1 Factory Index {#factory_index}
6 Functions that create objects of a given type:
8 See also [Argument Index](@ref argument_index), [Class Examples](@ref class_example_index), [Function Examples](@ref function_example_index)
9 # IMP.algebra # {#factory_index_algebra}
11 <th>Class</th><th>Factories</th></tr>
12 <tr><td>@ref
IMP::algebra::BoundingBoxD</td><td><a href=
"classIMP_1_1algebra_1_1BoundingBoxD.html#aa8092895377c9aca82b78050456b33c9">
IMP::algebra::BoundingBoxD::operator+=()</a>, <a href=
"classIMP_1_1algebra_1_1BoundingBoxD.html#abe7e39f1ee5d58dae32272ee29e51f0b">
IMP::algebra::BoundingBoxD::operator+=()</a>, <a href=
"classIMP_1_1algebra_1_1BoundingBoxD.html#a83c31adcb8aafca645af67822d996eed">
IMP::algebra::BoundingBoxD::operator+=()</a>, <a href=
"classIMP_1_1algebra_1_1Cone3D.html#a42215f5c82c6b41689887aee272d6f29">
IMP::algebra::Cone3D::get_bounding_box()</a>, <a href=
"classIMP_1_1algebra_1_1Cylinder3D.html#a2c0e1a36a0080caf666ff5e8657c44ea">
IMP::algebra::Cylinder3D::get_bounding_box()</a>, <a href=
"classIMP_1_1algebra_1_1DefaultEmbeddingD.html#aa939cc38c61633c05ba8f512671c9922">IMP::algebra::DefaultEmbeddingD::get_bounding_box()</a>, <a href=
"classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a2ef44b764283d6da46c20bfbf17dbff7">IMP::algebra::DefaultEmbeddingD::get_bounding_box()</a>, <a href=
"classIMP_1_1algebra_1_1Ellipsoid3D.html#a51e51989d370ac6d1f72605ea2b55659">
IMP::algebra::Ellipsoid3D::get_bounding_box()</a>, <a href=
"classIMP_1_1algebra_1_1GridD.html#a008aec5907f2445fdb9ab7f0ad9857b4">IMP::algebra::GridD::get_bounding_box()</a>, <a href=
"classIMP_1_1algebra_1_1LogEmbeddingD.html#afcefc82a3dc1a028efd0ef7a76ae3f62">IMP::algebra::LogEmbeddingD::get_bounding_box()</a>, <a href=
"classIMP_1_1algebra_1_1LogEmbeddingD.html#a19437cca74047a689ad5622534007858">IMP::algebra::LogEmbeddingD::get_bounding_box()</a>, <a href=
"classIMP_1_1algebra_1_1Plane3D.html#aedce7034965a145fc52252f640761b26">
IMP::algebra::Plane3D::get_bounding_box()</a>, <a href=
"classIMP_1_1algebra_1_1Segment3D.html#abd21d39499ca4acd3616d7a9355b90fd">
IMP::algebra::Segment3D::get_bounding_box()</a>, <a href=
"classIMP_1_1algebra_1_1SpherePatch3D.html#ae5375e21b4c4a14ecf4278d36cab2387">
IMP::algebra::SpherePatch3D::get_bounding_box()</a>, <a href=
"classIMP_1_1display_1_1BoundingBoxGeometry.html#ac2655fba9566ec3dc3e1063f8f29077d">IMP::display::BoundingBoxGeometry::get_geometry()</a>, <a href=
"classIMP_1_1em_1_1SampledDensityMap.html#aae468b468f722cb9c6745407171a969f">
IMP::em::SampledDensityMap::calculate_particles_bounding_box()</a>, <a href=
"classIMP_1_1statistics_1_1HistogramD.html#a1076a15bf53877cf192b36b1f7aa7b9f">IMP::statistics::HistogramD::get_bounding_box()</a>, <a href=
"namespaceIMP_1_1algebra.html#aecec6f9c6ca668315e6693773ac1c15f">
IMP::algebra::get_cube_kd()</a>, <a href=
"namespaceIMP_1_1algebra.html#aec3bea2d24fbbf621216822517ca1593">
IMP::algebra::get_transformed()</a>, <a href=
"namespaceIMP_1_1algebra.html#aa88ff22c3c9a9a857314e714d69dea62">
IMP::algebra::get_unit_bounding_box_kd()</a>, <a href=
"namespaceIMP_1_1atom.html#a45b3b96085fb5dbf171f218e95c73f22">
IMP::atom::get_bounding_box()</a>, <a href=
"namespaceIMP_1_1core.html#a0ba3b6f5fba01f4ecf8a3b8f18a311f2">
IMP::core::get_bounding_box()</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></td></tr>
15 <tr><td>@ref
IMP::algebra::DenseGridStorageD</td><td><a href=
"classIMP_1_1algebra_1_1DenseGridStorageD.html#a5cd0208038b5008c73248047c91f38a7">IMP::algebra::DenseGridStorageD::operator=()</a>, <a href=
"namespaceIMP_1_1em.html#a9c72b01f6d6bbe0c84a0779fc08b809c">
IMP::em::get_grid()</a></td></tr>
17 <tr><td>@ref
IMP::algebra::ExtendedGridIndexD</td><td><a href=
"classIMP_1_1algebra_1_1BoundedGridRangeD.html#a7daff516adaa890c3d2ce985fcf8c432">IMP::algebra::BoundedGridRangeD::get_extended_indexes()</a>, <a href=
"classIMP_1_1algebra_1_1BoundedGridRangeD.html#a61d03caf63e70aa0c0e6d6d74130c27c">
IMP::algebra::BoundedGridRangeD::get_end_index()</a>, <a href=
"classIMP_1_1algebra_1_1BoundedGridRangeD.html#a395874afecb718cda8209087070b9aaa">
IMP::algebra::BoundedGridRangeD::get_maximum_extended_index()</a>, <a href=
"classIMP_1_1algebra_1_1BoundedGridRangeD.html#a3630e2bb1873a86f4606a04b5bf7c847">
IMP::algebra::BoundedGridRangeD::get_minimum_extended_index()</a>, <a href=
"classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a7c5f5633d6495ade19fa00cca4dccff5">
IMP::algebra::DefaultEmbeddingD::get_extended_index()</a>, <a href=
"classIMP_1_1algebra_1_1ExtendedGridIndexD.html#a950308f6221c222ca73d04480a595f4b">IMP::algebra::ExtendedGridIndexD::get_offset()</a>, <a href=
"classIMP_1_1algebra_1_1ExtendedGridIndexD.html#a68dba8692dbf509e79f7c884a030996e">IMP::algebra::ExtendedGridIndexD::get_uniform_offset()</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#a1f513a99898cd34a8f760b887b4f9220">
IMP::algebra::GridD::get_extended_index()</a>, <a href=
"classIMP_1_1algebra_1_1LogEmbeddingD.html#a333cca1384be415a4beb6423dc4e6273">
IMP::algebra::LogEmbeddingD::get_extended_index()</a>, <a href=
"classIMP_1_1algebra_1_1UnboundedGridRangeD.html#a8ff58568320c5e193c8111f06a4b54d8">IMP::algebra::UnboundedGridRangeD::get_extended_indexes()</a></td></tr>
21 <tr><td>@ref
IMP::algebra::GridIndexD</td><td><a href=
"classIMP_1_1algebra_1_1BoundedGridRangeD.html#a93f5e4dae6e89c016220dd535b628539">IMP::algebra::BoundedGridRangeD::get_all_indexes()</a>, <a href=
"classIMP_1_1algebra_1_1BoundedGridRangeD.html#a2cc3b3ebbceaf09645e7243039a54743">IMP::algebra::BoundedGridRangeD::get_indexes()</a>, <a href=
"classIMP_1_1algebra_1_1BoundedGridRangeD.html#acf1f33b1c1d7957330f442f15d656ac9">
IMP::algebra::BoundedGridRangeD::get_index()</a>, <a href=
"classIMP_1_1algebra_1_1DefaultEmbeddingD.html#ae4437a1c4ca95b4abbf58c9531209d02">IMP::algebra::DefaultEmbeddingD::get_index()</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#a24ba706b342d7dc7e3c5cb42ed64fccf">IMP::algebra::GridD::add_voxel()</a>, <a href=
"classIMP_1_1algebra_1_1LogEmbeddingD.html#a09613ab4444befc995178b6b8a416358">IMP::algebra::LogEmbeddingD::get_index()</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#abcf4643d745ad8f61ac711026cb9a5cb">
IMP::algebra::SparseGridStorageD::get_index()</a></td></tr>
23 <tr><td>@ref
IMP::algebra::ReferenceFrame3D</td><td><a href=
"classIMP_1_1algebra_1_1Ellipsoid3D.html#a64cdd46002ef8528e8583d5de98b749a">IMP::algebra::Ellipsoid3D::get_reference_frame()</a>, <a href=
"classIMP_1_1algebra_1_1Gaussian3D.html#a455df294c6db94bd0407f2b7fe56577a">IMP::algebra::Gaussian3D::get_reference_frame()</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#ac13846a110676d06ea4baaa5530f4a49">
IMP::core::RigidBody::get_reference_frame()</a>, <a href=
"classIMP_1_1display_1_1ReferenceFrameGeometry.html#a78238ec0ea014903e5da1a323ace6fd2">IMP::display::ReferenceFrameGeometry::get_geometry()</a>, <a href=
"classIMP_1_1domino_1_1RigidBodyStates.html#accb521c129d1f71f3e5388e4a7d6aaa7">IMP::domino::RigidBodyStates::get_reference_frame()</a>, <a href=
"classIMP_1_1kinematics_1_1KinematicForest.html#ae9aea73c759c2ceeb7c88c46553fdc47">IMP::kinematics::KinematicForest::get_reference_frame_safe()</a>, <a href=
"namespaceIMP_1_1algebra.html#ad1ae16d9089296d2d7f458c2d667e587">
IMP::algebra::get_transformed()</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></td></tr>
25 <tr><td>@ref
IMP::algebra::Rotation3D</td><td><a href=
"classIMP_1_1algebra_1_1Ellipsoid3D.html#ab7b41bd7f224e14be6505a9871c2a078">
IMP::algebra::Ellipsoid3D::get_rotation()</a>, <a href=
"classIMP_1_1algebra_1_1Rotation3D.html#a64277befc08357d6768b5f8cba5fdf56">
IMP::algebra::Rotation3D::get_inverse()</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#af38f7b53af59c4d73defebca22893b14">
IMP::algebra::Transformation3D::get_rotation()</a>, <a href=
"classIMP_1_1em2d_1_1GridStates.html#ac3e4528519d25658257b5f01a6bf10ce">
IMP::em2d::GridStates::get_orientation()</a>, <a href=
"classIMP_1_1em2d_1_1ProjectionParameters.html#ae1773e9f6d26fced9d3511e6d8ffdca2">IMP::em2d::ProjectionParameters::get_rotation()</a>, <a href=
"classIMP_1_1em2d_1_1RegistrationResult.html#acd2c31e953d155a20d200440af0331e6">
IMP::em2d::RegistrationResult::get_rotation()</a>, <a href=
"classIMP_1_1em_1_1PCAAligner.html#a717801d249ab2dd4b3b33eb5849be168">IMP::em::PCAAligner::get_rotation_matrix()</a>, <a href=
"namespaceIMP_1_1algebra.html#a50728b3c7c4674d610b353a58510b601">
IMP::algebra::get_rotation_from_fixed_xyz()</a>, <a href=
"namespaceIMP_1_1algebra.html#a25e458f2015410be98a7805c50178c75">
IMP::algebra::get_rotation_from_fixed_zxz()</a>, <a href=
"namespaceIMP_1_1algebra.html#a0d07cdae4fbf65960b6d02ecdc4501f6">
IMP::algebra::get_rotation_from_fixed_zyz()</a>, <a href=
"namespaceIMP_1_1algebra.html#a216ec1243a72a2c3f9ddf6bd8bc22ece">
IMP::algebra::compose()</a>, <a href=
"namespaceIMP_1_1algebra.html#a98a32dfffbb6b9f5f20a12dd479f1b9b">
IMP::algebra::get_identity_rotation_3d()</a>, <a href=
"namespaceIMP_1_1algebra.html#aad56f25091896ce8e87f8e5f1098bf79">
IMP::algebra::get_interpolated()</a>, <a href=
"namespaceIMP_1_1algebra.html#a139712da5a82968a06bb71b09196bc5b">
IMP::algebra::get_random_rotation_3d()</a>, <a href=
"namespaceIMP_1_1algebra.html#abd23e8a25dda2d4acf8c00db35e2537f">
IMP::algebra::get_random_rotation_3d()</a>, <a href=
"namespaceIMP_1_1algebra.html#a283f1463563e2c38fd3f4ae788c11484">
IMP::algebra::get_rotation_about_axis()</a>, <a href=
"namespaceIMP_1_1algebra.html#ad96b1551c23f1f62de05e9ebbcbf3429">
IMP::algebra::get_rotation_about_normalized_axis()</a>, <a href=
"namespaceIMP_1_1algebra.html#a28b2093fb8db4340e11cce11de658572">
IMP::algebra::get_rotation_from_matrix()</a>, <a href=
"namespaceIMP_1_1algebra.html#a6028d3e347fbe4dff0cac83a0af30ce2">
IMP::algebra::get_rotation_from_matrix()</a>, <a href=
"namespaceIMP_1_1algebra.html#a3003fd1a5254db165a8600f2979e7146">
IMP::algebra::get_rotation_from_vector4d()</a>, <a href=
"namespaceIMP_1_1algebra.html#a010dd03d5d6e849ea7b0991f646d6b53">
IMP::algebra::get_rotation_from_x_y_axes()</a>, <a href=
"namespaceIMP_1_1algebra.html#a6af4099df3f5babb4891be41ed215978">
IMP::algebra::get_rotation_taking_first_to_second()</a></td></tr>
26 <tr><td>@ref
IMP::algebra::Segment3D</td><td><a href=
"classIMP_1_1algebra_1_1Cylinder3D.html#a4b84e7480a5b89054d7f4a7e401b86be">IMP::algebra::Cylinder3D::get_segment()</a>, <a href=
"classIMP_1_1algebra_1_1Segment3D.html#af5c43b376efc839be7570ffa3ee7825b">
IMP::algebra::Segment3D::get_segment_3d_geometry()</a>, <a href=
"classIMP_1_1core_1_1RigidBodyTorque.html#a7353f5b14547af12c64c90e2415bc1bd">IMP::core::RigidBodyTorque::extract_geometry()</a>, <a href=
"classIMP_1_1core_1_1RigidBodyTorque.html#abe94f37a6c3008811e61f39ec445a553">IMP::core::RigidBodyTorque::get_geometry()</a>, <a href=
"classIMP_1_1display_1_1SegmentGeometry.html#a6a445735008db1fa269f7846dcd40943">IMP::display::SegmentGeometry::get_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></td></tr>
27 <tr><td>@ref
IMP::algebra::SphereD</td><td><a href=
"namespaceIMP_1_1algebra.html#a4834da35487ef0d191fbc1a9371724eb">IMP::algebra::get_unit_sphere_kd()</a></td></tr>
30 <tr><td>@ref
IMP::algebra::Transformation3D</td><td><a href=
"classIMP_1_1algebra_1_1Ellipsoid3D.html#af697d30feba4be5d1e03bb325696e577">
IMP::algebra::Ellipsoid3D::get_transformation()</a>, <a href=
"classIMP_1_1algebra_1_1ReferenceFrame3D.html#a9a62f89fecbe2d134d417038a0272b47">IMP::algebra::ReferenceFrame3D::get_inverse()</a>, <a href=
"classIMP_1_1algebra_1_1ReferenceFrame3D.html#a0ea138451954b123f39698f67903f5ce">
IMP::algebra::ReferenceFrame3D::get_transformation_from()</a>, <a href=
"classIMP_1_1algebra_1_1ReferenceFrame3D.html#a1e26b1d2ad062f25d54acdceb4566976">
IMP::algebra::ReferenceFrame3D::get_transformation_to()</a>, <a href=
"classIMP_1_1algebra_1_1Transformation3D.html#a11749e8dd0e6454fa96ffb626b39949b">IMP::algebra::Transformation3D::get_inverse()</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#a1b2de56684ac4d70d7bf185f037e5a45">
IMP::core::RigidBodyMember::get_internal_transformation()</a>, <a href=
"classIMP_1_1domino_1_1NestedRigidBodyStates.html#a12dda30d492ea96fa4ef79242abc9f8c">IMP::domino::NestedRigidBodyStates::get_transformation()</a>, <a href=
"classIMP_1_1em_1_1EnvelopeFitRestraint.html#a0de188aa0a38a78ec85e898b09b763f8">IMP::em::EnvelopeFitRestraint::get_transformation()</a>, <a href=
"classIMP_1_1em_1_1FittingSolutions.html#a46b28b36a52016e65285fba309ae3d5b">
IMP::em::FittingSolutions::get_transformation()</a>, <a href=
"classIMP_1_1kinematics_1_1Joint.html#a3e4b1f2fa4792d300278ebda6c091b5d">
IMP::kinematics::Joint::get_transformation_child_to_parent()</a>, <a href=
"classIMP_1_1kinematics_1_1Joint.html#ac31f8b3fff9145b88f5f9bb4d7b4b021">
IMP::kinematics::Joint::get_transformation_child_to_parent_no_checks()</a>, <a href=
"classIMP_1_1kinematics_1_1RevoluteJoint.html#a7b6f7b757bf908b57e23c481bbfd06bf">
IMP::kinematics::RevoluteJoint::get_rotation_about_joint_in_parent_coordinates()</a>, <a href=
"classIMP_1_1multifit_1_1FittingSolutionRecord.html#a42ee92b9006f1854437cbd96d8a03223">IMP::multifit::FittingSolutionRecord::get_dock_transformation()</a>, <a href=
"classIMP_1_1multifit_1_1FittingSolutionRecord.html#ae71f26cdfc8fdb94a616687222cb3a69">IMP::multifit::FittingSolutionRecord::get_fit_transformation()</a>, <a href=
