Class | Examples |
IMP::core::BallMover | BallMover.py, core/move_aware_mc.py, core/optimize_balls.py, core/restrain_minimum_distance.py, display/display_log.py, temperature_rem.py |
IMP::core::ChildrenRefiner | core/connectivity_restraint.py, core/cover_particles.py |
IMP::core::CoinFlipPairPredicate | misc/decay.py |
IMP::core::ConjugateGradients | container/bipartite_nonbonded_interactions.py, container/nonbonded_interactions.py, core/optimize_balls.py, core/restrain_diameter.py, core/rigid_collisions.py, core/simple.py, core/symmetry.py, em/analyze_convergence.py |
IMP::core::ConnectivityRestraint | core/connectivity_restraint.py |
IMP::core::DiameterRestraint | core/restrain_diameter.py |
IMP::core::DistancePairScore | core/linear_and_harmonic_scores.py, core/ms_connectivity_restraint.py, core/pair_restraint.py, core/simple.py, kernel/basic_optimization.py |
IMP::core::DistanceRestraint | domino/domino_approach.py, em2d/optimize_em2d_with_montecarlo.py, gsl/simplex.py, modeller/imp_restraints_in_modeller.py, parallel/tasks.py, temperature_rem.py |
IMP::core::EdgePairsGeometry | container/connectivity.py |
IMP::core::ExcludedVolumeRestraint | atom/rigid_brownian_dynamics.py, core/excluded_volume.py, core/move_aware_mc.py, core/optimize_balls.py, core/symmetry.py, display/display_log.py, domino/rigid_body_excluded_volume.py, misc/decay.py, rmf/simulation.py |
IMP::core::GenericAttributeSingletonScore | domino/multiscale.py |
IMP::core::GenericBoundingBox3DSingletonScore | core/move_aware_mc.py, core/optimize_balls.py, misc/decay.py, rmf/simulation.py |
IMP::core::GenericDistanceToSingletonScore | container/restrain_in_sphere.py, core/restrain_in_sphere.py, core/simple.py, domino/multiscale.py, domino/six_particles_optimization.py |
IMP::core::GridClosePairsFinder | domino/merge_tree.py |
IMP::core::Harmonic | BallMover.py, atom/charmm_forcefield_verbose.py, atom/load_protein_restrain_bonds.py, core/linear_and_harmonic_scores.py, core/pair_restraint.py, core/simple.py, domino/domino_approach.py, domino/multiscale.py, em2d/optimize_em2d_with_montecarlo.py, gsl/simplex.py, modeller/imp_restraints_in_modeller.py, parallel/tasks.py, temperature_rem.py |
IMP::core::HarmonicDistancePairScore | container/statistical.py, core/optimize_balls.py, domino/custom_filter.py, domino/interactive.py, domino/interactive_with_containers.py, domino/six_particles_optimization.py, kernel/chain.py, rotamer/rotamer_pdb2.py |
IMP::core::HarmonicLowerBound | container/bipartite_nonbonded_interactions.py, core/excluded_volume.py, core/rigid_collisions.py, kernel/basic_optimization.py |
IMP::core::HarmonicSphereDistancePairScore | core/restrain_minimum_distance.py, domino/multiscale.py |
IMP::core::HarmonicUpperBound | container/restrain_in_sphere.py, core/connectivity_restraint.py, core/move_aware_mc.py, core/ms_connectivity_restraint.py, core/optimize_balls.py, core/restrain_diameter.py, core/restrain_in_sphere.py, display/displaying_ensembles.py, domino/six_particles_optimization.py, misc/decay.py, rmf/simulation.py |
IMP::core::HarmonicUpperBoundSphereDistancePairScore | domino/restraint_cache.py, misc/decay.py, rmf/simulation.py |
IMP::core::HierarchyTraits | core/custom_hierarchy.py |
IMP::core::KClosePairsPairScore | core/connectivity_restraint.py, core/restrain_minimum_distance.py, display/displaying_ensembles.py |
IMP::core::LeavesRefiner | display/displaying_ensembles.py, em/local_fitting.py |
IMP::core::Linear | core/linear_and_harmonic_scores.py |
IMP::core::MCCGSampler | kernel/basic_optimization.py, kernel/chain.py |
IMP::core::MSConnectivityRestraint | core/ms_connectivity_restraint.py |
IMP::core::MonteCarlo | BallMover.py, core/move_aware_mc.py, core/optimize_balls.py, core/restrain_minimum_distance.py, display/display_log.py, em2d/optimize_em2d_with_montecarlo.py, temperature_rem.py |
IMP::core::PairRestraint | BallMover.py, core/linear_and_harmonic_scores.py, core/pair_restraint.py, core/restrain_minimum_distance.py, core/simple.py, domino/marina_party.py, domino/multiscale.py, kernel/chain.py |
IMP::core::RestraintsScoringFunction | atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/rigid_brownian_dynamics.py, container/statistical.py, core/excluded_volume.py, core/move_aware_mc.py, core/optimize_balls.py, core/restrain_diameter.py, core/rigid_collisions.py, core/simple.py, core/symmetry.py, domino/custom_filter.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py, em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py, kernel/basic_optimization.py, kernel/dependency_graph.py, modeller/imp_restraints_in_modeller.py, modeller/load_modeller_model.py, modeller/modeller_restraints_in_imp.py, parallel/tasks.py, rmf/simulation.py, temperature_rem.py |
IMP::core::RigidBodyMover | em2d/optimize_em2d_with_montecarlo.py, pmi/protein_residue_binding.py |
IMP::core::RigidClosePairsFinder | core/rigid_collisions.py |
IMP::core::RigidMember | display/displaying_ensembles.py, domino/rigid_body_excluded_volume.py, em/local_fitting.py |
IMP::core::SerialMover | BallMover.py, core/move_aware_mc.py, core/optimize_balls.py, temperature_rem.py |
IMP::core::SingletonConstraint | core/symmetry.py |
IMP::core::SingletonRestraint | core/restrain_in_sphere.py, core/simple.py, domino/multiscale.py, domino/six_particles_optimization.py |
IMP::core::SoftSpherePairScore | container/nonbonded_interactions.py, core/optimize_balls.py, domino/merge_tree.py, kernel/chain.py |
IMP::core::SphereDistancePairScore | BallMover.py, container/bipartite_nonbonded_interactions.py, core/connectivity_restraint.py, core/excluded_volume.py, core/linear_and_harmonic_scores.py, core/rigid_collisions.py, display/displaying_ensembles.py |
IMP::core::TableRefiner | core/restrain_minimum_distance.py |
IMP::core::Transform | em2d/clustering_of_pdb_models.py |
IMP::core::TransformationSymmetry | core/symmetry.py |
IMP::core::XYZ | atom/score_protein_with_ligand.py, core/XYZR_Decorator.py, core/restrain_diameter.py, core/simple.cpp, core/symmetry.py, display/displaying_ensembles.py, domino/custom_filter.py, domino/six_particles_optimization.py, pmi/ambiguity.py, rmf/pdb.py, rotamer/rotamer_pdb.py |
IMP::core::XYZDerivativeGeometry | em/analyze_convergence.py |
IMP::core::XYZR | BallMover.py, atom/markers.py, core/linear_and_harmonic_scores.py, core/optimize_balls.py, display/show_particles_as_spheres.py |
IMP::core::XYZRGeometry | atom/markers.py, core/move_aware_mc.py, core/optimize_balls.py, display/displaying_ensembles.py, domino/multiscale.py |
IMP::core::XYZRsGeometry | display/display_log.py, display/show_particles_as_spheres.py |