::container::PredicatePairsRestraint::set_score()</a>, <a href="classIMP_1_1container_1_1PredicatePairsRestraint.html#aa636e8bd01657e7ad168f10d60247574">IMP::container::PredicatePairsRestraint::set_unknown_score()</a></td></tr>
200 <tr><td>@ref IMP::kernel::Particle</td><td><a href="classIMP_1_1atom_1_1BondEndpointsRefiner.html#a881add2324125a8d236b332b8fd82f79">IMP::atom::BondEndpointsRefiner::get_can_refine()</a>, <a href="classIMP_1_1atom_1_1BondEndpointsRefiner.html#a15e350d5bc62ba304febc2c7a1c99bde">IMP::atom::BondEndpointsRefiner::get_refined()</a>, <a href="classIMP_1_1atom_1_1BondGeometry.html#a13e03f266d94717cfb1529d9941cffd4">IMP::atom::BondGeometry::BondGeometry()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#ab9e89e0e6448c516389a46b7b3e31971">IMP::atom::CHARMMParameters::add_angle()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a7493e32f1b5534c11661f4ae1d283e8b">IMP::atom::CHARMMParameters::add_dihedral()</a>, <a href="classIMP_1_1atom_1_1SecondaryStructureResidue.html#a88683613171ac3d0d20d14ca3aa31f57">IMP::atom::SecondaryStructureResidue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a737bfa5dad795bf45b59d84c90143f58">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#a453f7d6449287dc809890dada03059bd">IMP::atom::Simulator::remove_particle()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#aea0020aee9fb1abdfbbe4d9eb43d413a">IMP::atom::Simulator::add_particle()</a>, <a href="classIMP_1_1container_1_1DynamicListSingletonContainer.html#aef8216dd098eb6070d7dcf6649d09055">IMP::container::DynamicListSingletonContainer::add_particle()</a>, <a href="classIMP_1_1container_1_1InContainerSingletonFilter.html#af780e2aee9aed1b849285603f61edd8b">IMP::container::InContainerSingletonFilter::get_value()</a>, <a href="classIMP_1_1core_1_1AllSameSingletonPredicate.html#a3e4c8b804d78d5a660cd9681953623f9">IMP::core::AllSameSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1AngleRestraint.html#a99ac631f348a1f4a080ca5d4dd763852">IMP::core::AngleRestraint::AngleRestraint()</a>, <a href="classIMP_1_1core_1_1AttributeSingletonPredicate.html#a61ac2de33f5f127e9af2d01239e71e0f">IMP::core::AttributeSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1ChildrenRefiner.html#a46d4648ed609952a2a0f8dac017daaca">IMP::core::ChildrenRefiner::get_can_refine()</a>, <a href="classIMP_1_1core_1_1ChildrenRefiner.html#a742dc731ef07bd773f8db1cdaf714330">IMP::core::ChildrenRefiner::get_refined()</a>, <a href="classIMP_1_1core_1_1CoinFlipSingletonPredicate.html#ad46dd8ae0419335bc3e3c44f0437113f">IMP::core::CoinFlipSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1ConstantSingletonPredicate.html#a9a89d3930592f84a4d53acc47fed514e">IMP::core::ConstantSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1DihedralRestraint.html#a702dec9e658d484bf5407b05d01741dd">IMP::core::DihedralRestraint::DihedralRestraint()</a>, <a href="classIMP_1_1core_1_1DistanceRestraint.html#a68e4b1141ea56c41bfc5399c80e5fcc6">IMP::core::DistanceRestraint::DistanceRestraint()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#ac33749ef6b6b7e6845b6e8a87a3590e7">IMP::core::FixedRefiner::get_can_refine()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#a2f392daaed2b6ffb00cfd7e95bc7aacc">IMP::core::FixedRefiner::get_refined()</a>, <a href="classIMP_1_1core_1_1InBoundingBox3DSingletonPredicate.html#a004c54f4c141a8da233a4d270058e1f8">IMP::core::InBoundingBox3DSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1LeavesRefiner.html#aecaac2b73136e7de8cb7134e53908523">IMP::core::LeavesRefiner::get_can_refine()</a>, <a href="classIMP_1_1core_1_1LeavesRefiner.html#a081798ad59ec6104b1a5644166cb086c">IMP::core::LeavesRefiner::get_refined()</a>, <a href="classIMP_1_1core_1_1OrderedTypeSingletonPredicate.html#a2bc16b36155f3a89e6c1d99b9aef11b3">IMP::core::OrderedTypeSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1QuadraticClosePairsFinder.html#a41650fddebd7cb3de0876526664939e2">IMP::core::QuadraticClosePairsFinder::get_are_close()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a7af0bef69680d9dcf62a249092eb27c2">IMP::core::RigidBody::add_member_internal()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a07388790001f624673905224265738c3">IMP::core::RigidBody::teardown_constraints()</a>, <a href="classIMP_1_1core_1_1RigidBodyDerivativeGeometry.html#a9bdbd80db7a9475ba05404562b82d096">IMP::core::RigidBodyDerivativeGeometry::RigidBodyDerivativeGeometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyFrameGeometry.html#adaef015fc8b782806000b23bde14941c">IMP::core::RigidBodyFrameGeometry::RigidBodyFrameGeometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyTorque.html#a7353f5b14547af12c64c90e2415bc1bd">IMP::core::RigidBodyTorque::extract_geometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyTorque.html#a4297f187743f0cd4da28c9b5535488da">IMP::core::RigidBodyTorque::RigidBodyTorque()</a>, <a href="classIMP_1_1core_1_1SingletonConstraint.html#a0940e711460fc379959c023c46a717b2">IMP::core::SingletonConstraint::SingletonConstraint()</a>, <a href="classIMP_1_1core_1_1SingletonRestraint.html#a9be13480cd22aef28e757bde6ec5b7e2">IMP::core::SingletonRestraint::SingletonRestraint()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a7615780047e92e9962c3ccdb70a6cab0">IMP::core::TableRefiner::add_particle()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#ac247b8e2d5c7ce74db467f52e7797586">IMP::core::TableRefiner::get_can_refine()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a3236d90a596b17e41e89664e4704e14b">IMP::core::TableRefiner::get_refined()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#ade7002d288eefa3dab2ca8cdc4c8942b">IMP::core::TableRefiner::remove_particle()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a359aebec2be2b5f56e477e62424e6700">IMP::core::TableRefiner::set_particle()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#ab18aa9dea7778b1ae9b00308bc6ab41d">IMP::core::TypedPairScore::set_particle_type()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeSingletonPredicate.html#a885ee02ab9c5cf213bd99b36d4f8a208">IMP::core::UnorderedTypeSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1XYZDerivativeGeometry.html#a99f55e7a0f1689cfebcfed0d2d1287b4">IMP::core::XYZDerivativeGeometry::XYZDerivativeGeometry()</a>, <a href="classIMP_1_1core_1_1XYZRGeometry.html#ac027b28cbb5bac03a42082166a1c07cc">IMP::core::XYZRGeometry::XYZRGeometry()</a>, <a href="classIMP_1_1display_1_1SingletonGeometry.html#a15751265e830ccc0a7b76f48de9a7f4b">IMP::display::SingletonGeometry::SingletonGeometry()</a>, <a href="classIMP_1_1domino_1_1CompoundStates.html#ad4f5da427326e33468dd1bb0d786d46e">IMP::domino::CompoundStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#afc500a620288204808f5fb15e0e9cff9">IMP::domino::DiscreteSampler::set_particle_states()</a>, <a href="classIMP_1_1domino_1_1DisjointSetsSubsetFilterTable.html#ae717b7e37ce3609b6a8be9726bdc94b0">IMP::domino::DisjointSetsSubsetFilterTable::get_index()</a>, <a href="classIMP_1_1domino_1_1IndexStates.html#a20fa5c5f87108fe06bd3b2dfdcede8df">IMP::domino::IndexStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#a9d3812f6d072fb1881a6577001164e1e">IMP::domino::ListSubsetFilterTable::get_number_of_particle_states()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#a659e91c76608443663f97e57e0ebe473">IMP::domino::ListSubsetFilterTable::set_allowed_states()</a>, <a href="classIMP_1_1domino_1_1NestedRigidBodyStates.html#a1656c12ca730835fe08af5225a1cb59b">IMP::domino::NestedRigidBodyStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1ParticleStates.html#a509911de42b3bb5427df6fe49a2fdbe3">IMP::domino::ParticleStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1ParticleStatesTable.html#a4c62739e84633af7111315ef655465f3">IMP::domino::ParticleStatesTable::get_has_particle()</a>, <a href="classIMP_1_1domino_1_1ParticleStatesTable.html#aa0827374f14a45cc57eef6a08f734f0a">IMP::domino::ParticleStatesTable::get_particle_states()</a>, <a href="classIMP_1_1domino_1_1ParticleStatesTable.html#a2f3ecc856aa1e60fcbd0d213f0f45dfb">IMP::domino::ParticleStatesTable::set_particle_states()</a>, <a href="classIMP_1_1domino_1_1PermutationStates.html#a5bd3cf83f08fe328504d199ea4e3b33e">IMP::domino::PermutationStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1RecursiveStates.html#aab5b5225450b5ce8ff2ffbdb5f15f517">IMP::domino::RecursiveStates::RecursiveStates()</a>, <a href="classIMP_1_1domino_1_1RecursiveStates.html#a3fdd52a35961b4c835e301f2e20cb285">IMP::domino::RecursiveStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1RigidBodyStates.html#ac81a8b0a26c8a73696d7609496aa8925">IMP::domino::RigidBodyStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1XYZStates.html#ad7567641498035edf1e6b34ec1af2994">IMP::domino::XYZStates::load_particle_state()</a>, <a href="classIMP_1_1em2d_1_1DummyRestraint.html#a3d8aadd607964b6805f8de2c99f958c4">IMP::em2d::DummyRestraint::DummyRestraint()</a>, <a href="classIMP_1_1em2d_1_1GridStates.html#addaa0456b1db6ee3dedecb4c74633e68">IMP::em2d::GridStates::load_particle_state()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParametersScoreState.html#a4ced005fce6faf3f178335fe5f8b841a">IMP::em2d::ProjectionParametersScoreState::ProjectionParametersScoreState()</a>, <a href="classIMP_1_1em2d_1_1ProjectionStates.html#ac72009a54e8f1d45c5bdb976cf167e5d">IMP::em2d::ProjectionStates::load_particle_state()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#a4c9e30e2cd297f3fb36d12d6c293ec22">IMP::em::DensityFillingRestraint::add_particle()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#aa432a147469e6a76827169da7e40e5ee">IMP::em::DensityFillingRestraint::remove_particle()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#aab72347fd0017474d391ef515b00f69a">IMP::em::EnvelopePenetrationRestraint::add_particle()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#aa2faede58b3a9a0a2a7db7ccdfcb3e48">IMP::em::EnvelopePenetrationRestraint::remove_particle()</a>, <a href="classIMP_1_1em_1_1FitRestraint.html#a9ec51efebd6e24b6f7705ec849c41195">IMP::em::FitRestraint::add_particle()</a>, <a href="classIMP_1_1em_1_1FitRestraint.html#a1c71edc9a6e8c38017d0e48e28e557f5">IMP::em::FitRestraint::remove_particle()</a>, <a href="classIMP_1_1em_1_1PCAFitRestraint.html#acfad3e22c1e7f09380df42ffe6a5389b">IMP::em::PCAFitRestraint::add_particle()</a>, <a href="classIMP_1_1em_1_1PCAFitRestraint.html#ae32ed246b482e7e88b011d70cc579b88">IMP::em::PCAFitRestraint::remove_particle()</a>, <a href="classIMP_1_1example_1_1ExampleConstraint.html#ad1f6a61bbe49ac41b403a1d1ad0b1d63">IMP::example::ExampleConstraint::ExampleConstraint()</a>, <a href="classIMP_1_1isd_1_1AmbiguousNOERestraint.html#ac4ba7253a939b4a86978febfab4a7ce4">IMP::isd::AmbiguousNOERestraint::AmbiguousNOERestraint()</a>, <a href="classIMP_1_1isd_1_1Covariance1DFunction.html#aab493a85aaa6cf685dd337c1a791f65b">IMP::isd::Covariance1DFunction::Covariance1DFunction()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#a33e047d45e77e1b6e5c71bba1ed7d6f0">IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#afc6082000216caa2d5a22f9813a317a2">IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#abe11ed410be3c9e949000e63bdaa33ea">IMP::isd::CysteineCrossLinkRestraint::add_contribution()</a>, <a href="classIMP_1_1isd_1_1FretRestraint.html#afc8350a1e661281aa25150827b1804c4">IMP::isd::FretRestraint::get_current_center()</a>, <a href="classIMP_1_1isd_1_1FretRestraint.html#acbe40c45131abcd07a3aded7cbb22ca1">IMP::isd::FretRestraint::get_current_centers()</a>, <a href="classIMP_1_1isd_1_1FretRestraint.html#a41cc9853f19ba5046fc14efacfcf944a">IMP::isd::FretRestraint::FretRestraint()</a>, <a href="classIMP_1_1isd_1_1FretRestraint.html#a701f942412b8255f1914d8850f6628e4">IMP::isd::FretRestraint::FretRestraint()</a>, <a href="classIMP_1_1isd_1_1FretRestraint.html#a8b6683ce3a6ec845b6b4a0b22e4861b5">IMP::isd::FretRestraint::FretRestraint()</a>, <a href="classIMP_1_1isd_1_1GaussianProcessInterpolation.html#ab41bc7acf66cea95ad3b8be03f8015b9">IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation()</a>, <a href="classIMP_1_1isd_1_1GaussianRestraint.html#ac6cd8199094e4365de4176264339796e">IMP::isd::GaussianRestraint::GaussianRestraint()</a>, <a href="classIMP_1_1isd_1_1GaussianRestraint.html#aea0904a099b0334a7c3f82122625bed1">IMP::isd::GaussianRestraint::GaussianRestraint()</a>, <a href="classIMP_1_1isd_1_1GaussianRestraint.html#a865f1a418dc9d6ef0cab42dad54a0aed">IMP::isd::GaussianRestraint::GaussianRestraint()</a>, <a href="classIMP_1_1isd_1_1GaussianRestraint.html#a6712b26f7304b9ca523041c926170108">IMP::isd::GaussianRestraint::GaussianRestraint()</a>, <a href="classIMP_1_1isd_1_1GaussianRestraint.html#acc25f7fdf315ceba3b4ef884e959b5f0">IMP::isd::GaussianRestraint::GaussianRestraint()</a>, <a href="classIMP_1_1isd_1_1GaussianRestraint.html#a182ffe29233c1d1a1ef8cb556867b8c5">IMP::isd::GaussianRestraint::GaussianRestraint()</a>, <a href="classIMP_1_1isd_1_1GaussianRestraint.html#a15ed1d70056edf790a3e46ff3f3d786d">IMP::isd::GaussianRestraint::GaussianRestraint()</a>, <a href="classIMP_1_1isd_1_1GeneralizedGuinierPorodFunction.html#a72bc8414bf6dc21ca0f94699a87ba010">IMP::isd::GeneralizedGuinierPorodFunction::GeneralizedGuinierPorodFunction()</a>, <a href="classIMP_1_1isd_1_1Linear1DFunction.html#aa75d824c318965362baa120456ac50e0">IMP::isd::Linear1DFunction::Linear1DFunction()</a>, <a href="classIMP_1_1isd_1_1LognormalRestraint.html#aab7627b0f4b4c79d143d6e87cc3d7f1a">IMP::isd::LognormalRestraint::LognormalRestraint()</a>, <a href="classIMP_1_1isd_1_1LognormalRestraint.html#ab21edfbbaf2dde87bb382eb3ba5f6c39">IMP::isd::LognormalRestraint::LognormalRestraint()</a>, <a href="classIMP_1_1isd_1_1LognormalRestraint.html#aaacdade753b9c8f079bb4d7816bf17bc">IMP::isd::LognormalRestraint::LognormalRestraint()</a>, <a href="classIMP_1_1isd_1_1LognormalRestraint.html#a9a76c0f2c7298a51427fd68ea2a29ce4">IMP::isd::LognormalRestraint::LognormalRestraint()</a>, <a href="classIMP_1_1isd_1_1LognormalRestraint.html#a7d3c5f59a476f3e52b14ac77b2c25f5d">IMP::isd::LognormalRestraint::LognormalRestraint()</a>, <a href="classIMP_1_1isd_1_1LognormalRestraint.html#aa036071da00bf609efe95cddcef6d786">IMP::isd::LognormalRestraint::LognormalRestraint()</a>, <a href="classIMP_1_1isd_1_1LognormalRestraint.html#a232a03903e5defa10b8b1bb59c6f13bd">IMP::isd::LognormalRestraint::LognormalRestraint()</a>, <a href="classIMP_1_1isd_1_1MarginalHBondRestraint.html#ab53cc71e064352545db0de0508e9d80c">IMP::isd::MarginalHBondRestraint::add_contribution()</a>, <a href="classIMP_1_1isd_1_1MarginalNOERestraint.html#a5a1a7423c4a376322da5703edc19c567">IMP::isd::MarginalNOERestraint::add_contribution()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#a948bdab7b6443bfe5699819a53070110">IMP::isd::Nuisance::set_lower()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#ab98a25ed363b10532718768357e55f32">IMP::isd::Nuisance::set_upper()</a>, <a href="classIMP_1_1isd_1_1TALOSRestraint.html#af02391c24e080b14395854a84e2f7369">IMP::isd::TALOSRestraint::TALOSRestraint()</a>, <a href="classIMP_1_1isd_1_1TALOSRestraint.html#a1363aeb8875066903b5e3fa7c5782a96">IMP::isd::TALOSRestraint::TALOSRestraint()</a>, <a href="classIMP_1_1isd_1_1TALOSRestraint.html#aaac74730bac287751f2f442dcfd74ddc">IMP::isd::TALOSRestraint::TALOSRestraint()</a>, <a href="classIMP_1_1isd_1_1TALOSRestraint.html#ad7b9a4e42e2d1c34266d136d71d79467">IMP::isd::TALOSRestraint::TALOSRestraint()</a>, <a href="classIMP_1_1isd_1_1WeightMover.html#ae5c4dcef1a30c4c50602c5f619be6c14">IMP::isd::WeightMover::WeightMover()</a>, <a href="classIMP_1_1isd_1_1WeightRestraint.html#a061fce4a8b58b3a454d262d040a45dae">IMP::isd::WeightRestraint::WeightRestraint()</a>, <a href="classIMP_1_1isd_1_1vonMisesKappaConjugateRestraint.html#a331ae31255cc6226c53410f16ca69fdc">IMP::isd::vonMisesKappaConjugateRestraint::vonMisesKappaConjugateRestraint()</a>, <a href="classIMP_1_1isd_1_1vonMisesKappaJeffreysRestraint.html#a69c0b213ef8e9ca483f36243c1bd4826">IMP::isd::vonMisesKappaJeffreysRestraint::vonMisesKappaJeffreysRestraint()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a460a5dbcaccba75573a169f3f928ce96">IMP::kernel::Model::add_particle_internal()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a3291c4ec720ed8d76cabd5a587d55219">IMP::kernel::Model::remove_particle()</a>, <a href="classIMP_1_1kernel_1_1ParticleAdaptor.html#ad1622f002cda2d25b9dcbdf7da5d93db">IMP::kernel::ParticleAdaptor::ParticleAdaptor()</a>, <a href="classIMP_1_1kernel_1_1ParticleAdaptor.html#a6692ab4d3f67b4e41d58e693e87eac4c">IMP::kernel::ParticleAdaptor::ParticleAdaptor()</a>, <a href="classIMP_1_1kernel_1_1ParticleAdaptor.html#a096327f901a3c6448424b382719214f9">IMP::kernel::ParticleAdaptor::ParticleAdaptor()</a>, <a href="classIMP_1_1kernel_1_1ParticleAdaptor.html#a493d09a04c2c9ee3eea29810bbc71fcf">IMP::kernel::ParticleAdaptor::ParticleAdaptor()</a>, <a href="classIMP_1_1kernel_1_1ParticleIndexAdaptor.html#a4fbbe53f93ca78bd3027514fb7979247">IMP::kernel::ParticleIndexAdaptor::ParticleIndexAdaptor()</a>, <a href="classIMP_1_1kernel_1_1ParticleInputs.html#aea84f881ca580e30fc4b5e9cfc5a855d">IMP::kernel::ParticleInputs::get_input_containers()</a>, <a href="classIMP_1_1kernel_1_1ParticleInputs.html#a4d6a4e5b57e6b82f7dde638f568545b9">IMP::kernel::ParticleInputs::get_input_particles()</a>, <a href="classIMP_1_1kernel_1_1ParticleOutputs.html#ad94b41b09fff3aa24dccae9a78f4fd99">IMP::kernel::ParticleOutputs::get_output_containers()</a>, <a href="classIMP_1_1kernel_1_1ParticleOutputs.html#a14e9a5b1ee506e8630100ed2d7e6117b">IMP::kernel::ParticleOutputs::get_output_particles()</a>, <a href="classIMP_1_1kernel_1_1Refiner.html#a76c480339c33da8136014a17f968ed3f">IMP::kernel::Refiner::refined_begin()</a>, <a href="classIMP_1_1kernel_1_1Refiner.html#a2a88cd95e141e3ba6c943f61b0de6bd2">IMP::kernel::Refiner::refined_end()</a>, <a href="classIMP_1_1kernel_1_1Refiner.html#a4defd8991c0d465c953f5d2b9a0e2af4">IMP::kernel::Refiner::get_can_refine()</a>, <a href="classIMP_1_1kernel_1_1Refiner.html#a515635f617b363ae512c35e83f9dfca9">IMP::kernel::Refiner::get_number_of_refined()</a>, <a href="classIMP_1_1kernel_1_1Refiner.html#a24fcaeb8596469c3ed61ce48cb7eef90">IMP::kernel::Refiner::get_refined()</a>, <a href="classIMP_1_1kernel_1_1Refiner.html#afd5f1e512319f876a63c4982ffd4a62b">IMP::kernel::Refiner::get_refined()</a>, <a href="classIMP_1_1kernel_1_1ScopedAddCacheAttribute.html#a1db5f418c0098f0e6dc69e2798ec5e2f">IMP::kernel::ScopedAddCacheAttribute::ScopedAddCacheAttribute()</a>, <a href="classIMP_1_1kernel_1_1ScopedAddCacheAttribute.html#ab25b8a051593ef26d399b58c7f1db660">IMP::kernel::ScopedAddCacheAttribute::set()</a>, <a href="classIMP_1_1kernel_1_1ScopedSetAttribute.html#a7331eb389d48ee743e093960a6730c45">IMP::kernel::ScopedSetAttribute::ScopedSetAttribute()</a>, <a href="classIMP_1_1kernel_1_1ScopedSetAttribute.html#af608ed2c60f0aafa29889b115520c9af">IMP::kernel::ScopedSetAttribute::set()</a>, <a href="classIMP_1_1kernel_1_1SingletonModifier.html#a935a39852ba19e4c2ed2170b32b2c7d2">IMP::kernel::SingletonModifier::apply()</a>, <a href="classIMP_1_1kernel_1_1SingletonPredicate.html#aad5d6e93d67b69f43d6489761576e05a">IMP::kernel::SingletonPredicate::get_value()</a>, <a href="classIMP_1_1kernel_1_1SingletonScore.html#a5e6728362848f96275e177442406bebf">IMP::kernel::SingletonScore::evaluate()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a329513be624b6cdec905a9abd97a1f1b">IMP::kinematics::KinematicForest::reset_root()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#aecd41fea74ef0ba7c87067dbef28e5fa">IMP::kinematics::KinematicForest::get_children()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a14b1bae2e1548367fe8f9c1dc0cd6ed5">IMP::kinematics::KinematicForest::get_parent()</a>, <a href="classIMP_1_1multifit_1_1DummyRestraint.html#a3877741eb79414251e58cfd047c90dbb">IMP::multifit::DummyRestraint::DummyRestraint()</a>, <a href="classIMP_1_1multifit_1_1FittingStates.html#a130a3911d39bd7ea8fbed12f71815cb3">IMP::multifit::FittingStates::load_particle_state()</a>, <a href="classIMP_1_1multifit_1_1ProbabilisticAnchorGraph.html#a5a6d2990189fd23771966e9e3f1c4052">IMP::multifit::ProbabilisticAnchorGraph::get_are_probabilities_for_particle_set()</a>, <a href="classIMP_1_1multifit_1_1ProbabilisticAnchorGraph.html#add5926e503f54bfebe3d3041bfe4a884">IMP::multifit::ProbabilisticAnchorGraph::get_particle_anchors()</a>, <a href="classIMP_1_1multifit_1_1ProbabilisticAnchorGraph.html#a5a049f7aba2c003fdb24b79bcf698987">IMP::multifit::ProbabilisticAnchorGraph::get_particle_probabilities()</a>, <a href="classIMP_1_1multifit_1_1ProbabilisticAnchorGraph.html#a686526609738393520f85c2b7c44761a">IMP::multifit::ProbabilisticAnchorGraph::set_particle_probabilities_on_anchors()</a>, <a href="classIMP_1_1multifit_1_1RadiusOfGyrationRestraint.html#a760c99763396d94c38fd817220b63f57">IMP::multifit::RadiusOfGyrationRestraint::add_particle()</a>, <a href="classIMP_1_1multifit_1_1RadiusOfGyrationRestraint.html#a5d2be470e8ce919341b1c859c13d4a39">IMP::multifit::RadiusOfGyrationRestraint::remove_particle()</a>, <a href="classIMP_1_1multifit_1_1WeightedExcludedVolumeRestraint.html#ac8715c7130d23290d5a58ed5b3868a3a">IMP::multifit::WeightedExcludedVolumeRestraint::add_particle()</a>, <a