"namespaceIMP_1_1algebra.html#ac1d0008195a1cf08b39038c2d7dc44a8">
IMP::algebra::get_transformation_aligning_first_to_second()</a>, <a href=
"namespaceIMP_1_1algebra.html#af2121b116324f67ee007e4aef258555c">
IMP::algebra::compose()</a>, <a href=
"namespaceIMP_1_1algebra.html#a5c675979c1dfb0467246764a7e1e2cbf">
IMP::algebra::get_identity_transformation_3d()</a>, <a href=
"namespaceIMP_1_1algebra.html#a1b3cdecd88bb99e7cf34d42117199775">
IMP::algebra::get_random_local_transformation()</a>, <a href=
"namespaceIMP_1_1algebra.html#a07063149bf0d6fd24bd5a1116d6b5115">
IMP::algebra::get_rotation_about_point()</a>, <a href=
"namespaceIMP_1_1algebra.html#a95b9c2466fd2ba29cddff88efc887aff">
IMP::algebra::get_transformation_3d()</a>, <a href=
"namespaceIMP_1_1algebra.html#a2e7851e2cdd810e68bb3235699c0f5ba">IMP::algebra::get_transformation_from_first_to_second()</a>, <a href=
"namespaceIMP_1_1algebra.html#a40b9b1290fa21102bda8255d8eb3c4d8">
IMP::algebra::get_transformation_from_first_triangle_to_second()</a>, <a href=
"namespaceIMP_1_1cnmultifit.html#a2e56b936c9db947d7febcc93a1389a2f">IMP::cnmultifit::calc_transformation_around_axis()</a>, <a href=
"namespaceIMP_1_1core.html#a805c9dce8eeee77af7354cec81a3991a">
IMP::core::get_transformation_aligning_first_to_second()</a></td></tr>
31 <tr><td>@ref
IMP::algebra::Triangle3D</td><td><a href=
"classIMP_1_1display_1_1TriangleGeometry.html#a3fb7310b1377825c917fe57545de7c0a">IMP::display::TriangleGeometry::get_geometry()</a>, <a href=
"namespaceIMP_1_1algebra.html#a3619d60308d5ac5c78e601d1e6426dee">
IMP::algebra::get_largest_triangle()</a></td></tr>
32 <tr><td>@ref
IMP::algebra::VectorD</td><td><a href=
"classIMP_1_1algebra_1_1BoundingBoxD.html#aa31f8295a3ecc17ce469438df678617b">
IMP::algebra::BoundingBoxD::get_corner()</a>, <a href=
"classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a42f36edf378dc3cb21d8b8320b2262d9">IMP::algebra::DefaultEmbeddingD::get_center()</a>, <a href=
"classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a584a87ad7db962f804e65beb46356e8a">IMP::algebra::DefaultEmbeddingD::get_center()</a>, <a href=
"classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a339984d8e099583b0cadaad5e6bf47c8">IMP::algebra::DefaultEmbeddingD::get_origin()</a>, <a href=
"classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a243f6b777d32aa49cc8e585edfaf79f6">
IMP::algebra::DefaultEmbeddingD::get_unit_cell()</a>, <a href=
"classIMP_1_1algebra_1_1LogEmbeddingD.html#a6f4d8f177ef76a4b4f05dbc3e26489f1">IMP::algebra::LogEmbeddingD::get_center()</a>, <a href=
"classIMP_1_1algebra_1_1LogEmbeddingD.html#a5cb83dd94de983716f6591c717d1b47a">IMP::algebra::LogEmbeddingD::get_center()</a>, <a href=
"classIMP_1_1algebra_1_1LogEmbeddingD.html#a3a3ab44f98c54855268ef87cb10080b9">IMP::algebra::LogEmbeddingD::get_origin()</a>, <a href=
"classIMP_1_1algebra_1_1LogEmbeddingD.html#adb20715e237723bf9de57872e11fb515">
IMP::algebra::LogEmbeddingD::get_unit_cell()</a>, <a href=
"classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a514a16c972ceea192e39bb308896e28d">IMP::algebra::PrincipalComponentAnalysisD::get_centroid()</a>, <a href=
"classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a87432e5b75325d5988dddc9c69d0a0e9">IMP::algebra::PrincipalComponentAnalysisD::get_principal_component()</a>, <a href=
"classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a4b29d9d2bc65cc38bcdc15a834dba392">IMP::algebra::PrincipalComponentAnalysisD::get_principal_components()</a>, <a href=
"classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a8bc34c872d7d80a7693bea12b91dc530">IMP::algebra::PrincipalComponentAnalysisD::get_principal_values()</a>, <a href=
"classIMP_1_1algebra_1_1SphereD.html#a66db928fc3b3bdcf01e891ba3507a3a0">IMP::algebra::SphereD::get_center()</a>, <a href=
"classIMP_1_1algebra_1_1VectorD.html#ae812e3f853fb6b2aa3c28be0cac1068a">IMP::algebra::VectorD::get_unit_vector()</a>, <a href=
"classIMP_1_1algebra_1_1VectorD.html#a78101a1171a91a39f8fa48c21fc88b02">IMP::algebra::VectorD::operator*()</a>, <a href=
"classIMP_1_1algebra_1_1VectorD.html#a04bc1569ddb15624437312ac6dcea370">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#a465db28829855dc1e2b4130ccf4970ad">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_1algebra_1_1VectorD.html#a70fee54ca37221cefb8dd755d51dbd21">IMP::algebra::VectorD::operator/()</a>, <a href=
"classIMP_1_1algebra_1_1VectorD.html#a3e0204ea98d9a5067400d54e3e48029a">IMP::algebra::VectorD::operator/=()</a>, <a href=
"classIMP_1_1core_1_1RigidBody.html#aa571733d4c574e3874777daef1f10d86">
IMP::core::RigidBody::get_rotational_derivatives()</a>, <a href=
"classIMP_1_1example_1_1ExampleTemplateClassD.html#a86ede654e64072869b8c25f23bfde3d6">
IMP::example::ExampleTemplateClassD::get_point()</a>, <a href=
"classIMP_1_1multifit_1_1GeometricHash.html#a27b2114018cc42b24e194589452e6e23">IMP::multifit::GeometricHash::from_bucket()</a>, <a href=
"classIMP_1_1statistics_1_1HistogramD.html#a3f95e629bfea515462d2554860205422">IMP::statistics::HistogramD::get_mean()</a>, <a href=
"classIMP_1_1statistics_1_1HistogramD.html#aa8f8a40723844f8f480074771dc3f0d2">IMP::statistics::HistogramD::get_standard_deviation()</a>, <a href=
"namespaceIMP_1_1algebra.html#a13112e2dae882f9c03a368a64986c198">
IMP::algebra::get_random_vector_in()</a>, <a href=
"namespaceIMP_1_1algebra.html#a15788395c438b5a87b99281375c9e1e7">
IMP::algebra::get_random_vector_on_unit_sphere()</a>, <a href=
"namespaceIMP_1_1algebra.html#a8d47beff6c7a5ffa59ef4317f1a8e604">
IMP::algebra::get_basis_vector_kd()</a></td></tr>
34 # IMP.atom # {#factory_index_atom}
36 <th>Class</th><th>Factories</th></tr>
39 <tr><td>@ref
IMP::atom::AtomType</td><td><a href=
"classIMP_1_1atom_1_1Atom.html#a867718443d203a8fdf69d0518b30fb1b">IMP::atom::Atom::get_atom_type()</a>, <a href=
"namespaceIMP_1_1atom.html#af4a6c11848aec861d0ef55068cf6261a">IMP::atom::get_atom_type()</a>, <a href=
"namespaceIMP_1_1atom.html#a02a38fbf0485b7d9642be56a9ee6bdc1">
IMP::atom::add_atom_type()</a></td></tr>
43 <tr><td>@ref
IMP::atom::CHARMMAtomTopology</td><td><a href=
"classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#afadfc33ed67175c434cad952d0d11307">IMP::atom::CHARMMResidueTopologyBase::get_atom()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a91fff9329d2a36aa42719d443fb5fc35">IMP::atom::CHARMMResidueTopologyBase::get_atom()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a42f75fbdc90c3d0ffc6da888c8a05d26">IMP::atom::CHARMMResidueTopologyBase::get_atom()</a></td></tr>
44 <tr><td>@ref
IMP::atom::CHARMMBondEndpoint</td><td><a href=
"classIMP_1_1atom_1_1CHARMMConnection.html#a5b2b5a53429c6cb8335145581de19850">IMP::atom::CHARMMConnection::get_endpoint()</a></td></tr>
45 <tr><td>@ref
IMP::atom::CHARMMConnection</td><td><a href=
"classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#add4b79ec748e743f8c1517428af553a6">IMP::atom::CHARMMResidueTopologyBase::get_angle()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a55335589fdb6c359612a1fd37f8658e8">IMP::atom::CHARMMResidueTopologyBase::get_bond()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#ade44e2c67bf8499b944f2574db441373">IMP::atom::CHARMMResidueTopologyBase::get_dihedral()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#aa4f8390a6d5efc7d3a94689490a32808">IMP::atom::CHARMMResidueTopologyBase::get_improper()</a></td></tr>
46 <tr><td>@ref
IMP::atom::CHARMMIdealResidueTopology</td><td><a href=
"classIMP_1_1atom_1_1CHARMMParameters.html#a93c5e6fbf6e839294e91ec2a179f74af">IMP::atom::CHARMMParameters::get_residue_topology()</a></td></tr>
47 <tr><td>@ref
IMP::atom::CHARMMInternalCoordinate</td><td><a href=
"classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#ad610c4fa66857daaad66e9ab60c548c1">IMP::atom::CHARMMResidueTopologyBase::get_internal_coordinate()</a></td></tr>
49 <tr><td>@ref
IMP::atom::CHARMMPatch</td><td><a href=
"classIMP_1_1atom_1_1CHARMMParameters.html#a7c83e58f1cea31a16484c15f8762635b">IMP::atom::CHARMMParameters::get_patch()</a></td></tr>
50 <tr><td>@ref
IMP::atom::CHARMMResidueTopology</td><td><a href=
"classIMP_1_1atom_1_1CHARMMSegmentTopology.html#a8e36b0b1c1bf882994cc5c7b0cfc782f">IMP::atom::CHARMMSegmentTopology::get_residue()</a></td></tr>
51 <tr><td>@ref
IMP::atom::CHARMMSegmentTopology</td><td><a href=
"classIMP_1_1atom_1_1CHARMMTopology.html#aae6f4e51cdf79001c102f679ebfc0a32">IMP::atom::CHARMMTopology::get_segment()</a></td></tr>
60 <tr><td>@ref
IMP::atom::ElementTable</td><td><a href=
"namespaceIMP_1_1atom.html#a5d562e4bead78d6882240505705d996e">IMP::atom::get_element_table()</a></td></tr>
62 <tr><td>@ref
IMP::atom::Hierarchy</td><td><a href=
"classIMP_1_1atom_1_1CHARMMTopology.html#aa146bec02d74a3610fcb85b2087c6bc5">
IMP::atom::CHARMMTopology::create_hierarchy()</a>, <a href=
"classIMP_1_1atom_1_1Hierarchy.html#a4c26db6d0879ccf5d7fc72c30e9ec54e">
IMP::atom::Hierarchy::get_child()</a>, <a href=
"classIMP_1_1atom_1_1Hierarchy.html#a3fa6740c3fcbf678ce64fb1db22a832e">
IMP::atom::Hierarchy::get_parent()</a>, <a href=
"classIMP_1_1atom_1_1Hierarchy.html#ac1a4d74fd46b7137273656725a0e6f6f">
IMP::atom::Hierarchy::setup_particle()</a>, <a href=
"classIMP_1_1atom_1_1Representation.html#af2cb8658482ff38369223b34bbb70d64">
IMP::atom::Representation::get_representation()</a>, <a href=
"namespaceIMP_1_1atom.html#a1b4c863b0fefde1c1d95cdf6fed794a8">
IMP::atom::create_simplified_along_backbone()</a>, <a href=
"namespaceIMP_1_1atom.html#af12315103e56599289223816dc3b3aeb">
IMP::atom::create_simplified_along_backbone()</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#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#aaccceee6a56745c2892b75ad9a0ca456">
IMP::atom::create_fragment()</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#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#a2cadcc607aa4c1f8b1ec4c0c8d493312">
IMP::atom::get_next_residue()</a>, <a href=
"namespaceIMP_1_1atom.html#ad329e5c66a8de2f49304492c5a690d90">
IMP::atom::get_previous_residue()</a>, <a href=
"namespaceIMP_1_1atom.html#addc26081dbfab30a1c5c74af47bbc93d">
IMP::atom::get_residue()</a>, <a href=
"namespaceIMP_1_1atom.html#ae6a2b0d20131a9186cfbea24d9320574">
IMP::atom::get_root()</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></td></tr>
64 <tr><td>@ref
IMP::atom::Mass</td><td><a href=
"classIMP_1_1atom_1_1Hierarchy.html#a6b500477d175cb9685399250a2b1bc9b">IMP::atom::Hierarchy::get_as_mass()</a>, <a href=
"classIMP_1_1atom_1_1Mass.html#abfed869368b4b4012be33932c65e9b1e">
IMP::atom::Mass::setup_particle()</a>, <a href=
"classIMP_1_1atom_1_1Mass.html#aa596392acbc82bee5e18f480d7a12706">
IMP::atom::Mass::setup_particle()</a></td></tr>
66 <tr><td>@ref
IMP::atom::PDBSelector</td><td><a href=
"namespaceIMP_1_1atom.html#af8a720ac93e90e948bd016b3e367663d">IMP::atom::get_default_pdb_selector()</a></td></tr>
69 <tr><td>@ref
IMP::atom::ResidueType</td><td><a href=
"classIMP_1_1atom_1_1CHARMMParameters.html#ad3151d18a8caed725aede9f667ea3a8d">IMP::atom::CHARMMParameters::parse_residue_line()</a>, <a href=
"classIMP_1_1atom_1_1Residue.html#ab4ca594e94407184dadbcf3f0fe4f9c7">IMP::atom::Residue::get_residue_type()</a>, <a href=
"namespaceIMP_1_1atom.html#a7bc45846fa709afb3ea73f2e9a3ad923">
IMP::atom::get_residue_type()</a>, <a href=
"namespaceIMP_1_1atom.html#a4069a6db716b4d4a269df0aed8db5287">
IMP::atom::get_residue_type()</a></td></tr>
74 <tr><td>@ref
IMP::atom::State</td><td><a href=
"classIMP_1_1atom_1_1Hierarchy.html#a6c1146092aa4d8a617722ae7a2d40cc3">IMP::atom::Hierarchy::get_as_state()</a>, <a href=
"classIMP_1_1atom_1_1State.html#ae1eb1ec30ed86385357f7146252f9d05">
IMP::atom::State::setup_particle()</a>, <a href=
"classIMP_1_1atom_1_1State.html#ad2579a58341559b9ef210e6b485f4886">
IMP::atom::State::setup_particle()</a></td></tr>
77 # IMP.base # {#factory_index_base}
79 <th>Class</th><th>Factories</th></tr>
80 <tr><td>@ref
IMP::base::AdvancedFlag</td><td><a href=
"classIMP_1_1base_1_1AdvancedFlag.html#af7fa344cc2fd88a1a85c5250366d824a">IMP::base::AdvancedFlag::operator=()</a></td></tr>
81 <tr><td>@ref
IMP::base::Flag</td><td><a href=
"classIMP_1_1base_1_1Flag.html#a1225a8ad318ecfcbd73f0efdabe1240e">IMP::base::Flag::operator=()</a></td></tr>
83 <tr><td>@ref
IMP::base::TextOutput</td><td><a href=
"namespaceIMP_1_1base.html#a8809c4162912b7c52f329795756f6ef9">
IMP::base::create_temporary_file()</a>, <a href=
"namespaceIMP_1_1base.html#a7780a106896f89443bc9e6a1e89d2466">IMP::base::get_log_target()</a></td></tr>
84 <tr><td>@ref
IMP::base::Vector</td><td><a href=
"classIMP_1_1algebra_1_1BoundedGridRangeD.html#a93f5e4dae6e89c016220dd535b628539">IMP::algebra::BoundedGridRangeD::get_all_indexes()</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_1DenseGridStorageD.html#acc097f0375f6180adbf9eb745f8ff11b">IMP::algebra::DenseGridStorageD::get_all_voxels()</a>, <a href=
"classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a4b29d9d2bc65cc38bcdc15a834dba392">IMP::algebra::PrincipalComponentAnalysisD::get_principal_components()</a>, <a href=
"classIMP_1_1algebra_1_1SparseGridStorageD.html#a1b65e9c70a1684711065212bf2de936e">IMP::algebra::SparseGridStorageD::get_indexes()</a>, <a href=
"classIMP_1_1algebra_1_1UnboundedGridRangeD.html#a8ff58568320c5e193c8111f06a4b54d8">IMP::algebra::UnboundedGridRangeD::get_extended_indexes()</a>, <a href=
