IMP  2.1.1
The Integrative Modeling Platform
Deprecated List
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.