IMP
2.0.0
The Integrative Modeling Platform
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Functions that create objects of a given type:
IMP::algebra::BoundingBoxD
:
IMP::algebra::BoundingBoxD::operator+=()
IMP::algebra::BoundingBoxD::operator+=()
IMP::algebra::BoundingBoxD::operator+=()
IMP::algebra::BoundingBoxD::get_bounding_box()
IMP::algebra::BoundingBoxD::get_cube_kd()
IMP::algebra::BoundingBoxD::get_unit_bounding_box_kd()
IMP::algebra::Cone3D::get_bounding_box()
IMP::algebra::Cylinder3D::get_bounding_box()
IMP::algebra::DefaultEmbeddingD::get_bounding_box()
IMP::algebra::DefaultEmbeddingD::get_bounding_box()
IMP::algebra::Ellipsoid3D::get_bounding_box()
IMP::algebra::GridD::get_bounding_box()
IMP::algebra::LogEmbeddingD::get_bounding_box()
IMP::algebra::LogEmbeddingD::get_bounding_box()
IMP::algebra::Plane3D::get_bounding_box()
IMP::algebra::Segment3D::get_bounding_box()
IMP::algebra::SpherePatch3D::get_bounding_box()
IMP::display::BoundingBoxGeometry::get_geometry()
IMP::em::SampledDensityMap::calculate_particles_bounding_box()
IMP::statistics::HistogramD::get_bounding_box()
IMP::algebra::get_transformed()
IMP::atom::get_bounding_box()
IMP::core::get_bounding_box()
IMP::em::get_bounding_box()
IMP::em::get_bounding_box()
IMP::kernel::get_bounding_box_d_geometry()
IMP::algebra::Cone3D
:
IMP::algebra::Cone3D::get_cone_3d_geometry()
IMP::algebra::Cylinder3D
:
IMP::algebra::Cylinder3D::get_cylinder_3d_geometry()
IMP::display::CylinderGeometry::get_geometry()
IMP::algebra::DenseGridStorageD
:
IMP::algebra::DenseGridStorageD::operator=()
IMP::em::get_grid()
IMP::algebra::Ellipsoid3D
:
IMP::algebra::Ellipsoid3D::get_ellipsoid_3d_geometry()
IMP::display::EllipsoidGeometry::get_geometry()
IMP::algebra::ExtendedGridIndexD
:
IMP::algebra::BoundedGridRangeD::get_extended_indexes()
IMP::algebra::BoundedGridRangeD::get_end_index()
IMP::algebra::BoundedGridRangeD::get_maximum_extended_index()
IMP::algebra::BoundedGridRangeD::get_minimum_extended_index()
IMP::algebra::DefaultEmbeddingD::get_extended_index()
IMP::algebra::ExtendedGridIndexD::get_offset()
IMP::algebra::ExtendedGridIndexD::get_uniform_offset()
IMP::algebra::GridD::get_nearest_extended_index()
IMP::algebra::GridD::get_extended_index()
IMP::algebra::LogEmbeddingD::get_extended_index()
IMP::algebra::SparseGridStorageD::get_maximum_extended_index()
IMP::algebra::SparseGridStorageD::get_minimum_extended_index()
IMP::algebra::UnboundedGridRangeD::get_extended_indexes()
IMP::algebra::FixedXYZ
:
IMP::algebra::get_fixed_xyz_from_rotation()
IMP::algebra::FixedZXZ
:
IMP::algebra::FixedZXZ::get_fixed_zxz_from_rotation()
IMP::algebra::get_fixed_zxz_from_rotation()
IMP::algebra::FixedZYZ
:
IMP::algebra::FixedZYZ::get_fixed_zyz_from_rotation()
IMP::algebra::get_fixed_zyz_from_rotation()
IMP::algebra::GridD
:
IMP::em::get_grid()
IMP::algebra::GridIndexD
:
IMP::algebra::BoundedGridRangeD::get_all_indexes()
IMP::algebra::BoundedGridRangeD::get_indexes()
IMP::algebra::BoundedGridRangeD::get_index()
IMP::algebra::DefaultEmbeddingD::get_index()
IMP::algebra::GridD::get_nearest_index()
IMP::algebra::GridD::add_voxel()
IMP::algebra::LogEmbeddingD::get_index()
IMP::algebra::SparseGridStorageD::get_all_indexes()
IMP::algebra::SparseGridStorageD::get_indexes()
IMP::algebra::SparseGridStorageD::add_voxel()
IMP::algebra::SparseGridStorageD::get_index()
IMP::algebra::Plane3D
:
IMP::algebra::Cone3D::get_base_plane()
IMP::algebra::Plane3D::get_opposite()
IMP::algebra::Plane3D::get_plane_3d_geometry()
IMP::algebra::SpherePatch3D::get_plane()
IMP::algebra::ReferenceFrame3D
:
IMP::algebra::ReferenceFrame3D::get_global_reference_frame()
IMP::algebra::ReferenceFrame3D::get_local_reference_frame()
IMP::core::RigidBody::get_reference_frame()
IMP::display::ReferenceFrameGeometry::get_geometry()
IMP::domino::RigidBodyStates::get_reference_frame()
IMP::algebra::get_transformed()
IMP::core::get_initial_reference_frame()
IMP::algebra::Rotation2D
:
IMP::algebra::Rotation2D::get_inverse()
IMP::algebra::Transformation2D::get_rotation()
IMP::algebra::compose()