"classIMP_1_1atom_1_1BondEndpointsRefiner.html#a15e350d5bc62ba304febc2c7a1c99bde">
IMP::atom::BondEndpointsRefiner::get_refined()</a>, <a href=
"classIMP_1_1atom_1_1BondPairContainer.html#a23acf10f2633e68d84946ebccc95b5c4">
IMP::atom::BondPairContainer::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1atom_1_1Bonded.html#a6d24f4e95a57f542cbd492cc5ad156ea">IMP::atom::Bonded::get_bond_indexes()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMConnection.html#adf29f3ca8131dfa961d939a35ce4af60">
IMP::atom::CHARMMConnection::get_atoms()</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_1CHARMMTopology.html#a27ba1dfd62880570d47a5084af6e9c4c">
IMP::atom::CHARMMTopology::add_bonds()</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_1Hierarchy.html#ad21bb9279754451fbe57bdebd170faf3">
IMP::atom::Hierarchy::get_children()</a>, <a href=
"classIMP_1_1atom_1_1Representation.html#ab31fd97c8a0dda88abe16f0744c17d6a">
IMP::atom::Representation::get_representations()</a>, <a href=
"classIMP_1_1atom_1_1Selection.html#afe161e06395cbac13aa681457cad1a24">
IMP::atom::Selection::get_hierarchies()</a>, <a href=
"classIMP_1_1atom_1_1Selection.html#adcf3ecd4cf8e2c04a906cf272b0330e6">
IMP::atom::Selection::get_selected_particle_indexes()</a>, <a href=
"classIMP_1_1atom_1_1Selection.html#a2295bcd24896c8fcbdcea743f4f01fa8">
IMP::atom::Selection::get_selected_particles()</a>, <a href=
"classIMP_1_1atom_1_1Simulator.html#ac7a7e5c70ed788dba3ff241ad8e4d08b">IMP::atom::Simulator::get_particles()</a>, <a href=
"classIMP_1_1atom_1_1Simulator.html#aad17d9691ac2c5c40120b465a97a1e94">
IMP::atom::Simulator::get_simulation_particle_indexes()</a>, <a href=
"classIMP_1_1atom_1_1Simulator.html#a8c5f3ba6aed31a4f12b222db512abdc7">
IMP::atom::Simulator::get_simulation_particles()</a>, <a href=
"classIMP_1_1base_1_1ConstVector.html#a7b870fecc340684d904178713569c610">IMP::base::ConstVector::ConstVector()</a>, <a href=
"classIMP_1_1base_1_1LRUCache.html#a351d089d68f749394302a47e73021a8e">IMP::base::LRUCache::get_keys()</a>, <a href=
"classIMP_1_1container_1_1AllBipartitePairContainer.html#acdb3725183c918e36ee7611f5edf7bb3">
IMP::container::AllBipartitePairContainer::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1container_1_1AllPairContainer.html#a2d99e88e79d7834a254eb4d29618f5ae">
IMP::container::AllPairContainer::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1container_1_1CloseBipartitePairContainer.html#ae94c2fccdbba6d333c7f4e62ec64c660">
IMP::container::CloseBipartitePairContainer::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1container_1_1ClosePairContainer.html#aefd1af460efe6a4fe525aa879020eaca">
IMP::container::ClosePairContainer::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1container_1_1ConnectingPairContainer.html#afb4dd9494a62f127a39e4008d175ebcd">
IMP::container::ConnectingPairContainer::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1container_1_1ConsecutivePairContainer.html#a652f450c1b4c0dc7538b3927dacb16f6">
IMP::container::ConsecutivePairContainer::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1container_1_1ExclusiveConsecutivePairContainer.html#ab911e09a56a6e01c2cb37f33b34c254f">
IMP::container::ExclusiveConsecutivePairContainer::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1container_1_1PairContainerSet.html#ae565aec6b5a58613b88751a55cf4085d">
IMP::container::PairContainerSet::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1container_1_1PredicateSingletonsRestraint.html#a69a2eac8197f893fc2a2dca9480504af">
IMP::container::PredicateSingletonsRestraint::get_indexes()</a>, <a href=
"classIMP_1_1container_1_1QuadContainerSet.html#a035285a8631c0bf40dd3c12ceefebf3b">
IMP::container::QuadContainerSet::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1container_1_1SingletonContainerSet.html#abb09dc6d6cf515e93d8c9a954d4fba13">
IMP::container::SingletonContainerSet::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1container_1_1TripletContainerSet.html#a2be70d6afd3e7fd3f18fbcf4015e0052">
IMP::container::TripletContainerSet::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1core_1_1ChildrenRefiner.html#a742dc731ef07bd773f8db1cdaf714330">
IMP::core::ChildrenRefiner::get_refined()</a>, <a href=
"classIMP_1_1core_1_1FixedRefiner.html#a2f392daaed2b6ffb00cfd7e95bc7aacc">
IMP::core::FixedRefiner::get_refined()</a>, <a href=
"classIMP_1_1core_1_1FixedRefiner.html#acfcca12623f9a956b362202add802112">
IMP::core::FixedRefiner::get_refined_indexes()</a>, <a href=
"classIMP_1_1core_1_1Hierarchy.html#a102cb65d695eda3395a4fe614dc9030c">IMP::core::Hierarchy::get_children_indexes()</a>, <a href=
"classIMP_1_1core_1_1IncrementalScoringFunction.html#acf54daedfadca1561d3cea1f0ba0cd24">IMP::core::IncrementalScoringFunction::get_movable_indexes()</a>, <a href=
"classIMP_1_1core_1_1LeavesRefiner.html#a081798ad59ec6104b1a5644166cb086c">
IMP::core::LeavesRefiner::get_refined()</a>, <a href=
"classIMP_1_1core_1_1MonteCarlo.html#a1b5e2563bc31d82bf3379fbe490b6143">
IMP::core::MonteCarlo::get_movable_particles()</a>, <a href=
"classIMP_1_1core_1_1NeighborsTable.html#afcaa38d09d2a2bf2431932e770d3e4d7">
IMP::core::NeighborsTable::get_neighbors()</a>, <a href=
"classIMP_1_1core_1_1RigidBody.html#a39ed4cacf1afe45cc7afa3bea10c01f7">
IMP::core::RigidBody::get_body_member_particle_indexes()</a>, <a href=
"classIMP_1_1core_1_1RigidBody.html#a0f259e96ce32e2f69a3cdaba83c5e8f2">
IMP::core::RigidBody::get_member_indexes()</a>, <a href=
"classIMP_1_1core_1_1RigidBody.html#ab1209e9e9104e54642c18021f014b824">
IMP::core::RigidBody::get_member_particle_indexes()</a>, <a href=
"classIMP_1_1core_1_1RigidBody.html#a4fee01a8f48567c5b52d574a4784b006">
IMP::core::RigidBody::get_members()</a>, <a href=
"classIMP_1_1core_1_1RigidBody.html#a01768cb77a2b5321ce1d5c49eb18e77a">IMP::core::RigidBody::get_rigid_members()</a>, <a href=
"classIMP_1_1core_1_1TableRefiner.html#a3236d90a596b17e41e89664e4704e14b">
IMP::core::TableRefiner::get_refined()</a>, <a href=
"classIMP_1_1domino_1_1DisjointSetsSubsetFilterTable.html#ac351865eed1eca742b3dd0c1409fdb68">IMP::domino::DisjointSetsSubsetFilterTable::get_set()</a>, <a href=
"classIMP_1_1domino_1_1ParticleStatesTable.html#a52b6df3813342fe80097eb02e8e8e2a1">IMP::domino::ParticleStatesTable::get_particles()</a>, <a href=
"classIMP_1_1domino_1_1Subset.html#ad7e9718aca30793514b4a6c7e6a39738">IMP::domino::Subset::get_sorted()</a>, <a href=
"classIMP_1_1em_1_1DensityFillingRestraint.html#a9ff22a93da5a31e6b38a08cb8f2a5854">IMP::em::DensityFillingRestraint::get_particles()</a>, <a href=
"classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#a003aed90e880b05e7dfe66ba78f0b5a4">IMP::em::EnvelopePenetrationRestraint::get_particles()</a>, <a href=
"classIMP_1_1em_1_1FitRestraint.html#a7621d91fe6797f70ff69179f81f3025c">IMP::em::FitRestraint::get_particles()</a>, <a href=
"classIMP_1_1em_1_1PCAFitRestraint.html#a6a0ea455dc900abda5c6220dd1347ccb">IMP::em::PCAFitRestraint::get_particles()</a>, <a href=
"classIMP_1_1em_1_1SampledDensityMap.html#a1576d99d6fef05e5a4d0fbd0eb77098c">IMP::em::SampledDensityMap::get_sampled_particles()</a>, <a href=
"classIMP_1_1em_1_1SampledDensityMap.html#ae745f6d6ea9515917c359ef7505bfc4e">IMP::em::SampledDensityMap::get_xyzr_particles()</a>, <a href=
"classIMP_1_1isd_1_1BivariateFunction.html#a58b70e738a4cd38768b7113b16342086">
IMP::isd::BivariateFunction::get_input_particles()</a>, <a href=
"classIMP_1_1isd_1_1Covariance1DFunction.html#a034b4c112463b121bb7694ffe58194ab">
IMP::isd::Covariance1DFunction::get_input_particles()</a>, <a href=
"classIMP_1_1isd_1_1GaussianProcessInterpolation.html#a202c3a0d47f67eff19e0eb52a40bcafb">IMP::isd::GaussianProcessInterpolation::get_input_particles()</a>, <a href=
"classIMP_1_1isd_1_1GeneralizedGuinierPorodFunction.html#acd7d5d0ead5ce483249ad8e2f7addd8e">
IMP::isd::GeneralizedGuinierPorodFunction::get_input_particles()</a>, <a href=
"classIMP_1_1isd_1_1Linear1DFunction.html#adda056d7c00df2aa480c59e0c8dbe74d">
IMP::isd::Linear1DFunction::get_input_particles()</a>, <a href=
"classIMP_1_1isd_1_1UnivariateFunction.html#a0383ed5c41021e192e6c5c514ef0ad78">
IMP::isd::UnivariateFunction::get_input_particles()</a>, <a href=
"classIMP_1_1kernel_1_1Container.html#a0b945de854e6a5632fec678750d74271">
IMP::kernel::Container::get_all_possible_indexes()</a>, <a href=
"classIMP_1_1kernel_1_1Key.html#afcbc1154cb2a92ef91e5801d9d127310">
IMP::kernel::Key::get_all_strings()</a>, <a href=
"classIMP_1_1kernel_1_1Model.html#a077fd785f8ef3e8c29cc325ef65517f5">
IMP::kernel::Model::get_particle_indexes()</a>, <a href=
"classIMP_1_1kernel_1_1Model.html#a6a60322aa9f700386154cfe5843d7ab9">
IMP::kernel::Model::get_particles()</a>, <a href=
"classIMP_1_1kernel_1_1ModelObject.html#a26115222b8c1beefd5b4268535d694e2">
IMP::kernel::ModelObject::get_interactions()</a>, <a href=
"classIMP_1_1kernel_1_1ModelObject.html#a8b73beced0b4144619206e5048c1e6ff">
IMP::kernel::ModelObject::do_get_interactions()</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#a14e9a5b1ee506e8630100ed2d7e6117b">
IMP::kernel::ParticleOutputs::get_output_particles()</a>, <a href=
"classIMP_1_1kernel_1_1Refiner.html#a24fcaeb8596469c3ed61ce48cb7eef90">
IMP::kernel::Refiner::get_refined()</a>, <a href=
"classIMP_1_1kernel_1_1Refiner.html#adf5ed7b069a84249fe87fdd355430d89">
IMP::kernel::Refiner::get_refined_indexes()</a>, <a href=
"classIMP_1_1kernel_1_1Refiner.html#a6e2efdd8eb25bfcfd3d6a014d9e80bd5">
IMP::kernel::Refiner::get_refined_indexes_by_ref()</a>, <a href=
"classIMP_1_1kernel_1_1SingletonContainer.html#a49fefaac36dc54528da734483d57a76e">IMP::kernel::SingletonContainer::get_contents()</a>, <a href=
"classIMP_1_1kernel_1_1SingletonContainer.html#a6a588f7389ee6e974601b2530f77d855">
IMP::kernel::SingletonContainer::get_indexes()</a>, <a href=
"classIMP_1_1kernel_1_1SingletonContainer.html#aaa9bd5cc661c6be9175d0b38ab6f4fde">
IMP::kernel::SingletonContainer::get_particles()</a>, <a href=
"classIMP_1_1kernel_1_1SingletonContainer.html#a4a9b733bca7387760314f96935fecb21">
IMP::kernel::SingletonContainer::get_range_indexes()</a>, <a href=
"classIMP_1_1kinematics_1_1KinematicForest.html#aecd41fea74ef0ba7c87067dbef28e5fa">IMP::kinematics::KinematicForest::get_children()</a>, <a href=
"classIMP_1_1kinematics_1_1ProteinKinematics.html#ac5551e3a3cc799adb3cdd2b005472d12">IMP::kinematics::ProteinKinematics::get_rigid_bodies()</a>, <a href=
"classIMP_1_1multifit_1_1AnchorsData.html#a509474f60ff186cab194c0afd1ebd66b">IMP::multifit::AnchorsData::get_secondary_structure_particles()</a>, <a href=
"classIMP_1_1multifit_1_1Ensemble.html#a4156aa95772ba0636c50f0528ff278ac">IMP::multifit::Ensemble::get_molecules()</a>, <a href=
"classIMP_1_1multifit_1_1Ensemble.html#a90987f6d8f5bcdaa856b3effcc6b224b">IMP::multifit::Ensemble::get_rigid_bodies()</a>, <a href=
"classIMP_1_1multifit_1_1GeometricHash.html#ad836b61873521a48bf1a0211f2d139f2">IMP::multifit::GeometricHash::neighbors_data()</a>, <a href=
"classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a8a3bce24cdbd4c2ff9fca7e726560fd0">IMP::multifit::ProteomicsEMAlignmentAtomic::get_molecules()</a>, <a href=
"classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a8db692880725a7de95df804f50deaeed">IMP::multifit::ProteomicsEMAlignmentAtomic::get_rigid_bodies()</a>, <a href=
"classIMP_1_1multifit_1_1RadiusOfGyrationRestraint.html#a09c80e8c2dbceb86ee8a7ee03da4af7b">IMP::multifit::RadiusOfGyrationRestraint::get_particles()</a>, <a href=
"classIMP_1_1multifit_1_1WeightedExcludedVolumeRestraint.html#ab28a624345ce084900dbfc60e2c2b00b">IMP::multifit::WeightedExcludedVolumeRestraint::get_particles()</a>, <a href=
"classIMP_1_1rmf_1_1SimpleLoadLink.html#a96c9b933510a0cde95f96d60b777fec5">
IMP::rmf::SimpleLoadLink::create()</a>, <a href=
"classIMP_1_1rmf_1_1SimpleLoadLink.html#a5fdf2b7e30282dddb88de9ee4cb47af6">
IMP::rmf::SimpleLoadLink::create()</a>, <a href=
"classIMP_1_1symmetry_1_1RigidBodyMover.html#a7713970249e18a6a78ec578cd4ad35ae">IMP::symmetry::RigidBodyMover::get_particles()</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>, <a href=
"namespaceIMP_1_1atom.html#a3b3f1f1666e2a122bd766f10a9eb84a9">
IMP::atom::get_by_type()</a>, <a href=
"namespaceIMP_1_1atom.html#a8f2e62640647e36570c22b0328283a9c">
IMP::atom::get_charmm_untyped_atoms()</a>, <a href=
"namespaceIMP_1_1atom.html#ac90fe977731f00cc049724fdeb3b6532">
IMP::atom::get_internal_bonds()</a>, <a href=
"namespaceIMP_1_1atom.html#af5b0cc808be9672d3996baeb2f9210fd">
IMP::atom::get_leaves()</a>, <a href=
"namespaceIMP_1_1atom.html#ae40f2053c2f95c317a034bdcb0e38478">
IMP::atom::get_leaves()</a>, <a href=
"namespaceIMP_1_1atom.html#acb0e2875f7d5b8fd8b51b89dbdc0cf3a">
IMP::atom::get_leaves()</a>, <a href=
"namespaceIMP_1_1atom.html#a6ef3ab3e84fd5ab0e83ce40fdc675455">
IMP::atom::get_phi_dihedral_atoms()</a>, <a href=
"namespaceIMP_1_1atom.html#a1c15e940e47a1a8f5872029fcb93c601">
IMP::atom::get_psi_dihedral_atoms()</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_1domino.html#ad555f4012dda95f5e23001941b79c735">
IMP::domino::get_order()</a>, <a href=
"namespaceIMP_1_1em.html#a97bf357f626dfeaa62507d51614db63d">
IMP::em::density2particles()</a>, <a href=
"namespaceIMP_1_1kernel.html#a6aa93f9052d5827a668743bf73753a86">
IMP::kernel::get_input_particles()</a>, <a href=
