Member IMP::algebra::Ellipsoid3D::get_center () const: As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_reference_frame()
Member IMP::algebra::Ellipsoid3D::get_radius (unsigned int i) const: As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_radii()
Member IMP::algebra::Ellipsoid3D::get_rotation () const: As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_reference_frame()
Member IMP::algebra::Ellipsoid3D::get_transformation () const: As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_reference_frame()
Member IMP::atom::Chain::get_id_char () const: As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the string version.
Member IMP::atom::get_chain_id_char (Hierarchy h): As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the string version.
Member IMP::atom::get_rmsd (const core::XYZs &s0, const core::XYZs &s1, const IMP::algebra::Transformation3D &tr_for_second): As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP::algebra::get_rmsd_transforming_first() or IMP::algebra::get_rmsd()
Member IMP::atom::get_rmsd (const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const algebra::Transformation3D &tr_for_second=algebra::get_identity_transformation_3d()): As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_rmsd_transforming_first()
Member IMP::atom::get_rmsd (const Selection &s0, const Selection &s1, const algebra::Transformation3D &tr_for_second): As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_rmsd_transforming_first()
Member IMP::atom::get_rmsd (const algebra::Vector3Ds &s0, const algebra::Vector3Ds &s1, const algebra::Transformation3D &tr_for_second): As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP::algebra::get_rmsd_transforming_first() or IMP::algebra::get_rmsd()
Member IMP::atom::Selection::set_chain (char c): As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Pass a string
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 one 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 one instead.
Member IMP::core::MonteCarlo::get_number_of_forward_steps () const: As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_number_of_accepted_steps() instead
Member IMP::core::PairConstraint::PairConstraint (PairModifier *before, PairDerivativeModifier *after, const kernel::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 kernel::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::RigidBody::get_members () const: As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_rigid_members() instead.
Member IMP::core::SingletonConstraint::SingletonConstraint (SingletonModifier *before, SingletonDerivativeModifier *after, kernel::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::TripletConstraint::TripletConstraint (TripletModifier *before, TripletDerivativeModifier *after, const kernel::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.
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.
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_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 () 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_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_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_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::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 kernel::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 kernel::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 kernel::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 kernel::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_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 kernel::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 kernel::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 kernel::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 kernel::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::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 (kernel::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 (kernel::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 kernel::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 (kernel::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_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 kernel::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 kernel::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 kernel::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 kernel::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::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::rmf::load_frame (RMF::FileConstHandle file, unsigned int frame): As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Pass the frame as an RMF::FrameID.
Member IMP::rmf::save_frame (RMF::FileHandle file, unsigned int, std::string name=""): As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. You cannot specify the frame. Drop it.