IMP::algebra::get_identity_rotation_2d()
IMP::algebra::get_random_rotation_2d()
IMP::algebra::get_rotation_to_x_axis()
IMP::algebra::Rotation3D
:
IMP::algebra::Ellipsoid3D::get_rotation()
IMP::algebra::FixedXYZ::get_rotation_from_fixed_xyz()
IMP::algebra::FixedZYZ::get_rotation_from_fixed_zyz()
IMP::algebra::Rotation3D::get_rotation_from_fixed_zxz()
IMP::algebra::Rotation3D::get_inverse()
IMP::algebra::Rotation3D::operator*()
IMP::algebra::Rotation3D::operator/()
IMP::algebra::Rotation3D::operator/=()
IMP::algebra::Rotation3D::compose()
IMP::algebra::Rotation3D::get_identity_rotation_3d()
IMP::algebra::Rotation3D::get_interpolated()
IMP::algebra::Rotation3D::get_random_rotation_3d()
IMP::algebra::Rotation3D::get_random_rotation_3d()
IMP::algebra::Rotation3D::get_rotation_about_axis()
IMP::algebra::Rotation3D::get_rotation_from_matrix()
IMP::algebra::Rotation3D::get_rotation_from_vector4d()
IMP::algebra::Rotation3D::get_rotation_taking_first_to_second()
IMP::algebra::Transformation3D::get_rotation()
IMP::em2d::GridStates::get_orientation()
IMP::em2d::ProjectionParameters::get_rotation()
IMP::em2d::RegistrationResult::get_rotation()
IMP::em::PCAAligner::get_rotation_matrix()
IMP::algebra::get_rotation_from_fixed_xyz()
IMP::algebra::get_rotation_from_fixed_zxz()
IMP::algebra::get_rotation_from_fixed_zyz()
IMP::algebra::compose()
IMP::algebra::get_identity_rotation_3d()
IMP::algebra::get_interpolated()
IMP::algebra::get_random_rotation_3d()
IMP::algebra::get_random_rotation_3d()
IMP::algebra::get_rotation_about_axis()
IMP::algebra::get_rotation_from_matrix()
IMP::algebra::get_rotation_from_vector4d()
IMP::algebra::get_rotation_from_x_y_axes()
IMP::algebra::get_rotation_taking_first_to_second()
IMP::algebra::Segment3D
:
IMP::algebra::Cylinder3D::get_segment()
IMP::algebra::Segment3D::get_shortest_segment()
IMP::algebra::Segment3D::get_segment_3d_geometry()
IMP::core::RigidBodyTorque::extract_geometry()
IMP::core::RigidBodyTorque::get_geometry()
IMP::display::SegmentGeometry::get_geometry()
IMP::algebra::get_shortest_segment()
IMP::algebra::get_shortest_segment()
IMP::algebra::SphereD
:
IMP::algebra::get_unit_sphere_kd()
IMP::algebra::SpherePatch3D
:
IMP::algebra::SpherePatch3D::get_sphere_patch_3d_geometry()
IMP::algebra::Transformation2D
:
IMP::algebra::Transformation2D::get_inverse()
IMP::algebra::Transformation2D::operator*()
IMP::algebra::Transformation2D::operator*=()
IMP::algebra::Transformation2D::operator/()
IMP::algebra::Transformation2D::operator/=()
IMP::algebra::Transformation2D::compose()
IMP::algebra::Transformation2D::get_identity_transformation_2d()
IMP::algebra::Transformation2D::get_rotation_about_point()
IMP::algebra::compose()
IMP::algebra::get_identity_transformation_2d()
IMP::algebra::get_rotation_about_point()
IMP::algebra::get_transformation_aligning_pair()
IMP::algebra::Transformation3D
:
IMP::algebra::Ellipsoid3D::get_transformation()
IMP::algebra::ReferenceFrame3D::get_inverse()
IMP::algebra::ReferenceFrame3D::get_transformation_from()
IMP::algebra::ReferenceFrame3D::get_transformation_to()
IMP::algebra::Transformation3D::get_inverse()
IMP::algebra::Transformation3D::operator*()
IMP::algebra::Transformation3D::operator*=()
IMP::algebra::Transformation3D::operator/()
IMP::algebra::Transformation3D::operator/=()
IMP::algebra::Transformation3D::compose()
IMP::algebra::Transformation3D::get_identity_transformation_3d()
IMP::algebra::Transformation3D::get_rotation_about_point()
IMP::core::NonRigidMember::get_internal_transformation()
IMP::core::RigidMember::get_internal_transformation()
IMP::domino::NestedRigidBodyStates::get_transformation()
IMP::em::EnvelopeFitRestraint::get_transformation()
IMP::em::FittingSolutions::get_transformation()
IMP::multifit::FittingSolutionRecord::get_dock_transformation()
IMP::multifit::FittingSolutionRecord::get_fit_transformation()
IMP::algebra::get_transformation_aligning_first_to_second()
IMP::algebra::compose()
IMP::algebra::get_identity_transformation_3d()
IMP::algebra::get_random_local_transformation()
IMP::algebra::get_rotation_about_point()