"namespaceIMP_1_1kernel.html#a4733ccf457063ebf4f7cafaa251a6a68">
IMP::kernel::get_output_particles()</a>, <a href=
"namespaceIMP_1_1kernel.html#a1efb3ada8f4005237b39e4f0efd605c6">
IMP::kernel::write_particles_to_buffer()</a>, <a href=
"namespaceIMP_1_1kernel.html#a59562be47760e4ee3424b80f4ca2a5ba">
IMP::kernel::get_dependent_particles()</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_1rmf.html#a31eaf33429ccc15ba6662fae46b59c6a">
IMP::rmf::create_hierarchies()</a>, <a href=
"namespaceIMP_1_1rmf.html#a2375a307294df39c42545c028c25f2cc">
IMP::rmf::create_particles()</a></td></tr>
85 <tr><td>@ref
IMP::base::VersionInfo</td><td><a href=
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IMP::algebra::DynamicNearestNeighbor3D::get_version_info()</a>, <a href=
"classIMP_1_1algebra_1_1EuclideanVectorKDMetric.html#af704a0d10194ddcb4c6c537bf1676e29">
IMP::algebra::EuclideanVectorKDMetric::get_version_info()</a>, <a href=
"classIMP_1_1algebra_1_1MaxVectorKDMetric.html#aa9c0a20e33ee7c304124744c21d53b2c">
IMP::algebra::MaxVectorKDMetric::get_version_info()</a>, <a href=
"classIMP_1_1algebra_1_1NearestNeighborD.html#a6f9d80efbac0ebfdb8477a602cb4e4a4">
IMP::algebra::NearestNeighborD::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1ATOMPDBSelector.html#aa169d6dac990448600cc7865ded83a28">
IMP::atom::ATOMPDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1AllMol2Selector.html#a4ddb917093303048b46785f78b533cbf">
IMP::atom::AllMol2Selector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1AllPDBSelector.html#aff3b9f57b750d453aa49510d5ad442b4">
IMP::atom::AllPDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1AndPDBSelector.html#a33f7bfb1b6fd2d547ab6ec79bd85376c">
IMP::atom::AndPDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1AngleSingletonScore.html#a84b09bffae08c88cd9b793d99cab3d84">
IMP::atom::AngleSingletonScore::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1BackbonePDBSelector.html#aac44df734c94bf99290149aa244ce0e7">
IMP::atom::BackbonePDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1BerendsenThermostatOptimizerState.html#a4f54ff8eff2631ef67314e3a14475023">
IMP::atom::BerendsenThermostatOptimizerState::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1BondEndpointsRefiner.html#aed4c8200fd76d53564acc751c7bdd62e">
IMP::atom::BondEndpointsRefiner::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1BondGeometry.html#a899a3ae88f39d70041281c7d97ef0ebf">
IMP::atom::BondGeometry::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1BondPairContainer.html#a4d1a66371a6f18e824cbdc0cd525f173">
IMP::atom::BondPairContainer::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1BondSingletonScore.html#abdc76b9a87703cf0696707ceabcb8aa5">
IMP::atom::BondSingletonScore::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1BondedPairFilter.html#a5f6b632f79583e3e69d4dba91cbcf648">
IMP::atom::BondedPairFilter::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1BondsGeometry.html#a9b10041993847edce5793ffe48613ddc">
IMP::atom::BondsGeometry::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1BrownianDynamics.html#a0ea192b6f608390b90ec21f0129d5491">
IMP::atom::BrownianDynamics::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CAlphaPDBSelector.html#a3e742f95aa37613f7912439b042d9b74">
IMP::atom::CAlphaPDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CBetaPDBSelector.html#a6de8b0c0def5f3f0b22f04fb1971166d">
IMP::atom::CBetaPDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMIdealResidueTopology.html#a5678ffba8f5901875f041b42fa0df56d">
IMP::atom::CHARMMIdealResidueTopology::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMParameters.html#a26bd6cddf07ef609bdbefa5308df9f2f">
IMP::atom::CHARMMParameters::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMPatch.html#a61ec3fc4927c472a91ea788edd6f59da">
IMP::atom::CHARMMPatch::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMResidueTopology.html#acbcb03693ffb55359a94dfe2b83b71ab">
IMP::atom::CHARMMResidueTopology::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a77fd0f7b08f651d481167c215c62809a">
IMP::atom::CHARMMResidueTopologyBase::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMSegmentTopology.html#ae0010344c0201f858dd770d4cdcb2e4e">
IMP::atom::CHARMMSegmentTopology::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#aecb095b55db8c1b73ab429a54070d5f2">
IMP::atom::CHARMMStereochemistryRestraint::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CHARMMTopology.html#ac8626c8cd465f80ba857a5ebd942491e">
IMP::atom::CHARMMTopology::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CPDBSelector.html#af656b68c38336528b088888a72a34360">
IMP::atom::CPDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1ChainPDBSelector.html#aa4c07c3a2b7238f88d72f15d7acbbd09">
IMP::atom::ChainPDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CoulombPairScore.html#aa909befa7b556624e40de64c86e89e2e">
IMP::atom::CoulombPairScore::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1CoverBond.html#a84c1604339969214752c645d5d7d31a5">
IMP::atom::CoverBond::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1DihedralSingletonScore.html#aaa5639fdb12e9eea87645e135cec8cf6">
IMP::atom::DihedralSingletonScore::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1EzRestraint.html#a516f413991f8b1fe9bb2ae984c13c980">
IMP::atom::EzRestraint::get_version_info()</a>, <a href=
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IMP::atom::ForceSwitch::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1HierarchiesGeometry.html#a625262e00f6d0e3fd5b7fa15ab54e960">
IMP::atom::HierarchiesGeometry::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1HierarchyGeometry.html#ab538334ff3b9656f18ad3a3143b6e797">
IMP::atom::HierarchyGeometry::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1HydrogenPDBSelector.html#a648b842f0e4eb87273b82a85d52e1b51">
IMP::atom::HydrogenPDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1ImproperSingletonScore.html#aec80cf5dd7bda09ecc2c06175b47a105">
IMP::atom::ImproperSingletonScore::get_version_info()</a>, <a href=
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IMP::atom::LangevinThermostatOptimizerState::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1LennardJonesPairScore.html#ab47b4987c0bd89298d47cde5326b6f35">
IMP::atom::LennardJonesPairScore::get_version_info()</a>, <a href=
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IMP::atom::MolecularDynamics::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1NPDBSelector.html#a09eb4a9123dd5c22945d70966ee475e9">
IMP::atom::NPDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1NonAlternativePDBSelector.html#a536a9a8fb83a58dac83fc478212e54f1">
IMP::atom::NonAlternativePDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1NonHydrogenMol2Selector.html#ad94c2263d7246a854b936326d50cf27b">
IMP::atom::NonHydrogenMol2Selector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1NonWaterNonHydrogenPDBSelector.html#a3712169041601585316d540b10c4154d">
IMP::atom::NonWaterNonHydrogenPDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1NonWaterPDBSelector.html#acb269259f381c2a7c1129631d00edf2f">
IMP::atom::NonWaterPDBSelector::get_version_info()</a>, <a href=
"classIMP_1_1atom_1_1NotPDBSelector.html#a1367e594ada0e0030c2b20d148509e57">
IMP::atom::NotPDBSelector::get_version_info()</a>, <a href=
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IMP::atom::OrPDBSelector::get_version_info()</a>, <a href=
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IMP::pmi::CompositeRestraint::get_version_info()</a>, <a href=
"classIMP_1_1pmi_1_1SigmoidRestraintSphere.html#adf8d33e12762cd33deb0054f2d2a55ba">
IMP::pmi::SigmoidRestraintSphere::get_version_info()</a>, <a href=
"classIMP_1_1pmi_1_1TransformMover.html#abc4b92bd8e5fe5b134f2ef1f736cf82a">
IMP::pmi::TransformMover::get_version_info()</a>, <a href=
"classIMP_1_1rmf_1_1HierarchyLoadLink.html#aa166418ed1c04d0ca493dfad32c972eb">
IMP::rmf::HierarchyLoadLink::get_version_info()</a>, <a href=
"classIMP_1_1rmf_1_1HierarchySaveLink.html#a527f2c931b54b5124e5160a3b9ca1cfa">
IMP::rmf::HierarchySaveLink::get_version_info()</a>, <a href=
"classIMP_1_1rmf_1_1SaveOptimizerState.html#afd68c21536f429bb19605464743f8996">
IMP::rmf::SaveOptimizerState::get_version_info()</a>, <a href=
"classIMP_1_1rotamer_1_1RotamerCalculator.html#a5c91eaa6b47114d0080edec58af929c3">
IMP::rotamer::RotamerCalculator::get_version_info()</a>, <a href=
"classIMP_1_1rotamer_1_1RotamerLibrary.html#a2aaef0fa97e7e1959ad60e539b1edbf6">
IMP::rotamer::RotamerLibrary::get_version_info()</a>, <a href=
"classIMP_1_1saxs_1_1Profile.html#adaf18a5f0229233c96a131de9a2218d0">
IMP::saxs::Profile::get_version_info()</a>, <a href=
"classIMP_1_1saxs_1_1RadiusOfGyrationRestraint.html#a9821a13382dc7a0c51fd66fe94ee2f42">
IMP::saxs::RadiusOfGyrationRestraint::get_version_info()</a>, <a href=
"classIMP_1_1saxs_1_1Restraint.html#ab22d1bcc639e6fd17f41a5a96d934828">
IMP::saxs::Restraint::get_version_info()</a>, <a href=
"classIMP_1_1saxs_1_1RigidBodiesProfileHandler.html#a2163e5a8f700814bf03486d4ccebb0e7">
IMP::saxs::RigidBodiesProfileHandler::get_version_info()</a>, <a href=
"classIMP_1_1score__functor_1_1DistancePairScore.html#a8606f47228c4ed5f06a20a13371cf799">
IMP::score_functor::DistancePairScore::get_version_info()</a>, <a href=
"classIMP_1_1score__functor_1_1ScoreUnaryFunction.html#af648b81d20df03dca58d124da8f3fa36">
IMP::score_functor::ScoreUnaryFunction::get_version_info()</a>, <a href=
"classIMP_1_1statistics_1_1ChiSquareMetric.html#a54b9640892959b2be3dca39b240ffaea">
IMP::statistics::ChiSquareMetric::get_version_info()</a>, <a href=
"classIMP_1_1statistics_1_1ConfigurationSetRMSDMetric.html#a0f929a42ccd5c945df88d7a1f01d463a">
IMP::statistics::ConfigurationSetRMSDMetric::get_version_info()</a>, <a href=
"classIMP_1_1statistics_1_1ConfigurationSetXYZEmbedding.html#a9fc0079127a998ef7194664bd07c0a8d">
IMP::statistics::ConfigurationSetXYZEmbedding::get_version_info()</a>, <a href=
"classIMP_1_1statistics_1_1EuclideanMetric.html#aa9637e0ba9f52d69f23d699375ffe622">
IMP::statistics::EuclideanMetric::get_version_info()</a>, <a href=
"classIMP_1_1statistics_1_1ParticleEmbedding.html#aa29dc462e3d140dd6f3a6810f62ce31a">
IMP::statistics::ParticleEmbedding::get_version_info()</a>, <a href=
"classIMP_1_1statistics_1_1PartitionalClusteringWithCenter.html#a52224c2192bf65eb1386811e6233989b">
IMP::statistics::PartitionalClusteringWithCenter::get_version_info()</a>, <a href=
"classIMP_1_1statistics_1_1RecursivePartitionalClusteringEmbedding.html#ab93782821b1ad754dad40ea7dbc80fd6">
IMP::statistics::RecursivePartitionalClusteringEmbedding::get_version_info()</a>, <a href=
"classIMP_1_1statistics_1_1RecursivePartitionalClusteringMetric.html#ac6f641d694bd964c3b56eb57d704df21">
IMP::statistics::RecursivePartitionalClusteringMetric::get_version_info()</a>, <a href=
"classIMP_1_1statistics_1_1VectorDEmbedding.html#ac26c8b992e86a4c6c72f81e45c6514c7">
IMP::statistics::VectorDEmbedding::get_version_info()</a>, <a href=
"classIMP_1_1symmetry_1_1BallMover.html#a2cb4a3ebefd0935a4a308516c955958d">
IMP::symmetry::BallMover::get_version_info()</a>, <a href=
"classIMP_1_1symmetry_1_1RigidBodyMover.html#a895d6420a2b94f7e57dd5e9b59cba025">
IMP::symmetry::RigidBodyMover::get_version_info()</a></td></tr>
87 # IMP.container # {#factory_index_container}
89 <th>Class</th><th>Factories</th></tr>
95 <tr><td>@ref
IMP::container::PairContainerSet</td><td><a href=
"classIMP_1_1container_1_1PairContainerSet.html#ad73b337edcd61026138832c505587c47">IMP::container::PairContainerSet::get_set()</a></td></tr>
96 <tr><td>@ref
IMP::container::QuadContainerSet</td><td><a href=
"classIMP_1_1container_1_1QuadContainerSet.html#ac2a1a54aa5fed2f2d5394c0a4734229c">IMP::container::QuadContainerSet::get_set()</a></td></tr>
97 <tr><td>@ref
IMP::container::SingletonContainerSet</td><td><a href=
"classIMP_1_1container_1_1SingletonContainerSet.html#a3053d32ea57216bae48fa420198bcf95">IMP::container::SingletonContainerSet::get_set()</a></td></tr>
98 <tr><td>@ref
IMP::container::TripletContainerSet</td><td><a href=
"classIMP_1_1container_1_1TripletContainerSet.html#a5650d9c2999046961450a95b98d1ff26">IMP::container::TripletContainerSet::get_set()</a></td></tr>
100 # IMP.core # {#factory_index_core}
102 <th>Class</th><th>Factories</th></tr>
105 <tr><td>@ref
IMP::core::DataObject</td><td><a href=
"classIMP_1_1multifit_1_1ComplementarityRestraint.html#a1c372e35090c02f005c21761512c986c">IMP::multifit::ComplementarityRestraint::get_grid_object()</a></td></tr>
108 <tr><td>@ref
IMP::core::HierarchyTraits</td><td><a href=
"classIMP_1_1atom_1_1Hierarchy.html#ab99b617e046d339ee51649f3eeb218e3">
IMP::atom::Hierarchy::get_traits()</a>, <a href=
"classIMP_1_1core_1_1Hierarchy.html#a21ff4285e9aa013c1914f59a54f7b02c">IMP::core::Hierarchy::get_decorator_traits()</a>, <a href=
"classIMP_1_1core_1_1Hierarchy.html#ab576c86a2116587699523d583391824b">IMP::core::Hierarchy::get_traits()</a>, <a href=
"classIMP_1_1core_1_1Hierarchy.html#a0c6a95216a6e527ffee2f054faa8cdd6">IMP::core::Hierarchy::get_default_decorator_traits()</a>, <a href=
"classIMP_1_1core_1_1Hierarchy.html#aba2834d7467a9a41e0ba54d7f09044c5">
IMP::core::Hierarchy::get_default_traits()</a></td></tr>
109 <tr><td>@ref
