Member IMP::atom::Angle::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Angle::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Angle::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Atom::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Atom::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Atom::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Bond::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Bond::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Bond::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Bonded::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Bonded::get_bonds () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_bond_indexes() instead.
Member IMP::atom::Bonded::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Bonded::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Chain::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Chain::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Chain::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Charged::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Charged::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Charged::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::CHARMMAtom::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::CHARMMAtom::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::CHARMMAtom::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Copy::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Copy::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Copy::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Diffusion::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Diffusion::get_d () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_diffusion_coefficient().
Member IMP::atom::Diffusion::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Diffusion::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Diffusion::set_d (double d): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set_diffusion_coefficient().
Member IMP::atom::Dihedral::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Dihedral::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Dihedral::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Domain::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Domain::get_begin_index () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_index_range() instead.
Member IMP::atom::Domain::get_end_index () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_index_range() instead.
Member IMP::atom::Domain::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Domain::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Domain::setup_particle (kernel::Model *m, kernel::ParticleIndex pi, Int residues_begin, Int residues_end): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the IntRange setup_particle.
Member IMP::atom::Domain::setup_particle (IMP::kernel::ParticleAdaptor decorator, Int residues_begin, Int residues_end): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the IntRange setup_particle.
Member IMP::atom::Fragment::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Fragment::get_residue_index_ranges () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the get_residue_indexes() method instead.
Member IMP::atom::Fragment::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Fragment::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::LangevinThermostatOptimizerState::LangevinThermostatOptimizerState (const kernel::ParticlesTemp &pis, double temperature, double gamma): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use constructor that takes indexes.
Member IMP::atom::LennardJones::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::LennardJones::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::LennardJones::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Mass::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Mass::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Mass::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Molecule::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Molecule::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Molecule::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::RemoveRigidMotionOptimizerState::RemoveRigidMotionOptimizerState (const kernel::ParticlesTemp &pis, unsigned skip_steps): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set_period() instead.
Member IMP::atom::RemoveTranslationOptimizerState::RemoveTranslationOptimizerState (const kernel::Particles &pis, unsigned skip_steps): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set_period() instead.
Member IMP::atom::Residue::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::Residue::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::Residue::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::RigidBodyDiffusion::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::RigidBodyDiffusion::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::RigidBodyDiffusion::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::SecondaryStructureResidue::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::atom::SecondaryStructureResidue::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::SecondaryStructureResidue::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::atom::VelocityScalingOptimizerState::VelocityScalingOptimizerState (const kernel::Particles &pis, Float temperature, unsigned skip_steps): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set_period() instead.
Member IMP::base::Object::Object (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Provide a name.
Class IMP::base::OwnerPointer< O >: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use ObjectMember instead
Member IMP::base::OwnerPointer< O >::OwnerPointer (const Any &o): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use ObjectMember instead
Member IMP::base::OwnerPointer< O >::OwnerPointer (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use ObjectMember instead
Member IMP::base::RefCounted: As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Just use Object.
Member IMP::core::Centroid::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::core::Centroid::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::Centroid::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::ClosePairsFinder::get_close_pairs (const kernel::ParticlesTemp &pc) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use the index-based on instead.
Member IMP::core::ClosePairsFinder::get_close_pairs (const kernel::ParticlesTemp &pca, const kernel::ParticlesTemp &pcb) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use the index-based on instead.
Member IMP::core::ConjugateGradients::ConjugateGradients (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the constructor that takes a kernel::Model.
Member IMP::core::ConnectivityRestraint::ConnectivityRestraint (PairScore *ps): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use constructor that takes a container instead.
Member IMP::core::Cover::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::core::Cover::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::Cover::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::Hierarchy::decorate_particle (IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits()): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::core::Hierarchy::particle_is_instance (IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits()): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::Hierarchy::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi, const HierarchyTraits &tr=get_default_traits()): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::IncrementalScoringFunction::get_movable_particles () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_movable_indexes() instead.
Member IMP::core::MonteCarlo::MonteCarlo (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the one that takes a model.
