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IMP Reference Guide
develop.d97d4ead1f,2024/11/22
The Integrative Modeling Platform
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This is the complete list of members for IMP::bff::AV, including all inherited members.
| add_member(ParticleIndexAdaptor p) | IMP::core::RigidBody | |
| add_non_rigid_member(ParticleIndexAdaptor p) | IMP::core::RigidBody | |
| add_to_derivative(int i, Float v, DerivativeAccumulator &d) | IMP::core::XYZ | |
| add_to_derivatives(const algebra::Vector3D &local_derivative, const algebra::Vector3D &local_location, DerivativeAccumulator &da) | IMP::core::RigidBody | |
| add_to_derivatives(const algebra::Vector3D &local_derivative, const algebra::Vector3D &global_derivative, const algebra::Vector3D &local_location, const algebra::Rotation3D &rot_local_to_global, DerivativeAccumulator &da) | IMP::core::RigidBody | |
| IMP::core::XYZ::add_to_derivatives(const algebra::Vector3D &v, DerivativeAccumulator &d) | IMP::core::XYZ | |
| add_to_rotational_derivatives(const algebra::Vector4D &other_qderiv, const algebra::Rotation3D &rot_other_to_local, const algebra::Rotation3D &rot_local_to_global, DerivativeAccumulator &da) | IMP::core::RigidBody | |
| add_to_rotational_derivatives(const algebra::Vector4D &qderiv, DerivativeAccumulator &da) | IMP::core::RigidBody | |
| add_to_torque(const algebra::Vector3D &torque_local, DerivativeAccumulator &da) | IMP::core::RigidBody | |
| AV() (defined in IMP::bff::AV) | IMP::bff::AV | |
| AV(::IMP::Model *m,::IMP::ParticleIndex id) (defined in IMP::bff::AV) | IMP::bff::AV | |
| AV(const IMP::ParticleAdaptor &d) (defined in IMP::bff::AV) | IMP::bff::AV | explicit |
| create_path_map_header() | IMP::bff::AV | |
| Decorator(Model *m, ParticleIndex pi) (defined in IMP::Decorator) | IMP::Decorator | protected |
| Decorator() (defined in IMP::Decorator) | IMP::Decorator | protected |
| Decorator(ParticleAdaptor p) (defined in IMP::Decorator) | IMP::Decorator | explicitprotected |
| do_setup_particle(Model *m, ParticleIndex pi, ParticleIndex pi_source, double linker_length=20.0, const algebra::Vector3D radii=algebra::Vector3D(3.5, 0, 0), double linker_width=0.5, double allowed_sphere_radius=1.5, double contact_volume_thickness=0.0, double contact_volume_trapped_fraction=-1, double simulation_grid_resolution=1.5) | IMP::bff::AV | static |
| Gaussian() (defined in IMP::core::Gaussian) | IMP::core::Gaussian | |
| Gaussian(::IMP::Model *m,::IMP::ParticleIndex id) (defined in IMP::core::Gaussian) | IMP::core::Gaussian | |
| Gaussian(const IMP::ParticleAdaptor &d) (defined in IMP::core::Gaussian) | IMP::core::Gaussian | explicit |
| get_allowed_sphere_radius() const | IMP::bff::AV | |
| get_av_key(unsigned int i) | IMP::bff::AV | static |
| get_body_member_particle_indexes() const | IMP::core::RigidBody | |
| get_contact_volume_thickness() const | IMP::bff::AV | |
| get_contact_volume_trapped_fraction() const | IMP::bff::AV | |
| get_coordinate(int i) const | IMP::core::XYZ | |
| get_coordinate_key(unsigned int i) (defined in IMP::core::XYZ) | IMP::core::XYZ | static |
| get_coordinates() const | IMP::core::RigidBody | |
| get_coordinates_are_optimized() const | IMP::core::RigidBody | |
| get_derivative(int i) const | IMP::core::XYZ | |
| get_derivatives() const | IMP::bff::AV | |
| get_gaussian() const | IMP::core::Gaussian | |
| get_global_covariance() | IMP::core::Gaussian | |
| get_global_covariance_key() (defined in IMP::core::Gaussian) | IMP::core::Gaussian | static |
| get_is_setup(const IMP::ParticleAdaptor &p) (defined in IMP::bff::AV) | IMP::bff::AV | static |
| get_is_setup(Model *m, ParticleIndex pi) (defined in IMP::bff::AV) | IMP::bff::AV | static |
