IMP  2.4.0
The Integrative Modeling Platform
Deprecated List
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.