Class IMP::core::Mover: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use MonteCarloMover instead
Class IMP::core::MoverBase: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP::core::MonteCarloMover instead
Member IMP::core::NonRigidMember::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::core::NonRigidMember::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::NonRigidMember::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::PairConstraint::PairConstraint (PairModifier *before, PairDerivativeModifier *after, const ParticlePair &vt, std::string name="PairConstraint %1%"): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the model/index constructor.
Member IMP::core::QuadConstraint::QuadConstraint (QuadModifier *before, QuadDerivativeModifier *after, const ParticleQuad &vt, std::string name="QuadConstraint %1%"): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the model/index constructor.
Member IMP::core::Reference::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::core::Reference::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::Reference::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::RigidBody::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::core::RigidBody::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::RigidBody::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::RigidBodyMember::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::core::RigidBodyMember::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::RigidBodyMember::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::RigidMember::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::core::RigidMember::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::RigidMember::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::SerialMover::get_acceptance_probability (int i) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the functions on the individual movers.
Member IMP::core::SerialMover::get_number_of_movers () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the functions on the individual movers.
Member IMP::core::SerialMover::reset_acceptance_probabilities (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the functions on the individual movers.
Member IMP::core::SingletonConstraint::SingletonConstraint (SingletonModifier *before, SingletonDerivativeModifier *after, Particle *vt, std::string name="SingletonConstraint %1%"): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the model/index constructor.
Member IMP::core::SteepestDescent::SteepestDescent (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the constructor that takes a kernel::Model.
Member IMP::core::TripletConstraint::TripletConstraint (TripletModifier *before, TripletDerivativeModifier *after, const ParticleTriplet &vt, std::string name="TripletConstraint %1%"): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the model/index constructor.
Member IMP::core::Typed::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::core::Typed::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::Typed::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::XYZ::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::core::XYZ::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::XYZ::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::XYZR::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::core::XYZR::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::core::XYZR::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Class IMP::display::BildWriter: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP::rmf when interfacing with Chimera.
Class IMP::display::ChimeraWriter: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP::rmf instead when interfacing with Chimera.
Class IMP::display::CMMWriter: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP::rmf for interfacing with Chimera.
Member IMP::display::Colored::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::display::Colored::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::display::Colored::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::display::WriteOptimizerState::WriteOptimizerState (WriterAdaptor w): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the method that takes a kernel::Model.
Member IMP::em2d::ProjectionParameters::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::em2d::ProjectionParameters::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::em2d::ProjectionParameters::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::em::Voxel::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::em::Voxel::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::em::Voxel::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::example::ExampleDecorator::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::example::ExampleDecorator::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::example::ExampleDecorator::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::gsl::ConjugateGradients::ConjugateGradients (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Pass a model to the constructor.
Member IMP::gsl::QuasiNewton::QuasiNewton (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Pass a model to the constructor.
Member IMP::gsl::Simplex::Simplex (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Pass a model to the constructor.
Member IMP::isd::Nuisance::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::isd::Nuisance::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::isd::Nuisance::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::isd::Scale::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::isd::Scale::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::isd::Scale::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::isd::Switching::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::isd::Switching::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::isd::Switching::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::isd::Weight::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::isd::Weight::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::isd::Weight::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::kernel::AttributeOptimizer::AttributeOptimizer (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the constructor with a Model and a name.
Member IMP::kernel::Container::get_all_possible_particles () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use get_all_possible_indexes() instead
Member IMP::kernel::Container::get_is_changed () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_contents_version() instead as that is safer.
Class IMP::kernel::GenericScopedRemoveRestraint< SS >: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. With the advent of the ScoringFunction, this should not be needed.
Class IMP::kernel::GenericScopedRemoveScoreState< SS >: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. This doesn't actually do anything any more.
Class IMP::kernel::GenericScopedRestraint< SS >: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. With the advent of the ScoringFunction, this should not be needed.
Class IMP::kernel::GenericScopedScoreState< SS >: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. No longer needed, just destroy the ScoreState itself.