href="classIMP_1_1multifit_1_1WeightedExcludedVolumeRestraint.html#a458f1aa5469e0f7ac6606d86bfc5a6f9">IMP::multifit::WeightedExcludedVolumeRestraint::remove_particle()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#aca7a14315caadb93ffa341dd6f9c3ac2">IMP::rmf::HierarchyLoadLink::do_add_link()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#a4d94ce2f7207e313ce1d10e5d8bcc4cd">IMP::rmf::HierarchyLoadLink::do_load_one()</a>, <a href="classIMP_1_1rmf_1_1HierarchySaveLink.html#aa327654ade5a9c5f53328618012c2cc7">IMP::rmf::HierarchySaveLink::do_add()</a>, <a href="classIMP_1_1rmf_1_1HierarchySaveLink.html#ad2a8dc31d99fd4c3c273ba6cd7fd1194">IMP::rmf::HierarchySaveLink::do_save_one()</a>, <a href="classIMP_1_1rmf_1_1HierarchySaveLink.html#ae1076c852f2f6f0c85bbbf87a8d65159">IMP::rmf::HierarchySaveLink::get_type()</a>, <a href="classIMP_1_1saxs_1_1DeltaDistributionFunction.html#ae70e019a7011cb378348489780810bf2">IMP::saxs::DeltaDistributionFunction::calculate_derivative_distribution()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#ae612d93963cb67999e8abe7f0911e79f">IMP::saxs::FormFactorTable::get_dummy_form_factor()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#af6d32b6e379786bfb7f62f12462691be">IMP::saxs::FormFactorTable::get_dummy_form_factors()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a9e25ffbf46da18d1cdad24c3035b6c53">IMP::saxs::FormFactorTable::get_form_factor()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a39c32ec8caec51b314be5cb7bdecf527">IMP::saxs::FormFactorTable::get_form_factors()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a822959aede7253c4f91412214fa62e4d">IMP::saxs::FormFactorTable::get_radius()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#ac885012f0955bcaf0a0af5dac4616abd">IMP::saxs::FormFactorTable::get_vacuum_form_factor()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a795458236d9909d53f70a8bd58a318ca">IMP::saxs::FormFactorTable::get_vacuum_form_factors()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a4fd68b35421b688fb6f3123fef5e1dc6">IMP::saxs::FormFactorTable::get_volume()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a805ad06ff8096e2e30819837da5e3453">IMP::saxs::FormFactorTable::get_form_factor_atom_type()</a>, <a href="classIMP_1_1symmetry_1_1BallMover.html#a83bd205b0f959f73bfbbfe0ed7cddcf6">IMP::symmetry::BallMover::BallMover()</a>, <a href="namespaceIMP_1_1atom.html#a990dcd12c2cfff8656227b9e059090f4">IMP::atom::setup_as_approximation()</a>, <a href="namespaceIMP_1_1base.html#a190a3e39c4f6fde040a8f13f6242ec9f">IMP::base::get_vector_geometry()</a>, <a href="namespaceIMP_1_1base.html#a19683c128f3107240bf38b3f83da647b">IMP::base::get_vector_geometry()</a>, <a href="namespaceIMP_1_1base.html#a26835ce0ab921c25fa31bbda21ab85f9">IMP::base::set_vector_geometry()</a>, <a href="namespaceIMP_1_1base.html#a68196dab65291e9ea53d1e03655279ee">IMP::base::set_vector_geometry()</a>, <a href="namespaceIMP_1_1em.html#af2e9693e484be616d4b490bc7e0ceafc">IMP::em::local_rigid_fitting()</a>, <a href="namespaceIMP_1_1em.html#a2d77c6d77688fed98290030953698a82">IMP::em::local_rigid_fitting_around_point()</a>, <a href="namespaceIMP_1_1em.html#a79ed07d59b449e5f31b1479b73b4b054">IMP::em::local_rigid_fitting_around_points()</a>, <a href="namespaceIMP_1_1kernel.html#a684ed8a7985d5c677235f2168a03a370">IMP::kernel::get_vector_geometry()</a>, <a href="namespaceIMP_1_1kernel.html#abe44f3d88c4d392b793248a8e95f3cae">IMP::kernel::set_vector_geometry()</a>, <a href="namespaceIMP_1_1multifit.html#a0a9580f83f49e4fb5dd13fc36465448b">IMP::multifit::get_close_to_point()</a>, <a href="namespaceIMP_1_1rmf.html#aeb17c04ff261464a9589e576ffc92950">IMP::rmf::add_particle()</a></td></tr>
201 <tr><td>@ref IMP::kernel::ParticleAdaptor</td><td><a href="classIMP_1_1atom_1_1Angle.html#acbd8c3e070b2a1bdf52635fd0d0014bc">IMP::atom::Angle::Angle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a5676843c7fddf794657637733475a5cd">IMP::atom::Angle::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a12c690f31dfbd13226378ef50ef215ce">IMP::atom::Angle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a4cd7d17c692dedcb951f6725577aa53a">IMP::atom::Atom::Atom()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a1b6727d2097ecfd96a13094167554ffb">IMP::atom::Atom::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a27acf841df41fc228ce9dd3c644b531c">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a43d9352c21c8b5827fe20d860cafb82c">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Bond.html#ae8e902f228b00f9da2b52ba71a3f2498">IMP::atom::Bond::Bond()</a>, <a href="classIMP_1_1atom_1_1Bond.html#a095bbeb2e720921f51c0771ba41ccf8e">IMP::atom::Bond::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#addb9c702fb7d2edaa8cc0efb3a58f6bc">IMP::atom::Bonded::Bonded()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#ab194e1eafa2f3fcde0471b050d642262">IMP::atom::Bonded::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#a5cacba235d9528c7e39044f6b368bd18">IMP::atom::Bonded::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#a5281802d14da5179cf7f6e591e0e8b6b">IMP::atom::CHARMMAtom::CHARMMAtom()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#a15932b664cbc3bc766a580ad03c2b646">IMP::atom::CHARMMAtom::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#a7d7857586ef2914062b6d6e099fa6e24">IMP::atom::CHARMMAtom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#ae8e0895c5aff6f1aa3662a36a64530e3">IMP::atom::CenterOfMass::CenterOfMass()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#ae65022cb3eb257987e7a828affe9cfe5">IMP::atom::CenterOfMass::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a6ea9ed4611f2dee1779632be0208e147">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a94025a54d4143236b175967d547da0fe">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a2cd4daccb63126418493fa915563d01b">IMP::atom::Chain::Chain()</a>, <a href="classIMP_1_1atom_1_1Chain.html#aabfcc3675ca8bbeedd5e3d55583a803b">IMP::atom::Chain::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Chain.html#addd22405a2289238d9b8f2df48b6cc74">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a716c01079e79acc8085ecdb2b6cd8d72">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a97cc8e8cf2ba8e7cef878150a3c4eb8b">IMP::atom::Chain::setup_particle()</a>, <a 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href="classIMP_1_1atom_1_1Hierarchy.html#af057dca372a1e08cec421b975079bb5f">IMP::atom::Hierarchy::Hierarchy()</a>, <a href="classIMP_1_1atom_1_1LennardJones.html#a4be748c53f26dccb193ed6f5ebec8030">IMP::atom::LennardJones::LennardJones()</a>, <a href="classIMP_1_1atom_1_1LennardJones.html#aeb64d0f59be9f2fa5fd6c4132ee96f55">IMP::atom::LennardJones::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1LennardJones.html#a07bf305d8b957b9e62d431466352c3a0">IMP::atom::LennardJones::setup_particle()</a>, <a href="classIMP_1_1atom_1_1LennardJones.html#a09984a7d8f26e4d55029f852e1d22308">IMP::atom::LennardJones::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Mass.html#af407b6c7332a1d5a1187933fff76782e">IMP::atom::Mass::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Mass.html#aa596392acbc82bee5e18f480d7a12706">IMP::atom::Mass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Mass.html#adf9ba2326c929e43eb576bfdd09d332e">IMP::atom::Mass::Mass()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#adc07538ca1382ffa73ff33910a6e5948">IMP::atom::Molecule::Molecule()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#a4587c01feb981dde0d060b614646f667">IMP::atom::Molecule::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#a494b80da9ab16e69258188ad614bdcd4">IMP::atom::Molecule::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#a7ba1ec0b5c5a38cd30156fc42d2d1316">IMP::atom::Molecule::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#a671c63f48506751b5b51d3b76f85f4f3">IMP::atom::Representation::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Representation.html#a6432fe14f4dddc96cd575d0cc2020ab9">IMP::atom::Representation::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#a3086e40c0518364751d0fe8098b07335">IMP::atom::Representation::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#ae81ff2bc5ee07f4dc22ca49810deb921">IMP::atom::Representation::Representation()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a4ea107653d78b5e651241dcb5846fb8a">IMP::atom::Residue::Residue()</a>, <a href="classIMP_1_1atom_1_1Residue.html#ac28ea9775081d5bb90f139a7bb34c047">IMP::atom::Residue::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a438d28031569985e208a7fff1e33471a">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#aa4ffa278f6ca0abeac027c259b607afd">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a8d590f34cd5ffeb959672af4bdccd514">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a54f33948b4d60dad09738d4ce504b43a">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1RigidBodyDiffusion.html#ac14a27770323569fc1ac37bbc6feb45b">IMP::atom::RigidBodyDiffusion::RigidBodyDiffusion()</a>, <a 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href="classIMP_1_1atom_1_1State.html#affdca86d304d9d3fe2b3385b8f029b8a">IMP::atom::State::State()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a79eb8be363343d6484e3d84294984f8c">IMP::core::Centroid::Centroid()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a01e84ba4fd96e667d1402b085d152934">IMP::core::Centroid::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a3cb848c883d70aa346f6d69ff856a484">IMP::core::Centroid::setup_particle()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a9bfdbc1331708d006ddd14b2c40855e1">IMP::core::Centroid::setup_particle()</a>, <a href="classIMP_1_1core_1_1Cover.html#a61712334f980f0108ad5884db044a7e1">IMP::core::Cover::Cover()</a>, <a href="classIMP_1_1core_1_1Cover.html#a594d7ca033d78c7106a7e34a3d689384">IMP::core::Cover::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Cover.html#aea1abd021d9a5f8de8673fb8eacee1d8">IMP::core::Cover::setup_particle()</a>, <a href="classIMP_1_1core_1_1Cover.html#a4f040b20d4c0354d0bbabf61683096b4">IMP::core::Cover::setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#ae8bf0d95736696835510296e17f77d3c">IMP::core::Gaussian::Gaussian()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a131245ddcce2124b0cf0b9919aa6fa14">IMP::core::Gaussian::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#ab4f457369ef9f11dfd0a848df46bdc5b">IMP::core::Gaussian::setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a3604f4f66e86521693d77592bfd6b892">IMP::core::Gaussian::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#aff9b158507f67597bca45f4d9cf12443">IMP::core::Hierarchy::Hierarchy()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#aff10f327112a0edbcf34bc8c58f85b91">IMP::core::Hierarchy::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a071bdca8bec3e0429efc652d79883372">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a603057a8541c1768f5bc917ac204ad1f">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a83a803677b4aa43ad2016e00a1963179">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1NonRigidMember.html#a63f636312a73a18f5c0202a634812cb4">IMP::core::NonRigidMember::NonRigidMember()</a>, <a href="classIMP_1_1core_1_1NonRigidMember.html#a68396f1d0910cb0e8007ca5ff4eb6831">IMP::core::NonRigidMember::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Reference.html#ac8ce31079e9c08a753be4b9c2288c2c9">IMP::core::Reference::Reference()</a>, <a href="classIMP_1_1core_1_1Reference.html#a6439d3e1d24db20721325b509dd25b8d">IMP::core::Reference::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Reference.html#a84c7fd0083e01ca749f93c3caad5efa5">IMP::core::Reference::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ae367d51bb9b7c3236b943579cd889935">IMP::core::RigidBody::RigidBody()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a2c395a4a73301b20e1ad26acdbad5486">IMP::core::RigidBody::get_is_setup()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#aabd4f6c3f08a7c3e24405aab08b1f135">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a2d18a7d5d57b5bf9e7d824928c94a88a">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBodyMember.html#a2265ab4fd3404532938e7780969ce361">IMP::core::RigidBodyMember::RigidBodyMember()</a>, <a href="classIMP_1_1core_1_1RigidBodyMember.html#ae5fcd33ed4497449a70748d9165838ea">IMP::core::RigidBodyMember::get_is_setup()</a>, <a href="classIMP_1_1core_1_1RigidMember.html#a0f8d67a987d29525609336f1542ced5d">IMP::core::RigidMember::RigidMember()</a>, <a href="classIMP_1_1core_1_1RigidMember.html#ac8dde5eb73d99b038ee7fed4ccaa3a1c">IMP::core::RigidMember::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Typed.html#a9f21084ed0919c2ec16c087d408c81e9">IMP::core::Typed::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Typed.html#a2bccb060c4748713b048d4454c87e6b8">IMP::core::Typed::setup_particle()</a>, <a href="classIMP_1_1core_1_1Typed.html#aef896276af07b03a76fb7b7f0078cbfe">IMP::core::Typed::Typed()</a>, <a href="classIMP_1_1core_1_1XYZ.html#a78c8372be16774189f0781c282e63e8e">IMP::core::XYZ::get_is_setup()</a>, <a href="classIMP_1_1core_1_1XYZ.html#a900745cd43644a9cb402a7fc2636a879">IMP::core::XYZ::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZ.html#ae8e6067ab1a5182a317f2d7b42fd4d64">IMP::core::XYZ::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZ.html#a7a756fac30dbb4a485ca0d9f54d651e8">IMP::core::XYZ::XYZ()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a2cb137b831bf12cf654d7d3abf4ff27f">IMP::core::XYZR::XYZR()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a7551726c3af6ffe25bdf3962f4776a6c">IMP::core::XYZR::get_is_setup()</a>, <a href="classIMP_1_1core_1_1XYZR.html#abea1181840755a6caffe6ab9f4d07fb2">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#aa301c5a743c45801291cf6b0e1981331">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a1d6da45a902f1bf244a951591b1dc3a9">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1display_1_1Colored.html#a09b59813213ca6df8eb390d7f131ec9a">IMP::display::Colored::Colored()</a>, <a href="classIMP_1_1display_1_1Colored.html#a7f24e93ad3f4e3ae64d63e9f397ee691">IMP::display::Colored::get_is_setup()</a>, <a href="classIMP_1_1display_1_1Colored.html#a9ed326bb7aab6bf5263d51e007f7e30b">IMP::display::Colored::setup_particle()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#af5d81aded23fbbc8ccb4cbc1e4edff53">IMP::em2d::ProjectionParameters::ProjectionParameters()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#a3c4df409b08f7e54c5284d8853915d49">IMP::em2d::ProjectionParameters::get_is_setup()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#af56d4dc965959a20883fe34a197b2fd6">IMP::em2d::ProjectionParameters::setup_particle()</a>, <a href="classIMP_1_1em_1_1Voxel.html#ab3270cd25e910c180527546dbf18587d">IMP::em::Voxel::get_is_setup()</a>, <a href="classIMP_1_1em_1_1Voxel.html#aecda3812c331af9989ca2d21b41f455d">IMP::em::Voxel::setup_particle()</a>, <a href="classIMP_1_1em_1_1Voxel.html#ab405891deaade218de4b53e1ef100dc4">IMP::em::Voxel::Voxel()</a>, <a href="classIMP_1_1example_1_1ExampleDecorator.html#a0ca7189e9cf6acfc668be33e2b70f0ab">IMP::example::ExampleDecorator::get_is_setup()</a>, <a href="classIMP_1_1example_1_1ExampleDecorator.html#a6561ed5f6d1c7a8baade1e94db560a6f">IMP::example::ExampleDecorator::setup_particle()</a>, <a href="classIMP_1_1example_1_1ExampleDecorator.html#a752ab0bc9c88c21908c5b57da544bc6f">IMP::example::ExampleDecorator::ExampleDecorator()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#ace0e060378c780736124296409708ae6">IMP::isd::Nuisance::Nuisance()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#aeafaf6681ae99c900ffaa05718ccf628">IMP::isd::Nuisance::get_is_setup()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#adb6c778a5206c24a48fe1ed1b4eab3bd">IMP::isd::Nuisance::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#ae984c3de90b9c6a4fe5448882d99466b">IMP::isd::Nuisance::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Scale.html#a5f4c917e97841eed0a58a91a0ee1de07">IMP::isd::Scale::Scale()</a>, <a href="classIMP_1_1isd_1_1Scale.html#a1c4ea1069548c472aac95d8baba35e43">IMP::isd::Scale::get_is_setup()</a>, <a href="classIMP_1_1isd_1_1Scale.html#ae5980af780760a651f53e3aec2e3f927">IMP::isd::Scale::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Scale.html#a64846198147a18dd2961296f9c505e15">IMP::isd::Scale::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Switching.html#adbe93c6f655fc3889e6f1aa3c4c9c5d7">IMP::isd::Switching::Switching()</a>, <a href="classIMP_1_1isd_1_1Switching.html#a636bbf5600566b34962294ff82477ab4">IMP::isd::Switching::get_is_setup()</a>, <a href="classIMP_1_1isd_1_1Switching.html#a25a8d0541741548d52c6b8a899603ce1">IMP::isd::Switching::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Switching.html#a7629c9f295be4a6ec397577a46168a4e">IMP::isd::Switching::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Weight.html#aa4caee859369a998a57f898dd077eee7">IMP::isd::Weight::Weight()</a>, <a href="classIMP_1_1isd_1_1Weight.html#a602e5611d8003055d3a8bd5f61b0cd70">IMP::isd::Weight::get_is_setup()</a>, <a href="classIMP_1_1isd_1_1Weight.html#a630585629ee22f806b53d8bc2a722d12">IMP::isd::Weight::setup_particle()</a>, <a href="classIMP_1_1kernel_1_1Decorator.html#a581c19e071fc4e34c0495768f839185f">IMP::kernel::Decorator::Decorator()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#ad85b97916de8136de25e5bbaae1395d3">IMP::kinematics::KinematicNode::KinematicNode()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a4fc3cc92cb23c1368c5adc6233baa101">IMP::kinematics::KinematicNode::get_is_setup()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a8c79d455a1b16bec5d8fb8c8cbb58865">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a99d86fe93aedd095bf27f4bd44aa798e">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#addbb41f5314b854c1abb0727962c548c">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#af6132d8ebe861d1fe20e504d0d35ebd0">IMP::misc::CustomXYZR::CustomXYZR()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a0cddf72d54e957440de09f724d9a4c7c">IMP::misc::CustomXYZR::get_is_setup()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a5536f1effbec7e595f7aaacf1a076eea">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a01fb1f7ade9751fb227788a9710d20e9">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a3c29f8066699269d333aee62e7f37c61">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Resolution.html#aea8e9de929b1c7509b5caeae270b6c12">IMP::pmi::Resolution::get_is_setup()</a>, <a href="classIMP_1_1pmi_1_1Resolution.html#a07e0c32c35432d0bd9261f29903b6c9d">IMP::pmi::Resolution::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Resolution.html#aecc4b8482477f9c7fdea21d9cf56967d">IMP::pmi::Resolution::Resolution()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#a989deccba99f30f6c8cf87fa05ff0958">IMP::pmi::Symmetric::get_is_setup()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#a8271d81d8ea67b68dfc2a5d6c4ee906f">IMP::pmi::Symmetric::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#ab893cd58674082efc59b1e20d7aacb21">IMP::pmi::Symmetric::Symmetric()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#a91990017cd3dac707c5229bbfbf6b4a9">IMP::pmi::Uncertainty::get_is_setup()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#ada189b2935cf9659fec64ca96e566b77">IMP::pmi::Uncertainty::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#af52ba4afd39a94ea16f11498422814eb">IMP::pmi::Uncertainty::Uncertainty()</a></td></tr>
202 <tr><td>@ref IMP::kernel::ParticleIndexAdaptor</td><td><a href="classIMP_1_1atom_1_1Representation.html#a70250fa1e9d4645dccde0f47df733346">IMP::atom::Representation::add_representation()</a>, <a href="classIMP_1_1core_1_1Reference.html#a84c7fd0083e01ca749f93c3caad5efa5">IMP::core::Reference::setup_particle()</a>, <a href="classIMP_1_1core_1_1Reference.html#ad9a2510e4cbd4392393e15cf43f48950">IMP::core::Reference::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#adf747d47d9a5fc85a39ee2b8f2ec7b62">IMP::core::RigidBody::add_member()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ad8f626bb808ec049e9f70861314014a6">IMP::core::RigidBody::add_non_rigid_member()</a>, <a href="classIMP_1_1core_1_1RigidBodyMember.html#a3cc86dc6aa5d02aad989100bce5aa30a">IMP::core::RigidBodyMember::get_is_setup()</a>, <a href="classIMP_1_1core_1_1RigidMember.html#adefac1c9947ca771287f4d1f4c9287bf">IMP::core::RigidMember::get_is_setup()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#a26757b4c5f6c39ea35a39d2d6f16f69f">IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint()</a>, <a href="classIMP_1_1pmi_1_1SigmoidRestraintSphere.html#a07bf22f2814d86f43e0e71a662fd346b">IMP::pmi::SigmoidRestraintSphere::SigmoidRestraintSphere()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#a9cb0cc97ac03a5405a0ccd355537b57b">IMP::pmi::TransformMover::add_rigid_body_particle()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#a62e7d5dd4d04ef113d70591ae92bb093">IMP::pmi::TransformMover::add_xyz_particle()</a></td></tr>
