Deprecated List

Class IMP.pmi.macros.BuildModel1

As of IMP release 2.5.

Member IMP::container::DynamicListPairContainer::add_particle_pair (const ParticlePair &vt)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use add() with indexes instead

Member IMP::container::DynamicListPairContainer::add_particle_pairs (const ParticlePairsTemp &c)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use add() with indexes instead

Member IMP::container::DynamicListPairContainer::clear_particle_pairs ()

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use clear() instead

Member IMP::container::DynamicListPairContainer::set_particle_pairs (ParticlePairsTemp c)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() instead

Member IMP::container::DynamicListQuadContainer::add_particle_quad (const ParticleQuad &vt)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use add() with indexes instead

Member IMP::container::DynamicListQuadContainer::add_particle_quads (const ParticleQuadsTemp &c)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use add() with indexes instead

Member IMP::container::DynamicListQuadContainer::clear_particle_quads ()

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use clear() instead

Member IMP::container::DynamicListQuadContainer::set_particle_quads (ParticleQuadsTemp c)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() instead

Member IMP::container::DynamicListSingletonContainer::add_particle (Particle *vt)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use add() with indexes instead

Member IMP::container::DynamicListSingletonContainer::add_particles (const ParticlesTemp &c)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use add() with indexes instead

Member IMP::container::DynamicListSingletonContainer::clear_particles ()

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use clear() instead

Member IMP::container::DynamicListSingletonContainer::set_particles (ParticlesTemp c)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() instead

Member IMP::container::DynamicListTripletContainer::add_particle_triplet (const ParticleTriplet &vt)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use add() with indexes instead

Member IMP::container::DynamicListTripletContainer::add_particle_triplets (const ParticleTripletsTemp &c)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use add() with indexes instead

Member IMP::container::DynamicListTripletContainer::clear_particle_triplets ()

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use clear() instead

Member IMP::container::DynamicListTripletContainer::set_particle_triplets (ParticleTripletsTemp c)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() instead

Member IMP::container::ListPairContainer::set_particle_pairs (const ParticlePairsTemp &ps)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() with indexes instead

Member IMP::container::ListPairContainer::set_particle_pairs (const ParticleIndexPairs &contents)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() instead

Member IMP::container::ListQuadContainer::set_particle_quads (const ParticleQuadsTemp &ps)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() with indexes instead

Member IMP::container::ListQuadContainer::set_particle_quads (const ParticleIndexQuads &contents)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() instead

Member IMP::container::ListSingletonContainer::set_particles (const ParticlesTemp &ps)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() with indexes instead

Member IMP::container::ListSingletonContainer::set_particles (const ParticleIndexes &contents)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() instead

Member IMP::container::ListTripletContainer::set_particle_triplets (const ParticleTripletsTemp &ps)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() with indexes instead

Member IMP::container::ListTripletContainer::set_particle_triplets (const ParticleIndexTriplets &contents)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set() 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::PairRestraint::PairRestraint (PairScore *ss, const ParticlePair &vt, std::string name="PairRestraint %1%")

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index-based constructor instead.

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::QuadRestraint::QuadRestraint (QuadScore *ss, const ParticleQuad &vt, std::string name="QuadRestraint %1%")

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index-based constructor instead.

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::SingletonRestraint::SingletonRestraint (SingletonScore *ss, Particle *vt, std::string name="SingletonRestraint %1%")

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index-based constructor instead.

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::TripletRestraint::TripletRestraint (TripletScore *ss, const ParticleTriplet &vt, std::string name="TripletRestraint %1%")

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index-based constructor instead.

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::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::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::misc::DecayPairContainerOptimizerState::DecayPairContainerOptimizerState (PairPredicate *pred, const ParticlePairsTemp &initial_list, std::string name="DecayPairContainerOptimizerState%1%")

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index-based constructor instead

Member IMP::Model::add_restraint (Restraint *r)

As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Add to a ScoringFunction instead.

Member IMP::Model::create_model_scoring_function ()

As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use a ScoringFunction instead.

Member IMP::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::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::modeller.load_restraints_file

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use ModelLoader instead.

Member IMP::modeller.read_pdb

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Use IMP::atom::read_pdb() instead to read a PDB file, or ModelLoader to read a Modeller model.

Member IMP::multifit::create_coarse_molecule_from_molecule (const atom::Hierarchy &mh, int num_beads, Model *mdl, float bead_radius, bool add_conn_restraint=false)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Unused and will be removed.

Parameters

[in]	mh	the molecule to coarsen
[in]	num_beads	the output number of beads
[in]	mdl	model to add the new molecule to
[in]	bead_radius	bead radius
[in]	add_conn_restraint	if true a connectivity restraint between the particles of the new molecule is added

Member IMP::multifit::create_coarse_molecules_from_molecules (const atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool add_conn_restraint=false)

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Unused and will be removed.

Parameters

[in]	mhs	the molecules to coarsen
[in]	frag_len	the number of beads for each molecule will be its number of residues / frag_len
[in]	mdl	model to add the new molecule to
[in]	bead_radius	bead radius
[in]	add_conn_restraint	if true a connectivity restraint between the particles of the new molecule is added

Member IMP::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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.