Member IMP::kernel::get_dependent_particles (ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should act directly on the ModelObjects instead.
Member IMP::kernel::get_dependent_restraints (ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should act directly on the ModelObjects instead.
Member IMP::kernel::get_dependent_score_states (ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should act directly on the ModelObjects instead.
Member IMP::kernel::get_required_particles (ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should act directly on the ModelObjects instead.
Member IMP::kernel::get_required_score_states (ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should act directly on the ModelObjects instead.
Member IMP::kernel::Model::evaluate (bool tf, bool warn=true): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use a ScoringFunction instead.
Member IMP::kernel::Model::get_maximum_score (Restraint *r) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Get the maximum directly from the restraint.
Member IMP::kernel::Model::get_maximum_score () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should use a ScoringFunction or a RestraintSet.
Member IMP::kernel::Model::get_number_of_particles () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_particle_indexes().
Member IMP::kernel::Model::get_number_of_restraints () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use a RestraintSet instead.
Member IMP::kernel::Model::get_optimized_particles () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Do not use.
Member IMP::kernel::Model::get_particles () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_particle_indexes().
Member IMP::kernel::Model::get_restraint (unsigned int i) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use a RestraintSet instead.
Member IMP::kernel::Model::get_root_restraint_set (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Using a ScoringFunction instead.
Member IMP::kernel::Model::operator Restraint * () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use a ScoringFunction instead.
Member IMP::kernel::Model::particles_begin () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_particle_indexes().
Member IMP::kernel::Model::particles_end () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_particle_indexes().
Member IMP::kernel::Model::remove_particle (Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the ParticleIndex version.
Member IMP::kernel::Model::set_maximum_score (Restraint *r, double s): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Set get the maximum directly on the restraint.
Member IMP::kernel::Model::set_maximum_score (double s): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should use a ScoringFunction or a RestraintSet.
Member IMP::kernel::ModelObject::do_set_model (kernel::Model *): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. As it should always be part of a model.
Member IMP::kernel::ModelObject::get_is_part_of_model () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Should always be true.
Member IMP::kernel::ModelObject::ModelObject (std::string name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the constructor that takes a Model.
Member IMP::kernel::ModelObject::set_model (kernel::Model *m): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the constructor that takes a Model.
Member IMP::kernel::Optimizer::clear_range_cache (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.
Member IMP::kernel::Optimizer::get_derivative (FloatIndex fi) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.
Member IMP::kernel::Optimizer::get_optimized_attributes () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.
Member IMP::kernel::Optimizer::get_restraints () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use Optimizer::get_scoring_function() instead.
Member IMP::kernel::Optimizer::get_scaled_derivative (FloatIndex fi) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.
Member IMP::kernel::Optimizer::get_scaled_value (FloatIndex fi) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.
Member IMP::kernel::Optimizer::get_score_threshold () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Do not use as it is not reliably supported.
Member IMP::kernel::Optimizer::get_value (FloatIndex fi) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.
Member IMP::kernel::Optimizer::get_width (FloatKey k) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.
Member IMP::kernel::Optimizer::Optimizer (): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the constructor with a Model and a name.
Member IMP::kernel::Optimizer::set_restraints (const RestraintsTemp &rs): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set_scoring_function() instead.
Member IMP::kernel::Optimizer::set_scaled_value (FloatIndex fi, Float v) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.
Member IMP::kernel::Optimizer::set_score_threshold (double s): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Do not use as it is not reliably supported.
Member IMP::kernel::Optimizer::set_value (FloatIndex fi, double v) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.
Member IMP::kernel::Optimizer::width (FloatKey k) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.
Member IMP::kernel::OptimizerState::OptimizerState (std::string name="OptimizerState %1%"): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the constructor that takes a Model.
Member IMP::kernel::PairContainer::get_contains_particle_pair (ParticlePair v) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. This is slow and dependent on the order of elements in the tuple.