203 <tr><td>@ref IMP::kernel::ParticleIndexesAdaptor</td><td><a href="classIMP_1_1atom_1_1Hierarchy.html#ac1a4d74fd46b7137273656725a0e6f6f">IMP::atom::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1atom_1_1RemoveRigidMotionOptimizerState.html#a8690af4e278d0499caa9e6bbc75bcb38">IMP::atom::RemoveRigidMotionOptimizerState::RemoveRigidMotionOptimizerState()</a>, <a href="classIMP_1_1atom_1_1RemoveTranslationOptimizerState.html#a208b5b2293fda1bfe89ba18170c33407">IMP::atom::RemoveTranslationOptimizerState::RemoveTranslationOptimizerState()</a>, <a href="classIMP_1_1atom_1_1VelocityScalingOptimizerState.html#a3ad919aac9c59b9a54789a3730acc073">IMP::atom::VelocityScalingOptimizerState::VelocityScalingOptimizerState()</a>, <a href="classIMP_1_1atom_1_1WritePDBOptimizerState.html#a68b2ab1f1b0591a78103dc96888a1b87">IMP::atom::WritePDBOptimizerState::WritePDBOptimizerState()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a6d174083c79ddd582cc07c2ef8954a32">IMP::core::RigidBody::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ae678bfb4d66a2934b449f3079989d65e">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#aabd4f6c3f08a7c3e24405aab08b1f135">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1CompositeRestraint.html#a55c398ef529347aa33425d3fbf55dbb2">IMP::pmi::CompositeRestraint::CompositeRestraint()</a>, <a href="classIMP_1_1pmi_1_1CompositeRestraint.html#a88ad8bf14f66ca4b66c600b34b6f52f4">IMP::pmi::CompositeRestraint::add_composite_particle()</a></td></tr>
204 <tr><td>@ref IMP::kernel::QuadContainer</td><td><a href="classIMP_1_1kernel_1_1QuadContainerAdaptor.html#a5984ee97a816ccceba6577109ba6255e">IMP::kernel::QuadContainerAdaptor::QuadContainerAdaptor()</a></td></tr>
205 <tr><td>@ref IMP::kernel::QuadContainerAdaptor</td><td><a href="classIMP_1_1container_1_1QuadsRestraint.html#a367897bc174f30e434f34d74f53f4103">IMP::container::QuadsRestraint::QuadsRestraint()</a></td></tr>
206 <tr><td>@ref IMP::kernel::QuadModifier</td><td><a href="classIMP_1_1kernel_1_1QuadContainer.html#acba02b751f223bb3692140f2d84110ba">IMP::kernel::QuadContainer::apply()</a>, <a href="classIMP_1_1kernel_1_1QuadContainer.html#a3182c008cef32e9083ca30d74719e1b4">IMP::kernel::QuadContainer::apply_generic()</a>, <a href="classIMP_1_1kernel_1_1QuadContainer.html#ae6886994a8f5d508a7ad084bf4f990f0">IMP::kernel::QuadContainer::do_apply()</a></td></tr>
207 <tr><td>@ref IMP::kernel::QuadScore</td><td><a href="classIMP_1_1container_1_1PredicateQuadsRestraint.html#a8dcc6bfe455a32f7171586037c40933a">IMP::container::PredicateQuadsRestraint::set_score()</a>, <a href="classIMP_1_1container_1_1PredicateQuadsRestraint.html#af0f1f7fba8656efc296f561266fbc5dc">IMP::container::PredicateQuadsRestraint::set_unknown_score()</a>, <a href="classIMP_1_1container_1_1QuadsRestraint.html#a367897bc174f30e434f34d74f53f4103">IMP::container::QuadsRestraint::QuadsRestraint()</a></td></tr>
208 <tr><td>@ref IMP::kernel::Restraint</td><td><a href="classIMP_1_1core_1_1IncrementalScoringFunction.html#a8d25412bb974210851c1c18ad8567f36">IMP::core::IncrementalScoringFunction::create_data()</a>, <a href="classIMP_1_1core_1_1MinimumRestraint.html#a414ca9e46291af1312373013622806b9">IMP::core::MinimumRestraint::add_restraint()</a>, <a href="classIMP_1_1core_1_1MinimumRestraint.html#a0655caf1e29255f0a421a48bb3215190">IMP::core::MinimumRestraint::remove_restraint()</a>, <a href="classIMP_1_1display_1_1RestraintGeometry.html#a8d29dbc06176c8b4e3234bdd7b9a744d">IMP::display::RestraintGeometry::RestraintGeometry()</a>, <a href="classIMP_1_1display_1_1RestraintGeometry.html#a7b0089ae5cae2cbdffd2947653c7ab4e">IMP::display::RestraintGeometry::RestraintGeometry()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#adb2fa9c11b8890d5fb8c45e0bb6ddf32">IMP::domino::RestraintCache::add_restraint_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a1912bee15e6361f9c9bb37fc566d0ddb">IMP::domino::RestraintCache::add_restraint_set_child_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#abe89754d9654db827f15ecdfbd92bad1">IMP::domino::RestraintCache::get_subset()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#ad0fd79f89825f4a73b169de2bcf1aaeb">IMP::domino::RestraintCache::get_score()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#aeacabf8b40ea4789ca165cd4773a0acb">IMP::domino::RestraintCache::get_score()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a8e10e0f3973fe941986e8cbf1674582d">IMP::domino::RestraintCache::get_slice()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a7cde8be9e50ebe392c39f47c24316a42">IMP::domino::RestraintCache::load_last_score()</a>, <a href="classIMP_1_1isd_1_1AmbiguousRestraint.html#a938caaca683e045e9bbf97269112a72b">IMP::isd::AmbiguousRestraint::AmbiguousRestraint()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a25e3738a5b7ee7c207c2d6dcc56e8162">IMP::kernel::Model::get_maximum_score()</a>, <a href="classIMP_1_1kernel_1_1Model.html#aa1b7b2ae87bdf52a34bdd05c75c36b29">IMP::kernel::Model::set_maximum_score()</a>, <a href="classIMP_1_1kernel_1_1RestraintSet.html#af1ee3b95150728ba171915bf4aa71bbe">IMP::kernel::RestraintSet::remove_restraint()</a>, <a href="classIMP_1_1kernel_1_1RestraintSet.html#aabcb9cf37bbaf3cd92ebdac391960faf">IMP::kernel::RestraintSet::add_restraint()</a>, <a href="classIMP_1_1kernel_1_1RestraintSet.html#a59310ca8b3c2f564a938e83910c716af">IMP::kernel::RestraintSet::on_add()</a>, <a href="classIMP_1_1kernel_1_1RestraintSet.html#a522ec1e65fbf250480ad2e8f6329465c">IMP::kernel::RestraintSet::on_remove()</a>, <a href="classIMP_1_1kernel_1_1RestraintsAdaptor.html#a2fd493fedcf2b313941e4080d0af17e4">IMP::kernel::RestraintsAdaptor::get()</a>, <a href="classIMP_1_1kernel_1_1RestraintsAdaptor.html#ab647eb485e8f992351685a8e7faa4a59">IMP::kernel::RestraintsAdaptor::RestraintsAdaptor()</a>, <a href="classIMP_1_1kernel_1_1ScoreAccumulator.html#a5e8120bd80573c65eff7b170335a3c8e">IMP::kernel::ScoreAccumulator::ScoreAccumulator()</a>, <a href="classIMP_1_1kernel_1_1ScoringFunctionAdaptor.html#aa62e2a283f933338f99272a4d0cbcd8f">IMP::kernel::ScoringFunctionAdaptor::get()</a>, <a href="classIMP_1_1kernel_1_1ScoringFunctionAdaptor.html#a5dd11fc681341466b9235199ec039ee9">IMP::kernel::ScoringFunctionAdaptor::ScoringFunctionAdaptor()</a>, <a href="namespaceIMP_1_1rmf.html#af9a247d8d35e90e6a73c740dc81cd3d3">IMP::rmf::add_restraint()</a></td></tr>
209 <tr><td>@ref IMP::kernel::RestraintSet</td><td><a href="classIMP_1_1display_1_1RestraintSetGeometry.html#a23bc10f065a47fba6b6ddbc628f94bc3">IMP::display::RestraintSetGeometry::RestraintSetGeometry()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#adb2fa9c11b8890d5fb8c45e0bb6ddf32">IMP::domino::RestraintCache::add_restraint_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a1912bee15e6361f9c9bb37fc566d0ddb">IMP::domino::RestraintCache::add_restraint_set_child_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a56bb538e2a59268eb5de499e909b2a2e">IMP::domino::RestraintCache::add_restraint_set_internal()</a>, <a href="classIMP_1_1kernel_1_1RestraintSet.html#a522ec1e65fbf250480ad2e8f6329465c">IMP::kernel::RestraintSet::on_remove()</a>, <a href="namespaceIMP_1_1domino.html#a54f68c619a127b816e0cadcf94638b7d">IMP::domino::get_restraints()</a></td></tr>
210 <tr><td>@ref IMP::kernel::RestraintsAdaptor</td><td><a href="classIMP_1_1core_1_1RestraintsScoringFunction.html#a115859daee8e31add0cadbdf933475ed">IMP::core::RestraintsScoringFunction::RestraintsScoringFunction()</a>, <a href="classIMP_1_1core_1_1RestraintsScoringFunction.html#a5ab60172ece02701b836846239c71c9a">IMP::core::RestraintsScoringFunction::RestraintsScoringFunction()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a4bd5f4f7ce9d342c5bfea7fcf0b8d951">IMP::domino::RestraintCache::add_restraints()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#a7f12cfb50a6614eeed2d4ecc0f968d2c">IMP::domino::RestraintScoreSubsetFilterTable::RestraintScoreSubsetFilterTable()</a></td></tr>
211 <tr><td>@ref IMP::kernel::ScoreAccumulator</td><td><a href="classIMP_1_1example_1_1ExampleRestraint.html#aaee98dfa83c4a5ba78673890312894cb">IMP::example::ExampleRestraint::do_add_score_and_derivatives()</a>, <a href="classIMP_1_1kernel_1_1Restraint.html#a58d5464f91a4bb7e509820c6c9fc6e37">IMP::kernel::Restraint::add_score_and_derivatives()</a>, <a href="classIMP_1_1kernel_1_1Restraint.html#aa68def3a588577ee90f2fc499b3cc6aa">IMP::kernel::Restraint::do_add_score_and_derivatives()</a>, <a href="classIMP_1_1kernel_1_1ScoreAccumulator.html#a5e8120bd80573c65eff7b170335a3c8e">IMP::kernel::ScoreAccumulator::ScoreAccumulator()</a>, <a href="classIMP_1_1kernel_1_1ScoreAccumulator.html#a6d755effd9cdd0f406e82dc84da7ad47">IMP::kernel::ScoreAccumulator::ScoreAccumulator()</a>, <a href="classIMP_1_1kernel_1_1ScoringFunction.html#af930088aae1a36132431c0182648b427">IMP::kernel::ScoringFunction::do_add_score_and_derivatives()</a></td></tr>
212 <tr><td>@ref IMP::kernel::ScoreState</td><td><a href="classIMP_1_1kernel_1_1Model.html#a3ddb10c31882c286e33d7b30349f2500">IMP::kernel::Model::remove_score_state()</a>, <a href="classIMP_1_1kernel_1_1Model.html#ac51e7485d85aeb49f2c04c978e4c3631">IMP::kernel::Model::add_score_state()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a0c9c4d8039260ee30fbd8e3e0dc77798">IMP::kernel::Model::do_add_score_state()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a7061aa7a185e9a11f60001bf485f3a8a">IMP::kernel::Model::do_check_update_order()</a>, <a href="classIMP_1_1kernel_1_1Model.html#a3fcde81d8effa700f4cd573c4f953201">IMP::kernel::Model::do_remove_score_state()</a></td></tr>
213 <tr><td>@ref IMP::kernel::ScoringFunction</td><td><a href="classIMP_1_1kernel_1_1ScoringFunctionAdaptor.html#a8088f5512b14874d08d0709b862e1945">IMP::kernel::ScoringFunctionAdaptor::get()</a>, <a href="classIMP_1_1kernel_1_1ScoringFunctionAdaptor.html#a100aea4cd2c5956e4ef751a326936e07">IMP::kernel::ScoringFunctionAdaptor::ScoringFunctionAdaptor()</a>, <a href="namespaceIMP_1_1kernel.html#ab7088bbe1134f1f8bc2e71c1b10651a3">IMP::kernel::create_decomposition()</a></td></tr>
214 <tr><td>@ref IMP::kernel::ScoringFunctionAdaptor</td><td><a href="classIMP_1_1kernel_1_1Optimizer.html#a6b2d98e35b2e13aaac651f0564e04a9b">IMP::kernel::Optimizer::set_scoring_function()</a>, <a href="classIMP_1_1kernel_1_1Sampler.html#ace92771391bfa4ecf077eea508c41ee5">IMP::kernel::Sampler::set_scoring_function()</a>, <a href="namespaceIMP_1_1kernel.html#aa91d78acab6fce9481d7464cdabfde9d">IMP::kernel::show_restraint_hierarchy()</a></td></tr>
215 <tr><td>@ref IMP::kernel::SingletonContainer</td><td><a href="classIMP_1_1container_1_1ConnectingPairContainer.html#ae67fa5cdec44c33d283ebeee886ae640">IMP::container::ConnectingPairContainer::ConnectingPairContainer()</a>, <a href="classIMP_1_1kernel_1_1SingletonContainerAdaptor.html#a09653008a1e8054a0a9b39aa5e9e60fc">IMP::kernel::SingletonContainerAdaptor::SingletonContainerAdaptor()</a></td></tr>
216 <tr><td>@ref IMP::kernel::SingletonContainerAdaptor</td><td><a href="classIMP_1_1container_1_1SingletonsRestraint.html#a0846e4ed2f4734d79ce283c39d9a9d7f">IMP::container::SingletonsRestraint::SingletonsRestraint()</a></td></tr>
217 <tr><td>@ref IMP::kernel::SingletonModifier</td><td><a href="classIMP_1_1kernel_1_1SingletonContainer.html#a57656d80f22e75703d8e61ea87996c52">IMP::kernel::SingletonContainer::apply()</a>, <a href="classIMP_1_1kernel_1_1SingletonContainer.html#a669f4f90296988ce7536b0268049eb2f">IMP::kernel::SingletonContainer::apply_generic()</a>, <a href="classIMP_1_1kernel_1_1SingletonContainer.html#a4f0cf13d2bb449f5ff6912ced77e065e">IMP::kernel::SingletonContainer::do_apply()</a></td></tr>
218 <tr><td>@ref IMP::kernel::SingletonScore</td><td><a href="classIMP_1_1container_1_1PredicateSingletonsRestraint.html#ac46ccba91d098a03a244672ceefd70ab">IMP::container::PredicateSingletonsRestraint::set_score()</a>, <a href="classIMP_1_1container_1_1PredicateSingletonsRestraint.html#af1cc16c7967776642909cb915524455b">IMP::container::PredicateSingletonsRestraint::set_unknown_score()</a>, <a href="classIMP_1_1container_1_1SingletonsRestraint.html#a0846e4ed2f4734d79ce283c39d9a9d7f">IMP::container::SingletonsRestraint::SingletonsRestraint()</a></td></tr>
219 <tr><td>@ref IMP::kernel::TripletContainer</td><td><a href="classIMP_1_1kernel_1_1TripletContainerAdaptor.html#abaef4074f879e45a2057e002d14f177c">IMP::kernel::TripletContainerAdaptor::TripletContainerAdaptor()</a></td></tr>
220 <tr><td>@ref IMP::kernel::TripletContainerAdaptor</td><td><a href="classIMP_1_1container_1_1TripletsRestraint.html#a9ea55bd7a7c97ee7e91eab54912845d1">IMP::container::TripletsRestraint::TripletsRestraint()</a></td></tr>
221 <tr><td>@ref IMP::kernel::TripletModifier</td><td><a href="classIMP_1_1kernel_1_1TripletContainer.html#abcb9bef4b61921b61249e0ac30f578bd">IMP::kernel::TripletContainer::apply()</a>, <a href="classIMP_1_1kernel_1_1TripletContainer.html#a05104d94e8b34133e4b2311f59f9dcdf">IMP::kernel::TripletContainer::apply_generic()</a>, <a href="classIMP_1_1kernel_1_1TripletContainer.html#a17e2dc52d73b0403d5eb537a4330939e">IMP::kernel::TripletContainer::do_apply()</a></td></tr>
222 <tr><td>@ref IMP::kernel::TripletScore</td><td><a href="classIMP_1_1container_1_1PredicateTripletsRestraint.html#a67ebf185ac6ba39a364b80a45096259f">IMP::container::PredicateTripletsRestraint::set_score()</a>, <a href="classIMP_1_1container_1_1PredicateTripletsRestraint.html#a54200937e033d6f669040ecdf3258f84">IMP::container::PredicateTripletsRestraint::set_unknown_score()</a>, <a href="classIMP_1_1container_1_1TripletsRestraint.html#a9ea55bd7a7c97ee7e91eab54912845d1">IMP::container::TripletsRestraint::TripletsRestraint()</a></td></tr>
223 <tr><td>@ref IMP::kernel::Undecorator</td><td><a href="classIMP_1_1kernel_1_1Model.html#ab9c6350c374b17d2435efa39a531b9d5">IMP::kernel::Model::add_undecorator()</a></td></tr>
224 </table>
225 # IMP.kinematics # {#argument_index_kinematics}
226 <table><tr>
227 <th>Class</th><th>Users</th></tr>
228 <tr><td>@ref IMP::kinematics::DOFsSampler</td><td><a href="classIMP_1_1kinematics_1_1LocalPlanner.html#a421139b1883cf862cfd30224846c2ca5">IMP::kinematics::LocalPlanner::LocalPlanner()</a>, <a href="classIMP_1_1kinematics_1_1PathLocalPlanner.html#a2241b79259d029b1e5c3808862073591">IMP::kinematics::PathLocalPlanner::PathLocalPlanner()</a>, <a href="classIMP_1_1kinematics_1_1RRT.html#ae36363751a8efa44da943d348b05f630">IMP::kinematics::RRT::RRT()</a></td></tr>
229 <tr><td>@ref IMP::kinematics::Joint</td><td><a href="classIMP_1_1kinematics_1_1CompositeJoint.html#a5c53ae6c3e1d44be15e303bb88dc624b">IMP::kinematics::CompositeJoint::add_downstream_joint()</a>, <a href="classIMP_1_1kinematics_1_1CompositeJoint.html#a16faab96024055e41874f66e7e64819a">IMP::kinematics::CompositeJoint::add_upstream_joint()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#aa327ed003021277f339df961628efb2f">IMP::kinematics::KinematicForest::add_edge()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a4ab04dfa734b150d38cd7f41ad7a357f">IMP::kinematics::KinematicNode::do_setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a99d86fe93aedd095bf27f4bd44aa798e">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a1dfb8c5b9763fb616f354c95a78c53d7">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a56e69b049f4e9237d5a7933cc5a53cd0">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#addbb41f5314b854c1abb0727962c548c">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#ae89ff1d8121a770643723f6b11d59016">IMP::kinematics::KinematicNode::add_out_joint()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#af6fbf6325f2d75517cc9c6199f6e1c98">IMP::kinematics::KinematicNode::set_in_joint()</a></td></tr>
230 <tr><td>@ref IMP::kinematics::KinematicForest</td><td><a href="classIMP_1_1kinematics_1_1Joint.html#a55f61a87ca11cf493e0465e9136af62f">IMP::kinematics::Joint::set_owner_kf()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForestScoreState.html#a45bac4078cf476eb4921c90bbddec56b">IMP::kinematics::KinematicForestScoreState::KinematicForestScoreState()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a4ab04dfa734b150d38cd7f41ad7a357f">IMP::kinematics::KinematicNode::do_setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#ae2ec41979137f8a5524687b105e94760">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a8c79d455a1b16bec5d8fb8c8cbb58865">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a99d86fe93aedd095bf27f4bd44aa798e">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a1dfb8c5b9763fb616f354c95a78c53d7">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a56e69b049f4e9237d5a7933cc5a53cd0">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#addbb41f5314b854c1abb0727962c548c">IMP::kinematics::KinematicNode::setup_particle()</a></td></tr>
231 <tr><td>@ref IMP::kinematics::LocalPlanner</td><td><a href="classIMP_1_1kinematics_1_1RRT.html#ae36363751a8efa44da943d348b05f630">IMP::kinematics::RRT::RRT()</a></td></tr>
232 </table>
233 # IMP.misc # {#argument_index_misc}
234 <table><tr>
235 <th>Class</th><th>Users</th></tr>
236 <tr><td>@ref IMP::misc::CustomXYZR</td><td><a href="namespaceIMP_1_1misc.html#a65ae63767baf9a8606e74158c6ef2ade">IMP::misc::get_distance()</a>, <a href="namespaceIMP_1_1misc.html#a4754647ec2a9fab5886f7c0ff31c27a0">IMP::misc::get_sphere_d_geometry()</a>, <a href="namespaceIMP_1_1misc.html#a1cca898df2ee830b5c161c85f0a1dd81">IMP::misc::set_sphere_d_geometry()</a></td></tr>
237 <tr><td>@ref IMP::misc::LogPairScore</td><td><a href="classIMP_1_1misc_1_1LogPairScore.html#a959fd9c4aaa38c637a9fc8ad23201e65">IMP::misc::LogPairScore::IMP_PAIR_SCORE_METHODS()</a></td></tr>
238 </table>
239 # IMP.modeller # {#argument_index_modeller}
240 <table><tr>
241 <th>Class</th><th>Users</th></tr>
242 <tr><td>@ref IMP::modeller::BinormalTerm</td><td><a href="classIMP_1_1modeller_1_1MultipleBinormalRestraint.html#ab1a685860093cf225410b76ff99e002a">IMP::modeller::MultipleBinormalRestraint::add_term()</a></td></tr>
243 </table>
244 # IMP.multifit # {#argument_index_multifit}
245 <table><tr>
246 <th>Class</th><th>Users</th></tr>
247 <tr><td>@ref IMP::multifit::AnchorsData</td><td><a href="classIMP_1_1multifit_1_1ProteinsAnchorsSamplingSpace.html#a897a2e3f157111ff53f6b1f94687c217">IMP::multifit::ProteinsAnchorsSamplingSpace::set_anchors()</a>, <a href="namespaceIMP_1_1multifit.html#a173eff7add1e1652a69ce9c1365ddf2f">IMP::multifit::get_anchor_indices_matching_secondary_structure()</a>, <a href="namespaceIMP_1_1multifit.html#ae4ba0e88472d3177de3ea67a7583d5c0">IMP::multifit::write_cmm()</a>, <a href="namespaceIMP_1_1multifit.html#ae2e18c9a8f1e3e81cf1a561a93e235c0">IMP::multifit::write_txt()</a></td></tr>
248 <tr><td>@ref IMP::multifit::AssemblyHeader</td><td><a href="classIMP_1_1multifit_1_1SettingsData.html#aaa24862022bf887ad2291a4e9e488a48">IMP::multifit::SettingsData::set_assembly_header()</a></td></tr>
249 <tr><td>@ref IMP::multifit::ComponentHeader</td><td><a href="classIMP_1_1multifit_1_1SettingsData.html#a991309d896089e3fd7ec4f9b70ad0ecb">IMP::multifit::SettingsData::add_component_header()</a>, <a href="classIMP_1_1multifit_1_1SettingsData.html#a6c99c0e9881422ed66c90ffd42a6d9e4">IMP::multifit::SettingsData::remove_component_header()</a></td></tr>
250 <tr><td>@ref IMP::multifit::DataPointsAssignment</td><td><a href="namespaceIMP_1_1multifit.html#a6945fa68efec8cd7f189ebd51b7af727">IMP::multifit::get_segment_maximum()</a>, <a href="namespaceIMP_1_1multifit.html#ab1ebb302ab2e310015f0f643bcef86f7">IMP::multifit::get_segment_maximum()</a>, <a href="namespaceIMP_1_1multifit.html#a1ab8b06464f3c9727f0a710d4f1e2f0a">IMP::multifit::write_chimera()</a>, <a href="namespaceIMP_1_1multifit.html#a3f44dc59f3fb41dfdd084270d6a10a61">IMP::multifit::write_pdb()</a>, <a href="namespaceIMP_1_1multifit.html#a8009ecb4c53812a36bf544ed7e9fe9a0">IMP::multifit::write_segment_as_mrc()</a>, <a href="namespaceIMP_1_1multifit.html#afa9365426346e3cbf57346e724da4691">IMP::multifit::write_segment_as_pdb()</a>, <a href="namespaceIMP_1_1multifit.html#ac66c9128b0009595989bc520e3e6dcd3">IMP::multifit::write_segments_as_mrc()</a>, <a href="namespaceIMP_1_1multifit.html#a52c63362745917843277eb7ba97d76d5">IMP::multifit::write_segments_as_pdb()</a></td></tr>
251 <tr><td>@ref IMP::multifit::ProteinsAnchorsSamplingSpace</td><td><a href="classIMP_1_1multifit_1_1Ensemble.html#ac3c46ee809eda56b27ed47c510d6b70b">IMP::multifit::Ensemble::Ensemble()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a5951962f4133ac2a456960ced4511253">IMP::multifit::ProteomicsEMAlignmentAtomic::ProteomicsEMAlignmentAtomic()</a>, <a href="namespaceIMP_1_1multifit.html#a1cc01cbbbb1cf9bb7f226524e0616e12">IMP::multifit::get_part_of_sampling_space()</a>, <a href="namespaceIMP_1_1multifit.html#a990fc248adf46233d96011ab77130eec">IMP::multifit::load_ensemble()</a>, <a href="namespaceIMP_1_1multifit.html#a11b1f20be441ca935aedaf5947b01cb6">IMP::multifit::write_protein_anchors_mapping()</a></td></tr>
252 <tr><td>@ref IMP::multifit::ProteomicsData</td><td><a href="classIMP_1_1multifit_1_1ProteinsAnchorsSamplingSpace.html#a5611298f4d66c2966344bb6f37783df5">IMP::multifit::ProteinsAnchorsSamplingSpace::ProteinsAnchorsSamplingSpace()</a>, <a href="namespaceIMP_1_1multifit.html#aac05dae9e06cb11ef27e820cf54be014">IMP::multifit::get_partial_proteomics_data()</a>, <a href="namespaceIMP_1_1multifit.html#adbd924144aee36a0b6dd9789ca164da8">IMP::multifit::read_protein_anchors_mapping()</a></td></tr>