| get_is_valid() const | IMP::Decorator | |
| get_linker_length() const | IMP::bff::AV | |
| get_linker_width() const | IMP::bff::AV | |
| get_local_covariance() const | IMP::core::Gaussian | |
| get_local_covariance_key() (defined in IMP::core::Gaussian) | IMP::core::Gaussian | static |
| get_map() const | IMP::bff::AV | |
| get_mean_position(bool include_source=true) const | IMP::bff::AV | |
| get_member_indexes() const | IMP::core::RigidBody | |
| get_member_particle_indexes() const | IMP::core::RigidBody | |
| get_model() const | IMP::Decorator | |
| get_parameter() const (defined in IMP::bff::AV) | IMP::bff::AV | protected |
| get_parameters_are_optimized() const | IMP::bff::AV | |
| get_particle() const | IMP::bff::AV | |
| get_particle(unsigned int i) const | IMP::bff::AV | |
| get_particle_index() const | IMP::bff::AV | |
| get_particle_index(unsigned int i) const | IMP::bff::AV | |
| get_particle_key(unsigned int i) | IMP::bff::AV | static |
| get_radii() | IMP::bff::AV | |
| get_radius1() const | IMP::bff::AV | |
| get_radius2() const | IMP::bff::AV | |
| get_radius3() const | IMP::bff::AV | |
| get_reference_frame() const | IMP::core::RigidBody | |
| get_rigid_members() const (defined in IMP::core::RigidBody) | IMP::core::RigidBody | |
| get_rotation() const | IMP::core::RigidBody | |
| get_rotation_keys() | IMP::core::RigidBody | static |
| get_rotational_derivatives() const | IMP::core::RigidBody | |
| get_simulation_grid_resolution() const | IMP::bff::AV | |
| get_source() const | IMP::bff::AV | |
| get_source_coordinates() const | IMP::bff::AV | |
| get_torque() const | IMP::core::RigidBody | |
| get_variances() const | IMP::core::Gaussian | |
| get_vector_to(const XYZ &b) const | IMP::core::XYZ | |
| get_x() const | IMP::core::XYZ | |
| get_xyz_keys() | IMP::core::XYZ | static |
| get_y() const | IMP::core::XYZ | |
| get_z() const | IMP::core::XYZ | |
| init_path_map() | IMP::bff::AV | |
| normalize_rotation() | IMP::core::RigidBody | |
| operator Particle *() const (defined in IMP::Decorator) | IMP::Decorator | |
| operator ParticleIndex() const (defined in IMP::Decorator) | IMP::Decorator | |
| operator->() const (defined in IMP::Decorator) | IMP::Decorator | |
| operator=(const RigidBody &)=default (defined in IMP::core::RigidBody) | IMP::core::RigidBody | |
| pull_back_body_member_adjoints(ParticleIndex pi, DerivativeAccumulator &da) | IMP::core::RigidBody | |
| pull_back_body_member_adjoints(ParticleIndex pi, const algebra::Transformation3D &TA, algebra::Transformation3D &TB, algebra::Transformation3DAdjoint &DTC, algebra::Transformation3DAdjoint &DTA, algebra::Transformation3DAdjoint &DTB, algebra::Vector3D &betatorque, DerivativeAccumulator &da) | IMP::core::RigidBody | |
| pull_back_member_adjoints(ParticleIndex pi, DerivativeAccumulator &da) | IMP::core::RigidBody | |
| pull_back_member_adjoints(ParticleIndex pi, const algebra::Transformation3D &T, algebra::Vector3D &x, algebra::Vector3D &Dy, algebra::Vector3D &Dx, algebra::Transformation3DAdjoint &DT, algebra::Vector3D &xtorque, DerivativeAccumulator &da) | IMP::core::RigidBody | |
| pull_back_members_adjoints(DerivativeAccumulator &da) | IMP::core::RigidBody | |
| remove_member(ParticleIndexAdaptor p) | IMP::core::RigidBody | |
| resample(bool shift_xyz=true) | IMP::bff::AV | |
| RigidBody() (defined in IMP::core::RigidBody) | IMP::core::RigidBody | |
| RigidBody(::IMP::Model *m,::IMP::ParticleIndex id) (defined in IMP::core::RigidBody) | IMP::core::RigidBody | |
| RigidBody(const IMP::ParticleAdaptor &d) (defined in IMP::core::RigidBody) | IMP::core::RigidBody | explicit |