IMP::core::IncrementalScoringFunction</td><td><a href=
"classIMP_1_1core_1_1MonteCarlo.html#a3276d3742cfacf2d09713a140cb5beeb">IMP::core::MonteCarlo::get_incremental_scoring_function()</a></td></tr>
112 <tr><td>@ref
IMP::core::RigidBody</td><td><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_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_1core_1_1RigidBodyMember.html#a37e8c45b0652cac4b1257e1773d9dc54">IMP::core::RigidBodyMember::get_rigid_body()</a>, <a href=
"classIMP_1_1kinematics_1_1Joint.html#a1c1015cacfabeb732fc45df58a914389">IMP::kinematics::Joint::get_child_node()</a>, <a href=
"classIMP_1_1kinematics_1_1Joint.html#a00109e3ad33f43ef6ab7b715ad529e9c">IMP::kinematics::Joint::get_parent_node()</a>, <a href=
"classIMP_1_1symmetry_1_1RigidBodyMover.html#a5569015e9d07f620ba5cb39921844cdc">IMP::symmetry::RigidBodyMover::get_rigid_bodies()</a>, <a href=
"namespaceIMP_1_1atom.html#a70ac55d293e6851c67b45d7fd55a3163">
IMP::atom::create_compatible_rigid_body()</a>, <a href=
"namespaceIMP_1_1atom.html#a1b72819ad85249bfe290fe31b4084e9e">
IMP::atom::create_rigid_body()</a>, <a href=
"namespaceIMP_1_1atom.html#a40da5b3553d98acf020078b4e435b12a">
IMP::atom::create_rigid_body()</a></td></tr>
117 # IMP.display # {#factory_index_display}
119 <th>Class</th><th>Factories</th></tr>
121 <tr><td>@ref
IMP::display::Color</td><td><a href=
"classIMP_1_1display_1_1Colored.html#af4eb5de7d7025ed94a665ad53e22521c">IMP::display::Colored::get_color()</a>, <a href=
"classIMP_1_1display_1_1Geometry.html#a1812713ecd15573825afeca59b69e570">IMP::display::Geometry::get_color()</a>, <a href=
"classIMP_1_1display_1_1PairGeometry.html#a73836b021934ef22979a48111b9974f6">IMP::display::PairGeometry::get_color()</a>, <a href=
"classIMP_1_1display_1_1SingletonGeometry.html#a7c51782da5aced5cfa497f0543647646">IMP::display::SingletonGeometry::get_color()</a>, <a href=
"namespaceIMP_1_1display.html#a8873da49642f951ec86570656e98e908">
IMP::display::get_jet_color()</a>, <a href=
"namespaceIMP_1_1display.html#ae15042a6bb4f4548ec2876ceddfd3165">
IMP::display::get_hot_color()</a>, <a href=
"namespaceIMP_1_1display.html#a3ea1c11940d14e4ac022768e96514dff">
IMP::display::get_rgb_color()</a>, <a href=
"namespaceIMP_1_1display.html#abd278fa3123b329c7fe1784b02f4ca31">
IMP::display::get_gray_color()</a>, <a href=
"namespaceIMP_1_1display.html#ad982e4a6182db9aa8157f3fc020da33f">
IMP::display::get_gnuplot_color()</a>, <a href=
"namespaceIMP_1_1display.html#a7139e3c2ffdf998ca304a7f01e6e237e">
IMP::display::get_display_color()</a>, <a href=
"namespaceIMP_1_1display.html#ada2a3156a15dd0217840bfc8675724d8">
IMP::display::get_interpolated_rgb()</a></td></tr>
125 <tr><td>@ref
IMP::display::Geometry</td><td><a href=
"classIMP_1_1display_1_1WriteOptimizerState.html#ab7308b24bd03e46f14de9693ab613535">IMP::display::WriteOptimizerState::get_geometry()</a></td></tr>
132 <tr><td>@ref
IMP::display::Writer</td><td><a href=
"classIMP_1_1display_1_1WriterAdaptor.html#afe4e8faa43b0dcc21116c1b0e2c4b252">IMP::display::WriterAdaptor::get_writer()</a>, <a href=
"classIMP_1_1display_1_1WriterAdaptor.html#a108d1a11ac10a1f30477d9209779f9d6">IMP::display::WriterAdaptor::operator->()</a>, <a href=
"namespaceIMP_1_1display.html#a55414a3681ffd79c126fabdbf13abb2d">
IMP::display::create_writer()</a></td></tr>
134 # IMP.domino # {#factory_index_domino}
136 <th>Class</th><th>Factories</th></tr>
137 <tr><td>@ref
IMP::domino::Assignment</td><td><a href=
"classIMP_1_1domino_1_1AssignmentContainer.html#aa81ef13a668c41da618439be20b6f2aa">IMP::domino::AssignmentContainer::get_assignment()</a>, <a href=
"classIMP_1_1domino_1_1CappedAssignmentContainer.html#a6dbc1dfc0bfb89a2574fa0aeb8c73dc7">IMP::domino::CappedAssignmentContainer::get_assignment()</a>, <a href=
"classIMP_1_1domino_1_1HeapAssignmentContainer.html#ac55e0371c4e26e56dbdbca445a68ae94">IMP::domino::HeapAssignmentContainer::get_assignment()</a>, <a href=
"classIMP_1_1domino_1_1ListAssignmentContainer.html#a270c0846741f2dd93ad6354143d6df14">IMP::domino::ListAssignmentContainer::get_assignment()</a>, <a href=
"classIMP_1_1domino_1_1Order.html#a5073cfaca05e214fb48cc38d76f2df51">IMP::domino::Order::get_subset_ordered()</a>, <a href=
"classIMP_1_1domino_1_1PackedAssignmentContainer.html#aebe9e10ef7d4deb7838107299c3e50ea">IMP::domino::PackedAssignmentContainer::get_assignment()</a>, <a href=
"classIMP_1_1domino_1_1RangeViewAssignmentContainer.html#a23e721abb0c1663ffd5371429bdbbf31">IMP::domino::RangeViewAssignmentContainer::get_assignment()</a>, <a href=
"classIMP_1_1domino_1_1ReadAssignmentContainer.html#ab47cc3fdca3d5944feca00a0c2126f2e">IMP::domino::ReadAssignmentContainer::get_assignment()</a>, <a href=
"classIMP_1_1domino_1_1ReadHDF5AssignmentContainer.html#a41f70ad327cee3330443e35a48167d67">IMP::domino::ReadHDF5AssignmentContainer::get_assignment()</a>, <a href=
"classIMP_1_1domino_1_1SampleAssignmentContainer.html#a8d3cb4c2cc32f4a8f5199a18033cbca1">IMP::domino::SampleAssignmentContainer::get_assignment()</a>, <a href=
"classIMP_1_1domino_1_1Slice.html#ab3c699a06268f2fa405c296149c4515b">IMP::domino::Slice::get_sliced()</a>, <a href=
"classIMP_1_1domino_1_1WriteAssignmentContainer.html#a1a1945c99b7a742323dd516df4fd88cf">IMP::domino::WriteAssignmentContainer::get_assignment()</a>, <a href=
"classIMP_1_1domino_1_1WriteHDF5AssignmentContainer.html#a955539a2e20a90cc06b9d7afa94ac07b">IMP::domino::WriteHDF5AssignmentContainer::get_assignment()</a>, <a href=
"namespaceIMP_1_1domino.html#abd8a69ba2cc2b8fea2f49c99189d8711">
IMP::domino::get_nearest_assignment()</a></td></tr>
138 <tr><td>@ref
IMP::domino::AssignmentsTable</td><td><a href=
"classIMP_1_1domino_1_1DiscreteSampler.html#a4e75f4975c1009934c6c594f93ca31e1">IMP::domino::DiscreteSampler::get_assignments_table_to_use()</a></td></tr>
139 <tr><td>@ref
IMP::domino::ParticleStates</td><td><a href=
"classIMP_1_1domino_1_1ParticleStatesTable.html#aa0827374f14a45cc57eef6a08f734f0a">IMP::domino::ParticleStatesTable::get_particle_states()</a></td></tr>
140 <tr><td>@ref
IMP::domino::ParticleStatesTable</td><td><a href=
"classIMP_1_1domino_1_1DiscreteSampler.html#add8262de16a05f7912617cb655f37831">IMP::domino::DiscreteSampler::get_particle_states_table()</a>, <a href=
"classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#af4484a70172a58bed5eedfe9a42a0705">IMP::multifit::ProteomicsEMAlignmentAtomic::set_particle_states_table()</a></td></tr>
142 <tr><td>@ref
IMP::domino::Subset</td><td><a href=
"classIMP_1_1domino_1_1ParticleStatesTable.html#ad199188132a371bdf4d086cc82ad2735">
IMP::domino::ParticleStatesTable::get_subset()</a>, <a href=
"classIMP_1_1domino_1_1RestraintCache.html#abe89754d9654db827f15ecdfbd92bad1">IMP::domino::RestraintCache::get_subset()</a>, <a href=
"classIMP_1_1domino_1_1Slice.html#a2f4e028d276be06d17293141b9a472c1">IMP::domino::Slice::get_sliced()</a>, <a href=
"namespaceIMP_1_1domino.html#a1e91ca287b91fd6144aeeff14960c14a">IMP::domino::get_difference()</a>, <a href=
"namespaceIMP_1_1domino.html#a399d7344a0696fbab4a6ca6c2796157b">IMP::domino::get_intersection()</a>, <a href=
"namespaceIMP_1_1domino.html#adc940e96eb944fe259a8fba40830a251">IMP::domino::get_union()</a></td></tr>
143 <tr><td>@ref
IMP::domino::SubsetFilter</td><td><a href=
"classIMP_1_1domino_1_1EqualitySubsetFilterTable.html#a0e41d167243f8bb91c8ebdf1e68fa66b">
IMP::domino::EqualitySubsetFilterTable::get_subset_filter()</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#a88463fb614a2dcb2b155e62b77d64a23">
IMP::domino::EquivalenceSubsetFilterTable::get_subset_filter()</a>, <a href=
"classIMP_1_1domino_1_1ExclusionSubsetFilterTable.html#ab21a7dbe5fd65a957b80d37cecb05e10">
IMP::domino::ExclusionSubsetFilterTable::get_subset_filter()</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#a04cfce4e5e82589e9a958780ec276853">
IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_subset_filter()</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#ad96b79309670a8ed32b79f69c2ac15de">
IMP::domino::ProbabilisticSubsetFilterTable::get_subset_filter()</a>, <a href=
"classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#afe6c067399f81400198864d011a90efb">
IMP::domino::RestraintScoreSubsetFilterTable::get_subset_filter()</a>, <a href=
"classIMP_1_1domino_1_1SubsetFilterTable.html#ac455bb060804addf2274c8304a2aa5fd">
IMP::domino::SubsetFilterTable::get_subset_filter()</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#a8fe7c10211739dd503ff88579ad18434">
IMP::example::ExampleSubsetFilterTable::get_subset_filter()</a></td></tr>
144 <tr><td>@ref
IMP::domino::SubsetFilterTable</td><td><a href=
"classIMP_1_1domino_1_1DiscreteSampler.html#ae77e8ad6a8313ae2970f192df444cf85">IMP::domino::DiscreteSampler::get_subset_filter_table()</a></td></tr>
146 # IMP.em # {#factory_index_em}
148 <th>Class</th><th>Factories</th></tr>
150 <tr><td>@ref
IMP::em::DensityMap</td><td><a href=
"classIMP_1_1em_1_1DensityMap.html#a3cbce8f549241438b9e02fbcc5e9f47f">
IMP::em::DensityMap::get_cropped()</a>, <a href=
"classIMP_1_1em_1_1DensityMap.html#a152abc77a04a0eddaedca4a61643c7e4">
IMP::em::DensityMap::get_cropped()</a>, <a href=
"classIMP_1_1em_1_1DensityMap.html#a8f5c966aab9fb6fa41e89500efc7f7e3">
IMP::em::DensityMap::pad_margin()</a>, <a href=
"classIMP_1_1multifit_1_1FFTFitting.html#a37d65339d5125709922ec82eba2ce9ed">IMP::multifit::FFTFitting::crop_margin()</a>, <a href=
"namespaceIMP_1_1cnmultifit.html#a3733609ff3265bd070779045acf03fca">IMP::cnmultifit::build_cn_dens_assembly()</a>, <a href=
"namespaceIMP_1_1em.html#a1c88424c8b24a5802ef048175e22787b">
IMP::em::binarize()</a>, <a href=
"namespaceIMP_1_1em.html#aa873c569e58e5c5d66dac1c0420f3e6c">
IMP::em::create_density_map()</a>, <a href=
"namespaceIMP_1_1em.html#ad6586b38abb58a2ebc6b64b10f60f734">
IMP::em::create_density_map()</a>, <a href=
"namespaceIMP_1_1em.html#ace9a6d63b63146fcaac428d8995ade7b">
IMP::em::create_density_map()</a>, <a href=
"namespaceIMP_1_1em.html#a325cd7401c937376cfb3504606e4ffd3">
IMP::em::create_density_map()</a>, <a href=
"namespaceIMP_1_1em.html#a6cde45849d9d1b0fbdc1ed54b6dd74b6">
IMP::em::get_binarized_interior()</a>, <a href=
"namespaceIMP_1_1em.html#ae7eacf1de1781ba22d2169b635d87753">
IMP::em::get_max_map()</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#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#a7ca59d2a3aa688060c280efa250d80a7">
IMP::em::interpolate_map()</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#ac570c6b6325f74c8a4ffa8df6ba6c4c9">
IMP::em::read_map()</a>, <a href=
"namespaceIMP_1_1em.html#aadebe0a2bd375bdcea106df7660ad840">
IMP::em::read_map()</a>, <a href=
"namespaceIMP_1_1multifit.html#a3359231b0601df5803958afcd8d93184">IMP::multifit::create_hit_map()</a>, <a href=
"namespaceIMP_1_1multifit.html#ae2668faf165711107665d494a73351a2">IMP::multifit::grid2map()</a>, <a href=
"namespaceIMP_1_1multifit.html#a8528245410468cfc40ab674d0ef64d70">
IMP::multifit::remove_background()</a></td></tr>
151 <tr><td>@ref
IMP::em::FittingSolutions</td><td><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#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#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_1multifit.html#a2a2ca63805bc102fbf07209c85e2ce44">IMP::multifit::convert_multifit_to_em_format()</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></td></tr>
153 <tr><td>@ref
IMP::em::KernelParameters</td><td><a href=
"classIMP_1_1em_1_1SampledDensityMap.html#a583657d98547c95dceb6130ea3bf1e02">IMP::em::SampledDensityMap::get_kernel_params()</a></td></tr>
159 # IMP.em2d # {#factory_index_em2d}
161 <th>Class</th><th>Factories</th></tr>
166 # IMP.example # {#factory_index_example}
168 <th>Class</th><th>Factories</th></tr>
171 # IMP.isd # {#factory_index_isd}
173 <th>Class</th><th>Factories</th></tr>
174 <tr><td>@ref
IMP::isd::MolecularDynamics</td><td><a href=
"classIMP_1_1isd_1_1HybridMonteCarlo.html#a126896181fdc35049811f2a1cd3d9980">IMP::isd::HybridMonteCarlo::get_md()</a>, <a href=
"classIMP_1_1isd_1_1MolecularDynamicsMover.html#a8536ffc5917d63f065ee68239b450e93">IMP::isd::MolecularDynamicsMover::get_md()</a></td></tr>
180 # IMP.kernel # {#factory_index_kernel}
182 <th>Class</th><th>Factories</th></tr>
183 <tr><td>@ref
IMP::kernel::ConfigurationSet</td><td><a href=
"classIMP_1_1kernel_1_1Sampler.html#ab6479a4cbe255d2b46348f45de6017f8">IMP::kernel::Sampler::create_sample()</a>, <a href=
"classIMP_1_1kernel_1_1Sampler.html#a542c10952c2df0d99774bfbfe25a690e">IMP::kernel::Sampler::do_sample()</a></td></tr>
184 <tr><td>@ref
IMP::kernel::DerivativeAccumulator</td><td><a href=
"classIMP_1_1kernel_1_1ScoreAccumulator.html#ae29bacf400fbddaa827731dc4e52527b">IMP::kernel::ScoreAccumulator::get_derivative_accumulator()</a></td></tr>
185 <tr><td>@ref
IMP::kernel::Key</td><td><a href=
"classIMP_1_1kernel_1_1Key.html#a4abb29cb1ab7b46fffa35648847f67a5">IMP::kernel::Key::operator+()</a>, <a href=
"classIMP_1_1kernel_1_1Key.html#a3212eae42b7777e11830559fc137125e">
IMP::kernel::Key::operator++()</a>, <a href=
"classIMP_1_1kernel_1_1Key.html#a399d5e3c520766550b77c0116ae395b0">IMP::kernel::Key::operator--()</a>, <a href=
"classIMP_1_1kernel_1_1Key.html#aac9bb4e342b6ce2213d6ec348911443a">
IMP::kernel::Key::add_alias()</a>, <a href=
"classIMP_1_1misc_1_1CustomXYZR.html#abf684f0db593d848979dc60276e353ee">IMP::misc::CustomXYZR::get_decorator_traits()</a>, <a href=