253 <tr><td>@ref IMP::multifit::SettingsData</td><td><a href="classIMP_1_1multifit_1_1Ensemble.html#ac3c46ee809eda56b27ed47c510d6b70b">IMP::multifit::Ensemble::Ensemble()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a5951962f4133ac2a456960ced4511253">IMP::multifit::ProteomicsEMAlignmentAtomic::ProteomicsEMAlignmentAtomic()</a>, <a href="namespaceIMP_1_1multifit.html#a3746dc39094e607667c55bde5aca85e6">IMP::multifit::get_partial_assembly_setting_data()</a>, <a href="namespaceIMP_1_1multifit.html#a990fc248adf46233d96011ab77130eec">IMP::multifit::load_ensemble()</a>, <a href="namespaceIMP_1_1multifit.html#aa9401684ce59f4d47aaa1e519e1d574b">IMP::multifit::write_settings()</a></td></tr>
254 </table>
255 # IMP.rotamer # {#argument_index_rotamer}
256 <table><tr>
257 <th>Class</th><th>Users</th></tr>
258 <tr><td>@ref IMP::rotamer::RotamerLibrary</td><td><a href="classIMP_1_1rotamer_1_1RotamerCalculator.html#ae6d0ae1fea1b6f90e0ac4f4698f9e0a9">IMP::rotamer::RotamerCalculator::RotamerCalculator()</a></td></tr>
259 </table>
260 # IMP.saxs # {#argument_index_saxs}
261 <table><tr>
262 <th>Class</th><th>Users</th></tr>
263 <tr><td>@ref IMP::saxs::DeltaDistributionFunction</td><td><a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a45d083d21f25cf20251b2e8d464f2ad5">IMP::saxs::DerivativeCalculator::compute_intensity_derivatives()</a></td></tr>
264 <tr><td>@ref IMP::saxs::DerivativeCalculator</td><td><a href="classIMP_1_1saxs_1_1RigidBodiesProfileHandler.html#a6876a8b69d19ec3454147d08096dd100">IMP::saxs::RigidBodiesProfileHandler::compute_derivatives()</a></td></tr>
265 <tr><td>@ref IMP::saxs::FormFactorTable</td><td><a href="classIMP_1_1saxs_1_1Profile.html#a8a1d10d7b06c24dbc9cc3b70d7b56a92">IMP::saxs::Profile::set_ff_table()</a>, <a href="namespaceIMP_1_1saxs.html#a22b0c7ea0b5f4f9d34870ce78131518a">IMP::saxs::compute_profile()</a>, <a href="namespaceIMP_1_1saxs.html#a480827857014751342a217cf2fcc91e8">IMP::saxs::get_form_factors()</a></td></tr>
266 <tr><td>@ref IMP::saxs::Profile</td><td><a href="classIMP_1_1saxs_1_1ChiFreeScore.html#a11612b0a90e33cf33c78b768f5e12385">IMP::saxs::ChiFreeScore::compute_offset()</a>, <a href="classIMP_1_1saxs_1_1ChiFreeScore.html#a82e82ff7311acdcefd00a0a70c98940b">IMP::saxs::ChiFreeScore::compute_scale_factor()</a>, <a href="classIMP_1_1saxs_1_1ChiFreeScore.html#a89e56f3ee6a11aa44c858fd9df34df52">IMP::saxs::ChiFreeScore::compute_score()</a>, <a href="classIMP_1_1saxs_1_1ChiScore.html#ae080a79a6123544ddc4a7fe45464aecb">IMP::saxs::ChiScore::compute_offset()</a>, <a href="classIMP_1_1saxs_1_1ChiScore.html#a1822d7514bcd7a160a3886a8e7e4bb8e">IMP::saxs::ChiScore::compute_scale_factor()</a>, <a href="classIMP_1_1saxs_1_1ChiScore.html#a645388040b29ba0020b1284fc518c0f2">IMP::saxs::ChiScore::compute_score()</a>, <a href="classIMP_1_1saxs_1_1ChiScore.html#aad0e336b0331021611a3fe8c7ec9924f">IMP::saxs::ChiScore::compute_score()</a>, <a href="classIMP_1_1saxs_1_1ChiScoreLog.html#a26c8ad2094d11e4c9a0a669adf85a80a">IMP::saxs::ChiScoreLog::compute_offset()</a>, <a href="classIMP_1_1saxs_1_1ChiScoreLog.html#a24f356fa7ed3bb6231f902ccb303266e">IMP::saxs::ChiScoreLog::compute_scale_factor()</a>, <a href="classIMP_1_1saxs_1_1ChiScoreLog.html#acb8349968f31784d24a629b9ad425e28">IMP::saxs::ChiScoreLog::compute_score()</a>, <a href="classIMP_1_1saxs_1_1ChiScoreLog.html#a42f40d6e3682f038cb09524430061f88">IMP::saxs::ChiScoreLog::compute_score()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a6d74d86a67d1ba3aefceccb71578c63f">IMP::saxs::DerivativeCalculator::DerivativeCalculator()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a8d39938ff78a4e9c586e38a3d3b1d771">IMP::saxs::DerivativeCalculator::compute_chisquare_derivative()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a2311d2c49eb961cdff56694e44ce655d">IMP::saxs::DerivativeCalculator::compute_chisquare_derivative()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a897bafc64ce5737232d679960a682bd8">IMP::saxs::DerivativeCalculator::compute_gaussian_effect_size()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#aacf9ff590d52121ddc187cefd9739766">IMP::saxs::DerivativeCalculator::precompute_derivative_helpers()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a48c1b3ab8114d572ccb2644ac89410e5">IMP::saxs::DerivativeCalculator::compute_sinc_cos()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a82536430388b99179eaf494ab3c4a227">IMP::saxs::Profile::add()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#ad2161d03baaa5af6d03d72b7de77bd49">IMP::saxs::Profile::add()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a66a17a8754a50ea50f3f2313aed786c0">IMP::saxs::Profile::add_partial_profiles()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a0a1d33df12a2c8468a675327e5d2bb3c">IMP::saxs::Profile::add_partial_profiles()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#aad86fc9975dd25aadd81a698410918ac">IMP::saxs::Profile::copy_errors()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#ab89bf550f73ed2bdc93addcf0b62d23d">IMP::saxs::Profile::downsample()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a2da7f760b5f7c057cf2856a613c681b9">IMP::saxs::Profile::resample()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a344f7cdb6981bb1b9d568a9a8927987b">IMP::saxs::ProfileFitter::ProfileFitter()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#aa2b22f8b8ce22da520317058a8c75c36">IMP::saxs::ProfileFitter::ProfileFitter()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a233de38809e2bb451fb014661d089535">IMP::saxs::ProfileFitter::compute_offset()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a5a88beabc5360854406a1bf76d42d154">IMP::saxs::ProfileFitter::compute_scale_factor()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#aee47b52058b10ed9943f843bb543a797">IMP::saxs::ProfileFitter::compute_score()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#aede1b48c837b0dd74cafb1e783ae0819">IMP::saxs::ProfileFitter::compute_score()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a689741a9f31fc98782a4af93aa29d943">IMP::saxs::ProfileFitter::fit_profile()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a66edb60e5085c5f369a4e786ef0aa4e4">IMP::saxs::ProfileFitter::resample()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a543990fbe9169e6f3b850e9406c949a7">IMP::saxs::ProfileFitter::write_SAXS_fit_file()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#acd1027cc3eff7ffd93e55ad39fd60d93">IMP::saxs::ProfileFitter::search_fit_parameters()</a>, <a href="classIMP_1_1saxs_1_1RadiusOfGyrationRestraint.html#aa1802c804fb1f62b6678c9b2b860b1f8">IMP::saxs::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint()</a>, <a href="classIMP_1_1saxs_1_1Restraint.html#abbc4fdbf88d78283813ae690fae73e6f">IMP::saxs::Restraint::Restraint()</a>, <a href="classIMP_1_1saxs_1_1RigidBodiesProfileHandler.html#a6876a8b69d19ec3454147d08096dd100">IMP::saxs::RigidBodiesProfileHandler::compute_derivatives()</a>, <a href="classIMP_1_1saxs_1_1RigidBodiesProfileHandler.html#ac0113e2be22d5d7c176ff06c81da89e3">IMP::saxs::RigidBodiesProfileHandler::compute_profile()</a>, <a href="classIMP_1_1saxs_1_1WeightedProfileFitter.html#a28c1f37cd4f8ee6ed7ce7ffde6bdfda4">IMP::saxs::WeightedProfileFitter::WeightedProfileFitter()</a></td></tr>
267 <tr><td>@ref IMP::saxs::RadialDistributionFunction</td><td><a href="classIMP_1_1saxs_1_1Profile.html#a1c170e6a2d3867d31fb0a6104093cd33">IMP::saxs::Profile::distribution_2_profile()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#af9badf8c5270bd3431674c24fbd7aeae">IMP::saxs::Profile::profile_2_distribution()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a9dd95cf18dd18cd346ab6185dad2004e">IMP::saxs::Profile::squared_distribution_2_profile()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#ac2aec4005556b0c401702ccdc54f3442">IMP::saxs::Profile::squared_distributions_2_partial_profiles()</a>, <a href="classIMP_1_1saxs_1_1RadialDistributionFunction.html#aeb53667c6c8b782418cc9189c9bd0a12">IMP::saxs::RadialDistributionFunction::add()</a>, <a href="classIMP_1_1saxs_1_1RadialDistributionFunction.html#ae721522ec9a73d6d7a0ca6d70f8c26b0">IMP::saxs::RadialDistributionFunction::fit()</a>, <a href="classIMP_1_1saxs_1_1RadialDistributionFunction.html#a6db926a74bb65954241a8ed464bc21e0">IMP::saxs::RadialDistributionFunction::R_factor_score()</a>, <a href="classIMP_1_1saxs_1_1RadialDistributionFunction.html#a11b8ee90b83286aad0ea5313c7b9a26f">IMP::saxs::RadialDistributionFunction::write_fit_file()</a></td></tr>
268 </table>
269 # IMP.statistics # {#argument_index_statistics}
270 <table><tr>
271 <th>Class</th><th>Users</th></tr>
272 <tr><td>@ref IMP::statistics::Embedding</td><td><a href="classIMP_1_1statistics_1_1EuclideanMetric.html#a5d5bcbea89a38c0c4cdb29b2a6aad159">IMP::statistics::EuclideanMetric::EuclideanMetric()</a>, <a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringEmbedding.html#ad2e702ad3bd288cff7f34307c124456c">IMP::statistics::RecursivePartitionalClusteringEmbedding::RecursivePartitionalClusteringEmbedding()</a>, <a href="namespaceIMP_1_1statistics.html#a2ccc84a060553c450d17b18bce708436">IMP::statistics::create_bin_based_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#a19eae7a22f877948e0582872cb42e760">IMP::statistics::create_centrality_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#ad6ac98231fe5e79078029b821e5d2417">IMP::statistics::create_connectivity_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#a84d813a09204387c1b2af83e6fb5e014">IMP::statistics::create_lloyds_kmeans()</a>, <a href="namespaceIMP_1_1statistics.html#ac31b5cbb1a3c6722e837341ce0ee872d">IMP::statistics::get_centroids()</a>, <a href="namespaceIMP_1_1statistics.html#a974ae5760db93ab3cf0afced47455a29">IMP::statistics::get_representatives()</a></td></tr>
273 <tr><td>@ref IMP::statistics::HistogramD</td><td><a href="namespaceIMP_1_1statistics.html#a6f2a5df02a675039a03a695b45947498">IMP::statistics::show_histogram()</a></td></tr>
274 <tr><td>@ref IMP::statistics::Metric</td><td><a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringMetric.html#a0eb7c7bea72016758a63d42ddcd0552a">IMP::statistics::RecursivePartitionalClusteringMetric::RecursivePartitionalClusteringMetric()</a>, <a href="namespaceIMP_1_1statistics.html#a033ac0d9e680dc724a782c219391dc5c">IMP::statistics::create_centrality_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#a7fa3185254b0cf61b8baa2b04e3461c6">IMP::statistics::create_connectivity_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#ae34d7252a499c1f7a6948fa5283f88a6">IMP::statistics::create_diameter_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#a739c887af40a30b27d360f052f3d001b">IMP::statistics::create_gromos_clustering()</a></td></tr>
275 <tr><td>@ref IMP::statistics::PartitionalClustering</td><td><a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringEmbedding.html#ad2e702ad3bd288cff7f34307c124456c">IMP::statistics::RecursivePartitionalClusteringEmbedding::RecursivePartitionalClusteringEmbedding()</a>, <a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringEmbedding.html#ad985a95838650906b20fab33bf23b3ea">IMP::statistics::RecursivePartitionalClusteringEmbedding::create_full_clustering()</a>, <a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringMetric.html#a0eb7c7bea72016758a63d42ddcd0552a">IMP::statistics::RecursivePartitionalClusteringMetric::RecursivePartitionalClusteringMetric()</a>, <a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringMetric.html#a298cc8279d3029e200a24ce9fb247942">IMP::statistics::RecursivePartitionalClusteringMetric::create_full_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#ac31b5cbb1a3c6722e837341ce0ee872d">IMP::statistics::get_centroids()</a>, <a href="namespaceIMP_1_1statistics.html#a974ae5760db93ab3cf0afced47455a29">IMP::statistics::get_representatives()</a>, <a href="namespaceIMP_1_1statistics.html#a5935bfa801d76e543494e701665dd173">IMP::statistics::validate_partitional_clustering()</a></td></tr>
276 </table>
Restraints create_decomposition(const RestraintsTemp &rs)
Return the decomposition of a list of restraints.
const SpherePatch3D & get_sphere_patch_3d_geometry(const SpherePatch3D &g)
Definition: SpherePatch3D.h:48
static Residue setup_particle(kernel::Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)
Definition: Residue.h:157
Transform(const algebra::Transformation3D &t, bool ignore_non_xyz=false)
Initialize.
virtual void apply_indexes(kernel::Model *m, const kernel::ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
Definition: core/symmetry.h:66
TransformationAndReflectionSymmetry(const algebra::Transformation3D &t, const algebra::Reflection3D &r)
Create with both reflection and translation.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexTriplets &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
PairConstraint(PairModifier *before, PairDerivativeModifier *after, const kernel::ParticlePair &vt, std::string name="PairConstraint %1%")
PartitionalClusteringWithCenter * create_lloyds_kmeans(Embedding *embedding, unsigned int k, unsigned int iterations)
Hierarchies get_leaves(Hierarchy h)
Float fit(const RadialDistributionFunction &model_pr, const std::string &file_name="") const
fit the distributions by scaling according to maximum
int operator()(kernel::Model *m, const kernel::ParticleIndexQuad &vt) const
Enable them to be use as functors.
static State setup_particle(kernel::Model *m, ParticleIndex pi, unsigned int index)
Definition: State.h:36
void set_atom_type(AtomType t)
Set the name and corresponding element and mass.
void add_bonds(Hierarchy mhd) const
add bonds to the structure defined in the hierarchy
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
StateAdaptor(kernel::Model *m, OptimizerState *before, OptimizerState *after)
set the before and after states
void set_orientations(const core::RigidBody &rb, const algebra::Rotation3Ds &rots)
Set the possible rotations that a rigid body can have.
void get_transformed_into(const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true)
Rotate a density map into another map.
Detect cn symmetry in proteins and density maps.
base::Vector< VectorD< D > > get_uniform_upper_hemisphere_cover(const SphereD< D > &s, unsigned int n)
Generate a set of 3D points that uniformly cover a hemisphere.
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Float get_vacuum_form_factor(kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
f(0) in vacuum
virtual int get_value_index(kernel::Model *, kernel::ParticleIndex vt) const
Compute the predicate and the derivative if needed.
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
NOERestraint(kernel::Model *m, Particle *p0, Particle *p1, Particle *sigma, Particle *gamma, double Iexp)
Create the restraint.
void set_score(int predicate_value, kernel::SingletonScore *score)
double get_maximum_score() const
static Nuisance setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: Nuisance.h:31
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
Fine2DRegistrationRestraint(kernel::Model *m)
The ideal topology of a single residue.
Base class for functions of one variable.
virtual double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexTriplets &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
A class to store a set of configurations of a model.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
double get_radius_of_gyration(const kernel::ParticlesTemp &ps)
The base class for simulators.
Definition: Simulator.h:34
GridIndexD< D > get_index(const ExtendedGridIndexD< D > &v) const
Convert a ExtendedIndex into a real Index if possible.
Definition: grid_ranges.h:237
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
The base class to handle reading and writing of density maps.
ModelObjectsTemp get_outputs(kernel::Model *m, const ParticleIndexes &pis) const
RestraintSet(kernel::Model *m, double weight, const std::string &name="RestraintSet %1%")
Create an empty set that is registered with the model.
void set_rotation(double phi, double theta, double psi)
Rotation to apply to the model.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexTriplets &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual void apply_index(kernel::Model *m, kernel::ParticleIndex pi) const
Copies weighted derivatives to fine particles.
A Monte Carlo optimizer.
Definition: MonteCarlo.h:45
Restraints create_current_decomposition(kernel::Model *m, kernel::ParticleIndex vt) const
Simple 3D transformation class.
ParticleIndexes get_indexes(const ParticlesTemp &ps)
virtual int get_value_index(kernel::Model *, const kernel::ParticleIndexPair &pip) const
Compute the predicate and the derivative if needed.
A decorator to associate a particle with a part of a protein.
Definition: Domain.h:21
Float get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2)
Compares the secondary structure probabilities of two residues.
VectorD< D > get_random_vector_on(const BoundingBoxD< D > &bb)
Generate a random vector on a box with uniform density.
void add_restraints(const kernel::RestraintsAdaptor &rs)
A base class for Keys.
Definition: kernel/Key.h:46
A shared container for Triplets.
double get_shift_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
Distance between the two in-plane translations.
Restraint * create_restraint(Score *s, const typename Score::Argument &t, std::string name=std::string())
QuadRestraint(QuadScore *ss, const kernel::ParticleQuad &vt, std::string name="QuadRestraint %1%")
Create the restraint.
Definition: QuadRestraint.h:41
bool get_contains(const SphereD< D > &o) const
Return true if this sphere contains the other one.
Definition: SphereD.h:43
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
Restraints do_create_current_decomposition(kernel::Model *m, kernel::ParticleIndex vt) const
void show_timings(TextOutput out)
RotamerCalculator(const RotamerLibrary *rl)
constructor
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Hierarchies read_multimodel_pdb(base::TextInput input, kernel::Model *model, PDBSelector *selector=get_default_pdb_selector())
double score(const std::vector< IMP::algebra::Vector3D > &points) const
virtual void apply_index(kernel::Model *m, kernel::ParticleIndex p) const
Chain get_chain(Hierarchy h)
void do_project_particles(const kernel::ParticlesTemp &ps, cv::Mat &m2, const algebra::Rotation3D &R, const algebra::Vector3D &translation, const ProjectingOptions &options, MasksManagerPtr masks)
Projects a set of particles. This is the core function that others call.
static Typed setup_particle(kernel::Model *m, ParticleIndex pi, ParticleType t)
Definition: Typed.h:46
atom::Hierarchies create_hierarchies(RMF::FileConstHandle fh, kernel::Model *m)
static Charged setup_particle(kernel::Model *m, ParticleIndex pi, Float charge)
Definition: Charged.h:46
IntsList get_anchor_indices_matching_secondary_structure(const AnchorsData &ad, const atom::SecondaryStructureResidues &ssrs, Float max_rmsd=0.7)
Get lists of anchors that match a sequence of secondary structures.
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
bool same_origin(const DensityMap *other) const
Checks if two maps have the same origin.
Represent an RGB color.
Definition: Color.h:24
static void teardown_particle(RigidBody rb)
Make the rigid body no longer rigid.
BallMover(kernel::Particle *p, kernel::Particles ps, Float max_tr, algebra::Vector3Ds ctrs, algebra::Transformation3Ds trs)
Float get_threshold_for_approximate_mass(DensityMap *m, Float desired_mass, atom::ProteinDensityReference ref=atom::HARPAZ)
Computes the threshold to consider in an EM map to get a desired mass.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual bool get_can_refine(kernel::Particle *) const
Return true if this refiner can refine that particle.
A decorator to associate a particle with a part of a protein/DNA/RNA.
Definition: Fragment.h:20
ProfileFitter(const Profile *exp_profile)
Constructor.
Definition: ProfileFitter.h:36
kernel::Particles add_bonds(Hierarchy hierarchy) const
Add bonds to the given Hierarchy using this topology, and return them.
void link_particles(RMF::FileConstHandle fh, const kernel::ParticlesTemp &hs)
virtual kernel::ModelObjectsTemp do_get_outputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
MolecularDynamics(kernel::Model *m)
static ProjectionParameters setup_particle(kernel::Model *m, ParticleIndex pi)
virtual int get_value_index(kernel::Model *, const kernel::ParticleIndexTriplet &) const
Compute the predicate and the derivative if needed.
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
Atoms get_phi_dihedral_atoms(Residue rd)
Return the atoms comprising the phi dihedral.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
Abstract class for scoring object(s) of type ParticleQuad.
DensityMap * interpolate_map(DensityMap *in_map, double new_spacing)
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void write_pdb(const Selection &mhd, base::TextOutput out, unsigned int model=1)
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.
static RigidBody setup_particle(kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexesAdaptor ps)
Definition: rigid_bodies.h:168
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
static Weight setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: Weight.h:31
Class for adding derivatives from restraints to the model.
algebra::Vector3Ds density2vectors(DensityMap *dmap, Float threshold)
Converts a density grid to a set of paritlces.
void set_incremental_scoring_function(IncrementalScoringFunction *isf)
ConsecutivePairContainer(const kernel::ParticlesTemp &ps, std::string name="ConsecutivePairContainer%1%")
Get the individual particles from the passed SingletonContainer.