IMP::algebra::get_transformation_3d()
IMP::algebra::get_transformation_from_first_to_second()
IMP::algebra::get_transformation_from_first_triangle_to_second()
IMP::cnmultifit::calc_transformation_around_axis()
IMP::core::get_transformation_aligning_first_to_second()
IMP::algebra::Triangle3D
:
IMP::algebra::Triangle3D::get_largest_triangle()
IMP::display::TriangleGeometry::get_geometry()
IMP::algebra::get_largest_triangle()
IMP::algebra::VectorD
:
IMP::algebra::BoundingBoxD::get_corner()
IMP::algebra::DefaultEmbeddingD::get_center()
IMP::algebra::DefaultEmbeddingD::get_center()
IMP::algebra::DefaultEmbeddingD::get_origin()
IMP::algebra::DefaultEmbeddingD::get_unit_cell()
IMP::algebra::LogEmbeddingD::get_center()
IMP::algebra::LogEmbeddingD::get_center()
IMP::algebra::LogEmbeddingD::get_origin()
IMP::algebra::LogEmbeddingD::get_unit_cell()
IMP::algebra::PrincipalComponentAnalysisD::get_centroid()
IMP::algebra::PrincipalComponentAnalysisD::get_principal_component()
IMP::algebra::PrincipalComponentAnalysisD::get_principal_components()
IMP::algebra::PrincipalComponentAnalysisD::get_principal_values()
IMP::algebra::SphereD::get_random_vector_in()
IMP::algebra::SphereD::get_center()
IMP::algebra::VectorD::get_unit_vector()
IMP::core::RigidBody::get_rotational_derivatives()
IMP::example::ExampleTemplateClassD::get_point()
IMP::multifit::GeometricHash::from_bucket()
IMP::statistics::HistogramD::get_mean()
IMP::statistics::HistogramD::get_standard_deviation()
IMP::algebra::get_random_vector_in()
IMP::algebra::get_basis_vector_kd()
IMP::algebra::get_ones_vector_kd()
IMP::algebra::get_zero_vector_kd()
IMP::atom::Angle
:
IMP::atom::Angle::decorate_particle()
IMP::atom::Angle::setup_particle()
IMP::atom::Atom
:
IMP::atom::Atom::decorate_particle()
IMP::atom::Atom::setup_particle()
IMP::atom::Atom::setup_particle()
IMP::atom::Atom::setup_particle()
IMP::atom::CHARMMBondEndpoint::get_atom()
IMP::atom::Hierarchy::get_as_atom()
IMP::atom::Hierarchy::get_atom()
IMP::atom::get_atom()
IMP::atom::AtomType
:
IMP::atom::Atom::get_atom_type()
IMP::atom::AtomType::add_atom_type()
IMP::atom::get_atom_type()
IMP::atom::add_atom_type()
IMP::atom::Bond
:
IMP::atom::Bond::decorate_particle()
IMP::atom::BondGraph::get_bond()
IMP::atom::Bonded::get_bond()
IMP::atom::Bonded::create_bond()
IMP::atom::Bonded::create_bond()
IMP::atom::Bonded::create_custom_bond()
IMP::atom::Bonded::get_bond()
IMP::atom::create_bond()
IMP::atom::create_bond()
IMP::atom::create_custom_bond()
IMP::atom::get_bond()
IMP::atom::Bonded
:
IMP::atom::Bond::get_bonded()
IMP::atom::Bonded::get_bonded()
IMP::atom::Bonded::decorate_particle()
IMP::atom::Bonded::setup_particle()
IMP::atom::CHARMMAtom
:
IMP::atom::CHARMMAtom::decorate_particle()
IMP::atom::CHARMMAtom::setup_particle()
IMP::atom::CHARMMAtomTopology
:
IMP::atom::CHARMMResidueTopologyBase::get_atom()
IMP::atom::CHARMMResidueTopologyBase::get_atom()
IMP::atom::CHARMMResidueTopologyBase::get_atom()
IMP::atom::CHARMMBondEndpoint
:
IMP::atom::CHARMMConnection::get_endpoint()
IMP::atom::CHARMMConnection
:
IMP::atom::CHARMMResidueTopologyBase::get_angle()
IMP::atom::CHARMMResidueTopologyBase::get_bond()
IMP::atom::CHARMMResidueTopologyBase::get_dihedral()
IMP::atom::CHARMMResidueTopologyBase::get_improper()
IMP::atom::CHARMMIdealResidueTopology
:
IMP::atom::CHARMMParameters::get_residue_topology()
IMP::atom::CHARMMInternalCoordinate
:
IMP::atom::CHARMMResidueTopologyBase::get_internal_coordinate()
IMP::atom::CHARMMParameters
:
IMP::atom::CHARMMTopology::get_parameters()
IMP::atom::get_all_atom_CHARMM_parameters()
IMP::atom::get_heavy_atom_CHARMM_parameters()
IMP::atom::CHARMMPatch
:
IMP::atom::CHARMMParameters::get_patch()
IMP::atom::CHARMMResidueTopology
:
IMP::atom::CHARMMSegmentTopology::get_residue()
IMP::atom::CHARMMSegmentTopology
:
IMP::atom::CHARMMTopology::get_segment()
IMP::atom::CHARMMTopology
:
IMP::atom::CHARMMParameters::create_topology()
IMP::atom::Chain
:
IMP::atom::Chain::decorate_particle()
IMP::atom::Chain::setup_particle()
IMP::atom::Chain::setup_particle()
IMP::atom::Chain::setup_particle()