| RigidBody(const RigidBody &)=default (defined in IMP::core::RigidBody) | IMP::core::RigidBody | |
| set_allowed_sphere_radius(Float t) | IMP::bff::AV | |
| set_av_parameter(const nlohmann::json &j) | IMP::bff::AV | |
| set_av_parameters_are_optimized(bool tf) const | IMP::bff::AV | |
| set_contact_volume_thickness(Float t) | IMP::bff::AV | |
| set_contact_volume_trapped_fraction(Float t) | IMP::bff::AV | |
| set_coordinate(unsigned int i, Float v) | IMP::core::XYZ | |
| set_coordinates(const algebra::Vector3D &v) | IMP::core::XYZ | |
| set_coordinates_are_optimized(bool tf) | IMP::core::RigidBody | |
| IMP::core::XYZ::set_coordinates_are_optimized(bool tf) const | IMP::core::XYZ | |
| set_gaussian(const algebra::Gaussian3D &g) | IMP::core::Gaussian | |
| set_global_covariance(Eigen::Matrix3d covar) | IMP::core::Gaussian | |
| set_is_rigid_member(ParticleIndex pi, bool tf) | IMP::core::RigidBody | |
| set_linker_length(Float t) | IMP::bff::AV | |
| set_linker_width(Float t) | IMP::bff::AV | |
| set_local_covariance(const Eigen::Vector3d covar) | IMP::core::Gaussian | |
| set_radius1(Float t) | IMP::bff::AV | |
| set_radius2(Float t) | IMP::bff::AV | |
| set_radius3(Float t) | IMP::bff::AV | |
| set_reference_frame(const IMP::algebra::ReferenceFrame3D &tr) | IMP::core::RigidBody | |
| set_reference_frame_from_members(const ParticleIndexes &members) | IMP::core::RigidBody | |
| set_reference_frame_lazy(const IMP::algebra::ReferenceFrame3D &tr) | IMP::core::RigidBody | |
| set_simulation_grid_resolution(Float t) | IMP::bff::AV | |
| set_variances(const algebra::Vector3D v) | IMP::core::Gaussian | |
| set_x(Float t) | IMP::core::XYZ | |
| set_y(Float t) | IMP::core::XYZ | |
| set_z(Float t) | IMP::core::XYZ | |
| setup_particle(Model *m, ParticleIndex pi, IMP::ParticleIndex pi_source) | IMP::bff::AV | static |
| setup_particle(IMP::ParticleAdaptor pa, IMP::ParticleIndex pi_source) | IMP::bff::AV | static |
| IMP::core::Gaussian::setup_particle(Model *m, ParticleIndex pi) | IMP::core::Gaussian | static |
| IMP::core::Gaussian::setup_particle(IMP::ParticleAdaptor pa) | IMP::core::Gaussian | static |
| IMP::core::Gaussian::setup_particle(Model *m, ParticleIndex pi, algebra::Gaussian3D g) | IMP::core::Gaussian | static |
| IMP::core::Gaussian::setup_particle(IMP::ParticleAdaptor pa, algebra::Gaussian3D g) | IMP::core::Gaussian | static |
| IMP::core::RigidBody::setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps) | IMP::core::RigidBody | static |
| IMP::core::RigidBody::setup_particle(IMP::ParticleAdaptor pa, ParticleIndexesAdaptor ps) | IMP::core::RigidBody | static |
| IMP::core::RigidBody::setup_particle(Model *m, ParticleIndex pi, algebra::ReferenceFrame3D rf) | IMP::core::RigidBody | static |
| IMP::core::RigidBody::setup_particle(IMP::ParticleAdaptor pa, algebra::ReferenceFrame3D rf) | IMP::core::RigidBody | static |
| IMP::core::XYZ::setup_particle(Model *m, ParticleIndex pi, algebra::Vector3D v) | IMP::core::XYZ | static |
| IMP::core::XYZ::setup_particle(IMP::ParticleAdaptor pa, algebra::Vector3D v) | IMP::core::XYZ | static |
| show(std::ostream &out=std::cout) const (defined in IMP::bff::AV) | IMP::bff::AV | |
| teardown_particle(RigidBody rb) | IMP::core::RigidBody | static |
| update_global_covariance() | IMP::core::Gaussian | |
| update_members() | IMP::core::RigidBody | |
| Value() (defined in IMP::Value) | IMP::Value | protected |
| XYZ() (defined in IMP::core::XYZ) | IMP::core::XYZ | |
| XYZ(::IMP::Model *m,::IMP::ParticleIndex id) (defined in IMP::core::XYZ) | IMP::core::XYZ | |
| XYZ(const IMP::ParticleAdaptor &d) (defined in IMP::core::XYZ) | IMP::core::XYZ | explicit |
| ~RigidBody() (defined in IMP::core::RigidBody) | IMP::core::RigidBody |