Storage and access to force field.
void set_transformation(const algebra::Transformation3D &rot)
GaussianProcessInterpolationRestraint(kernel::Model *m, GaussianProcessInterpolation *gpi)
VectorD< D > get_elementwise_product(const algebra::VectorD< D > &a, const algebra::VectorD< D > &b)
Return the vector that is the elementwise product of the two.
Definition: VectorD.h:431
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
TALOSRestraint(kernel::Model *m, kernel::Particles p, Floats data, kernel::Particle *kappa)
Create restraint from a list of particles and the data.
algebra::Sphere3D get_bounding_sphere(const Hierarchy &h)
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
kernel::ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
base::Vector< VectorD< D > > get_uniform_surface_cover(const SphereD< D > &s, unsigned int n)
Generate a set of vectors which covers a sphere uniformly.
SingletonRestraint(SingletonScore *ss, kernel::Particle *vt, std::string name="SingletonRestraint %1%")
Create the restraint.
Storage of proteomics data.
A base class for modifiers of kernel::ParticleTripletsTemp.
virtual double evaluate_if_good_index(kernel::Model *m, const kernel::ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed.
A shared container for Quads.
BoundingBoxD< 3 > get_bounding_box(const Plane3D &g)
Definition: Plane3D.h:86
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
Ints get_index(const kernel::ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
EnvelopePenetrationRestraint(kernel::Particles ps, DensityMap *em_map, Float threshold)
Constructor.
A base class for algorithms to find spatial proximities.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
static KinematicNode setup_particle(kernel::Model *m, ParticleIndex pi, KinematicForest *owner)
Definition: KinematicNode.h:39
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
SurfaceShellDensityMap * particles2surface(const kernel::ParticlesTemp &ps, Float apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
virtual const ParticlesTemp get_refined(Particle *a) const =0
Refine the passed particle into a set of particles.
void set_score(int predicate_value, kernel::PairScore *score)
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexQuad &vt) const
Compute the predicate and the derivative if needed.
virtual const kernel::ParticlesTemp get_refined(kernel::Particle *) const
Refine the passed particle into a set of particles.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
GaussianRestraint(kernel::Particle *x, kernel::Particle *mu, kernel::Particle *sigma)
Gaussian restraint.
Hierarchy create_simplified_from_volume(Hierarchy h, double resolution)
A connection (bond, angle, dihedral) between some number of endpoints.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
void setup_secondary_structure(kernel::Model *mdl)
Sets up default secondary structure particles for every anchor (run first)
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
void propagate_velocities(const kernel::ParticleIndexes &ps, double step_size)
Second part of velocity Verlet (update velocity)
void set_maximum_score(Restraint *r, double s)
void setup_as_approximation(kernel::Particle *h, const kernel::ParticlesTemp &other)
kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual int get_value(kernel::Particle *vt) const
RadiusOfGyrationRestraint(kernel::Particles ps, int num_residues, Float scale=1.)
Constructor.
double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexQuads &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
ScoreStatesTemp get_dependent_score_states(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
double get_distance(CustomXYZR a, CustomXYZR b)
Compute the distance between a pair of particles.
Definition: CustomXYZR.h:85
void add_solution(const algebra::Transformation3D &t, Float score)
Add a solution to the fitting solution set.
O * object_cast(Object *o)
Definition: object_cast.h:24
PCAAligner(IMP::em::DensityMap *map, float density_threshold)
Definition: PCAAligner.h:33
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
const Floats & get_form_factors(kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
full form factor for reciprocal space profile calculation
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double get_volume(const Selection &s)
Get the total volume of a hierarchy, in cubic angstroms.
AmbiguousNOERestraint(kernel::Model *m, PairContainer *pc, kernel::Particle *sigma, kernel::Particle *gamma, double Iexp)
Create the restraint.
atom::Hierarchy create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, kernel::Model *mdl, float bead_radius)
Coarsen a density map based on voxels clustering.
Represent an ellipsoid in 3D.
Definition: Ellipsoid3D.h:22
Float get_dummy_form_factor(kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
f(0) for solvent
const BoundingBoxD< D > operator+(const BoundingBoxD< D > &o) const
Returning a bounding box containing both.
Definition: BoundingBoxD.h:109
static CHARMMAtom setup_particle(kernel::Model *m, ParticleIndex pi, String charmm_type)
Definition: CHARMMAtom.h:37
Restraints create_current_decomposition(kernel::Model *m, const kernel::ParticleIndexQuad &vt) const
internal::PredicateEquals< Pred, true > make_predicate_equal(const Pred *p, Model *m, int value)
Return a functor that returns true when the predicate has a certain value.
A decorator for a particle with x,y,z coordinates and a radius.
Definition: CustomXYZR.h:24
void do_add_score_and_derivatives(kernel::ScoreAccumulator sa) const
IntsList get_connected_components(em::DensityMap *dmap, float threshold, float edge_threshold)
Return connected components based on density values.
virtual void apply_index(kernel::Model *m, const kernel::ParticleIndexPair &v) const
void add_child(Hierarchy o)
Add a child and check that the types are appropriate.
void apply(const PairModifier *sm) const
Apply a SingletonModifier to the contents.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
Calculates kernel parameters as a function of a specific radius.
void add_charges(Hierarchy hierarchy) const
Add CHARMM charges to the given Hierarchy using this topology.
SampledDensityMap * particles2density(const kernel::ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexQuad &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual unsigned int get_number_of_refined(Particle *a) const
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexTriplet &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Restraint(kernel::Model *m, std::string name)
void show_restraint_hierarchy(ScoringFunctionAdaptor rs, std::ostream &out=std::cout)
Print the hierarchy of restraints.
virtual SubsetFilter * get_subset_filter(const Subset &s, const Subsets &prior_subsets) const =0
Class to deal with the header of Electron Microscopy images in IMP.
Definition: ImageHeader.h:28
static Atom setup_particle(kernel::Model *m, ParticleIndex pi, Atom other)
Definition: atom/Atom.h:242
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Rotation3D()
Create an invalid rotation.
Definition: Rotation3D.h:86
double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
BoundingBoxD< 3 > get_bounding_box(const Geometry &)
Compute the bounding box of any geometric object.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
Class for getting the distance from the map envelope.
virtual int get_value_index(kernel::Model *m, kernel::ParticleIndex vt) const
Compute the predicate and the derivative if needed.
void add_member(kernel::ParticleIndexAdaptor p)
void set_particles(const kernel::Particles &pis)
Set the particles to use.
Stores a 2D rotation matrix.
Definition: Rotation2D.h:36
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
Em2DRestraint(kernel::Model *m)
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual void apply(kernel::Particle *vt) const
kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Assignments get_state_clusters(const Subset &subset, const Assignments &states, ParticleStatesTable *pst, double resolution)
Return subset of the passed states which are representative.
PathLocalPlanner(kernel::Model *model, DOFsSampler *dofs_sampler, DirectionalDOF *directional_dof, int save_step_interval=1)
construct a path planner (default planning is linear)
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexQuad &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual kernel::ModelObjectsTemp do_get_outputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void resample(const Profile *exp_profile, Profile *resampled_profile, bool partial_profiles=false) const
return a profile that is sampled on the q values of the exp_profile
Rotation2D compose(const Rotation2D &a, const Rotation2D &b)
compose two rotations a and b
Definition: Rotation2D.h:108
algebra::Vector3D get_coordinates() const
Get the coordinates of the particle.
Definition: rigid_bodies.h:189
PairContainerSet(kernel::Model *m, std::string name="PairContainerSet %1%")
Construct and empty set.
The base class for geometry.
void get_correlation2d(const cv::Mat &A, const cv::Mat &B, cv::Mat &corr)
Correlation matrix between two 2D matrices using FFT.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
RadiusOfGyrationRestraint(const kernel::Particles &particles, const Profile *exp_profile, const double end_q_rg=1.3)
Constructor.
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
Hierarchy()
null constructor
CysteineCrossLinkRestraint(kernel::Particle *beta, kernel::Particle *sigma, kernel::Particle *epsilon, kernel::Particle *weight, CrossLinkData *data, double fexp)
Create the restraint.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexTriplets &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
unsigned int get_enclosing_image_size(const kernel::ParticlesTemp &ps, double pixel_size, unsigned int slack)
Get an automatic size for an image that contains the particles.
kernel::Restraints create_restraints(RMF::FileConstHandle fh, kernel::Model *m)
void after_evaluate(DerivativeAccumulator *accpt)
Do post evaluation work if needed.
A decorator for a particle which has bonds.
int score_alignment(atom::Hierarchies mhs, float max_allowed_diff)
Return the number of matching eigen vectors by their eigen values.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Class to provide all the parameters to the segmentation function.
kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void resample(const Profile *model_profile, Profile *resampled_profile) const
resampling of the modeled profile is required to fit the q
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Hierarchy create_clone(Hierarchy d)
Clone the Hierarchy.
DensityMap * binarize(DensityMap *orig_map, float threshold, bool reverse=false)
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
const algebra::Vector3D get_vector_geometry(Particle *p)
Definition: XYZ.h:145
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
BondGraph(Hierarchy bd)
The graph is on the leaves of the atom::Hierarchy.
DerivativeAccumulator(double weight=1.0)
the weight is one by default
ReferenceFrame3D get_local_reference_frame(const ReferenceFrame3D &v) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual void apply_index(kernel::Model *m, kernel::ParticleIndex p) const
FixedRefiner(const kernel::ParticlesTemp &ps)
Store the set of particles.
static void set_reduced_coordinates(kernel::Model *m, kernel::ParticleIndex target, kernel::ParticleIndex ref, Floats coords)
sets rigid body coordinates in the reference frame of ref
double get_sum(const DensityMap *m1)
Return the sum of all voxels.
SecondaryStructureResidues setup_coarse_secondary_structure_residues(const kernel::Particles &ssr_ps, kernel::Model *mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=false)
void set_proper_ranges_for_keys(kernel::Model *m, const algebra::Vector3D &min_translation_values, const algebra::Vector3D &max_translation_values)
Rotation3D operator/(const Rotation3D &r) const
Compute the rotation which when composed with r gives this.
Definition: Rotation3D.h:206
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double get_mass(ResidueType c)
Get the mass from the residue type.
void optimize_assembly(kernel::Model *m, const kernel::ParticlesTemp &components, const kernel::RestraintsTemp &interactions, const kernel::RestraintsTemp &other_restraints, const algebra::BoundingBox3D &bb, PairScore *ev, double cutoff, const PairPredicates &excluded=PairPredicates())
A single atom in a CHARMM topology.
virtual double evaluate_index(kernel::Model *m, kernel::ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
PrincipalComponentAnalysisD< D > get_principal_components(const base::Vector< VectorD< D > > &ps)
Perform principal components analysis on a set of vectors.
void set_assignments(const Subset &s, AssignmentContainer *lsc)
void get_projection(em2d::Image *img, const kernel::ParticlesTemp &ps, const RegistrationResult &reg, const ProjectingOptions &options, MasksManagerPtr masks=MasksManagerPtr(), String name="")
Generates a projection from particles.
void set_particles(const kernel::Particles &pis)
Set the particles to use.
FFTFittingOutput * do_local_fitting(em::DensityMap *dmap, double density_threshold, atom::Hierarchy mol2fit, double angle_sampling_interval_rad, double max_angle_sampling_rad, double max_translation, int num_fits_to_report, bool cluster_fits, int num_angle_per_voxel, double max_clustering_translation, double max_clustering_rotation, const std::string &angles_filename="")
Locally fit a molecule inside its density.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Represent a real cell in a grid (one within the bounding box)
Definition: grid_indexes.h:162
virtual bool get_is_ok(const IMP::domino::Assignment &assignment) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pi) const
Definition: predicates.h:30
const algebra::Vector3D get_vector_geometry(XYZ d)
Definition: XYZ.h:133
void set(TextOutput to)
Definition: file.h:147
virtual int get_value_index(kernel::Model *, const kernel::ParticleIndexQuad &vt) const
Compute the predicate and the derivative if needed.
Store a persistent ordering for a subset based on the list.
Definition: Order.h:29
void add_to_map(DensityMap *dm, const kernel::Particles &pis)
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void apply_variance_filter(Image *input, Image *filtered, int kernelsize)
Definition: Image.h:265
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
Storage of anchors (points and edges)
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
void write_segments_as_mrc(em::DensityMap *dmap, const DataPointsAssignment &dpa, Float resolution, Float apix, Float threshold, const std::string &filename)
Write segments in MRC format.
A class storing a whole rotamer library read from a file.
virtual double do_step(const kernel::ParticleIndexes &sc, double dt)
Perform a single time step.
Shared optimizer state that is invoked upon commitment of new coordinates.
Selection(Hierarchy hierarchy=None, Hierarchies hierarchies=[], Strings molecules=[], Ints residue_indexes=[], Strings chains=[], AtomTypes atom_types=[], ResidueTypes residue_types=[], Strings domains=[], double resolution=0, std::string molecule=None, int residue_index=None, std::string chain=None, AtomType atom_type=None, ResidueType residue_type=None, HierarchyType hierarchy_type=None, Terminus terminus=None, std::string domain=None, core::ParticleType particle_type=None, core::ParticleTypes particle_types=[], int copy_index=-1, Ints copy_indexs=[], int state_index=-1, Ints state_indexes=[])
void apply_diffusion_filter(Image *input, Image *filtered, double beta, double pixelsize, int time_steps)
Definition: Image.h:278
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
const algebra::Sphere3D get_sphere_d_geometry(CustomXYZR d)
Definition: CustomXYZR.h:90
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void write(const char *filename, const float *data, const DensityHeader &header)
Writes a density file in EM format with the header information.
RigidBodyTunneler(kernel::Model *m, kernel::ParticleIndexes pis, kernel::ParticleIndex ref, double k, double move_probability=1.)
double get_dihedral(XYZ a, XYZ b, XYZ c, XYZ d)
Compute the dihedral angle (in radians) between the four particles.
ParticlesTemp get_particles(kernel::Model *m, const ParticleIndexes &ps)
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexTriplet &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual ParticlesTemp get_input_particles(Particle *p) const
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
void apply_generic(const SingletonModifier *m) const
Just use apply() in the base class.
em::DensityMap * remove_background(em::DensityMap *dmap, float threshold, float edge_threshold)
Returns a map containing all density without the background.
A geometric relationship between four atoms.
Slice get_slice(kernel::Restraint *r, const Subset &s) const
Return the slice for that restraint given the subset.
FittingSolutions local_rigid_fitting_grid_search(const kernel::ParticlesTemp &ps, const FloatKey &wei_key, DensityMap *dmap, Int max_voxels_translation=2, Int translation_step=1, Float max_angle_in_radians=0.174, Int number_of_rotations=100)
Local grid search rigid fitting.
double get_resolution(kernel::Model *m, kernel::ParticleIndex pi)
DensityMap * mask_and_norm(em::DensityMap *dmap, em::DensityMap *mask)
Return a masked density, and normalize the output map within the mask region.
static Switching setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: Switching.h:34
void set_symmetric_difference(const Selection &s)
Select elements that are in this Selection or the passed one but not both.
StatisticalPairScore(IntKey k, double threshold, base::TextInput data_file)
An index in an infinite grid on space.
Definition: grid_indexes.h:30
algebra::ReferenceFrame3D get_initial_reference_frame(kernel::Model *m, const kernel::ParticleIndexes &pis)
double get_slack_estimate(const kernel::ParticlesTemp &ps, double upper_bound, double step, const kernel::RestraintsTemp &restraints, bool derivatives, Optimizer *opt, ClosePairContainer *cpc)
Virtual class for reader/writers of images.
double get_maximum_length(const BoundingBoxD< D > &a)
Return the maximum axis aligned extent.
Definition: BoundingBoxD.h:244
BoundingBoxD< 3 > get_transformed(const BoundingBoxD< 3 > &bb, const Transformation3D &tr)
Return a bounding box containing the transformed box.
Ints get_numbers_of_particles_outside_of_the_density(DensityMap *dmap, const kernel::Particles &ps, const IMP::algebra::Transformation3Ds &transformations, float thr=0.0)
Get numbers of particles (mult transforms) that are outside the density.
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexPair &pi) const
Compute the predicate and the derivative if needed.
TripletContainerSet(kernel::Model *m, std::string name="TripletContainerSet %1%")
Construct and empty set.
const Floats & get_dummy_form_factors(kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
for reciprocal space profile calculation
Object used to hold a set of restraints.
double get_volume(const Cone3D &g)
Definition: Cone3D.h:64
void set_particle_states(kernel::Particle *p, ParticleStates *se)
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexTriplet &pi, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
A container which contains all consecutive particle pairs from an input list.
IntPairs get_edges(const BoundingBoxD< 3 > &)
Return the edges of the box as indices into the vertices list.
Definition: BoundingBoxD.h:289
A voxel grid in d-dimensional space space.
Definition: GridD.h:79
BrownianDynamics(kernel::Model *m, std::string name="BrownianDynamics%1%", double wave_factor=1.0)
Create the optimizer.
virtual int get_value_index(kernel::Model *m, kernel::ParticleIndex pi) const
Compute the predicate and the derivative if needed.
Definition: predicates.h:26
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
stores the anchors sampling space for each protein
virtual double evaluate_if_good_index(kernel::Model *m, kernel::ParticleIndex vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed.
void apply(CHARMMResidueTopology *res) const
Apply the patch to the residue, modifying its topology accordingly.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Bonds get_internal_bonds(Hierarchy mhd)
Get the bonds internal to this tree.
virtual double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
ProteinsAnchorsSamplingSpace get_part_of_sampling_space(const ProteinsAnchorsSamplingSpace &prots_ss, const Strings &prot_names)
Get the sampling space of few of the proteins.
Vector3D operator*(const Vector3D &v) const
Rotate a vector around the origin.
Definition: Rotation3D.h:171
BoundingBoxD< D > get_union(BoundingBoxD< D > a, const BoundingBoxD< D > &b)
Return the union bounding box.
Definition: BoundingBoxD.h:236
virtual int get_value_index(kernel::Model *m, kernel::ParticleIndex pi) const
Compute the predicate and the derivative if needed.
Definition: predicates.h:48
bool same_voxel_size(const DensityMap *other) const
Checks if two maps have the same voxel size.
void write_to_ints(const String &filename, em::ImageHeader &header, const cv::Mat &data) const
Writes an EM image in JPG format.
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexPair &vt) const
Compute the predicate and the derivative if needed.
Float get_radius(Atom atom) const
get radius
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void get_autocorrelation2d(const cv::Mat &m, cv::Mat &corr)
Computes the autocorrelation matrix.
A simple list of fitting solutions.
Definition: rigid_fitting.h:33
void apply_generic(const QuadModifier *m) const
Just use apply() in the base class.
DensityMap * get_threshold_map(const DensityMap *orig_map, float threshold)
void add(const DensityMap *other)
virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &) const
algebra::BoundingBoxD< 3 > get_bounding_box(const Hierarchy &h)
Get a bounding box for the Hierarchy.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
SigmoidRestraintSphere(IMP::kernel::Model *m, IMP::kernel::ParticleIndexAdaptor p1, IMP::kernel::ParticleIndexAdaptor p2, double inflection, double slope, double amplitude, double line_slope_=0, std::string name="SigmoidRestraintSphere%1%")
Create the restraint.
virtual bool get_can_refine(kernel::Particle *) const
Return true if this refiner can refine that particle.
Definition: FixedRefiner.h:33
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
DensityMap * get_segment_by_masking(DensityMap *map_to_segment, DensityMap *mask, float mas_threshold)
Get a segment of the map covered by another map.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
double get_squared_distance(const VectorD< D > &v1, const VectorD< D > &v2)
Compute the squared distance between two vectors.
Definition: VectorD.h:201
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Transformation3D get_transformation_from_first_triangle_to_second(Triangle3D first_tri, Triangle3D second_tri)
Return a transformation between two triangles.
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
Assignment get_nearest_assignment(const Subset &s, const algebra::VectorKD &embedding, ParticleStatesTable *pst)
Return the nearest assignment from an embedding.
IncrementalScoringFunction(const kernel::ParticlesTemp &to_move, const kernel::RestraintsTemp &rs, double weight=1.0, double max=NO_MAX, std::string name="IncrementalScoringFunction%1%")
void do_extend_borders(cv::Mat &orig, cv::Mat &dst, unsigned int pix)
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
A shared container for Pairs.
static XYZ setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: XYZ.h:51
void validate_partitional_clustering(PartitionalClustering *pc, unsigned int n)
Check that the clustering is a valid clustering of n elements.
virtual void apply_index(kernel::Model *m, kernel::ParticleIndex p) const
Parameters given as options to the get_projections() functions.
Definition: project.h:59
void set(const char *fname, const Object *object=nullptr)
Base class for writing geometry to a file.
Definition: Writer.h:28
static bool get_is_setup(kernel::Model *m, kernel::ParticleIndex p)
void write_multimodel_pdb(const Hierarchies &mhd, base::TextOutput out)
double get_surface_area(const Ellipsoid3D &g)
Definition: Ellipsoid3D.h:64
DependencyGraph get_pruned_dependency_graph(kernel::Model *m)
Represent a cylinder in 3D.
Definition: Cylinder3D.h:26
static Scale setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: Scale.h:30
void set_union(const Selection &s)
Select elements that are in either this Selection or the passed one.
void calculate_profile_constant_form_factor(const kernel::Particles &particles, Float form_factor=1.0)
calculate profile for any type of kernel::Particles that have coordinates
BoundingBoxD< 3 > get_bounding_box(const Cylinder3D &g)
Definition: Cylinder3D.h:78
virtual void do_add_score_and_derivatives(ScoreAccumulator sa) const
double get_distance_if_smaller_than(const Subset &s, const Assignment &a, const Assignment &b, ParticleStatesTable *pst, const statistics::Metrics &metrics, double max)
void apply_mean_outside_mask(Image *img, double radius)
IMP_Eigen::Matrix3d get_covariance(const Gaussian3D &g)
CompositeRestraint(kernel::Model *m, kernel::ParticleIndexesAdaptor handle_particle_indexes, double coffd, double l, bool tabprob, double plateau, std::string name="CompositeRestraint%1%")
Create the restraint.
void apply(const QuadModifier *sm) const
Apply a SingletonModifier to the contents.
Simulator(kernel::Model *m, std::string name="Simulator %1%", double wave_factor=1.0)
DihedralRestraint(UnaryFunction *score_func, kernel::Particle *p1, kernel::Particle *p2, kernel::Particle *p3, kernel::Particle *p4)
Create the dihedral restraint.
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
void apply_default_patches(const CHARMMParameters *ff)
Apply patches to the first and last residue in the segment.
kernel::RestraintsTemp get_restraints(const Subset &s, const ParticleStatesTable *pst, const DependencyGraph &dg, kernel::RestraintSet *rs)
static bool get_is_setup(kernel::Model *m, kernel::ParticleIndex pi)
return true if the particle has a name
multifit::SettingsData * get_partial_assembly_setting_data(multifit::SettingsData *prots_sd, const Strings &prot_names)
Get the assembly data for a few of the proteins.
Float R_factor_score(const RadialDistributionFunction &model_pr, const std::string &file_name="") const
analogy crystallographic R-factor score
ExampleRestraint(kernel::Model *m, kernel::ParticleIndex p, double k)
Create the restraint.
ParticlesTemp get_dependent_particles(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
virtual kernel::ModelObjectsTemp do_get_outputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
PairRestraint(PairScore *ss, const kernel::ParticlePair &vt, std::string name="PairRestraint %1%")
Create the restraint.