IMP::atom::Hierarchy::get_as_chain()
IMP::atom::get_chain()
IMP::atom::Charged
:
IMP::atom::Charged::decorate_particle()
IMP::atom::Charged::setup_particle()
IMP::atom::Charged::setup_particle()
IMP::atom::Copy
:
IMP::atom::Copy::decorate_particle()
IMP::atom::Copy::setup_particle()
IMP::atom::Diffusion
:
IMP::atom::Diffusion::decorate_particle()
IMP::atom::Diffusion::setup_particle()
IMP::atom::Diffusion::setup_particle()
IMP::atom::Diffusion::setup_particle()
IMP::atom::Dihedral
:
IMP::atom::Dihedral::decorate_particle()
IMP::atom::Dihedral::setup_particle()
IMP::atom::Domain
:
IMP::atom::Domain::decorate_particle()
IMP::atom::Domain::setup_particle()
IMP::atom::Domain::setup_particle()
IMP::atom::Hierarchy::get_as_domain()
IMP::atom::ElementTable
:
IMP::atom::get_element_table()
IMP::atom::Fragment
:
IMP::atom::Fragment::decorate_particle()
IMP::atom::Fragment::setup_particle()
IMP::atom::Fragment::setup_particle()
IMP::atom::Hierarchy::get_as_fragment()
IMP::atom::Hierarchy
:
IMP::atom::CHARMMTopology::create_hierarchy()
IMP::atom::Hierarchy::read_pdb()
IMP::atom::Hierarchy::get_child()
IMP::atom::Hierarchy::get_parent()
IMP::atom::Hierarchy::decorate_particle()
IMP::atom::Hierarchy::setup_particle()
IMP::atom::Hierarchy::setup_particle()
IMP::atom::Hierarchy::setup_particle()
IMP::atom::Hierarchy::create_clone()
IMP::atom::Hierarchy::create_clone_one()
IMP::atom::Hierarchy::create_fragment()
IMP::atom::Hierarchy::create_protein()
IMP::atom::Hierarchy::get_residue()
IMP::atom::Hierarchy::get_root()
IMP::atom::Residue::get_next_residue()
IMP::atom::Residue::get_previous_residue()
IMP::atom::create_simplified_along_backbone()
IMP::atom::create_simplified_along_backbone()
IMP::atom::read_mol2()
IMP::atom::read_pdb()
IMP::atom::read_pdb()
IMP::atom::create_clone()
IMP::atom::create_clone_one()
IMP::atom::create_fragment()
IMP::atom::create_protein()
IMP::atom::create_protein()
IMP::atom::get_next_residue()
IMP::atom::get_previous_residue()
IMP::atom::get_residue()
IMP::atom::get_root()
IMP::multifit::create_coarse_molecule_from_density()
IMP::multifit::create_coarse_molecule_from_molecule()
IMP::atom::LennardJones
:
IMP::atom::LennardJones::decorate_particle()
IMP::atom::LennardJones::setup_particle()
IMP::atom::Mass
:
IMP::atom::Hierarchy::get_as_mass()
IMP::atom::Mass::decorate_particle()
IMP::atom::Mass::setup_particle()
IMP::atom::Molecule
:
IMP::atom::Hierarchy::get_as_molecule()
IMP::atom::Molecule::decorate_particle()
IMP::atom::Molecule::setup_particle()
IMP::atom::Molecule::setup_particle()
IMP::atom::Residue
:
IMP::atom::Hierarchy::get_as_residue()
IMP::atom::Hierarchy::get_residue()
IMP::atom::Residue::decorate_particle()
IMP::atom::Residue::setup_particle()
IMP::atom::Residue::setup_particle()
IMP::atom::Residue::setup_particle()
IMP::atom::get_residue()
IMP::atom::ResidueType
:
IMP::atom::CHARMMParameters::parse_residue_line()
IMP::atom::Residue::get_residue_type()
IMP::atom::get_residue_type()
IMP::atom::get_residue_type()
IMP::atom::RigidBodyDiffusion
:
IMP::atom::RigidBodyDiffusion::decorate_particle()
IMP::atom::RigidBodyDiffusion::setup_particle()
IMP::atom::SecondaryStructureResidue
:
IMP::atom::SecondaryStructureResidue::decorate_particle()
IMP::atom::SecondaryStructureResidue::setup_particle()
IMP::atom::SecondaryStructureResidue::setup_particle()
IMP::atom::setup_coarse_secondary_structure_residue()
IMP::atom::StereochemistryPairFilter
:
IMP::atom::CHARMMStereochemistryRestraint::get_pair_filter()
IMP::base::LRUCache
:
IMP::domino::RestraintCache::Generator::operator()()
IMP::base::Object
:
IMP::kernel::Model::get_data()
IMP::base::TextOutput
:
IMP::base::create_temporary_file()
IMP::base::get_log_target()
IMP::base::Tracker
:
IMP::base::TrackedObject::get_tracker()
IMP::base::Vector
:
IMP::algebra::BoundedGridRangeD::get_all_indexes()
IMP::algebra::BoundedGridRangeD::get_indexes()
IMP::algebra::BoundedGridRangeD::get_extended_indexes()
IMP::algebra::DenseGridStorageD::get_all_voxels()
IMP::algebra::PrincipalComponentAnalysisD::get_principal_components()
IMP::algebra::SparseGridStorageD::get_all_indexes()