"classIMP_1_1misc_1_1CustomXYZR.html#a57fd04d203ea022563739fccb3e008e6">IMP::misc::CustomXYZR::get_default_decorator_traits()</a></td></tr>
186 <tr><td>@ref
IMP::kernel::Model</td><td><a href=
"classIMP_1_1domino_1_1Subset.html#ab20cbb20765364747449b8c70e1c4d0a">IMP::domino::Subset::get_model()</a>, <a href=
"classIMP_1_1kernel_1_1ConfigurationSet.html#a610e9e2a88ef2940633835400288f6c2">IMP::kernel::ConfigurationSet::get_model()</a>, <a href=
"classIMP_1_1kernel_1_1Decorator.html#a9784359e2cff233d1dc1a532c9c38c02">
IMP::kernel::Decorator::get_model()</a>, <a href=
"classIMP_1_1kernel_1_1ModelObject.html#ad4d078c66a305f154fdb6545bbba8eda">IMP::kernel::ModelObject::get_model()</a>, <a href=
"classIMP_1_1kernel_1_1ParticleAdaptor.html#a166d6e3ed9b396777fb04bce479a296a">IMP::kernel::ParticleAdaptor::get_model()</a>, <a href=
"classIMP_1_1kernel_1_1Sampler.html#ae85879514ca15f04e48d9f7420348f64">IMP::kernel::Sampler::get_model()</a>, <a href=
"classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a9ed2ed7369607ce99df2b93f968ae708">IMP::multifit::ProteomicsEMAlignmentAtomic::get_model()</a></td></tr>
187 <tr><td>@ref
IMP::kernel::Optimizer</td><td><a href=
"classIMP_1_1kernel_1_1OptimizerState.html#a50fd5b922eaf1932235e9100ff397f2d">IMP::kernel::OptimizerState::get_optimizer()</a></td></tr>
188 <tr><td>@ref
IMP::kernel::OptimizerState</td><td><a href=
"classIMP_1_1kernel_1_1Optimizer.html#a7af14a56930af85b9da147c380a9dd79">IMP::kernel::Optimizer::get_optimizer_state()</a></td></tr>
189 <tr><td>@ref
IMP::kernel::Particle</td><td><a href=
"classIMP_1_1atom_1_1Angle.html#a8a8b062f087cea3dc536ef77f3fa380b">IMP::atom::Angle::get_particle()</a>, <a href=
"classIMP_1_1atom_1_1Angle.html#a36a85bdaac96517eb018d67fd499b61b">IMP::atom::Angle::get_particle()</a>, <a href=
"classIMP_1_1atom_1_1Dihedral.html#abed8fb49fc981de36c19b3e4954fa401">IMP::atom::Dihedral::get_particle()</a>, <a href=
"classIMP_1_1atom_1_1Dihedral.html#ab0b1c16d0ba2589e532cce32ab92f9de">IMP::atom::Dihedral::get_particle()</a>, <a href=
"classIMP_1_1atom_1_1SecondaryStructureResidue.html#afc1a9d62ef75039f5b4b1d1403d97112">IMP::atom::SecondaryStructureResidue::get_particle()</a>, <a href=
"classIMP_1_1atom_1_1Simulator.html#af6e1bd7bf44a96d07a4c02b5240313f8">IMP::atom::Simulator::get_particle()</a>, <a href=
"classIMP_1_1core_1_1Reference.html#ae4895699d66bb17641c42c851e6457dd">IMP::core::Reference::get_reference_particle()</a>, <a href=
"classIMP_1_1display_1_1SingletonGeometry.html#a7bb89ab7817255ec811b9d5b290d2547">IMP::display::SingletonGeometry::get_particle()</a>, <a href=
"classIMP_1_1em_1_1DensityFillingRestraint.html#adad5e78616b287969dfd531512c8cc37">IMP::em::DensityFillingRestraint::get_particle()</a>, <a href=
"classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#af2738d460a2f98dd60790f44bbb1ca13">IMP::em::EnvelopePenetrationRestraint::get_particle()</a>, <a href=
"classIMP_1_1em_1_1FitRestraint.html#a3ac86b1f77f938a2eb685d1d1273ae55">IMP::em::FitRestraint::get_particle()</a>, <a href=
"classIMP_1_1em_1_1PCAFitRestraint.html#ae6e85e3976dcfb69abeb227e48985a72">IMP::em::PCAFitRestraint::get_particle()</a>, <a href=
"classIMP_1_1kernel_1_1Decorator.html#aed5bcdf3daba8b5e9a8c6c76dd0cd84c">
IMP::kernel::Decorator::get_particle()</a>, <a href=
"classIMP_1_1kernel_1_1Decorator.html#a5c525e74bba947abb4c48529a23d58aa">IMP::kernel::Decorator::operator->()</a>, <a href=
"classIMP_1_1kernel_1_1Model.html#afaae4848e02a7af53aba201c80fc947a">
IMP::kernel::Model::get_particle()</a>, <a href=
"classIMP_1_1kernel_1_1Refiner.html#afd5f1e512319f876a63c4982ffd4a62b">
IMP::kernel::Refiner::get_refined()</a>, <a href=
"classIMP_1_1kernel_1_1SingletonContainer.html#abb73910311fff9f5a158e23de20b668b">
IMP::kernel::SingletonContainer::get_particle()</a>, <a href=
"classIMP_1_1kinematics_1_1KinematicForest.html#a14b1bae2e1548367fe8f9c1dc0cd6ed5">IMP::kinematics::KinematicForest::get_parent()</a>, <a href=
"classIMP_1_1multifit_1_1RadiusOfGyrationRestraint.html#a68543208c02ba3168e41a5bda83316ea">IMP::multifit::RadiusOfGyrationRestraint::get_particle()</a>, <a href=
"classIMP_1_1multifit_1_1WeightedExcludedVolumeRestraint.html#a38622be55ae9f06164fb46e1b965066a">IMP::multifit::WeightedExcludedVolumeRestraint::get_particle()</a>, <a href=
"classIMP_1_1rmf_1_1HierarchyLoadLink.html#add7114279d7ee3371b052d7b2ad3e99a">IMP::rmf::HierarchyLoadLink::do_create()</a></td></tr>
190 <tr><td>@ref
IMP::kernel::Restraint</td><td><a href=
"classIMP_1_1core_1_1MinimumRestraint.html#a2dc7d93a3e7aa32c3eb5225f26fa46cf">IMP::core::MinimumRestraint::get_restraint()</a>, <a href=
"classIMP_1_1display_1_1RestraintGeometry.html#a1e9cc60ebd84150fdff2f7c29794593e">IMP::display::RestraintGeometry::get_restraint()</a>, <a href=
"classIMP_1_1kernel_1_1Model.html#a9ab76fcce74053435e0fb91fe96ac5d4">
IMP::kernel::Model::get_restraint()</a>, <a href=
"classIMP_1_1kernel_1_1Restraint.html#abad714322450bb54ecc15dbe8cfcc501">
IMP::kernel::Restraint::create_current_decomposition()</a>, <a href=
"classIMP_1_1kernel_1_1Restraint.html#ad9dc68fdb3e35bbbf54d56d4322fccce">
IMP::kernel::Restraint::create_decomposition()</a>, <a href=
"classIMP_1_1kernel_1_1RestraintSet.html#a021e7f95a753e52b53c30e51f5ab4273">IMP::kernel::RestraintSet::get_restraint()</a>, <a href=
"classIMP_1_1kernel_1_1RestraintsAdaptor.html#af5989cf6412cc59405b78c40acd6c533">IMP::kernel::RestraintsAdaptor::get()</a>, <a href=
"classIMP_1_1kernel_1_1RestraintsAdaptor.html#a2fd493fedcf2b313941e4080d0af17e4">IMP::kernel::RestraintsAdaptor::get()</a>, <a href=
"namespaceIMP_1_1atom.html#aa320a95736f890640f2b5980c2296157">
IMP::atom::create_connectivity_restraint()</a>, <a href=
"namespaceIMP_1_1atom.html#ac362c35eaf58b15b6bac53cba2b6aa2d">
IMP::atom::create_connectivity_restraint()</a>, <a href=
"namespaceIMP_1_1atom.html#af6c28249c49b2aa2f4eda4faf0bda484">
IMP::atom::create_distance_restraint()</a>, <a href=
"namespaceIMP_1_1atom.html#afd2757eb3f37160c3288198c7e647e44">
IMP::atom::create_excluded_volume_restraint()</a>, <a href=
"namespaceIMP_1_1atom.html#a269e6c721543f3ccd8306e0f188e5b4e">
IMP::atom::create_excluded_volume_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_1example.html#ab77a6d1a8b6ce3666ab2b28c607c053b">
IMP::example::create_chain_restraint()</a></td></tr>
191 <tr><td>@ref
IMP::kernel::RestraintSet</td><td><a href=
"classIMP_1_1display_1_1RestraintSetGeometry.html#a8086bac477686ba7266a8945ec3f5fea">IMP::display::RestraintSetGeometry::get_restraint_set()</a>, <a href=
"classIMP_1_1kernel_1_1Model.html#aeb21ac03874765df4f1fdff66d0c0788">
IMP::kernel::Model::get_root_restraint_set()</a></td></tr>
192 <tr><td>@ref
IMP::kernel::ScoreAccumulator</td><td><a href=
"classIMP_1_1kernel_1_1ScoringFunction.html#a9181216bab38bad6578ff3ba6379942f">IMP::kernel::ScoringFunction::get_score_accumulator()</a>, <a href=
"classIMP_1_1kernel_1_1ScoringFunction.html#a228beeb3fcb65d47e89247d47cd5b6f0">IMP::kernel::ScoringFunction::get_score_accumulator_if_below()</a>, <a href=
"classIMP_1_1kernel_1_1ScoringFunction.html#a8319292e3e9ff9e708de15736eeace03">IMP::kernel::ScoringFunction::get_score_accumulator_if_good()</a></td></tr>
193 <tr><td>@ref
IMP::kernel::ScoreState</td><td><a href=
"classIMP_1_1kernel_1_1Model.html#a7426a4cab582891f3550da5cadbb6aa7">IMP::kernel::Model::get_score_state()</a></td></tr>
194 <tr><td>@ref
IMP::kernel::ScoringFunction</td><td><a href=
"classIMP_1_1kernel_1_1Optimizer.html#a77dd769fb37f395720ca9f74e7002452">
IMP::kernel::Optimizer::get_scoring_function()</a>, <a href=
"classIMP_1_1kernel_1_1Restraint.html#ac6c2b795718f8af100ec7daab4aa9201">
IMP::kernel::Restraint::create_scoring_function()</a>, <a href=
"classIMP_1_1kernel_1_1Restraint.html#a2452878c23185500ff4ede41f683413b">IMP::kernel::Restraint::create_internal_scoring_function()</a>, <a href=
"classIMP_1_1kernel_1_1Sampler.html#a198648756f795d64bff3ff696eb688be">IMP::kernel::Sampler::get_scoring_function()</a>, <a href=
"classIMP_1_1kernel_1_1ScoringFunctionAdaptor.html#a8088f5512b14874d08d0709b862e1945">IMP::kernel::ScoringFunctionAdaptor::get()</a>, <a href=
"classIMP_1_1kernel_1_1ScoringFunctionAdaptor.html#a5c4f6b23714f5f11c8c049c9189f9e72">IMP::kernel::ScoringFunctionAdaptor::get()</a>, <a href=
"classIMP_1_1kernel_1_1ScoringFunctionAdaptor.html#a54411f2a1b7caa4d3c29c916880af609">IMP::kernel::ScoringFunctionAdaptor::get()</a>, <a href=
"classIMP_1_1kernel_1_1ScoringFunctionAdaptor.html#aaa85b61e8d642ff123988fc107327f46">IMP::kernel::ScoringFunctionAdaptor::get()</a>, <a href=
"classIMP_1_1kernel_1_1ScoringFunctionAdaptor.html#aa62e2a283f933338f99272a4d0cbcd8f">IMP::kernel::ScoringFunctionAdaptor::get()</a></td></tr>
196 # IMP.kinematics # {#factory_index_kinematics}
198 <th>Class</th><th>Factories</th></tr>
200 <tr><td>@ref
IMP::kinematics::DihedralAngleRevoluteJoint</td><td><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></td></tr>
201 <tr><td>@ref
IMP::kinematics::Joint</td><td><a href=
"classIMP_1_1kinematics_1_1KinematicForest.html#a4f4f75ae4464f9238edbd4f9f53da211">
IMP::kinematics::KinematicForest::add_edge()</a>, <a href=
"classIMP_1_1kinematics_1_1KinematicNode.html#a40ad561042d38de8f17e9732deeac344">IMP::kinematics::KinematicNode::get_in_joint()</a></td></tr>
202 <tr><td>@ref
IMP::kinematics::KinematicForest</td><td><a href=
"classIMP_1_1kinematics_1_1Joint.html#ace40f33493218a6909b5c5ec3747210e">IMP::kinematics::Joint::get_owner_kf()</a>, <a href=
"classIMP_1_1kinematics_1_1KinematicNode.html#afb08a98ef2a09bbfde3f86f65d886eb6">IMP::kinematics::KinematicNode::get_owner()</a>, <a href=
"classIMP_1_1kinematics_1_1ProteinKinematics.html#a7d362a387254728e698107b187ccabc9">IMP::kinematics::ProteinKinematics::get_kinematic_forest()</a></td></tr>
205 # IMP.misc # {#factory_index_misc}
207 <th>Class</th><th>Factories</th></tr>
210 # IMP.multifit # {#factory_index_multifit}
212 <th>Class</th><th>Factories</th></tr>
213 <tr><td>@ref
IMP::multifit::AnchorsData</td><td><a href=
"classIMP_1_1multifit_1_1ProteinsAnchorsSamplingSpace.html#a749cb63890e572b59c9b0b5e5e4075c1">IMP::multifit::ProteinsAnchorsSamplingSpace::get_anchors()</a>, <a href=
"namespaceIMP_1_1multifit.html#aedc64c26eefe139ef34e5cce89d13a51">IMP::multifit::molecule2anchors()</a>, <a href=
"namespaceIMP_1_1multifit.html#a1311b5448ea5d757a085c959a77e5fc2">IMP::multifit::read_anchors_data()</a></td></tr>
214 <tr><td>@ref
IMP::multifit::AssemblyHeader</td><td><a href=
"classIMP_1_1multifit_1_1SettingsData.html#ab907ede30470a45d77126d0ed631868e">IMP::multifit::SettingsData::get_assembly_header()</a></td></tr>
215 <tr><td>@ref
IMP::multifit::ComponentHeader</td><td><a href=
"classIMP_1_1multifit_1_1SettingsData.html#a64cd483a817da67778deb9fbbb0d90a9">IMP::multifit::SettingsData::get_component_header()</a></td></tr>
216 <tr><td>@ref
IMP::multifit::Ensemble</td><td><a href=
"namespaceIMP_1_1multifit.html#a990fc248adf46233d96011ab77130eec">IMP::multifit::load_ensemble()</a></td></tr>
219 <tr><td>@ref
IMP::multifit::ProteomicsData</td><td><a href=
"classIMP_1_1multifit_1_1ProteinsAnchorsSamplingSpace.html#ab6cfebe16d6ea30f264e390f01e73890">IMP::multifit::ProteinsAnchorsSamplingSpace::get_proteomics_data()</a>, <a href=
"namespaceIMP_1_1multifit.html#aac05dae9e06cb11ef27e820cf54be014">IMP::multifit::get_partial_proteomics_data()</a>, <a href=
"namespaceIMP_1_1multifit.html#ae4470dd25cd94e09c145556b62fd54b7">
IMP::multifit::read_proteomics_data()</a></td></tr>
222 # IMP.pmi # {#factory_index_pmi}
224 <th>Class</th><th>Factories</th></tr>
229 # IMP.rotamer # {#factory_index_rotamer}
231 <th>Class</th><th>Factories</th></tr>
234 # IMP.saxs # {#factory_index_saxs}
236 <th>Class</th><th>Factories</th></tr>
237 <tr><td>@ref
IMP::saxs::DeltaDistributionFunction</td><td><a href=
"classIMP_1_1saxs_1_1DerivativeCalculator.html#aacf9ff590d52121ddc187cefd9739766">IMP::saxs::DerivativeCalculator::precompute_derivative_helpers()</a></td></tr>
241 # IMP.statistics # {#factory_index_statistics}
243 <th>Class</th><th>Factories</th></tr>
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
const SpherePatch3D & get_sphere_patch_3d_geometry(const SpherePatch3D &g)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Residue setup_particle(kernel::Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
algebra::Rotation3D get_orientation(unsigned int i) const
Returns the orientation corresponding to the state i.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
An ensemble of fitting solutions.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
PartitionalClusteringWithCenter * create_lloyds_kmeans(Embedding *embedding, unsigned int k, unsigned int iterations)
Hierarchies get_leaves(Hierarchy h)
Rotation3D get_rotation_about_normalized_axis(const Vector3D &axis_norm, double angle)
static State setup_particle(kernel::Model *m, ParticleIndex pi, unsigned int index)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
TextOutput create_temporary_file(std::string prefix="imp_temp", std::string suffix="")
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Rotation2D get_inverse() const
Returns the matrix for the inverse rotation.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Nuisance setup_particle(kernel::Model *m, ParticleIndex pi)
The ideal topology of a single residue.