Definition: PairRestraint.h:41
ExtendedGridIndexD< D > get_extended_index(const VectorD< D > &o) const
Return the index that would contain the voxel if the grid extended there.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Vector3D get_reflected(const Plane3D &pln, const Vector3D &p)
Return the point reflected about the plane.
Definition: Plane3D.h:76
Track the pairs of particles passed.
Definition: LogPairScore.h:21
virtual kernel::ModelObjectsTemp do_get_outputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
double get_area(const SpherePatch3D &g)
Definition: SpherePatch3D.h:48
void optimize_balls(const kernel::ParticlesTemp &ps, const kernel::RestraintsTemp &rs=kernel::RestraintsTemp(), const PairPredicates &excluded=PairPredicates(), const OptimizerStates &opt_states=OptimizerStates(), base::LogLevel ll=base::DEFAULT)
void destroy_bond(Bond b)
Destroy the bond connecting two particles.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Represent a subset of the particles being optimized.
Definition: Subset.h:33
ModelObjectsTemp get_inputs(kernel::Model *m, const ParticleIndexes &pis) const
The type of an atom.
algebra::Vector3D get_centroid(const XYZs &ps)
Get the centroid.
HierarchyTree get_hierarchy_tree(Hierarchy h)
Get a graph for the passed Hierarchy.
void add_undecorator(ParticleIndex pi, Undecorator *d)
double get_maximum_range(kernel::Model *m, const base::Array< D, kernel::ParticleIndex > &p) const
Return an upper bound on the distance at which the score can be non-zero.
Definition: AddScores.h:49
double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
Get all atoms in the Hierarchy that do not have CHARMM types.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Statistical(IntKey k, double threshold, base::TextInput data_file)
Definition: Statistical.h:64
kernel::Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
bool get_is_heterogen(Hierarchy h)
Return true if the piece of hierarchy should be classified as a heterogen.
int get_value(kernel::Particle *a) const
void read_from_floats(const String &filename, em::ImageHeader &header, cv::Mat &data) const
virtual bool get_is_ok(const Assignment &state) const =0
static SecondaryStructureResidue setup_particle(kernel::Model *m, ParticleIndex pi, Float prob_helix, Float prob_strand, Float prob_coil)
Return all close unordered pairs of particles taken from the SingletonContainer.
const Plane3D & get_plane_3d_geometry(const Plane3D &g)
Definition: Plane3D.h:86
virtual void propagate_velocities(const kernel::ParticleIndexes &ps, double step_size)
Second part of velocity Verlet (update velocity)
virtual double evaluate(const kernel::ParticlePair &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void compute_chisquare_derivative(const Profile *model_profile, const kernel::Particles &particles1, const kernel::Particles &particles2, std::vector< algebra::Vector3D > &derivatives, const std::vector< double > &effect_size) const
compute derivatives for particles1 with respect to particles2
Restraints create_current_decomposition(kernel::Model *m, const kernel::ParticleIndexTriplet &vt) const
char get_one_letter_code(ResidueType c)
Get the 1-letter amino acid code from the residue type.
PartitionalClustering * create_gromos_clustering(Metric *d, double cutoff)
void add_hierarchies(RMF::FileHandle fh, const atom::Hierarchies &hs)
virtual double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
GenericHierarchies get_leaves(Hierarchy mhd)
Get all the leaves of the bit of hierarchy.
Represents a scoring function on the model.
LognormalRestraint(kernel::Particle *x, kernel::Particle *mu, kernel::Particle *sigma)
Gaussian restraint.
double operator()(unsigned int id1, unsigned int id2, const ClusterSet &cluster_set, const FloatsList &distances)
Distance between the clusters.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual kernel::ModelObjectsTemp do_get_outputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Color get_interpolated_rgb(const Color &a, const Color &b, double f)
Return a color interpolated between a and b in RGB space.
Definition: Color.h:143
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Restraints create_current_decomposition(kernel::Model *m, const kernel::ParticleIndexPair &vt) const
double get_rotation_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
Atom get_atom(Residue rd, AtomType at)
Return a particle atom from the residue.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pi) const
ScoreStates maintain invariants in the Model.
Represent a triangle in 3D.
Definition: Triangle3D.h:23
RigidBodyMover(core::RigidBody d, kernel::Particles ps, Float max_tr, Float max_ang, algebra::Vector3Ds ctrs, algebra::Transformation3Ds trs)
double get_score(Image *image, Image *projection) const
Given an image and a projection, returns the appropriate score.
Definition: scores2D.h:60
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual kernel::ModelObjectsTemp do_get_outputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
internal::PredicateEquals< Pred, false > make_predicate_not_equal(const Pred *p, Model *m, int value)
DensityMap * read_map(std::string filename, MapReaderWriter *reader)
Read a density map from a file and return it.
double get_percentage_of_voxels_covered_by_particles(DensityMap *dmap, const kernel::Particles &ps, float smoothing_radius=3., const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of density voxels that are not covered by particles.
void add_in_plane_transformation(algebra::Transformation2D t)
virtual void apply_index(kernel::Model *m, kernel::ParticleIndex v) const
GenericHierarchies get_all_descendants(Hierarchy mhd)
Get all the particles in the subtree.
DistanceRestraint(UnaryFunction *score_func, kernel::Particle *a, kernel::Particle *b, std::string name="DistanceRestraint %1%")
Create the distance restraint.
Atom get_atom(const CHARMMResidueTopology *current_residue, const CHARMMResidueTopology *previous_residue, const CHARMMResidueTopology *next_residue, const std::map< const CHARMMResidueTopology *, Hierarchy > &resmap) const
Map the endpoint to an Atom particle.
void create(const em::KernelParameters &KP, const em::RadiusDependentKernelParameters &params, double mass=1.0)
Generates the mask.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
Definition: predicates.h:130
CompositeJoint(IMP::core::RigidBody parent, IMP::core::RigidBody child, Joints joints=Joints())
The end of a bond, angle, dihedral, improper, or internal coordinate.
static Resolution setup_particle(kernel::Model *m, ParticleIndex pi, Float resolution)
Definition: Resolution.h:44
virtual kernel::ModelObjectsTemp do_get_outputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Hierarchy create_hierarchy(kernel::Model *model) const
Create a new Hierarchy in the given model using this topology.
virtual int get_value_index(kernel::Model *m, kernel::ParticleIndex pi) const
Compute the predicate and the derivative if needed.
double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual int get_value_index(kernel::Model *m, kernel::ParticleIndex pi) const
Compute the predicate and the derivative if needed.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
LogWrapper(kernel::Model *m, double weight, const std::string &name="LogWrapper %1%")
Create an empty set that is registered with the model.
Floats get_histogram(Image *img, int bins)
Definition: Image.h:254
FittingSolutions compute_fitting_scores(const kernel::ParticlesTemp &ps, DensityMap *em_map, const algebra::Transformation3Ds &transformations, bool fast_version=false, bool local_score=false, const FloatKey &wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
em::FittingSolutions pca_based_rigid_fitting(core::RigidBody rb, Refiner *rb_refiner, em::DensityMap *em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis())
Compute fitting scores for a given set of rigid transformations.
void add_non_rigid_member(kernel::ParticleIndexAdaptor p)
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pi) const
Definition: predicates.h:91
InteractionGraph get_interaction_graph(ScoringFunctionAdaptor rs, const ParticleStatesTable *pst)
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
Definition: LogPairScore.h:30
Transformation3D()
construct an invalid transformation
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
DependencyGraph get_dependency_graph(kernel::Model *m)
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
int operator()(kernel::Model *m, const kernel::ParticleIndexTriplet &vt) const
Enable them to be use as functors.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual double unprotected_evaluate(kernel::DerivativeAccumulator *accum) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void do_subtract_images(Image *first, Image *second, Image *result)
The topology of a single residue in a model.
A base class for modifiers of kernel::ParticlesTemp.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
const BoundingBoxD< D > & operator+=(const BoundingBoxD< D > &o)
extend the current bounding box to include the other
Definition: BoundingBoxD.h:82
A reference frame in 3D.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
ClosePairContainer(SingletonContainerAdaptor c, double distance_cutoff, double slack=1, std::string name="ClosePairContainer%1%")
Get the individual particles from the passed SingletonContainer.
kernel::Restraint * create_chain_restraint(const kernel::ParticlesTemp &ps, double length_factor, double k, std::string name)
CHARMM force field parameters.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
void do_combined_fill_holes_and_threshold(cv::Mat &m, cv::Mat &result, double n_stddevs, double threshold=0.0)
Combines the fill holes and thresholding operations together with normalize.
unsigned int get_number_of_incidences(const kernel::ParticlesTemp &psa, const kernel::ParticlesTemp &psb, double point_distance)
Definition: counting.h:23
Store an array of values of the same type.
Definition: ConstVector.h:27
virtual bool get_can_refine(Particle *) const
Return true if this refiner can refine that particle.
algebra::Transformation3Ds get_symm_axis_alignments_from_model_to_density(atom::Hierarchies mhs, bool sample_translation, bool fine_rotation_sampling=true) const
algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > get_grid(DensityMap *in_map)
void set_residue_type(ResidueType type)
Select only residues with the passed type.
void set_unknown_score(kernel::TripletScore *score)
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
void set_secondary_structure_probabilities(const kernel::Particles &ssres_ps, const Ints &indices=Ints())
Assign secondary structure particles. Provide indices if out of order.
SphereGeometry * create_geometry(const algebra::Sphere3D &t, std::string name="algebra::Sphere3D"+"%1""%")
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
SingletonContainerSet(kernel::Model *m, std::string name="SingletonContainerSet %1%")
Construct and empty set.
Segment3D get_shortest_segment(const Segment3D &s, const Vector3D &p)
algebra::Vector2Ds do_project_vectors(const algebra::Vector3Ds &ps, const algebra::Rotation3D &R, const algebra::Vector3D &translation)
Project the points contained in Vector3Ds to gen vectors in 2D.
void project(const kernel::ParticlesTemp &ps, int x_margin, int y_margin, int z_margin, algebra::Vector3D shift=algebra::Vector3D(0., 0., 0.), FloatKey mass_key=atom::Mass::get_mass_key())
Project particles on the grid by their mass value.
virtual double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexQuads &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual int get_value_index(kernel::Model *, const kernel::ParticleIndexPair &) const
Compute the predicate and the derivative if needed.
virtual int get_value_index(kernel::Model *, const kernel::ParticleIndexTriplet &vt) const
Compute the predicate and the derivative if needed.
static Reference setup_particle(kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexAdaptor reference)
Definition: core/symmetry.h:31
void assign_blame(const kernel::RestraintsTemp &rs, const kernel::ParticlesTemp &ps, FloatKey attribute)
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
A class to store an fixed array of same-typed values.
Definition: Array.h:33
void set_model_particles(const kernel::ParticlesTemp &ps)
kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Transformation2D()
constructor. An invalid transformation is built
void ImageHeader_to_DensityHeader(const ImageHeader &h, DensityHeader &header)
void set_log_target(TextOutput l)
Set the target for the log.
void set_reference_frame_safe(IMP::core::RigidBody rb, IMP::algebra::ReferenceFrame3D r)
void add_close_pair_score(PairScore *ps, double distance, const kernel::ParticlesTemp &particles, const PairPredicates &filters)
unsigned int get_number_of_masks(const core::RigidBody &rb) const
Return the number of precomputed masks associated with the rigid body.
Class for handling density maps.
Definition: DensityMap.h:94
Hierarchy read_pdb(base::TextInput input, kernel::Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Abstract class for scoring object(s) of type ParticlePair.
kernel::RestraintsTemp get_restraints(const Subset &s, const Subsets &exclusions) const
Store a subset of a subset or assignment.
Definition: Slice.h:27
A single binormal term in a MultipleBinormalRestraint.
ChildrenRefiner(HierarchyTraits tr)
Create a refiner for a particular type of hierarchy.
BoundingBoxD< D > get_intersection(const BoundingBoxD< D > &a, const BoundingBoxD< D > &b)
Return the intersecting bounding box.
Definition: BoundingBoxD.h:207
GaussianProcessInterpolation(FloatsList x, Floats sample_mean, Floats sample_std, unsigned n_obs, UnivariateFunction *mean_function, BivariateFunction *covariance_function, kernel::Particle *sigma, double sparse_cutoff=1e-7)
MergeTree get_merge_tree(ScoringFunctionAdaptor input, const ParticleStatesTable *pst)
Transformation2D get_rotation_about_point(const Vector2D &point, const Rotation2D &rotation)
Generates a Transformation2D object from a rotation around a point.
void profile_2_distribution(RadialDistributionFunction &rd, Float max_distance) const
convert to real space P(r) function P(r) = 1/2PI^2 Sum(I(q)*qr*sin(qr))
int get_value(kernel::Particle *a) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
A Gaussian distribution in 3D.
Definition: Gaussian3D.h:24
void read(String filename, const ImageReaderWriter *reader)
Definition: Image.h:125
void setup(ScoreFunction *score_function, const Em2DRestraintParameters &params)
Definition: Em2DRestraint.h:60
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
const VectorD< C::DIMENSION > & get_vector_geometry(const C &g)
Definition: VectorD.h:418
Class for sampling a density map from particles.
float cn_symm_score(atom::Hierarchies mhs, const algebra::Vector3D &center, const algebra::Vector3D &direction, int symm_deg)
scores an input vector as a symmetry axis
The class represents a molecule as shells of distance from the surface.
ReferenceFrame3D get_global_reference_frame(const ReferenceFrame3D &v) const
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
void apply(const TripletModifier *sm) const
Apply a SingletonModifier to the contents.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pi) const
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexPair &pip) const
Compute the predicate and the derivative if needed.
RestraintsTemp get_dependent_restraints(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexTriplet &pi) const
Compute the predicate and the derivative if needed.
display::Geometries create_blame_geometries(const kernel::RestraintsTemp &rs, const kernel::ParticlesTemp &ps, double max=NO_MAX, std::string name=std::string())
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
void calculate_profile_partial(const kernel::Particles &particles, const Floats &surface=Floats(), FormFactorType ff_type=HEAVY_ATOMS)
compute profile for fitting with hydration layer and excluded volume
void set_particles(const kernel::Particles &pis)
Set the particles to use.
virtual double evaluate_index(kernel::Model *m, kernel::ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
static XYZR setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: XYZR.h:48
static Angle setup_particle(kernel::Model *m, ParticleIndex pi, core::XYZ a, core::XYZ b, core::XYZ c)
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
double get_volume(const BoundingBoxD< D > &bb)
Definition: BoundingBoxD.h:147
Rotation3D get_random_rotation_3d()
Pick a rotation at random from all possible rotations.
double convolute(const DensityMap *m1, const DensityMap *m2)
virtual void apply_index(kernel::Model *m, const kernel::ParticleIndexTriplet &v) const
Float compute_scale_factor(const Profile *model_profile, Float offset=0.0) const
computes the scaling factor needed for fitting the modeled profile
Definition: ProfileFitter.h:81
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void read_particles_from_buffer(const base::Vector< char > &buffer, const ParticlesTemp &particles, const FloatKeys &keys)
load found attributes into the particles
Hierarchy create_fragment(const Hierarchies &ps)
Create a fragment containing the specified nodes.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void add_rigid_bodies_in_chain(IMP::core::RigidBodies rbs)
kernel::Particles add_impropers(Hierarchy hierarchy) const
Add impropers to the given Hierarchy using this topology, and return them.
BoundingBoxD< 3 > get_bounding_box(const Segment3D &g)
Definition: Segment3D.h:52
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
FloatPair get_component_placement_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the difference between two placements of the same set of points.
Vector2D operator*(const Vector2D &v) const
Perform the transformation on an 2D vector.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void do_fill_holes(const cv::Mat &m, cv::Mat &result, double h)
Fills the holes in the matrix m of height h.
vonMisesKappaJeffreysRestraint(kernel::Model *m, kernel::Particle *kappa)
Create the restraint.
void add_hierarchy(RMF::FileHandle fh, atom::Hierarchy hs)
double get_distance(const Plane3D &pln, const Vector3D &p)
Return the distance between a plane and a point in 3D.
Definition: Plane3D.h:71
Simple Brownian dynamics simulator.
static Bonded setup_particle(kernel::Model *m, ParticleIndex pi)
kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
TripletsRestraint(kernel::TripletScore *ss, kernel::TripletContainerAdaptor pc, std::string name="TripletsRestraint %1%")
Create the restraint with a shared container.
virtual double evaluate_if_good_index(kernel::Model *m, const kernel::ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed.
PartitionalClustering * create_diameter_clustering(Metric *d, double maximum_diameter)
ConsecutivePairFilter(ConsecutivePairContainer *cpc)
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
static Hierarchy setup_particle(kernel::Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
void add_surface_index(core::Hierarchy mhd, Float apix, FloatKey shell_key=FloatKey("surf_ind"), FloatKey radius_key=core::XYZR::get_radius_key(), FloatKey weight_key=atom::Mass::get_mass_key())
Add shell index to leaves.
Abstract class for containers of particles.
virtual double evaluate_index(kernel::Model *m, kernel::ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
static Molecule setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: Molecule.h:37
FretRestraint(kernel::Particles pd, kernel::Particles pa, kernel::Particle *kda, kernel::Particle *Ida, kernel::Particle *R0, kernel::Particle *sigma0, kernel::Particle *Pbl, double fexp, double m_d=1.0, double m_a=1.0)
Create the restraint.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
bool get_interiors_intersect(const BoundingBoxD< D > &a, const BoundingBoxD< D > &b)
Return true if they intersect.
Definition: BoundingBoxD.h:193
const Cone3D & get_cone_3d_geometry(const Cone3D &g)
Definition: Cone3D.h:64
static double cross_correlation_coefficient(const DensityMap *grid1, const DensityMap *grid2, float grid2_voxel_data_threshold, bool allow_padding=false, FloatPair norm_factors=FloatPair(0., 0.))
Calculates the cross correlation coefficient between two maps.
kernel::ParticlePairsTemp get_possible_interactions(const kernel::ParticlesTemp &ps, double max_distance, ParticleStatesTable *pst)
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
The standard decorator for manipulating molecular structures.
void set_reference_frame(const IMP::algebra::ReferenceFrame3D &tr)
Set the current reference frame.
void add_term(const BinormalTerm &term)
Add a single BinormalTerm to the restraint.
A Cartesian vector in D-dimensions.
Definition: VectorD.h:52
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
DensityMap * multiply(const DensityMap *m1, const DensityMap *m2)
BoundingBoxD()
Create an empty bounding box.
Definition: BoundingBoxD.h:37
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
static Hierarchy setup_particle(kernel::Model *m, kernel::ParticleIndex pi, kernel::ParticleIndexesAdaptor children=kernel::ParticleIndexesAdaptor())
static Cover setup_particle(kernel::Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
Definition: CoverRefined.h:72
void setup(kernel::ParticlesTemp &ps, const ProjectingParameters &params, kernel::Model *scoring_model, ScoreFunction *score_function, MasksManagerPtr masks=MasksManagerPtr())
EnvelopeFitRestraint(kernel::Particles particles, DensityMap *em_map, double density_threshold, double penetration_threshold)
Constructor.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Base class for all CHARMM residue-based topology.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
A decorator for wrapping a particle representing a molecular bond.
FixedXYZ get_fixed_xyz_from_rotation(const Rotation3D &r)
The inverse of rotation_from_fixed_xyz()
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void set_particles(const kernel::ParticlesTemp &ps, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key())
setting particles in case they were not set by the constructor
virtual void apply_indexes(kernel::Model *m, const kernel::ParticleIndexQuads &o, unsigned int lower_bound, unsigned int upper_bound) const
Atoms get_psi_dihedral_atoms(Residue rd)
Return the atoms comprising the psi dihedral.
void write_pts(const Vector3Ds &vs, base::TextOutput out)
Write a set of 3D vectors to a file.
A decorator for a particle representing an atom.
Definition: atom/Atom.h:234
void add_score_and_derivatives(ScoreAccumulator sa) const
Perform the actual restraint scoring.
virtual double evaluate(const kernel::ParticleTriplet &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual double evaluate_index(kernel::Model *m, kernel::ParticleIndex vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
bool get_has_index(const ExtendedGridIndexD< D > &i) const
Return true if the voxel has been added.
void write_pdb_of_c_alphas(const Selection &mhd, base::TextOutput out, unsigned int model=1)
Write a hierarchy to a PDB as C_alpha atoms.
void write_map(DensityMap *m, std::string filename, MapReaderWriter *writer)
Write a density map to a file.
RevoluteJoint(IMP::core::RigidBody parent, IMP::core::RigidBody child)
kernel::ParticlesTemp create_particles(RMF::FileConstHandle fh, kernel::Model *m)
static float convolution(const DensityMap *em_map, DensityMap *model_map, float voxel_data_threshold, bool recalc_ccnormfac=true)
void copy_map(const DensityMap *other)
copy map into this map
int compare(const VectorD< D > &a, const VectorD< D > &b)
lexicographic comparison of two vectors
Definition: VectorD.h:179
void set_atom_type(AtomType types)
Select atoms with only the passed type.
const IMP::algebra::Vector3D & get_coordinates(unsigned index, const IMP::atom::AtomType &at) const
get coordinates of the specified atom
void write_connolly_surface(atom::Atoms as, base::TextOutput fn, float density, float probe_radius)
Write the Connolly surface for a set of atoms to a file.
bool get_has_index(const ExtendedGridIndexD< D > &v) const
Return true if the ExtendedIndex is also a normal index value.
Definition: grid_ranges.h:242
double get_distance(XYZ a, XYZ b)
Compute the distance between a pair of particles.
Definition: XYZ.h:192
AngleRestraint(UnaryFunction *score_func, kernel::Particle *p1, kernel::Particle *p2, kernel::Particle *p3)
Create the angle restraint.
ExtendedGridIndexD< D > get_extended_index(const VectorD< D > &o) const
Return the index that would contain the voxel if the grid extended there.
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
FFTFittingOutput * do_global_fitting(em::DensityMap *dmap, double density_threshold, atom::Hierarchy mol2fit, double angle_sampling_interval_rad, int num_fits_to_report, double max_clustering_translation, double max_clustering_angle, bool cluster_fits=true, int num_angle_per_voxel=1, const std::string &angles_filename="")
Fit a molecule inside its density.
base::Vector< char > write_particles_to_buffer(const ParticlesTemp &particles, const FloatKeys &keys)
return a binary buffer with the data
virtual void apply_index(kernel::Model *m, kernel::ParticleIndex a) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pi) const
Hierarchies get_by_type(Hierarchy mhd, GetByType t)
WeightedExcludedVolumeRestraint(core::RigidBodies rbs, Refiner *refiner, FloatKey weight_key=IMP::atom::Mass::get_mass_key())
Constructor.
void set_transformation_child_to_parent(IMP::algebra::Transformation3D transformation)
void read(const char *filename, float **data, DensityHeader &header)
Reads a density file in EM format and stores the information.
void load_leaf_assignments(const Subset &subset, AssignmentsTable *at, AssignmentContainer *ac)
Fill in assignments for a leaf.
PartitionalClustering * create_connectivity_clustering(Metric *metric, double dist)
void calculate_profile(const kernel::Particles &particles, FormFactorType ff_type=HEAVY_ATOMS, bool reciprocal=false)
computes theoretical profile
Definition: Profile.h:44
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
QuadContainerSet(kernel::Model *m, std::string name="QuadContainerSet %1%")
Construct and empty set.
void read(const char *fn_in, float **data, DensityHeader &head)
Reads an MRC file and translates the header to the general DensityHeader.
void add_particles(RMF::FileHandle fh, const kernel::ParticlesTemp &hs)
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
Ints get_partial_index(const kernel::ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
virtual double evaluate_if_good_index(kernel::Model *m, const kernel::ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed.