IMP::algebra::SparseGridStorageD::get_indexes()
IMP::algebra::UnboundedGridRangeD::get_extended_indexes()
IMP::base::ConstVector::ConstVector()
IMP::base::LRUCache::get_keys()
IMP::base::Tracker::get_tracked()
IMP::core::MSConnectivityRestraint::ExperimentalTree::Node::get_label()
IMP::kernel::Container::get_all_possible_indexes()
IMP::kernel::Container::get_all_possible_particles()
IMP::kernel::Key::get_all_strings()
IMP::kernel::Model::get_particles()
IMP::kernel::ModelObject::get_interactions()
IMP::kernel::ModelObject::do_get_interactions()
IMP::kernel::PairModifier::get_input_particles()
IMP::kernel::PairModifier::get_output_particles()
IMP::kernel::PairPredicate::get_input_particles()
IMP::kernel::PairScore::get_input_particles()
IMP::kernel::QuadModifier::get_input_particles()
IMP::kernel::QuadModifier::get_output_particles()
IMP::kernel::QuadPredicate::get_input_particles()
IMP::kernel::QuadScore::get_input_particles()
IMP::kernel::Refiner::get_input_particles()
IMP::kernel::Refiner::get_refined()
IMP::kernel::Restraint::get_input_particles()
IMP::kernel::ScoreState::get_input_particles()
IMP::kernel::ScoreState::get_output_particles()
IMP::kernel::SingletonContainer::get_indexes()
IMP::kernel::SingletonContainer::get_particles()
IMP::kernel::SingletonContainer::get_range_indexes()
IMP::kernel::SingletonModifier::get_input_particles()
IMP::kernel::SingletonModifier::get_output_particles()
IMP::kernel::SingletonPredicate::get_input_particles()
IMP::kernel::SingletonScore::get_input_particles()
IMP::kernel::TripletModifier::get_input_particles()
IMP::kernel::TripletModifier::get_output_particles()
IMP::kernel::TripletPredicate::get_input_particles()
IMP::kernel::TripletScore::get_input_particles()
IMP::multifit::GeometricHash::neighbors_data()
IMP::rmf::SimpleLoadLink::create()
IMP::kernel::get_required_particles()
IMP::kernel::get_dependent_particles()
IMP::kernel::get_input_particles()
IMP::kernel::get_output_particles()
IMP::kernel::write_particles_to_buffer()
IMP::kernel::get_indexes()
IMP::kernel::get_particles()
IMP::base::VersionInfo
:
IMP::base::Object::get_version_info()
IMP::em::EnvelopeScore::get_version_info()
IMP::em::PCAAligner::get_version_info()
IMP::container::ClosePairContainer
:
IMP::example::create_excluded_volume()
IMP::container::DynamicListPairContainer
:
IMP::container::DistributePairsScoreState::add_predicate()
IMP::container::DynamicListQuadContainer
:
IMP::container::DistributeQuadsScoreState::add_predicate()
IMP::container::DynamicListSingletonContainer
:
IMP::container::DistributeSingletonsScoreState::add_predicate()
IMP::container::DynamicListTripletContainer
:
IMP::container::DistributeTripletsScoreState::add_predicate()
IMP::container::PairContainerSet
:
IMP::container::PairContainerSet::get_set()
IMP::container::QuadContainerSet
:
IMP::container::QuadContainerSet::get_set()
IMP::container::SingletonContainerSet
:
IMP::container::SingletonContainerSet::get_set()
IMP::container::TripletContainerSet
:
IMP::container::TripletContainerSet::get_set()
IMP::core::Centroid
:
IMP::core::Centroid::decorate_particle()
IMP::core::Centroid::setup_particle()
IMP::core::Centroid::setup_particle()
IMP::core::ConnectivityRestraint
:
IMP::restrainer::SimpleConnectivity::get_restraint()
IMP::core::Cover
:
IMP::core::Cover::decorate_particle()
IMP::core::Cover::setup_particle()
IMP::core::Cover::setup_particle()
IMP::core::DataObject
:
IMP::multifit::ComplementarityRestraint::get_grid_object()
IMP::core::DiameterRestraint
:
IMP::restrainer::SimpleDiameter::get_restraint()
IMP::core::DistanceRestraint
:
IMP::restrainer::SimpleDistance::get_restraint()
IMP::core::ExcludedVolumeRestraint
:
IMP::restrainer::SimpleExcludedVolume::get_restraint()
IMP::core::HarmonicUpperBound
:
IMP::restrainer::SimpleConnectivity::get_harmonic_upper_bound()
IMP::restrainer::SimpleDiameter::get_harmonic_upper_bound()
IMP::restrainer::SimpleDistance::get_harmonic_upper_bound()
IMP::core::Hierarchy
:
IMP::core::Hierarchy::get_child()
IMP::core::Hierarchy::get_parent()