Member IMP::kernel::PairContainer::get_number_of_particle_pairs () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. This can be very slow and is probably not useful
Member IMP::kernel::PairContainer::get_particle_pair (unsigned int i) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP.Use get_indexes() instead and thing about using the IMP_CONTAINER_FOREACH() macro.
Member IMP::kernel::PairContainer::get_particle_pairs () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_indexes() instead.
Member IMP::kernel::PairModifier::apply (const ParticlePair &vt) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use the index version instead
Member IMP::kernel::PairPredicate::get_value (const ParticlePair &vt) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index based version.
Member IMP::kernel::PairPredicate::get_value (const ParticlePairsTemp &o) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index based version.
Member IMP::kernel::PairScore::evaluate (const ParticlePair &vt, DerivativeAccumulator *da) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index-based evaluate instead.
Member IMP::kernel::ParticleInputs::get_input_containers (Particle *p) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_inputs instead.
Member IMP::kernel::ParticleInputs::get_input_particles (Particle *p) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_inputs instead.
Member IMP::kernel::ParticleOutputs::get_output_containers (Particle *p) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_inputs instead.
Member IMP::kernel::ParticleOutputs::get_output_particles (Particle *p) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_inputs instead.
Member IMP::kernel::QuadContainer::get_contains_particle_quad (ParticleQuad v) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. This is slow and dependent on the order of elements in the tuple.
Member IMP::kernel::QuadContainer::get_number_of_particle_quads () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. This can be very slow and is probably not useful
Member IMP::kernel::QuadContainer::get_particle_quad (unsigned int i) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP.Use get_indexes() instead and thing about using the IMP_CONTAINER_FOREACH() macro.
Member IMP::kernel::QuadContainer::get_particle_quads () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_indexes() instead.
Member IMP::kernel::QuadModifier::apply (const ParticleQuad &vt) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use the index version instead
Member IMP::kernel::QuadPredicate::get_value (const ParticleQuad &vt) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index based version.
Member IMP::kernel::QuadPredicate::get_value (const ParticleQuadsTemp &o) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index based version.
Member IMP::kernel::QuadScore::evaluate (const ParticleQuad &vt, DerivativeAccumulator *da) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index-based evaluate instead.
Member IMP::kernel::Restraint::get_input_containers () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use get_inputs() instead.
Member IMP::kernel::Restraint::get_input_particles () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use get_inputs() instead.
Member IMP::kernel::Restraint::Restraint (std::string name="Restraint %1%"): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the constructor that takes a model instead.
Member IMP::kernel::RestraintSet::RestraintSet (double weight, const std::string &name="RestraintSet %1%"): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the constructor that takes a Model.
Member IMP::kernel::RestraintSet::RestraintSet (const std::string &name="RestraintSet %1%"): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the constructor that takes a Model.
Member IMP::kernel::Sampler::get_sample () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use create_sample
Member IMP::kernel::ScoreState::get_input_containers () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use get_inputs() instead.
Member IMP::kernel::ScoreState::get_input_particles () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use get_inputs() instead.
Member IMP::kernel::ScoreState::get_output_containers () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use get_outputs() instead.
Member IMP::kernel::ScoreState::get_output_particles () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use get_outputs() instead.
Member IMP::kernel::ScoreState::ScoreState (kernel::Model *m): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use version that takes a name too.
Member IMP::kernel::ScoreState::ScoreState (std::string name="ScoreState %1%"): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use version that takes a Model instead.
Member IMP::kernel::SingletonContainer::get_contains_particle (Particle *v) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. This is slow and dependent on the order of elements in the tuple.
Member IMP::kernel::SingletonContainer::get_number_of_particles () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. This can be very slow and is probably not useful
Member IMP::kernel::SingletonContainer::get_particle (unsigned int i) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP.Use get_indexes() instead and thing about using the IMP_CONTAINER_FOREACH() macro.
Member IMP::kernel::SingletonContainer::get_particles () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_indexes() instead.