base::Vector< base::Pointer< O > > create(RMF::NodeConstHandle rt)
A class to store a set of configurations of a model.
GridIndexD< D > get_index(const ExtendedGridIndexD< D > &v) const
Convert a ExtendedIndex into a real Index if possible.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Transformation2D get_transformation_aligning_pair(const Vector2Ds &set_from, const Vector2Ds &set_to)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Restraint * get_restraint(unsigned int i) const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
algebra::Transformation3D get_transformation_aligning_first_to_second(XYZsOrVector3ds a, XYZsOrVector3ds b)
ParticleIndexes get_indexes(const ParticlesTemp &ps)
RegistrationResult get_final_registration() const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A decorator to associate a particle with a part of a protein.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchies read_multimodel_pdb(base::TextInput input, kernel::Model *model, PDBSelector *selector=get_default_pdb_selector())
ExtendedGridIndexD< D > get_end_index() const
Get the past-end voxel.
Add weights for a set of states to a particle.
Chain get_chain(Hierarchy h)
Hierarchy get_parent() const
virtual kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
static Typed setup_particle(kernel::Model *m, ParticleIndex pi, ParticleType t)
atom::Hierarchies create_hierarchies(RMF::FileConstHandle fh, kernel::Model *m)
static Charged setup_particle(kernel::Model *m, ParticleIndex pi, Float charge)
virtual ParticleIndexes get_all_possible_indexes() const =0
Get contained particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
const Rotation3D & get_rotation() const
A decorator to associate a particle with a part of a protein/DNA/RNA.
kernel::Particles add_bonds(Hierarchy hierarchy) const
Add bonds to the given Hierarchy using this topology, and return them.
ExtendedGridIndexD< D > get_maximum_extended_index() const
Return the index of the maximal cell.
static ProjectionParameters setup_particle(kernel::Model *m, ParticleIndex pi)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
DensityMap * interpolate_map(DensityMap *in_map, double new_spacing)
static RigidBody setup_particle(kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexesAdaptor ps)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Weight setup_particle(kernel::Model *m, ParticleIndex pi)
Class for adding derivatives from restraints to the model.
kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Rotation3D get_rotation_from_x_y_axes(const Vector3D &x, const Vector3D &y)
const VectorD< D > & get_corner(unsigned int i) const
For 0 return lower corner and 1 upper corner.
kernel::ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
const Transformation3D & get_transformation_from() const
Storage of proteomics data.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
BoundingBoxD< 3 > get_bounding_box(const Plane3D &g)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static KinematicNode setup_particle(kernel::Model *m, ParticleIndex pi, KinematicForest *owner)
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 ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual const ParticlesTemp get_refined(Particle *a) const =0
Refine the passed particle into a set of particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual const kernel::ParticlesTemp get_refined(kernel::Particle *) const
Refine the passed particle into a set of particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static const HierarchyTraits & get_default_traits()
Get the default hierarchy traits.
Hierarchy create_simplified_from_volume(Hierarchy h, double resolution)
A connection (bond, angle, dihedral) between some number of endpoints.
Rotation3D get_rotation_from_fixed_xyz(double xr, double yr, double zr)
Initialize a rotation in x-y-z order from three angles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
ParticlesTemp get_output_particles(const ModelObjectsTemp &mos)
Return all the output particles for a given ModelObject.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
DensityMap * pad_margin(int mrg_x, int mrg_y, int mrg_z, float val=0.0)
Create a new padded map.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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.
static CHARMMAtom setup_particle(kernel::Model *m, ParticleIndex pi, String charmm_type)
VectorD< 3 > get_random_vector_on_unit_sphere()
A decorator for a particle with x,y,z coordinates and a radius.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Calculates kernel parameters as a function of a specific radius.
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.
Particle * get_particle() const
Returns the particle decorated by this decorator.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual SubsetFilter * get_subset_filter(const Subset &s, const Subsets &prior_subsets) const =0
static Atom setup_particle(kernel::Model *m, ParticleIndex pi, Atom other)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Stores a 2D rotation matrix.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A a decorator for a particle with an associated reference particle.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Rotation2D compose(const Rotation2D &a, const Rotation2D &b)
compose two rotations a and b
Particle * get_particle(ParticleIndex p) const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
The base class for geometry.
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A decorator for a particle which has bonds.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
algebra::Transformation3D get_transformation(unsigned int i) const
Get the score of the i'th solution.
Hierarchy create_clone(Hierarchy d)
Clone the Hierarchy.
DensityMap * binarize(DensityMap *orig_map, float threshold, bool reverse=false)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Restraint * create_decomposition() const
Decompose this restraint into constituent terms.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
ReferenceFrame3D get_local_reference_frame(const ReferenceFrame3D &v) const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Rotation3D operator/(const Rotation3D &r) const
Compute the rotation which when composed with r gives this.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A single atom in a CHARMM topology.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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.
Store a kernel::ParticleIndexTriplets.
Represent a real cell in a grid (one within the bounding box)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A simple class for returning XYZ Euler angles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Storage of anchors (points and edges)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Triangle3D get_largest_triangle(const Vector3Ds &points)
Return the largest triangle defined by 3 points from the input.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Shared optimizer state that is invoked upon commitment of new coordinates.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
const kernel::ParticleIndexes & get_member_particle_indexes() const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
ParticlesTemp get_particles(kernel::Model *m, const ParticleIndexes &ps)
Color get_rgb_color(double f)
Return the color for f from the RGB color map.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A particle that is the geometric centroid of other particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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
kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Slice get_slice(kernel::Restraint *r, const Subset &s) const
Return the slice for that restraint given the subset.
kernel::ParticleIndexes get_selected_particle_indexes() const
Get the indexes of the selected particles.
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.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
An index in an infinite grid on space.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
algebra::ReferenceFrame3D get_initial_reference_frame(kernel::Model *m, const kernel::ParticleIndexes &pis)
BoundingBoxD< 3 > get_transformed(const BoundingBoxD< 3 > &bb, const Transformation3D &tr)
Return a bounding box containing the transformed box.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Object used to hold a set of restraints.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A voxel grid in d-dimensional space space.
Stores a set of SingletonContainers.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
Model * get_model() const
Returns the Model containing the particle.
kernel::ParticlesTemp get_simulation_particles() const
Returns the set of particles used in the simulation.
Bonds get_internal_bonds(Hierarchy mhd)
Get the bonds internal to this tree.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A simple list of fitting solutions.
DensityMap * get_threshold_map(const DensityMap *orig_map, float threshold)
algebra::BoundingBoxD< 3 > get_bounding_box(const Hierarchy &h)
Get a bounding box for the Hierarchy.
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 ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Transformation3D get_transformation_from_first_triangle_to_second(Triangle3D first_tri, Triangle3D second_tri)
Return a transformation between two triangles.
Add symmetric attribute to a particle.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Assignment get_nearest_assignment(const Subset &s, const algebra::VectorKD &embedding, ParticleStatesTable *pst)
Return the nearest assignment from an embedding.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static XYZ setup_particle(kernel::Model *m, ParticleIndex pi)
Base class for writing geometry to a file.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Represent a cylinder in 3D.
static Scale setup_particle(kernel::Model *m, ParticleIndex pi)
ParticlesTemp get_particles() const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
BoundingBoxD< 3 > get_bounding_box(const Cylinder3D &g)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Bond get_bond(unsigned int i) const
Get a Bond of the ith bond.
const RadiusDependentKernelParameters & set_params(float radius)
Sets the parameters that depend on the radius of a given particle.
ParticlesTemp get_input_particles(const ModelObjectsTemp &mos)
Return all the input particles for a given ModelObject.
Store a kernel::ParticleIndexQuads.
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.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
ParticlesTemp get_dependent_particles(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
ExtendedGridIndexD< D > get_extended_index(const VectorD< D > &o) const
Return the index that would contain the voxel if the grid extended there.
virtual kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
Add scale parameter to particle.
Represent a subset of the particles being optimized.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Add uncertainty to a particle.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
Get all atoms in the Hierarchy that do not have CHARMM types.
kernel::Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
FormFactorTable * get_default_form_factor_table()
kernel::ParticleIndexes get_simulation_particle_indexes() const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
PartitionalClustering * create_gromos_clustering(Metric *d, double cutoff)
em::ImageHeader & get_header()
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Represents a scoring function on the model.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
DynamicListTripletContainer * add_predicate(TripletPredicate *predicate, int value)
Color get_interpolated_rgb(const Color &a, const Color &b, double f)
Return a color interpolated between a and b in RGB space.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Color get_hot_color(double f)
Return the color for f from the hot color map.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Atom get_atom(Residue rd, AtomType at)
Return a particle atom from the residue.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
ScoreStates maintain invariants in the Model.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Represent a triangle in 3D.
Stores a set of QuadContainers.
Hierarchies get_children() const
Return the children in the order they were added.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
SampledDensityMap * get_model_dens_map() const
Return the predicted density map of the model.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
DensityMap * read_map(std::string filename, MapReaderWriter *reader)
Read a density map from a file and return it.
const Transformation3D get_transformation() const
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.
The end of a bond, angle, dihedral, improper, or internal coordinate.
static Resolution setup_particle(kernel::Model *m, ParticleIndex pi, Float resolution)
A class storing the rotated coordinates of the atoms in the residue.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchy create_hierarchy(kernel::Model *model) const
Create a new Hierarchy in the given model using this topology.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Plane3D get_base_plane() const
Get the plane supporting the base of the cone.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Restraint * create_current_decomposition() const
Decompose this restraint into constituent terms for the current conf.
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.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
The topology of a single residue in a model.
const BoundingBoxD< D > & operator+=(const BoundingBoxD< D > &o)
extend the current bounding box to include the other
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Add switching parameter to particle.
Add resolution to a particle.
kernel::Restraint * create_chain_restraint(const kernel::ParticlesTemp &ps, double length_factor, double k, std::string name)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
CHARMM force field parameters.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > get_grid(DensityMap *in_map)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A particle which covers a set of other particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
VectorD<-1 > get_basis_vector_kd(int D, unsigned int coordinate)
Return a dynamically sized basis vector.
Rotation3D get_rotation_about_axis(const Vector3D &axis, double angle)
Generate a Rotation3D object from a rotation around an axis.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
SphereGeometry * create_geometry(const algebra::Sphere3D &t, std::string name="algebra::Sphere3D"+"%1""%")
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Filter atom pairs for SOAP.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
base::Object * get_data(kernel::ModelKey mk) const
Segment3D get_shortest_segment(const Segment3D &s, const Vector3D &p)
DOF const * get_dof(unsigned int i) const
Returns the i'th dof over which this sampler works.
ModelObjectsTemps get_interactions() const
Get the interacting sets induced by this ModelObject.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Reference setup_particle(kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexAdaptor reference)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A decorator for a point particle that has an electrostatic charge.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A simple decorator which adds a name to a particle.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::Particle * get_particle(unsigned int i) const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Class for handling density maps.
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchy read_pdb(base::TextInput input, kernel::Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Store a subset of a subset or assignment.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
IMP::algebra::Transformation3D get_transformation_aligning_first_to_second(const Vector3DsOrXYZs0 &source, const Vector3DsOrXYZs1 &target)
Compute the rigid transform bringing the first point set to the second.
Transformation2D get_rotation_about_point(const Vector2D &point, const Rotation2D &rotation)
Generates a Transformation2D object from a rotation around a point.
A Gaussian distribution in 3D.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Display a reference frame.
Class for sampling a density map from particles.
A decorator for keeping track of copies of a molecule.