IMP::core::Hierarchy::decorate_particle()
IMP::core::Hierarchy::setup_particle()
IMP::core::Hierarchy::setup_particle()
IMP::core::Hierarchy::get_root()
IMP::core::get_root()
IMP::core::HierarchyTraits
:
IMP::atom::Hierarchy::get_traits()
IMP::core::Hierarchy::get_decorator_traits()
IMP::core::Hierarchy::get_traits()
IMP::core::Hierarchy::get_default_decorator_traits()
IMP::core::Hierarchy::get_default_traits()
IMP::core::IncrementalScoringFunction
:
IMP::core::MonteCarlo::get_incremental_scoring_function()
IMP::core::MonteCarloMover
:
IMP::core::MonteCarlo::get_mover()
IMP::example::create_serial_mover()
IMP::core::NonRigidMember
:
IMP::core::NonRigidMember::decorate_particle()
IMP::core::Reference
:
IMP::core::Reference::decorate_particle()
IMP::core::Reference::setup_particle()
IMP::core::RigidBody
:
IMP::core::NonRigidMember::get_rigid_body()
IMP::core::RigidBody::decorate_particle()
IMP::core::RigidBody::setup_particle()
IMP::core::RigidBody::setup_particle()
IMP::core::RigidBody::create_compatible_rigid_body()
IMP::core::RigidBody::create_rigid_body()
IMP::core::RigidMember::get_rigid_body()
IMP::atom::create_compatible_rigid_body()
IMP::atom::create_rigid_body()
IMP::atom::create_rigid_body()
IMP::core::RigidMember
:
IMP::core::RigidMember::decorate_particle()
IMP::core::SphereDistancePairScore
:
IMP::restrainer::SimpleConnectivity::get_sphere_distance_pair_score()
IMP::core::Typed
:
IMP::core::Typed::decorate_particle()
IMP::core::Typed::setup_particle()
IMP::core::XYZ
:
IMP::atom::Hierarchy::get_as_xyz()
IMP::core::XYZ::decorate_particle()
IMP::core::XYZ::setup_particle()
IMP::core::XYZ::setup_particle()
IMP::core::XYZR
:
IMP::atom::Hierarchy::get_as_xyzr()
IMP::atom::Selection::create_cover()
IMP::core::XYZR::decorate_particle()
IMP::core::XYZR::setup_particle()
IMP::core::XYZR::setup_particle()
IMP::core::XYZR::setup_particle()
IMP::core::XYZR::setup_particle()
IMP::atom::create_cover()
IMP::display::BoundingBoxGeometry
:
IMP::display::create_geometry()
IMP::display::Color
:
IMP::display::Color::get_jet_color()
IMP::display::Color::get_hot_color()
IMP::display::Color::get_rgb_color()
IMP::display::Color::get_grey_color()
IMP::display::Color::get_gnuplot_color()
IMP::display::Color::get_interpolated_rgb()
IMP::display::Colored::get_color()
IMP::display::Geometry::get_color()
IMP::display::PairGeometry::get_color()
IMP::display::SingletonGeometry::get_color()
IMP::display::get_jet_color()
IMP::display::get_hot_color()
IMP::display::get_rgb_color()
IMP::display::get_grey_color()
IMP::display::get_gnuplot_color()
IMP::display::get_display_color()
IMP::display::get_interpolated_rgb()
IMP::display::Colored
:
IMP::display::Colored::decorate_particle()
IMP::display::Colored::setup_particle()
IMP::display::CylinderGeometry
:
IMP::display::create_geometry()
IMP::display::EllipsoidGeometry
:
IMP::display::create_geometry()
IMP::display::Geometry
:
IMP::display::WriteOptimizerState::get_geometry()
IMP::display::PointGeometry
:
IMP::display::create_geometry()
IMP::display::PolygonGeometry
:
IMP::display::create_geometry()
IMP::display::ReferenceFrameGeometry
:
IMP::display::create_geometry()
IMP::display::SegmentGeometry
:
IMP::display::create_geometry()
IMP::display::SphereGeometry
:
IMP::display::create_geometry()
IMP::display::TriangleGeometry
:
IMP::display::create_geometry()
IMP::display::Writer
:
IMP::display::WriterAdaptor::get_writer()
IMP::display::WriterAdaptor::operator->()
IMP::display::create_writer()
IMP::domino::Assignment
:
IMP::domino::AssignmentContainer::get_assignment()
IMP::domino::Order::get_subset_ordered()
IMP::domino::Slice::get_sliced()
IMP::domino::get_nearest_assignment()
IMP::domino::AssignmentsTable
:
IMP::domino::DiscreteSampler::get_assignments_table_to_use()
IMP::domino::ParticleStates
:
IMP::domino::ParticleStatesTable::get_particle_states()
IMP::domino::ParticleStatesTable
:
IMP::domino::DiscreteSampler::get_particle_states_table()
IMP::domino::RestraintCache::Generator::get_particle_states_table()
IMP::multifit::ProteomicsEMAlignmentAtomic::set_particle_states_table()