Member IMP::kernel::SingletonModifier::apply (Particle *vt) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use the index version instead
Member IMP::kernel::SingletonPredicate::get_value (Particle *vt) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index based version.
Member IMP::kernel::SingletonPredicate::get_value (const ParticlesTemp &o) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index based version.
Member IMP::kernel::SingletonScore::evaluate (Particle *vt, DerivativeAccumulator *da) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index-based evaluate instead.
Member IMP::kernel::TripletContainer::get_contains_particle_triplet (ParticleTriplet v) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. This is slow and dependent on the order of elements in the tuple.
Member IMP::kernel::TripletContainer::get_number_of_particle_triplets () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. This can be very slow and is probably not useful
Member IMP::kernel::TripletContainer::get_particle_triplet (unsigned int i) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP.Use get_indexes() instead and thing about using the IMP_CONTAINER_FOREACH() macro.
Member IMP::kernel::TripletContainer::get_particle_triplets () const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_indexes() instead.
Member IMP::kernel::TripletModifier::apply (const ParticleTriplet &vt) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use the index version instead
Member IMP::kernel::TripletPredicate::get_value (const ParticleTriplet &vt) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index based version.
Member IMP::kernel::TripletPredicate::get_value (const ParticleTripletsTemp &o) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index based version.
Member IMP::kernel::TripletScore::evaluate (const ParticleTriplet &vt, DerivativeAccumulator *da) const: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index-based evaluate instead.
Member IMP::kinematics::KinematicNode::decorate_particle (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::kinematics::KinematicNode::particle_is_instance (IMP::kernel::Particle *p): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::kinematics::KinematicNode::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::misc::CustomXYZR::decorate_particle (IMP::kernel::Particle *p, const FloatKey &tr=IMP::core::XYZR::get_radius_key()): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.
Member IMP::misc::CustomXYZR::particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi, const FloatKey &tr=IMP::core::XYZR::get_radius_key()): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::misc::CustomXYZR::particle_is_instance (IMP::kernel::Particle *p, const FloatKey &tr=IMP::core::XYZR::get_radius_key()): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.
Member IMP::modeller.load_restraints_file: Use ModelLoader instead.
Member IMP::modeller.read_pdb: Use IMP::atom::read_pdb() instead to read a PDB file, or ModelLoader to read a Modeller model.
Member IMP::restrainer::set_rigid_bodies (atom::Hierarchies const &mhs): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use atom::create_rigid_body() instead.
Member IMP::rmf::SaveOptimizerState::SaveOptimizerState (RMF::FileHandle fh): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use one that takes a model.
Class IMP::statistics::Histogram: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use HistogramD instead.
Member IMP_ACTIVE_PAIR_CONTAINER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly and use IMP_PAIR_CONTAINER_METHODS
Member IMP_ACTIVE_QUAD_CONTAINER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly and use IMP_QUAD_CONTAINER_METHODS
Member IMP_ACTIVE_SINGLETON_CONTAINER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly and use IMP_SINGLETON_CONTAINER_METHODS
Member IMP_ACTIVE_TRIPLET_CONTAINER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly and use IMP_TRIPLET_CONTAINER_METHODS
Member IMP_ASSIGNMENT_CONTAINER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP_ASSIGNMENT_CONTAINER_METHODS instead
Member IMP_ASSIGNMENT_CONTAINER_INLINE (Name, show, dest): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP_ASSIGNMENT_CONTAINER_METHODS instead
Member IMP_ASSIGNMENTS_TABLE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Expand the macro inline
Member IMP_CLOSE_PAIRS_FINDER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods yourself.
Member IMP_CLUSTERING (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Do not use any more
Member IMP_COMPOSITE_PAIR_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Do it yourself.
Member IMP_COMPOSITE_QUAD_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Do it yourself.
Member IMP_COMPOSITE_SINGLETON_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Do it yourself.
Member IMP_COMPOSITE_TRIPLET_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Do it yourself.
Member IMP_CONSTRAINT (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the needed functions directly
Member IMP_CONSTRAINT_2 (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the needed functions directly
Member IMP_DECLARE_CONTROLLED_KEY_TYPE (Name, Tag): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Just declare the typedef directly.