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
void set_cone_3d_geometry(Cone3D &g, const Cone3D &v)
Definition: Cone3D.h:64
void show_histogram(HistogramD h, std::string xscale="linear", std::string yscale="linear", Functions curves=Functions())
A base class for classes which perturb particles.
void load_merged_assignments(const Subset &first_subset, AssignmentContainer *first, const Subset &second_subset, AssignmentContainer *second, const SubsetFilterTablesTemp &filters, AssignmentContainer *ret)
Fill in assignments for an internal node.
A class to store the clusters generated during hierarchical clustering.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexPair &pi) const
Compute the predicate and the derivative if needed.
Definition: predicates.h:67
BoundingBoxD< 3 > get_bounding_box(const Cone3D &g)
Definition: Cone3D.h:64
void get_anchors_for_density(em::DensityMap *dmap, int number_of_means, float density_threshold, std::string pdb_filename, std::string cmm_filename, std::string seg_filename, std::string txt_filename)
Generate anchors in several formats for a given density map.
virtual ModelObjectsTemp do_get_inputs(kernel::Model *m, const ParticleIndexes &pis) const
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexQuad &pi) const
Compute the predicate and the derivative if needed.
static Colored setup_particle(kernel::Model *m, ParticleIndex pi, Color color)
Definition: Colored.h:62
Images read_images(const Strings &names, const ImageReaderWriter *rw)
algebra::VectorKD get_embedding(const Subset &s, const Assignment &a, ParticleStatesTable *pst)
Return an embedding for an assignment.
void set_coordinates_safe(IMP::core::RigidBody rb, IMP::algebra::Vector3D c)
The type for a residue.
Float compute_score(const Profile *model_profile, bool use_offset=false, const std::string fit_file_name="") const
compute fit score
Represent a cone in 3D.
Definition: Cone3D.h:31
const Cylinder3D & get_cylinder_3d_geometry(const Cylinder3D &g)
Definition: Cylinder3D.h:78
kernel::Particles create_dihedrals(kernel::Particles bonds) const
Auto-generate Dihedral particles from the passed list of Bond particles.
kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Define the type for a type of hierarchy.
void set_model_particles(const kernel::ParticlesTemp &ps)
Set the particles where the em2D restraint is applied.
void set_particles(const kernel::Particles &pis)
Set the particles to use.
algebra::BoundingBoxD< 3 > get_bounding_box(const XYZRs &ps)
Get the bounding box.
virtual Restraints do_create_current_decomposition(kernel::Model *m, const kernel::ParticleIndexTriplet &vt) const
FilterGeometry(const algebra::Plane3D &p)
Pay attention to the orientation of the plane.
Class for adding up scores during ScoringFunction evaluation.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Hierarchy get_previous_residue(Residue rd)
Return the residue from the same chain with one lower index.
void write_to_floats(const String &filename, em::ImageHeader &header, const cv::Mat &data) const
Writes an EM image in Spider format.
DensityMap * get_binarized_interior(DensityMap *dmap)
Return a binaries density map with 1 for voxels that are internal.
virtual void apply_index(kernel::Model *m, const kernel::ParticleIndexQuad &v) const
void set(Object *o, CheckLevel l)
Definition: SetCheckState.h:43
A restraint is a term in an IMP ScoringFunction.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
static float calc_score(DensityMap *data, SampledDensityMap *model_map, float scalefactor, bool recalc_rms=true, bool resample=true, FloatPair norm_factors=FloatPair(0., 0.))
Calculates the value of the EM fitting term.
Float compute_fitting_score(const kernel::ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
DeltaDistributionFunction(const kernel::Particles &particles, Float max_distance=0.0, Float bin_size=pr_resolution)
Constructor.
A sphere patch is defined as all points above the plane and on the sphere.
Definition: SpherePatch3D.h:18
XYZRs create_xyzr_particles(kernel::Model *m, unsigned int num, Float radius, Float box_side=10)
Create a set of particles with random coordinates.
VectorD< D > get_random_vector_in(const BoundingBoxD< D > &bb)
Generate a random vector in a box with uniform density.
SingletonConstraint(SingletonModifier *before, SingletonDerivativeModifier *after, kernel::Particle *vt, std::string name="SingletonConstraint %1%")
Float calculate_I0(const kernel::Particles &particles, FormFactorType ff_type=HEAVY_ATOMS)
calculate Intensity at zero (= squared number of electrons)
QuadsRestraint(kernel::QuadScore *ss, kernel::QuadContainerAdaptor pc, std::string name="QuadsRestraint %1%")
Create the restraint with a shared container.
const Transformation2D & operator*=(const Transformation2D &o)
See help for operator*.
virtual Restraints do_create_current_decomposition(kernel::Model *m, const kernel::ParticleIndexPair &vt) const
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexTriplet &pi) const
Compute the predicate and the derivative if needed.
PartitionalClusteringWithCenter * create_bin_based_clustering(Embedding *embed, double side)
Simple 2D transformation class.
void DensityHeader_to_ImageHeader(const DensityHeader &header, ImageHeader &h)
AmbiguousRestraint(kernel::Model *m, int d, kernel::Restraint *r0, kernel::Restraint *r1)
Create the restraint.
virtual double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexes &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
GridIndexD< D > get_index(const ExtendedGridIndexD< D > &i) const
requires get_has_index(i) is true.
Base class for all scoring functions related to em2d.
Definition: scores2D.h:55
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexPair &pi) const
Compute the predicate and the derivative if needed.
virtual double evaluate(const kernel::ParticleQuad &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual int get_value_index(kernel::Model *, const kernel::ParticleIndexQuad &) const
Compute the predicate and the derivative if needed.
UniformPrior(IMP::kernel::Model *m, Particle *p, Float k, Float upperb, Float lowerb, std::string name="UniformPrior%1%")
Create the restraint.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
void set_size(int rows, int cols)
AlignSymmetric(em::DensityMap *dmap, float threshold, int cn_symm_deg)
Constructor.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double get_surface_area(const Cone3D &g)
Definition: Cone3D.h:64
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pi) const
SurfaceShellDensityMap()
Creates a new density map.
void save_cache(const kernel::ParticlesTemp &particle_ordering, const kernel::RestraintsTemp &restraints, RMF::HDF5::Group group, unsigned int max_entries)
std::pair< Vector3D, double > get_axis_and_angle(const Rotation3D &rot)
Decompose a Rotation3D object into a rotation around an axis.
Holds header data for optimization.
Definition: SettingsData.h:135
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double get_density(const DensityMap *m, const algebra::Vector3D &v)
Hierarchy read_mol2(base::TextInput mol2_file, kernel::Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
bool same_dimensions(const DensityMap *other) const
Checks if two maps have the same dimensions.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
int get_value(kernel::Particle *a) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void set_score(int predicate_value, kernel::QuadScore *score)
Restraint(const kernel::Particles &particles, const Profile *exp_profile, FormFactorType ff_type=HEAVY_ATOMS)
Constructor.
Vector3Ds read_pts(base::TextInput input)
Read a set of 3D vectors from a file.
void setup_hierarchy(Hierarchy hierarchy) const
Make the Hierarchy conform with this topology.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
double get_volume(const Ellipsoid3D &g)
Definition: Ellipsoid3D.h:64
virtual int get_value_index(kernel::Model *, kernel::ParticleIndex) const
Compute the predicate and the derivative if needed.
Hierarchy create_clone_one(Hierarchy d)
Clone the node in the Hierarchy.
bool is_penetrating(const std::vector< IMP::algebra::Vector3D > &points, float penetration_thr) const
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
Base class for functions of two variables.
virtual void apply_index(kernel::Model *m, kernel::ParticleIndex pi) const
static Chain setup_particle(kernel::Model *m, ParticleIndex pi, std::string id)
Definition: Chain.h:41
void set_in_image(em::ImageHeader &header) const
Sets the registration results to the header of an image.
void setup(ScoreFunction *score_function, const Em2DRestraintParameters &params)
Initializes the parameters to generate and match projections.
void crop(Image *img, const IntPair &center, int size)
void read_from_image(const em::ImageHeader &header)
Reads the registration parameters from an image.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
Transformation3Ds get_alignments_from_first_to_second(const PrincipalComponentAnalysisD< 3 > &pca1, const PrincipalComponentAnalysisD< 3 > &pca2)
ExtendedGridIndexD< D > get_extended_index(const GridIndexD< D > &index) const
Convert an index back to an extended index.
Definition: GridD.h:247
void transform(const IMP::atom::Hierarchy &protein, const IMP::PairScore *score, double thr, double K, int num_iter) const
set coordinates of side chains of the given protein
virtual double get_strength(const Subset &s, const Subsets &prior_subsets) const =0
The strength is a rough metric of how this filter restricts the subset.
void read(const char *filename, float **data, DensityHeader &header)
Reads a map in Spider format and transfers the data and header.
void set_particle(kernel::Particle *p, const kernel::ParticlesTemp &ps)
Set the mapping for a particular particle.
DensityMap * create_density_map(const DensityMap *other)
create a copy of another map
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
PCAFitRestraint(kernel::ParticlesTemp ps, DensityMap *em_map, float threahold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff, FloatKey weight_key=atom::Mass::get_mass_key())
Constructor.
void write_to_ints(const String &filename, em::ImageHeader &header, const cv::Mat &data) const
Writes an EM image in TIFF format.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pi) const
BondAngleRevoluteJoint(IMP::core::RigidBody parent, IMP::core::RigidBody child, IMP::core::XYZ a, IMP::core::XYZ b, IMP::core::XYZ c)
IMP::Restraint * create_weighted_excluded_volume_restraint(core::RigidBody rb1, core::RigidBody rb2, FloatKey shell_key=FloatKey("surf_ind"))
Create a weighted excluded volume restraint between two rigid bodies.
BoundingBoxD< 3 > get_bounding_box(const Ellipsoid3D &g)
Definition: Ellipsoid3D.h:64
LeavesRefiner(HierarchyTraits tr)
Create a refiner for a particular type of hierarchy.
Holds data about the assembly density needed for optimization.
Definition: SettingsData.h:76
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void write_mol2(Hierarchy rhd, base::TextOutput file_name)
Write a ligand hierarchy as a mol2 file.
double get_cross_correlation_coefficient(Image *im1, Image *im2)
Cross correlation between two images.
A decorator for a particle that has a Lennard-Jones potential well.
Definition: LennardJones.h:26
Rotation3D get_interpolated(const Rotation3D &a, const Rotation3D &b, double f)
Interpolate between two rotations.
Definition: Rotation3D.h:453
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexQuad &pi) const
Compute the predicate and the derivative if needed.
IMP::algebra::BoundingBoxD< 3 > calculate_particles_bounding_box(const kernel::Particles &ps)
Calculate the parameters of the particles bounding box.
void set_unknown_score(kernel::SingletonScore *score)
MapDistanceTransform(IMP::em::DensityMap *map, float density_threshold, float max_distance)
Class to handle individual model particles.
Rotation3D get_rotation_from_vector4d(const VectorD< 4 > &v)
Compute a rotation from an unnormalized quaternion.
Definition: Rotation3D.h:349
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual ParticleIndexes get_refined_indexes(Model *m, ParticleIndex pi) const
Return the indexes of the particles returned by get_refined()
RotamerAngleTuples get_rotamers(IMP::atom::ResidueType residue, float phi, float psi, float probability_thr) const
query the rotamer library for the rotamer data
double get_surface_area(const Cylinder3D &g)
Definition: Cylinder3D.h:78
Store data to be clustered for embedding based algorithms.
double get_area(const Plane3D &g)
Definition: Plane3D.h:86
const Storage::Value get_trilinearly_interpolated(const GridD< 3, Storage, typename Storage::Value, Embedding > &g, const Vector3D &v, const typename Storage::Value &outside=0)
Use trilinear interpolation to compute a smoothed value at v.
Definition: grid_utility.h:36
Transformation3D operator/(const Transformation3D &b) const
bool get_atom_exists(const IMP::atom::AtomType &at) const
check if a given atom is present in the data structure
void set_bounding_box(const BoundingBoxD< D > &bb3)
Change the bounding box but not the grid or contents.
Definition: GridD.h:270
int get_state_index(Hierarchy h)
Walk up the hierarchy to find the current state.
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexTriplet &pi) const
Compute the predicate and the derivative if needed.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
const Floats & get_vacuum_form_factors(kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
for reciprocal space profile calculation
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual double evaluate_index(kernel::Model *m, kernel::ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
static Domain setup_particle(kernel::Model *m, ParticleIndex pi, Domain other)
Definition: Domain.h:61
static Uncertainty setup_particle(kernel::Model *m, ParticleIndex pi, Float uncertainty)
Definition: Uncertainty.h:45
virtual int get_value_index(kernel::Model *, const kernel::ParticleIndexQuad &) const
Compute the predicate and the derivative if needed.
A CHARMM patch residue.
Holds data about a component needed for optimization.
Definition: SettingsData.h:22
virtual Restraints do_create_current_decomposition(kernel::Model *m, kernel::ParticleIndex vt) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
double get_score(kernel::Restraint *r, const Assignment &a) const
Get the score of a set or restraint.
void set_vector_geometry(base::WeakPointer< kernel::Particle > d, const algebra::Vector3D &v)
Definition: XYZ.h:168
void save_images(Images images, const Strings &names, const ImageReaderWriter *rw)
double operator()(unsigned int id1, unsigned int id2, const ClusterSet &cluster_set, const FloatsList &distances)
Distance between the clusters.
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
A class to store a configuration of a model.
void add_internal_transformations(core::RigidBody d, algebra::Transformation3Ds transforms)
GenericHierarchies get_internal(Hierarchy mhd)
Get all the non-leaves of the bit of hierarchy.
Common base class for heavy weight IMP objects.
Definition: Object.h:106
Base class for all optimizers.
void create_masks(const kernel::ParticlesTemp &ps)
virtual ContainersTemp get_output_containers(Particle *p) const
virtual Restraints do_create_current_decomposition(kernel::Model *m, const kernel::ParticleIndexQuad &vt) const
double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual void apply_indexes(kernel::Model *m, const kernel::ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
Definition: core/symmetry.h:88
algebra::Vector3Ds get_points_close_to_molecule(const atom::Hierarchy &mh, const algebra::Vector3Ds points, Float max_dist)
void write(const String &filename, const ImageReaderWriter *writer)
Definition: Image.h:138
virtual void apply_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &o, unsigned int lower_bound, unsigned int upper_bound) const
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
float get_cn_rmsd(atom::Hierarchies mh1, atom::Hierarchies mh2)
Find correspondence between the two rings and calculate rmsd.
Images create_evenly_distributed_projections(const kernel::ParticlesTemp &ps, unsigned int n, const ProjectingOptions &options)
static Copy setup_particle(kernel::Model *m, ParticleIndex pi, Int number)
Definition: Copy.h:40
void set_unknown_score(kernel::PairScore *score)
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Reflect about a plane in 3D.
Definition: Reflection3D.h:20
PairsRestraint(kernel::PairScore *ss, kernel::PairContainerAdaptor pc, std::string name="PairsRestraint %1%")
Create the restraint with a shared container.
Float approximate_molecular_mass(DensityMap *m, Float threshold)
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void add_data(kernel::ModelKey mk, base::Object *o)
virtual void apply_index(kernel::Model *m, kernel::ParticleIndex p) const
algebra::Vector3D get_vector_to(const XYZ &b) const
Get the vector from this particle to another.
Definition: XYZ.h:99
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual int get_value_index(kernel::Model *m, kernel::ParticleIndex pi) const
Compute the predicate and the derivative if needed.
void set_internal_transformation(const algebra::Transformation3D &v)
Definition: rigid_bodies.h:392
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pi) const
Definition: predicates.h:52
virtual void apply_indexes(kernel::Model *m, const kernel::ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
Definition: Transform.h:38
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void get_segmentation(em::DensityMap *dmap, double apix, double density_threshold, int num_means, const std::string pdb_filename, const std::string cmm_filename, const std::string seg_filename, const std::string txt_filename)
Segment a density map using the anchor graph.
unsigned get_number_of_cases(const IMP::atom::AtomType &at) const
get number of coordinate sets for a given atom
void do_normalize(Image *im, bool force=false)
DensityMap * get_transformed(const DensityMap *input, const algebra::Transformation3D &tr, double threshold)
Return a new density map containing a rotated version of the old one.
TextWriter(base::TextOutput fn)
Create a writer opening the file with the passed sink.
kernel::Restraint * create_internal_connectivity_restraint(const Selection &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selection.
void destroy(Hierarchy d)
Delete the Hierarchy.
void add_coordinates(Hierarchy hierarchy) const
Add atom Cartesian coordinates to the given Hierarchy using this topology.
Particle(kernel::Model *m, std::string name)
Construct a particle and add it to the Model.
virtual int get_value_index(kernel::Model *, const kernel::ParticleIndexPair &vt) const
Compute the predicate and the derivative if needed.
int operator()(kernel::Model *m, kernel::ParticleIndex vt) const
Enable them to be use as functors.
void add_protein_ligand_score_data(Hierarchy h)
Float get_radius(kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
radius
void downsample(Profile *downsampled_profile, unsigned int point_number) const
downsample the profile to a given number of points
atom::Hierarchy create_coarse_molecule_from_molecule(const atom::Hierarchy &mh, int num_beads, kernel::Model *mdl, float bead_radius, bool add_conn_restraint=false)
Coarsen a molecule based on atom clustering.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
An axis-aligned bounding box.
Definition: BoundingBoxD.h:27
Transformation2D operator/(const Transformation2D &b) const
static Mass setup_particle(kernel::Model *m, ParticleIndex pi, Float mass)
Definition: Mass.h:44
Parameters needed for the core projection routine.
Definition: project.h:30
static ExampleDecorator setup_particle(kernel::Model *m, ParticleIndex pi, std::string name)
3D rotation class.
Definition: Rotation3D.h:46
std::string get_molecule_name(Hierarchy h)
Ints get_nearest_neighbors(unsigned int i, unsigned int k) const
Search using the ith point in the input set.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
void set_particles(const kernel::Particles &pis)
Set the particles to use.
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
TripletConstraint(TripletModifier *before, TripletDerivativeModifier *after, const kernel::ParticleTriplet &vt, std::string name="TripletConstraint %1%")
void set_transformation_child_to_parent_no_checks(IMP::algebra::Transformation3D transformation)
Definition: Joint.h:99
void add_partial_profiles(const Profile *other_profile, Float weight=1.0)
add partial profiles
virtual double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexes &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
void add_atom_types(Hierarchy hierarchy) const
Add CHARMM atom types to the given Hierarchy using this topology.
Return 1 if two XYZRs collide.
Definition: predicates.h:63
base::Vector< VectorD< D > > get_grid_interior_cover_by_spacing(const BoundingBoxD< D > &bb, double s)
static Centroid setup_particle(kernel::Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
Float compute_offset(const Profile *model_profile) const
computes offset for fitting for fitting the modeled profile
Definition: ProfileFitter.h:93
const Segment3D & get_segment_3d_geometry(const Segment3D &g)
Definition: Segment3D.h:52
virtual bool get_can_refine(kernel::Particle *) const
Return true if this refiner can refine that particle.
virtual bool operator()(Hierarchy p)=0
Return true if the traversal should visit this node's children.
void set_sphere_d_geometry(CustomXYZR d, const algebra::Sphere3D &v)
Definition: CustomXYZR.h:95
virtual void do_add_score_and_derivatives(ScoreAccumulator sa, const ScoreStatesTemp &ss)=0
virtual const kernel::ParticlesTemp get_refined(kernel::Particle *) const
Refine the passed particle into a set of particles.
int get_value(kernel::Particle *a) const
void distribution_2_profile(const RadialDistributionFunction &r_dist)
convert to reciprocal space I(q) = Sum(P(r)*sin(qr)/qr)
Simple implementation of segments in 3D.
Definition: Segment3D.h:24
em2d::Images get_projections(const kernel::ParticlesTemp &ps, const algebra::SphericalVector3Ds &vs, int rows, int cols, const ProjectingOptions &options, Strings names=Strings())
Generates projections from particles.
virtual ModelObjectsTemp do_get_outputs(kernel::Model *m, const ParticleIndexes &pis) const
container::ClosePairContainer * create_excluded_volume(const kernel::ParticlesTemp &ps, double k, std::string name)
void set_owner_kf(KinematicForest *kf)
Definition: Joint.h:89
void do_resample_polar(Image *im1, Image *im2, const PolarResamplingParameters &polar_params)
const Ellipsoid3D & get_ellipsoid_3d_geometry(const Ellipsoid3D &g)
Definition: Ellipsoid3D.h:64
A decorator for a residue with probability of secondary structure.
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexQuad &pi) const
Compute the predicate and the derivative if needed.
SecondaryStructureResidue setup_coarse_secondary_structure_residue(const kernel::Particles &ssr_ps, kernel::Model *mdl, bool winner_takes_all_per_res=false)
Coarsen some SecondaryStructureResidues.
double get_pairwise_rmsd_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the RMSD between two placements of the same set of points.
SingletonsRestraint(kernel::SingletonScore *ss, kernel::SingletonContainerAdaptor pc, std::string name="SingletonsRestraint %1%")
Create the restraint with a shared container.
virtual double evaluate_index(kernel::Model *m, kernel::ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void pick_max(const DensityMap *other)
algebra::Sphere3D get_enclosing_sphere(const XYZs &v)
Get a sphere enclosing the set of XYZRs.
multifit::FittingSolutionRecords fft_based_rigid_fitting(atom::Hierarchy mol2fit, em::DensityMap *dmap, double density_threshold, double angle_sampling_interval_rad)
FFT fit of a molecule in the density.
TripletRestraint(TripletScore *ss, const kernel::ParticleTriplet &vt, std::string name="TripletRestraint %1%")
Create the restraint.
void load_merged_assignments_random_order(const Subset &first_subset, AssignmentContainer *first, const Subset &second_subset, AssignmentContainer *second, const SubsetFilterTablesTemp &filters, unsigned int maximum_tries, AssignmentContainer *ret)
Sample from the merged assignments.
static CustomXYZR setup_particle(kernel::Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
Definition: CustomXYZR.h:49
void write_spheres(const Sphere3Ds &vs, base::TextOutput out)
Write a set of 3d spheres to a file.
A decorator for a residue.
Definition: Residue.h:134
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
virtual bool get_can_refine(kernel::Particle *) const
Return true if this refiner can refine that particle.
MarginalNOERestraint(kernel::Model *m)
Create the restraint.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
Joint * add_edge(IMP::core::RigidBody parent, IMP::core::RigidBody child)
RotamerRange get_rotamers_fast(IMP::atom::ResidueType residue, float phi, float psi, float probability_thr) const
query the rotamer library for the rotamer data
FittingSolutionRecords get_close_to_point(const FittingSolutionRecords &fit_sols, atom::Hierarchy mh, IMP::kernel::Particle *ap, Float dist)
prune solutions by distance to an anchor point
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
kernel::ParticlePairsTemp get_close_pairs(const kernel::ParticlesTemp &pc) const
void propagate_coordinates(const kernel::ParticleIndexes &ps, double step_size)
First part of velocity Verlet (update coordinates and half-step velocity)
ConnectingPairContainer(kernel::SingletonContainer *sc, double error)
static LennardJones setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: LennardJones.h:36
Transformation3D get_transformation_3d(const Transformation2D &t2d)
Builds a 3D transformation from a 2D one.
void do_segmentation(const cv::Mat &m, cv::Mat &result, const SegmentationParameters &params)
Segmentation of images.
void add_radii(Hierarchy mhd, double scale=1.0, FloatKey radius_key=FloatKey("radius")) const
Add or replace radii in the structure defined in the hierarchy.
Vector3D operator*(const Vector3D &v) const
apply transformation (rotate and then translate)
void get_transformed(const cv::Mat &input, cv::Mat &transformed, const algebra::Transformation2D &T)
Parameters used by Em2DRestraint and ProjectionFinder.
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Value get_linearly_interpolated(const GridD< D, Storage, Value, Embedding > &g, const VectorD< D > &pt)
Definition: grid_utility.h:23
A class for fast alignment of a cyclic model to its density.
double get_rmsd(const core::XYZs &s0, const core::XYZs &s1)
Store a configuration of a subset.