IMP::domino::Slice
:
IMP::domino::RestraintCache::get_slice()
IMP::domino::get_slice()
IMP::domino::Subset
:
IMP::domino::ParticleStatesTable::get_subset()
IMP::domino::RestraintCache::get_subset()
IMP::domino::Slice::get_sliced()
IMP::domino::get_difference()
IMP::domino::get_intersection()
IMP::domino::get_union()
IMP::domino::SubsetFilter
:
IMP::domino::SubsetFilterTable::get_subset_filter()
IMP::domino::SubsetFilterTable
:
IMP::domino::DiscreteSampler::get_subset_filter_table()
IMP::em2d::Image
:
IMP::em2d::ProjectionStates::get_projection()
IMP::em2d::ProjectionParameters
:
IMP::em2d::ProjectionParameters::decorate_particle()
IMP::em2d::ProjectionParameters::setup_particle()
IMP::em2d::RegistrationResult
:
IMP::em2d::Fine2DRegistrationRestraint::get_final_registration()
IMP::em::DensityHeader
:
IMP::em::DensityHeader::create_density_header()
IMP::em::DensityMap::get_header()
IMP::em::DensityMap::get_header_writable()
IMP::em::create_density_header()
IMP::em::DensityMap
:
IMP::em::DensityMap::get_resampled()
IMP::em::DensityMap::get_transformed()
IMP::em::DensityMap::get_transformed()
IMP::em::DensityMap::read_map()
IMP::em::DensityMap::read_map()
IMP::em::DensityMap::get_cropped()
IMP::em::DensityMap::get_cropped()
IMP::em::DensityMap::pad_margin()
IMP::multifit::FFTFitting::crop_margin()
IMP::cnmultifit::build_cn_dens_assembly()
IMP::em::binarize()
IMP::em::create_density_map()
IMP::em::create_density_map()
IMP::em::create_density_map()
IMP::em::create_density_map()
IMP::em::get_binarized_interior()
IMP::em::get_max_map()
IMP::em::get_resampled()
IMP::em::get_segment()
IMP::em::get_segment()
IMP::em::get_segment_by_masking()
IMP::em::get_threshold_map()
IMP::em::get_transformed()
IMP::em::get_transformed()
IMP::em::interpolate_map()
IMP::em::mask_and_norm()
IMP::em::multiply()
IMP::em::read_map()
IMP::em::read_map()
IMP::multifit::create_hit_map()
IMP::multifit::grid2map()
IMP::multifit::remove_background()
IMP::restrainer::load_em_density_map()
IMP::em::FitRestraint
:
IMP::restrainer::SimpleEMFit::get_restraint()
IMP::em::FittingSolutions
:
IMP::cnmultifit::fit_cn_assembly()
IMP::cnmultifit::fit_cn_assembly()
IMP::cnmultifit::symmetry_local_fitting()
IMP::em::compute_fitting_scores()
IMP::em::compute_fitting_scores()
IMP::em::local_rigid_fitting()
IMP::em::local_rigid_fitting_around_point()
IMP::em::local_rigid_fitting_around_points()
IMP::em::local_rigid_fitting_grid_search()
IMP::multifit::convert_multifit_to_em_format()
IMP::multifit::fitting_clustering()
IMP::multifit::pca_based_rigid_fitting()
IMP::multifit::pca_based_rigid_fitting()
IMP::em::ImageHeader
:
IMP::em2d::Image::get_header()
IMP::em::KernelParameters
:
IMP::em::SampledDensityMap::get_kernel_params()
IMP::em::RadiusDependentKernelParameters
:
IMP::em::KernelParameters::get_params()
IMP::em::KernelParameters::set_params()
IMP::em::SampledDensityMap
:
IMP::em::FitRestraint::get_model_dens_map()
IMP::em::SampledDensityMap::particles2binarized_density()
IMP::em::SampledDensityMap::particles2density()
IMP::em::particles2binarized_density()
IMP::em::particles2density()
IMP::em::SurfaceShellDensityMap
:
IMP::em::SampledDensityMap::particles2surface()
IMP::em::particles2surface()
IMP::em::Voxel
:
IMP::em::Voxel::decorate_particle()
IMP::em::Voxel::setup_particle()
IMP::example::ExampleDecorator
:
IMP::example::ExampleDecorator::decorate_particle()
IMP::example::ExampleDecorator::setup_particle()
IMP::isd::MolecularDynamics
:
IMP::isd::HybridMonteCarlo::get_md()
IMP::isd::MolecularDynamicsMover::get_md()
IMP::isd::Nuisance
:
IMP::isd::Nuisance::decorate_particle()
IMP::isd::Nuisance::setup_particle()
IMP::isd::Scale
:
IMP::isd::Scale::decorate_particle()
IMP::isd::Scale::setup_particle()
IMP::isd::Switching
:
IMP::isd::Switching::decorate_particle()
IMP::isd::Switching::setup_particle()
IMP::kernel::ConfigurationSet
:
IMP::kernel::Sampler::create_sample()
IMP::kernel::Sampler::do_sample()
IMP::kernel::DerivativeAccumulator
:
IMP::kernel::ScoreAccumulator::get_derivative_accumulator()
IMP::kernel::Key
:
IMP::kernel::Key::operator+()