Member IMP_DECLARE_KEY_TYPE (Name, Tag): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Just declare the typedef directly.
Member IMP_DECORATOR (Name, Parent): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP_DECORATOR_METHODS() instead.
Member IMP_DECORATOR_WITH_TRAITS (Name, Parent, TraitsType, traits_name,default_traits): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP_DECORATOR_WITH_TRAITS_METHODS()
Member IMP_DEPRECATED_CLASS (classname, replacement_classname): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. As of IMP 2.1. Use IMPMODULE_DEPRECATED_CLASS_DEF() instead
Member IMP_DEPRECATED_FUNCTION (replacement): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. As of IMP 2.1. Use IMPMODULE_DEPRECATED_FUNCTION_DEF() instead
Member IMP_DEPRECATED_OBJECT (replacement_classname): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Deprecated as of IMP 2.1. Use IMPMODULE_DEPRECATED_CLASS_DEF().
Member IMP_DEPRECATED_WARN: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. As of IMP 2.1. Use IMPMODULE_DEPRECATED_FUNCTION_DEF() instead.
Member IMP_DISCRETE_SAMPLER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Expand the macro inline
Member IMP_INDEX_PAIR_MODIFIER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_PAIR_MODIFIER_METHODS to fill in the rest.
Member IMP_INDEX_PAIR_PREDICATE (Name, return_value, return_inputs): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_PAIR_PREDICATE_METHODS to fill in the rest.
Member IMP_INDEX_PAIR_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_PAIR_SCORE_METHODS() to fill in the rest.
Member IMP_INDEX_QUAD_MODIFIER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_QUAD_MODIFIER_METHODS to fill in the rest.
Member IMP_INDEX_QUAD_PREDICATE (Name, return_value, return_inputs): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_QUAD_PREDICATE_METHODS to fill in the rest.
Member IMP_INDEX_QUAD_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_QUAD_SCORE_METHODS() to fill in the rest.
Member IMP_INDEX_SINGLETON_MODIFIER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_SINGLETON_MODIFIER_METHODS to fill in the rest.
Member IMP_INDEX_SINGLETON_PREDICATE (Name, return_value, return_inputs): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_SINGLETON_PREDICATE_METHODS to fill in the rest.
Member IMP_INDEX_SINGLETON_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_SINGLETON_SCORE_METHODS() to fill in the rest.
Member IMP_INDEX_TRIPLET_MODIFIER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_TRIPLET_MODIFIER_METHODS to fill in the rest.
Member IMP_INDEX_TRIPLET_PREDICATE (Name, return_value, return_inputs): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_TRIPLET_PREDICATE_METHODS to fill in the rest.
Member IMP_INDEX_TRIPLET_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_TRIPLET_SCORE_METHODS() to fill in the rest.
Member IMP_INPUTS_DECL (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Just declare the methods yourself.
Member IMP_INTERNAL_METHOD (return_value, name, arguments, const_or_not, body): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Don't use this
Member IMP_MOVER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP::core::MonteCarloMover
Member IMP_OBJECT (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP_OBJECT_METHODS()
Member IMP_OBJECT_2 (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP_OBJECT_METHODS()
Member IMP_OBJECT_INLINE (Name, show, destructor): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP_OBJECT_METHODS()
Member IMP_OPTIMIZER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly.
Member IMP_OPTIMIZER_STATE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly.
Member IMP_OUTPUTS_DECL (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods yourself.
Member IMP_OUTPUTS_DEF (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods yourself
Member IMP_PAIR_CONTAINER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly and use IMP_PAIR_CONTAINER_METHODS
Member IMP_PAIR_MODIFIER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_PAIR_MODIFIER_METHODS to fill in the rest.
Member IMP_PAIR_PREDICATE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP_PAIR_PREDICATE_METHODS instead and declare the methods you implement.
Member IMP_PAIR_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_PAIR_SCORE_METHODS() to fill in the rest.