The class represents a molecule as shells of distance from the surface.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
ReferenceFrame3D get_global_reference_frame(const ReferenceFrame3D &v) const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static XYZR setup_particle(kernel::Model *m, ParticleIndex pi)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Angle setup_particle(kernel::Model *m, ParticleIndex pi, core::XYZ a, core::XYZ b, core::XYZ c)
Rotation3D get_random_rotation_3d()
Pick a rotation at random from all possible rotations.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
Hierarchy create_fragment(const Hierarchies &ps)
Create a fragment containing the specified nodes.
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)
virtual kernel::ParticleIndexes get_range_indexes() const =0
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Bonded setup_particle(kernel::Model *m, ParticleIndex pi)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Image * get_projection(unsigned int i) const
Returns the projection corresponding to the state i;.
PartitionalClustering * create_diameter_clustering(Metric *d, double maximum_diameter)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
const RadiusDependentKernelParameters & get_params(float radius, float eps=0.001)
Finds the precomputed parameters given a particle radius.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Hierarchy setup_particle(kernel::Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Molecule setup_particle(kernel::Model *m, ParticleIndex pi)
Hierarchy get_parent() const
A decorator for a representation.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
A particle that describes an angle between three particles.
const Cone3D & get_cone_3d_geometry(const Cone3D &g)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
The standard decorator for manipulating molecular structures.
A Cartesian vector in D-dimensions.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static base::Vector< std::string > get_all_strings()
Get a list of all of the keys of this type.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
DensityMap * multiply(const DensityMap *m1, const DensityMap *m2)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
ExtendedGridIndexD< D > get_minimum_extended_index() const
Return the ExtendedGridIndexD of all zeros.
IMP::algebra::Transformation3D get_rotation_about_joint_in_parent_coordinates() 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)
StereochemistryPairFilter * get_full_pair_filter()
Get a PairFilter including everything from original topology.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual kernel::ParticlesTemp get_input_particles() const =0
particle manipulation
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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()
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Atoms get_psi_dihedral_atoms(Residue rd)
Return the atoms comprising the psi dihedral.
A decorator for a particle representing an atom.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::ParticlesTemp create_particles(RMF::FileConstHandle fh, kernel::Model *m)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
base::Vector< char > write_particles_to_buffer(const ParticlesTemp &particles, const FloatKeys &keys)
return a binary buffer with the data
Rotation2D get_identity_rotation_2d()
Builds an identity rotation in 2D.
Plane3D get_opposite() const
Return the plane with the opposite normal.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchies get_by_type(Hierarchy mhd, GetByType t)
const IMP::algebra::VectorD< D > & get_point(unsigned int i) const
Get one of the endpoints.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
PartitionalClustering * create_connectivity_clustering(Metric *metric, double dist)
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
Add nuisance parameter to particle.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Rotation3D get_inverse() const
Return the rotation which undoes this rotation.
Use this to add an advanced flag to the program.
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A base class for classes which perturb particles.
Storage of the results from an FFT fit.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
BoundingBoxD< 3 > get_bounding_box(const Cone3D &g)
kernel::ParticleIndexes get_member_indexes() const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Colored setup_particle(kernel::Model *m, ParticleIndex pi, Color color)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
const Transformation3D & get_transformation_to() const
const VectorD< D > & get_unit_cell() const
Return the unit cell, relative to the origin.
const Cylinder3D & get_cylinder_3d_geometry(const Cylinder3D &g)
kernel::Particles create_dihedrals(kernel::Particles bonds) const
Auto-generate Dihedral particles from the passed list of Bond particles.
Define the type for a type of hierarchy.
Rotation3D get_rotation_from_fixed_zyz(double Rot, double Tilt, double Psi)
Generate a rotation object from Euler Angles.
algebra::BoundingBoxD< 3 > get_bounding_box(const XYZRs &ps)
Get the bounding box.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Class for adding up scores during ScoringFunction evaluation.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchy get_previous_residue(Residue rd)
Return the residue from the same chain with one lower index.
DensityMap * get_binarized_interior(DensityMap *dmap)
Return a binaries density map with 1 for voxels that are internal.
A restraint is a term in an IMP ScoringFunction.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A sphere patch is defined as all points above the plane and on the sphere.
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.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
DynamicListQuadContainer * add_predicate(QuadPredicate *predicate, int value)
BoundingBoxD<-1 > get_unit_bounding_box_kd(unsigned int d)
Box with radius one.
PartitionalClusteringWithCenter * create_bin_based_clustering(Embedding *embed, double side)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
GridIndexD< D > get_index(const ExtendedGridIndexD< D > &i) const
requires get_has_index(i) is true.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Color get_display_color(unsigned int i)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Holds header data for optimization.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchy read_mol2(base::TextInput mol2_file, kernel::Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
Hierarchy create_clone_one(Hierarchy d)
Clone the node in the Hierarchy.
A decorator for a particle with x,y,z coordinates.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Stores a set of TripletContainers.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Chain setup_particle(kernel::Model *m, ParticleIndex pi, std::string id)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
ExtendedGridIndexD< D > get_extended_index(const GridIndexD< D > &index) const
Convert an index back to an extended index.
DensityMap * get_max_map(DensityMaps maps)
DensityMap * create_density_map(const DensityMap *other)
create a copy of another map
Bonded get_bonded(unsigned int i) const
Get the atom i of the bond.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
DensityHeader * get_header_writable()
Returns a pointer to the header of the map in a writable version.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
ProteomicsData * read_proteomics_data(const char *proteomics_fn)
Proteomics reader.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
BoundingBoxD< 3 > get_bounding_box(const Ellipsoid3D &g)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A decorator for a particle that has a Lennard-Jones potential well.
Rotation3D get_interpolated(const Rotation3D &a, const Rotation3D &b, double f)
Interpolate between two rotations.
kernel::ParticlesTemp get_particles() const
IMP::algebra::BoundingBoxD< 3 > calculate_particles_bounding_box(const kernel::Particles &ps)
Calculate the parameters of the particles bounding box.
Hierarchy get_child(unsigned int i) const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::ParticleIndexes get_movable_particles() const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Class to handle individual model particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Rotation3D get_rotation_from_vector4d(const VectorD< 4 > &v)
Compute a rotation from an unnormalized quaternion.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
BoundingBoxD<-1 > get_cube_kd(unsigned int d, double radius)
Cube with radius of length side.
Rotation3D get_rotation_taking_first_to_second(const Vector3D &v1, const Vector3D &v2)
Create a rotation from the first vector to the second one.
virtual ParticleIndexes get_refined_indexes(Model *m, ParticleIndex pi) const
Return the indexes of the particles returned by get_refined()
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
ParticleIndexes get_particle_indexes()
static Domain setup_particle(kernel::Model *m, ParticleIndex pi, Domain other)
static Uncertainty setup_particle(kernel::Model *m, ParticleIndex pi, Float uncertainty)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Rotation2D get_rotation_to_x_axis(const Vector2D &v)
Writer * create_writer(std::string filename)
Common base class for heavy weight IMP objects.
Base class for all optimizers.
Color get_gnuplot_color(double f)
Return colors using the gnuplot default color map.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static const IMP::core::HierarchyTraits & get_traits()
Get the molecular hierarchy HierarchyTraits.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Stores a set of PairContainers.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Copy setup_particle(kernel::Model *m, ParticleIndex pi, Int number)
virtual kernel::ParticlesTemp get_input_particles() const =0
particle manipulation
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A particle that describes a dihedral angle between four particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
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.
kernel::Restraint * create_internal_connectivity_restraint(const Selection &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selection.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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.
kernel::ParticlesTemp get_input_particles() const
particle manipulation
An axis-aligned bounding box.
static Mass setup_particle(kernel::Model *m, ParticleIndex pi, Float mass)
static ExampleDecorator setup_particle(kernel::Model *m, ParticleIndex pi, std::string name)
kernel::ParticleIndexes get_indexes(int predicate_value) const
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Centroid setup_particle(kernel::Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
Transformation3D get_identity_transformation_3d()
Return a transformation that does not do anything.
const Segment3D & get_segment_3d_geometry(const Segment3D &g)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual const kernel::ParticlesTemp get_refined(kernel::Particle *) const
Refine the passed particle into a set of particles.
Simple implementation of segments in 3D.
container::ClosePairContainer * create_excluded_volume(const kernel::ParticlesTemp &ps, double k, std::string name)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
const Ellipsoid3D & get_ellipsoid_3d_geometry(const Ellipsoid3D &g)
A decorator for a residue with probability of secondary structure.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
SecondaryStructureResidue setup_coarse_secondary_structure_residue(const kernel::Particles &ssr_ps, kernel::Model *mdl, bool winner_takes_all_per_res=false)
Coarsen some SecondaryStructureResidues.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
HistogramD< D > get_probability_distribution_function() const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static CustomXYZR setup_particle(kernel::Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
A decorator for a residue.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Joint * add_edge(IMP::core::RigidBody parent, IMP::core::RigidBody child)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Rotation3D get_rotation_from_matrix(double m00, double m01, double m02, double m10, double m11, double m12, double m20, double m21, double m22)
Generate a Rotation3D object from a rotation matrix.
Gaussian3D get_gaussian_from_covariance(const IMP_Eigen::Matrix3d &covariance, const Vector3D ¢er)
Return a Gaussian centered at the origin from a covariance matrix.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static LennardJones setup_particle(kernel::Model *m, ParticleIndex pi)
Transformation3D get_transformation_3d(const Transformation2D &t2d)
Builds a 3D transformation from a 2D one.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ScoringFunction * create_scoring_function(double weight=1.0, double max=NO_MAX) const
Create a scoring function with only this restraint.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Store a configuration of a subset.
IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Version and module information for Objects.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Representation setup_particle(kernel::Model *m, ParticleIndex pi)
virtual kernel::ParticleIndexes get_indexes() const =0
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Associate an integer "state" index with a hierarchy node.
algebra::Rotation3D get_rotation() const
Returns the rotation for the 3 projection angles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchies get_hierarchies() const
Return the hierarchies that the Selection was constructed with.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchy get_representation(double resolution, RepresentationType type=BALLS)
virtual ModelObjectsTemps do_get_interactions() const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
core::MonteCarloMover * create_serial_mover(const kernel::ParticlesTemp &ps)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::ParticlesTemp create_rigid_bodies(kernel::Model *m, unsigned int n, bool no_members=false)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
algebra::VectorD< 4 > get_rotational_derivatives() const
Get the derivatives of the quaternion.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
kernel::Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A filter that excludes bonds, angles and dihedrals.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Rotation3D get_identity_rotation_3d()
Return a rotation that does not do anything.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Color get_gray_color(double f)
Return the a grayscale value for f.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
ScoringFunction * get_scoring_function() const
Return the scoring function that is being used.
static Diffusion setup_particle(kernel::Model *m, ParticleIndex pi, Float D)
const VectorD< D > & get_unit_cell() const
Return the unit cell, relative to the origin.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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.
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Molecular dynamics optimizer on 1-D and 3-D particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Class to manage registration results.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchies get_representations(RepresentationType type=BALLS)
Return all children at all resolutions.
static Voxel setup_particle(kernel::Model *m, ParticleIndex pi, algebra::Vector3D position, Float radius, Float density)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
The topology of a single CHARMM segment in a model.
Color get_jet_color(double f)
Return the color for f from the jet color map.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
RigidMembers get_members() const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A decorator for classifying particles in your system.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Fragment setup_particle(kernel::Model *m, ParticleIndex pi)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual const IMP::algebra::Transformation3D & get_transformation_child_to_parent() const
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.
Bonded get_bonded(unsigned int i) const
Get a Bonded of the ith bonded particle.
Store a kernel::ParticleIndexes.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static CenterOfMass setup_particle(kernel::Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::Particles density2particles(DensityMap *dmap, Float threshold, kernel::Model *m, int step=1)
Converts a density grid to a set of paritlces.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A decorator for helping deal with a hierarchy.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
algebra::Gaussian3D get_gaussian() const
create Gaussian3D from these attributes
virtual const kernel::ParticlesTemp get_refined(kernel::Particle *p) const
Returns the fixed set of particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Selection create_clone()
Make a clone of this Selection.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A decorator for a diffusing particle with a diffusion coefficient.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
A decorator for a rigid body.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
The topology of a complete CHARMM model.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Dynamically build a histogram embedded in D-dimensional space.
RestraintSet * get_root_restraint_set()
static Key< ID, LazyAdd > add_alias(Key< ID, LazyAdd > old_key, std::string new_name)
Make new_name an alias for old_key.
DynamicListSingletonContainer * add_predicate(SingletonPredicate *predicate, int value)
virtual const IMP::algebra::Transformation3D & get_transformation_child_to_parent_no_checks() const
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 ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
SoapPairFilter * get_pair_filter()
Get a filter that returns pairs that this score should use.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
algebra::Transformation3D get_internal_transformation() const
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())
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
const kernel::ParticleIndexes & get_neighbors(kernel::ParticleIndex pi) const
StereochemistryPairFilter * get_pair_filter()
Get a PairFilter that excludes all stereochemical pairs.
Subset get_subset() const
Return the subset corresponding to all the particles.
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
kernel::ParticlesTemp get_input_particles() const
particle manipulation
ResidueRotamer get_rotamer(const IMP::atom::Residue &rd, double thr) const
get the coordinates of the residue atoms
static Dihedral setup_particle(kernel::Model *m, ParticleIndex pi, core::XYZ a, core::XYZ b, core::XYZ c, core::XYZ d)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ParticlesTemp get_output_particles(Particle *p) const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual const kernel::ParticlesTemp get_refined(kernel::Particle *) const
Refine the passed particle into a set of particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
CHARMMParameters * get_all_atom_CHARMM_parameters()
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ParticleIndexes const & get_refined_indexes_by_ref(Model *m, ParticleIndex pi) const
Return the indexes of the particles returned by get_refined()
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Select which atoms to read from a PDB file.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
PartitionalClustering * create_centrality_clustering(Metric *d, double far, int k)
A decorator for a molecule.
Select hierarchy particles identified by the biological name.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::Particles add_dihedrals(Hierarchy hierarchy) const
Add dihedrals to the given Hierarchy using this topology, and return them.
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.
Store a kernel::ParticleIndexPairs.
kernel::Particles create_angles(kernel::Particles bonds) const
Auto-generate Angle particles from the passed list of Bond particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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.
virtual const kernel::ParticlesTemp get_refined(kernel::Particle *) const
Refine the passed particle into a set of particles.
static Gaussian setup_particle(kernel::Model *m, ParticleIndex pi)
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
const kernel::ParticleIndexes & get_body_member_particle_indexes() const
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Rotation3D get_rotation_from_fixed_zxz(double phi, double theta, double psi)
Initialize a rotation from Euler angles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Represent a sphere in D-dimensions.
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.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Hierarchy get_next_residue(Residue rd)
Return the residue from the same chain with one higher index.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
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 ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
DensityMap * get_cropped(float threshold)
Create a new cropped map.
ResidueType get_residue_type(char c)
Get the residue type from the 1-letter amino acid code.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::ParticlesTemp get_selected_particles() const
Get the selected particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static RigidBodyDiffusion setup_particle(kernel::Model *m, ParticleIndex pi)
A particle that is the center of mass of other particles.
A decorator for an atom that has a defined CHARMM type.
Transformation3D get_random_local_transformation(Vector3D origin, double max_translation=5., double max_angle_in_rad=0.26)
Get a local transformation.
2D Electron Microscopy images in IMP
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Transformation2D get_identity_transformation_2d()
Returns a transformation that does not do anything.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Class for storing model, its restraints, constraints, and particles.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
kernel::ParticlesTemp get_input_particles() const
particle manipulation
BoundingBoxD< 3 > get_bounding_box(const SpherePatch3D &g)
A base class for clustering results where each item is in one cluster.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
static Symmetric setup_particle(kernel::Model *m, ParticleIndex pi, Float symmetric)
IMP::algebra::ReferenceFrame3D get_reference_frame() const
Get the reference frame for the local coordinates.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
Slice get_slice(Subset outer, Subset inner, const Subsets &excluded)
Rotation2D get_random_rotation_2d()
Builds an identity rotation in 2D.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual ::IMP::base::VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual kernel::ParticleIndexes get_refined_indexes(Model *m, ParticleIndex) const
Return the indexes of the particles returned by get_refined()
kernel::ParticleIndexes get_all_possible_indexes() const
Get contained particles.
A decorator for a particle with x,y,z coordinates and a radius.