IMP::kernel::Key::operator++()
IMP::kernel::Key::operator–()
IMP::kernel::Key::add_alias()
IMP::misc::CustomXYZR::get_decorator_traits()
IMP::misc::CustomXYZR::get_default_decorator_traits()
IMP::kernel::Model
:
IMP::kernel::ConfigurationSet::get_model()
IMP::kernel::Decorator::get_model()
IMP::kernel::ModelObject::get_model()
IMP::kernel::Optimizer::get_model()
IMP::kernel::Sampler::get_model()
IMP::kernel::Optimizer
:
IMP::kernel::OptimizerState::get_optimizer()
IMP::kernel::OptimizerState
:
IMP::kernel::Optimizer::get_optimizer_state()
IMP::kernel::Particle
:
IMP::kernel::Decorator::get_particle()
IMP::kernel::Model::get_particle()
IMP::kernel::Refiner::get_refined()
IMP::kernel::SingletonContainer::get_particle()
IMP::kernel::Restraint
:
IMP::kernel::Restraint::create_current_decomposition()
IMP::kernel::Restraint::create_decomposition()
IMP::kernel::RestraintSet::get_restraint()
IMP::kernel::ScoreAccumulator
:
IMP::kernel::ScoringFunction::get_score_accumulator()
IMP::kernel::ScoringFunction::get_score_accumulator_if_below()
IMP::kernel::ScoringFunction::get_score_accumulator_if_good()
IMP::kernel::ScoreState
:
IMP::kernel::Model::get_score_state()
IMP::kernel::ScoringFunction
:
IMP::kernel::Model::create_model_scoring_function()
IMP::kernel::Optimizer::get_scoring_function()
IMP::kernel::Restraint::create_scoring_function()
IMP::kernel::Restraint::create_internal_scoring_function()
IMP::kernel::Sampler::get_scoring_function()
IMP::kernel::ScoringFunctionAdaptor::get()
IMP::kernel::ScoringFunctionAdaptor::get()
IMP::kernel::ScoringFunctionAdaptor::get()
IMP::kernel::ScoringFunctionAdaptor::get()
IMP::kernel::ScoringFunctionAdaptor::get()
IMP::misc::CustomXYZR
:
IMP::misc::CustomXYZR::decorate_particle()
IMP::misc::CustomXYZR::setup_particle()
IMP::misc::CustomXYZR::setup_particle()
IMP::misc::CustomXYZR::setup_particle()
IMP::multifit::AssemblyHeader
:
IMP::multifit::SettingsData::get_assembly_header()
IMP::multifit::ComponentHeader
:
IMP::multifit::SettingsData::get_component_header()
IMP::multifit::ProteinsAnchorsSamplingSpace
:
IMP::multifit::get_part_of_sampling_space()
IMP::multifit::read_protein_anchors_mapping()
IMP::multifit::SettingsData
:
IMP::multifit::get_partial_assembly_setting_data()
IMP::multifit::read_settings()
IMP::restrainer::SimpleConnectivity
:
IMP::restrainer::SimpleConnectivity::create_simple_connectivity_on_molecules()
IMP::restrainer::create_simple_connectivity_on_rigid_bodies()
IMP::restrainer::SimpleDiameter
:
IMP::restrainer::SimpleDiameter::create_simple_diameter()
IMP::restrainer::SimpleDistance
:
IMP::restrainer::SimpleDistance::create_simple_distance()
IMP::restrainer::SimpleEMFit
:
IMP::restrainer::SimpleEMFit::create_simple_em_fit()
IMP::restrainer::SimpleEMFit::create_simple_em_fit()
IMP::restrainer::SimpleExcludedVolume
:
IMP::restrainer::SimpleExcludedVolume::create_simple_excluded_volume_on_molecules()
IMP::restrainer::SimpleExcludedVolume::create_simple_excluded_volume_on_rigid_bodies()
IMP::rotamer::ResidueRotamer
:
IMP::rotamer::RotamerCalculator::get_rotamer()
IMP::saxs::DeltaDistributionFunction
:
IMP::saxs::DerivativeCalculator::precompute_derivative_helpers()
IMP::saxs::FormFactorTable
:
IMP::saxs::default_form_factor_table()
IMP::statistics::Histogram
:
IMP::cnmultifit::my_get_density_histogram()
IMP::multifit::get_density_histogram()
IMP::statistics::HistogramD
:
IMP::statistics::HistogramD::get_frequencies()
IMP::statistics::HistogramD::get_probability_distribution_function()
IMP::statistics::PartitionalClustering
:
IMP::statistics::RecursivePartitionalClusteringEmbedding::create_full_clustering()
IMP::statistics::RecursivePartitionalClusteringMetric::create_full_clustering()
IMP::statistics::create_centrality_clustering()
IMP::statistics::create_centrality_clustering()
IMP::statistics::create_connectivity_clustering()
IMP::statistics::create_diameter_clustering()
IMP::statistics::PartitionalClusteringWithCenter
:
IMP::statistics::create_bin_based_clustering()
IMP::statistics::create_connectivity_clustering()
IMP::statistics::create_lloyds_kmeans()