Member IMP_PARTICLE_STATES (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Expand the macro inline
Member IMP_PERIODIC_OPTIMIZER_STATE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Functionality is built into OptimizerState.
Member IMP_PROTECTED_CONSTRUCTOR (Name, arguments, body): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Don't use this
Member IMP_PROTECTED_CONSTRUCTOR_DECL (protection, Name, arguments, body): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Don't use this
Member IMP_PROTECTED_DESTRUCTOR (Name, arguments, body): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Don't use this
Member IMP_PROTECTED_DESTRUCTOR_DECL (protection, Name, arguments, body): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Don't use this
Member IMP_PROTECTED_METHOD (return_value, name, arguments, const_or_not, body): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Don't use this
Member IMP_PROTECTED_METHOD_DECL (protection, return_value, name, arguments, const_or_not, body): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Don't use this
Member IMP_QUAD_CONTAINER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly and use IMP_QUAD_CONTAINER_METHODS
Member IMP_QUAD_MODIFIER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_QUAD_MODIFIER_METHODS to fill in the rest.
Member IMP_QUAD_PREDICATE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP_QUAD_PREDICATE_METHODS instead and declare the methods you implement.
Member IMP_QUAD_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_QUAD_SCORE_METHODS() to fill in the rest.
Member IMP_REFINER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself.
Member IMP_RESTRAINT (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods yourself instead.
Member IMP_RESTRAINT_2 (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods yourself instead.
Member IMP_RESTRAINT_ACCUMULATOR (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods yourself instead.
Member IMP_SAMPLER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the needed methods directly.
Member IMP_SCORE_STATE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the needed functions directly
Member IMP_SCORE_STATE_2 (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the needed functions directly
Member IMP_SCORING_FUNCTION (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the needed methods yourself.
Member IMP_SIMPLE_PAIR_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_PAIR_SCORE_METHODS() to fill in the rest.
Member IMP_SIMPLE_QUAD_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_QUAD_SCORE_METHODS() to fill in the rest.
Member IMP_SIMPLE_REFINER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself.
Member IMP_SIMPLE_SINGLETON_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_SINGLETON_SCORE_METHODS() to fill in the rest.
Member IMP_SIMPLE_TRIPLET_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_TRIPLET_SCORE_METHODS() to fill in the rest.
Member IMP_SINGLETON_CONTAINER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly and use IMP_SINGLETON_CONTAINER_METHODS
Member IMP_SINGLETON_MODIFIER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_SINGLETON_MODIFIER_METHODS to fill in the rest.
Member IMP_SINGLETON_MODIFIER_FROM_REFINED (Name, refiner): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Just define the methods yourself.
Member IMP_SINGLETON_MODIFIER_TO_REFINED (Name, refiner): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Just define the methods yourself.
Member IMP_SINGLETON_PREDICATE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP_SINGLETON_PREDICATE_METHODS instead and declare the methods you implement.
Member IMP_SINGLETON_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_SINGLETON_SCORE_METHODS() to fill in the rest.
Member IMP_SUBSET_FILTER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Expand the macro inline
Member IMP_SUBSET_FILTER_TABLE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Expand the macro inline
Member IMP_SUBSET_GRAPH_TABLE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Expand the macro inline
Member IMP_TRIPLET_CONTAINER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly and use IMP_TRIPLET_CONTAINER_METHODS
Member IMP_TRIPLET_MODIFIER (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods yourself and use IMP_TRIPLET_MODIFIER_METHODS to fill in the rest.
Member IMP_TRIPLET_PREDICATE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP_TRIPLET_PREDICATE_METHODS instead and declare the methods you implement.
Member IMP_TRIPLET_SCORE (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare methods youself and use IMP_TRIPLET_SCORE_METHODS() to fill in the rest.
Member IMP_UNARY_FUNCTION (Name): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly.
Member IMP_UNARY_FUNCTION_INLINE (Name, value_expression,derivative_expression, show_expression): As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Declare the methods directly.