Definition: Assignment.h:32
double get_relative_projection_on_segment(const Segment3D &s, const algebra::Vector3D &p)
void set_subject_image(em2d::Image *subject)
void set_cylinder_3d_geometry(Cylinder3D &g, const Cylinder3D &v)
Definition: Cylinder3D.h:78
void set_simulator(atom::Simulator *sim)
Use the simulator to tag frames with current time.
virtual void propagate_coordinates(const kernel::ParticleIndexes &ps, double step_size)
First part of velocity Verlet (update coordinates and half-step velocity)
virtual double do_evaluate(const kernel::ParticleIndexes &moved) const
Get the current energy.
Definition: MonteCarlo.h:189
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Definition: predicates.h:130
void set_vector_geometry(XYZ d, const algebra::Vector3D &v)
Definition: XYZ.h:129
void set_particle_states(kernel::Particle *p, ParticleStates *e)
virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum) const
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
void show(Hierarchy h, std::ostream &out=std::cout)
Print out a molecular hierarchy.
Sphere3Ds read_spheres(base::TextInput input)
Read a set of 3d spheres from a file.
Float radius_of_gyration(const kernel::Particles &particles)
compute radius_of_gyration
Definition: saxs/utility.h:73
static Representation setup_particle(kernel::Model *m, ParticleIndex pi)
virtual int get_value_index(kernel::Model *, const kernel::ParticleIndexTriplet &) const
Compute the predicate and the derivative if needed.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void read_from_ints(const String &filename, em::ImageHeader &header, cv::Mat &data) const
Reads an image file in TIFF format.
virtual double evaluate_if_good_index(kernel::Model *m, const kernel::ParticleIndexQuad &vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed.
Abstract class for scoring object(s) of type Particle.
Joint(IMP::core::RigidBody parent, IMP::core::RigidBody child)
void apply_generic(const PairModifier *m) const
Just use apply() in the base class.
WeightRestraint(kernel::Particle *w, Float wmin, Float wmax, Float kappa)
Create the restraint.
core::MonteCarloMover * create_serial_mover(const kernel::ParticlesTemp &ps)
virtual void apply_indexes(kernel::Model *m, const kernel::ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
Definition: CoverRefined.h:60
Restraints do_create_current_decomposition(kernel::Model *m, const kernel::ParticleIndexQuad &vt) const
const Transformation2D & operator/=(const Transformation2D &o)
See help for operator/.
virtual double evaluate_index(kernel::Model *m, kernel::ParticleIndex vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void add(const RadialDistributionFunction &model_pr)
add another distribution
void show_rigid_body_hierarchy(RigidBody rb, base::TextOutput out=base::TextOutput(std::cout))
double operator()(unsigned int id1, unsigned int id2, const ClusterSet &cluster_set, const FloatsList &distances) const
kernel::ParticlesTemp create_rigid_bodies(kernel::Model *m, unsigned int n, bool no_members=false)
virtual void setup(const kernel::ParticleIndexes &)
Definition: Simulator.h:157
virtual void apply_index(kernel::Model *m, kernel::ParticleIndex p) const
Restraints do_create_current_decomposition(kernel::Model *m, const kernel::ParticleIndexTriplet &vt) const
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
Calculate the -Log of a list of restraints.
Definition: LogWrapper.h:19
FitRestraint(kernel::ParticlesTemp ps, DensityMap *em_map, FloatPair norm_factors=FloatPair(0., 0.), FloatKey weight_key=atom::Mass::get_mass_key(), float scale=1, bool use_rigid_bodies=true, KernelType kt=GAUSSIAN)
Constructor.
void add(const Profile *other_profile, Float weight=1.0)
add another profile - useful for rigid bodies
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
kernel::Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
OptimizerState(kernel::Model *m, std::string name)
virtual double evaluate_index(kernel::Model *m, kernel::ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
kernel::ParticleIndex get_root_rigid_body(RigidMember m)
Return the index of the outer-most rigid body containing the member.
Float get_volume(kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
volume
int get_value(kernel::Particle *a) const
Definition: predicates.h:58
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void multiply(const algebra::Transformation3D &t)
Definition: rigid_fitting.h:83
Hierarchy create_protein(kernel::Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
void set_enclosing_radius(XYZR b, const XYZs &v)
Set the radius of the first to enclose the list.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
virtual double do_step(const kernel::ParticleIndexes &sc, double dt)=0
Perform a single time step.
void link_hierarchies(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *, const kernel::ParticleIndexes &) const
Ints get_unique_index(const algebra::Rotation3D &rot)
For a unique 4 ints ( 2 first decimal positions) for a rotation.
CrossLinkMSRestraint(IMP::kernel::Model *m, double length, std::string name="CrossLinkMSRestraint%1%")
Create the restraint.
virtual void apply_indexes(kernel::Model *m, const kernel::ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
void set(Particle *p, Key key, const Value &value)
Definition: kernel/scoped.h:48
static Diffusion setup_particle(kernel::Model *m, ParticleIndex pi, Float D)
Definition: Diffusion.h:50
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pi) const
virtual double evaluate_index(kernel::Model *m, kernel::ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double get_surface_area(const Selection &s)
Get the total surface area of a hierarchy, in square angstroms.
void set_ellipsoid_3d_geometry(Ellipsoid3D &g, const Ellipsoid3D &v)
Definition: Ellipsoid3D.h:64
void set_plane_3d_geometry(Plane3D &g, const Plane3D &v)
Definition: Plane3D.h:86
em::FittingSolutions fit_cn_assembly(atom::Hierarchies mhs, int dn_symm_deg, em::DensityMap *dmap, float threshold, const AlignSymmetric &aligner, bool sample_translation=false, bool fine_rotational_sampling=true)
Fit a symmetric model to its density.
void add_dope_score_data(atom::Hierarchy h)
DistanceFilter(const domino::Subset &subset_to_act_on, const domino::Subset &subset_to_restrain, domino::ParticleStatesTable *ps_table, double max_distance)
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
void apply_generic(const TripletModifier *m) const
Just use apply() in the base class.
virtual bool get_can_refine(kernel::Particle *) const
Return true if this refiner can refine that particle.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
IMP::Floats get_solvent_accessibility(const core::XYZRs &points, float probe_radius=1.8, float density=5.0)
estimate surface accessibility of each atom.
Base class for smoothing nonbonded interactions as a function of distance.
SubsetGraph get_restraint_graph(ScoringFunctionAdaptor rs, const ParticleStatesTable *pst)
atom::Hierarchies create_coarse_molecules_from_molecules(const atom::Hierarchies &mhs, int frag_len, kernel::Model *mdl, float bead_radius, bool add_conn_restraint=false)
Coarsen molecules based on atom clustering.
void add_noise(cv::Mat &v, double op1, double op2, const String &mode="uniform", double df=3)
Add noise to the values of a matrix.
VectorD< D > operator*(double s, VectorD< D > o)
Definition: VectorD.h:193
void do_remove_small_objects(cvIntMat &m, double percentage, int background=0, int foreground=1)
Removes small objects from a matrix of integers.
void set_score(int predicate_value, kernel::TripletScore *score)
Restraints do_create_current_decomposition(kernel::Model *m, const kernel::ParticleIndexPair &vt) const
base::Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 8 bounding points for the bounding box.
Definition: BoundingBoxD.h:256
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
Class to manage registration results.
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void transform(RigidBody a, const algebra::Transformation3D &tr)
Transform a rigid body.
Definition: rigid_bodies.h:540
static Voxel setup_particle(kernel::Model *m, ParticleIndex pi, algebra::Vector3D position, Float radius, Float density)
Definition: Voxel.h:39
Auxiliary class for FRET_R restraint.
Definition: FretData.h:22
void set_vector_geometry(Particle *p, const algebra::Vector3D &v)
Definition: XYZ.h:149
FloatPair get_placement_score(const core::XYZs &source, const core::XYZs &target)
Measure the difference between two placements of the same set of points.
FitParameters fit_profile(Profile *partial_profile, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0, float max_c2=4.0, bool use_offset=false, const std::string fit_file_name="") const
fit experimental profile through optimization of c1 and c2 parameters
std::pair< double, algebra::Vector3Ds > evaluate(DensityMap *em_map, SampledDensityMap *model_map, const algebra::Vector3Ds &deriv, float scalefac, bool lderiv, unsigned long eval_interval)
Evaluate the cross-correlation value only every X calls to the function.
Ints get_in_ball(unsigned int i, double distance) const
virtual void apply_indexes(kernel::Model *m, const kernel::ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
The topology of a single CHARMM segment in a model.
SampledDensityMap(KernelType kt=GAUSSIAN)
Creates a new density map for sampled map.
Float compute_max_distance(const kernel::Particles &particles)
compute max distance
Definition: saxs/utility.h:39
virtual void apply_indexes(kernel::Model *m, const kernel::ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
Definition: CoverBond.h:34
void load_last_score(kernel::Restraint *r, const Subset &s, const Assignment &a)
Make it so kernel::Restraint::get_last_score() returns the score.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexPair &pi) const
Compute the predicate and the derivative if needed.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
RigidBodyUmbrella(kernel::Model *m, kernel::ParticleIndex pi, kernel::ParticleIndex ref, Floats x0, double alpha, double k, std::string name="RigidBodyUmbrella %1%")
Create the restraint by specifying directly.
void set_sphere_patch_3d_geometry(SpherePatch3D &g, const SpherePatch3D &v)
Definition: SpherePatch3D.h:48
CHARMMParameters(base::TextInput topology_file_name, base::TextInput par_file_name=base::TextInput(), bool translate_names_to_pdb=false)
Construction with CHARMM topology (and optionally parameters) file.
virtual double evaluate(kernel::Particle *vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
static Fragment setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: Fragment.h:63
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
void set_reference_frame_from_members(const kernel::ParticleIndexes &members)
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
bool get_contains(const VectorD< D > &o) const
True if the point o is contained within this bounding box.
Definition: BoundingBoxD.h:129
FittingSolutions local_rigid_fitting_around_points(kernel::Particle *p, Refiner *refiner, const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds &anchor_centroids, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3)
Local rigid fitting of a rigid body around a set of center points.
Store info for a chain of a protein.
Definition: Chain.h:21
TransformationSymmetry(const algebra::Transformation3D &t)
Create with both reflection and translation.
void add_well_depths(Hierarchy mhd) const
Add LennardJones well depths to the structure.
void set_ff_table(FormFactorTable *ff_table)
required for reciprocal space calculation
Definition: Profile.h:177
virtual double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexQuads &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void read_from_ints(const String &filename, em::ImageHeader &header, cv::Mat &data) const
Reads an image file in JPG format.
PrismaticJoint(IMP::core::RigidBody parent, IMP::core::RigidBody child, IMP::core::XYZ a, IMP::core::XYZ b)
static CenterOfMass setup_particle(kernel::Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
Definition: CenterOfMass.h:81
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexTriplets &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual int get_value_index(kernel::Model *, const kernel::ParticleIndexPair &) const
Compute the predicate and the derivative if needed.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
int get_copy_index(Hierarchy h)
Walk up the hierarchy to find the current copy index.
DensityFillingRestraint(kernel::Particles ps, DensityMap *em_map, Float threshold)
Constructor.
kernel::Particles density2particles(DensityMap *dmap, Float threshold, kernel::Model *m, int step=1)
Converts a density grid to a set of paritlces.
double get_rmsd_transforming_first(const IMP::algebra::Transformation3D &tr, const core::XYZs &s0, const core::XYZs &s1)
A decorator for helping deal with a hierarchy.
CHARMMResidueTopology(ResidueType type)
Create an empty topology, containing no atoms or bonds.
double get_maximum_time_step_estimate(BrownianDynamics *bd)
void write(const char *filename, const float *data, const DensityHeader &header)
Writes a map in Spider format from data and header.
MarginalHBondRestraint(kernel::Model *m)
Create the restraint.
virtual const kernel::ParticlesTemp get_refined(kernel::Particle *p) const
Returns the fixed set of particles.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
ReferenceFrame3D()
Create the default reference frame.
void add(const algebra::VectorD< D > &x, double weight=1)
Definition: HistogramD.h:35
void apply(const SingletonModifier *sm) const
Apply a SingletonModifier to the contents.
Float get_form_factor(kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
get f(0), ie q=0 for real space profile calculation
virtual int get_value_index(kernel::Model *, kernel::ParticleIndex) const
Compute the predicate and the derivative if needed.
void remove_particle(ParticleIndex pi)
void add_particle(kernel::Particle *p, const kernel::ParticlesTemp &ps)
Add a mapping to the table.
A decorator for a rigid body.
Definition: rigid_bodies.h:75
double get_rmsd_transforming_first(const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Calculate the root mean square deviation between two sets of 3D points.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
MolecularDynamics(kernel::Model *m=nullptr)
The topology of a complete CHARMM model.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
A Cartesian vector in D-dimensions.
Definition: VectorBaseD.h:50
Dynamically build a histogram embedded in D-dimensional space.
Definition: HistogramD.h:27
virtual void apply_indexes(kernel::Model *m, const kernel::ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
static Key< ID, LazyAdd > add_alias(Key< ID, LazyAdd > old_key, std::string new_name)
Make new_name an alias for old_key.
Definition: kernel/Key.h:143
virtual void set_scoring_function(ScoringFunctionAdaptor sf)
Represent a plane in 3D.
Definition: Plane3D.h:20
FittingSolutions local_rigid_fitting_around_point(kernel::Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D &anchor_centroid, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=false)
Local rigid fitting of a rigid body around a center point.
virtual double evaluate_index(kernel::Model *m, kernel::ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void set(Particle *p, Key key, const Value &value)
Definition: kernel/scoped.h:75
void remove_particle(kernel::Particle *p)
Remove a mapping from the table.
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
char get_chain_id_char(Hierarchy h)
SampledDensityMap * particles2binarized_density(const kernel::ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Definition: converters.h:80
void set(Object *o, LogLevel l)
Definition: SetLogState.h:43
WeightMover(kernel::Particle *w, Float radius)
void load_vertex_assignments(unsigned int node_index, AssignmentContainer *ac, unsigned int max_states=std::numeric_limits< int >::max()) const
Fill in assignments for a leaf.
Profile * compute_profile(IMP::kernel::Particles particles, float min_q=0.0, float max_q=0.5, float delta_q=0.001, FormFactorTable *ft=get_default_form_factor_table(), FormFactorType ff_type=HEAVY_ATOMS, float water_layer_c2=4.0, bool fit=true, bool reciprocal=false, bool ab_initio=false, bool vacuum=false, std::string beam_profile_file="")
profile calculation for particles and a given set of options
static Dihedral setup_particle(kernel::Model *m, ParticleIndex pi, core::XYZ a, core::XYZ b, core::XYZ c, core::XYZ d)
ResidueRotamer get_rotamer(const IMP::atom::Residue &rd, double thr) const
get the coordinates of the residue atoms
void add_particle(RMF::FileHandle fh, kernel::Particle *hs)
PCAFitRestraint(kernel::Particles particles, const std::vector< std::string > &image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=false)
Constructor.
virtual int get_next_state(int pos, const Assignment &state) const
Return a next possible acceptable state for the particle in pos.
void write(const char *fn_out, const float *data, const DensityHeader &head)
Writes an MRC file from the data and the general DensityHeader.
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
void load_particle_states(const Subset &s, const Assignment &ss, const ParticleStatesTable *pst)
void set_unknown_score(kernel::QuadScore *score)
void set_bounding_box(const algebra::BoundingBoxD< 3 > &bb)
Set the bounding box for randomizing the Cartesian coordinates.
std::string get_chain_id(Hierarchy h)
Float get_molecular_mass_at_threshold(DensityMap *m, Float threshold, atom::ProteinDensityReference ref=atom::HARPAZ)
Compute an approximate molecular mass.
virtual ParticlesTemp get_output_particles(Particle *p) const
void calculate_derivative_distribution(kernel::Particle *particle)
calculates distribution for an atom defined by particle
virtual const kernel::ParticlesTemp get_refined(kernel::Particle *) const
Refine the passed particle into a set of particles.
Assignments get_sample_assignments(const Subset &s) const
static Floats get_reduced_coordinates(kernel::Model *m, kernel::ParticleIndex target, kernel::ParticleIndex ref)
returns center of mass and quaternion of rotation wrt ref
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
void set_particle_probabilities_on_anchors(kernel::Particle *p, multifit::FittingSolutionRecords sols)
Set the probability of a component to be located at each anchor position.
virtual void set_particle_type(kernel::Particle *) const
Set the particle's type.
long get_number_of_particles_outside_of_the_density(DensityMap *dmap, const kernel::Particles &ps, const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of particles that are outside of the density.
WeightedProfileFitter(const Profile *exp_profile)
Constructor.
A base class for modifiers of kernel::ParticleQuadsTemp.
void set_residue_type(ResidueType t)
Update the stored ResidueType and the atom::Hierarchy::Name.
virtual ParticleIndexes const & get_refined_indexes_by_ref(Model *m, ParticleIndex pi) const
Return the indexes of the particles returned by get_refined()
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexQuads &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Select which atoms to read from a PDB file.
Definition: pdb.h:39
PartitionalClustering * create_centrality_clustering(Metric *d, double far, int k)
A decorator for a molecule.
Definition: Molecule.h:24
void add_restraint(RMF::FileHandle fh, kernel::Restraint *hs)
Select hierarchy particles identified by the biological name.
Definition: Selection.h:62
void set_reference_frame_lazy(const IMP::algebra::ReferenceFrame3D &tr)
Change the reference, delay updating the members until evaluate.
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexTriplet &vt) const
Compute the predicate and the derivative if needed.
DihedralAngleRevoluteJoint(IMP::core::RigidBody parent, IMP::core::RigidBody child, IMP::core::XYZ a, IMP::core::XYZ b, IMP::core::XYZ c, IMP::core::XYZ d)
kernel::Particles add_dihedrals(Hierarchy hierarchy) const
Add dihedrals to the given Hierarchy using this topology, and return them.
Abstract class for scoring object(s) of type ParticleTriplet.
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
int get_value(kernel::Particle *a) const
Definition: predicates.h:36
Vector3Ds get_grid_surface_cover(const Cylinder3D &cyl, int number_of_cycles, int number_of_points_on_cycle)
Generate a grid of 3d points on a cylinder surface.
kernel::Particles create_angles(kernel::Particles bonds) const
Auto-generate Angle particles from the passed list of Bond particles.
QuadConstraint(QuadModifier *before, QuadDerivativeModifier *after, const kernel::ParticleQuad &vt, std::string name="QuadConstraint %1%")
Atoms get_atoms(const CHARMMResidueTopology *current_residue, const CHARMMResidueTopology *previous_residue, const CHARMMResidueTopology *next_residue, const std::map< const CHARMMResidueTopology *, Hierarchy > &resmap) const
Map the bond to a list of Atom particles.
algebra::VectorKDs get_centroids(Embedding *d, PartitionalClustering *pc)
virtual const kernel::ParticlesTemp get_refined(kernel::Particle *) const
Refine the passed particle into a set of particles.
kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void add_missing_atoms(Hierarchy hierarchy) const
Add any missing atoms to the given Hierarchy using this topology.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
GridD()
An empty, undefined grid.
Definition: GridD.h:201
virtual double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexTriplets &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double do_evaluate(const kernel::ParticleIndexes &) const
Get the current energy.
static Gaussian setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: Gaussian.h:48
ScoreStatesTemp get_required_score_states(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
void set_intersection(const Selection &s)
Select elements that are in both this Selection and the passed one.
virtual double evaluate_if_good_index(kernel::Model *m, const kernel::ParticleIndexTriplet &vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed.
Represent a sphere in D-dimensions.
Definition: SphereD.h:25
virtual void apply_indexes(kernel::Model *m, const kernel::ParticleIndexTriplets &o, unsigned int lower_bound, unsigned int upper_bound) const
virtual double evaluate_index(kernel::Model *m, kernel::ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
A shared container for Singletons.
A base class for choosing which Mol2 atoms to read.
Definition: mol2.h:26
vonMisesKappaConjugateRestraint(kernel::Model *m, kernel::Particle *kappa, double c=10.0, double R0=0.0)
Create the restraint.
DensityMap * get_resampled(DensityMap *input, double scaling)
Get a resampled version of the map.
GridIndexD< D > add_voxel(const ExtendedGridIndexD< D > &i, const VT &gi)
Add a voxel to the storage, this voxel will now have a GridIndex3D.
DummyRestraint(IMP::kernel::Particle *p, IMP::kernel::Particle *q)
Hierarchy get_next_residue(Residue rd)
Return the residue from the same chain with one higher index.
CHARMMTopology * create_topology(Hierarchy hierarchy) const
Create topology that corresponds to the primary sequence of the Hierarchy.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
FittingSolutions local_rigid_fitting(kernel::Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=true)
Local rigid fitting of a rigid body.
virtual bool operator()(Hierarchy p)
Return true if the traversal should visit this node's children.
A base class for modifiers of kernel::ParticlePairsTemp.
double evaluate_if_good_indexes(kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void set_enclosing_sphere(XYZR b, const XYZs &v, double slack=0)
Set the coordinates and radius of the first to enclose the list.
virtual double evaluate_index(kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
ResidueType get_residue_type(char c)
Get the residue type from the 1-letter amino acid code.
RigidBodiesImageFitRestraint(ScoreFunction *scf, const core::RigidBodies &rbs, Image *img)
Initialize the class.
double get_volume(const Cylinder3D &g)
Definition: Cylinder3D.h:78
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
virtual int get_value_index(kernel::Model *m, const kernel::ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
static RigidBodyDiffusion setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: Diffusion.h:83
void set_moved_particles(const kernel::ParticleIndexes &p)
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
2D Electron Microscopy images in IMP
Definition: Image.h:27
double evaluate_indexes(kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
int operator()(kernel::Model *m, const kernel::ParticleIndexPair &vt) const
Enable them to be use as functors.
A text label for a ball in space.
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:73
void add_representation(kernel::ParticleIndexAdaptor rep, RepresentationType type=BALLS, double resolution=-1)
Add the representation for the given resolution.
virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis) const
BoundingBoxD< 3 > get_bounding_box(const SpherePatch3D &g)
Definition: SpherePatch3D.h:48
A base class for clustering results where each item is in one cluster.
Float get_threshold_for_approximate_volume(DensityMap *m, Float desired_volume)
Computes the threshold consider in an EM map to get a desired volume.
static Symmetric setup_particle(kernel::Model *m, ParticleIndex pi, Float symmetric)
Definition: Symmetric.h:44
static float local_cross_correlation_coefficient(const DensityMap *em_map, DensityMap *model_map, float voxel_data_threshold)
Local cross correlation function.
Ints get_representatives(Embedding *d, PartitionalClustering *pc)
Float get_epsilon(Atom atom) const
get epsilon for non bonded vdW
Float get_volume_at_threshold(DensityMap *m, Float threshold)
Compute an approximate volume.
VectorD(const Range &r)
Will accept a list of floats from Python.
Definition: VectorD.h:55
virtual void setup(const kernel::ParticleIndexes &ps)
void set_difference(const Selection &s)
Select elements that are in this Selection but not the passed one.
Slice get_slice(Subset outer, Subset inner, const Subsets &excluded)
Definition: Slice.h:66
double get_power_distance(const SphereD< D > &a, const SphereD< D > &b)
Return the power distance between the two spheres.
Definition: SphereD.h:114
ExclusiveConsecutivePairContainer(const kernel::ParticlesTemp &ps, std::string name="ExclusiveConsecutivePairContainer%1%")
Get the individual particles from the passed SingletonContainer.
Store data to be clustered for distance metric based algorithms.
Definition: Metric.h:25
virtual ContainersTemp get_input_containers(Particle *p) const
A decorator for a particle with x,y,z coordinates and a radius.
Definition: XYZR.h:27