IMP::kernel::Model | IMP::atom::Angle::do_setup_particle(), IMP::atom::Angle::Angle(), IMP::atom::Angle::get_is_setup(), IMP::atom::Angle::setup_particle(), IMP::atom::AngleSingletonScore::do_get_inputs(), IMP::atom::AngleSingletonScore::evaluate_if_good_indexes(), IMP::atom::AngleSingletonScore::evaluate_index(), IMP::atom::AngleSingletonScore::evaluate_indexes(), IMP::atom::Atom::do_setup_particle(), IMP::atom::Atom::do_setup_particle(), IMP::atom::Atom::Atom(), IMP::atom::Atom::get_is_setup(), IMP::atom::Atom::setup_particle(), IMP::atom::Atom::setup_particle(), IMP::atom::Bond::Bond(), IMP::atom::Bond::get_is_setup(), IMP::atom::BondEndpointsRefiner::do_get_inputs(), IMP::atom::BondSingletonScore::do_get_inputs(), IMP::atom::BondSingletonScore::evaluate_if_good_indexes(), IMP::atom::BondSingletonScore::evaluate_index(), IMP::atom::BondSingletonScore::evaluate_indexes(), IMP::atom::Bonded::do_setup_particle(), IMP::atom::Bonded::Bonded(), IMP::atom::Bonded::get_is_setup(), IMP::atom::Bonded::setup_particle(), IMP::atom::BondedPairFilter::do_get_inputs(), IMP::atom::BondedPairFilter::get_value_index(), IMP::atom::BondedPairFilter::get_value_index(), IMP::atom::BrownianDynamics::BrownianDynamics(), IMP::atom::CHARMMAtom::do_setup_particle(), IMP::atom::CHARMMAtom::CHARMMAtom(), IMP::atom::CHARMMAtom::get_is_setup(), IMP::atom::CHARMMAtom::setup_particle(), IMP::atom::CHARMMTopology::create_hierarchy(), IMP::atom::CenterOfMass::do_setup_particle(), IMP::atom::CenterOfMass::do_setup_particle(), IMP::atom::CenterOfMass::CenterOfMass(), IMP::atom::CenterOfMass::get_is_setup(), IMP::atom::CenterOfMass::setup_particle(), IMP::atom::CenterOfMass::setup_particle(), IMP::atom::Chain::do_setup_particle(), IMP::atom::Chain::do_setup_particle(), IMP::atom::Chain::do_setup_particle(), IMP::atom::Chain::Chain(), IMP::atom::Chain::get_is_setup(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Charged::do_setup_particle(), IMP::atom::Charged::do_setup_particle(), IMP::atom::Charged::Charged(), IMP::atom::Charged::get_is_setup(), IMP::atom::Charged::setup_particle(), IMP::atom::Charged::setup_particle(), IMP::atom::Copy::do_setup_particle(), IMP::atom::Copy::get_is_setup(), IMP::atom::Copy::setup_particle(), IMP::atom::Copy::Copy(), IMP::atom::CoulombPairScore::do_get_inputs(), IMP::atom::CoulombPairScore::evaluate_if_good_indexes(), IMP::atom::CoulombPairScore::evaluate_index(), IMP::atom::CoulombPairScore::evaluate_indexes(), IMP::atom::CoverBond::apply_index(), IMP::atom::CoverBond::apply_indexes(), IMP::atom::CoverBond::do_get_inputs(), IMP::atom::CoverBond::do_get_outputs(), IMP::atom::Diffusion::do_setup_particle(), IMP::atom::Diffusion::do_setup_particle(), IMP::atom::Diffusion::do_setup_particle(), IMP::atom::Diffusion::Diffusion(), IMP::atom::Diffusion::get_is_setup(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Dihedral::do_setup_particle(), IMP::atom::Dihedral::Dihedral(), IMP::atom::Dihedral::get_is_setup(), IMP::atom::Dihedral::setup_particle(), IMP::atom::DihedralSingletonScore::do_get_inputs(), IMP::atom::DihedralSingletonScore::evaluate_if_good_indexes(), IMP::atom::DihedralSingletonScore::evaluate_index(), IMP::atom::DihedralSingletonScore::evaluate_indexes(), IMP::atom::Domain::do_setup_particle(), IMP::atom::Domain::do_setup_particle(), IMP::atom::Domain::get_is_setup(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::Domain(), IMP::atom::Fragment::do_setup_particle(), IMP::atom::Fragment::do_setup_particle(), IMP::atom::Fragment::set_residue_indexes(), IMP::atom::Fragment::set_residue_indexes(), IMP::atom::Fragment::get_is_setup(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::Fragment(), IMP::atom::Hierarchy::Hierarchy(), IMP::atom::Hierarchy::get_is_setup(), IMP::atom::Hierarchy::setup_particle(), IMP::atom::ImproperSingletonScore::do_get_inputs(), IMP::atom::ImproperSingletonScore::evaluate_if_good_indexes(), IMP::atom::ImproperSingletonScore::evaluate_index(), IMP::atom::ImproperSingletonScore::evaluate_indexes(), IMP::atom::LennardJones::do_setup_particle(), IMP::atom::LennardJones::LennardJones(), IMP::atom::LennardJones::get_is_setup(), IMP::atom::LennardJones::setup_particle(), IMP::atom::LennardJones::setup_particle(), IMP::atom::LennardJonesPairScore::do_get_inputs(), IMP::atom::LennardJonesPairScore::evaluate_if_good_indexes(), IMP::atom::LennardJonesPairScore::evaluate_index(), IMP::atom::LennardJonesPairScore::evaluate_indexes(), IMP::atom::Mass::do_setup_particle(), IMP::atom::Mass::get_is_setup(), IMP::atom::Mass::setup_particle(), IMP::atom::Mass::Mass(), IMP::atom::MolecularDynamics::MolecularDynamics(), IMP::atom::Molecule::do_setup_particle(), IMP::atom::Molecule::Molecule(), IMP::atom::Molecule::get_is_setup(), IMP::atom::Molecule::setup_particle(), IMP::atom::Molecule::setup_particle(), IMP::atom::RemoveRigidMotionOptimizerState::RemoveRigidMotionOptimizerState(), IMP::atom::RemoveTranslationOptimizerState::RemoveTranslationOptimizerState(), IMP::atom::Representation::do_setup_particle(), IMP::atom::Representation::get_is_setup(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::Representation(), IMP::atom::Residue::do_setup_particle(), IMP::atom::Residue::do_setup_particle(), IMP::atom::Residue::Residue(), IMP::atom::Residue::get_is_setup(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::RigidBodyDiffusion::do_setup_particle(), IMP::atom::RigidBodyDiffusion::RigidBodyDiffusion(), IMP::atom::RigidBodyDiffusion::get_is_setup(), IMP::atom::RigidBodyDiffusion::setup_particle(), IMP::atom::SameResiduePairFilter::do_get_inputs(), IMP::atom::SameResiduePairFilter::get_value_index(), IMP::atom::SameResiduePairFilter::get_value_index(), IMP::atom::SecondaryStructureResidue::do_setup_particle(), IMP::atom::SecondaryStructureResidue::SecondaryStructureResidue(), IMP::atom::SecondaryStructureResidue::get_is_setup(), IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::Selection::search(), IMP::atom::Selection::set_hierarchies(), IMP::atom::Selection::Selection(), IMP::atom::Simulator::Simulator(), IMP::atom::SoapPairFilter::do_get_inputs(), IMP::atom::SoapPairFilter::get_value_index(), IMP::atom::SoapPairFilter::get_value_index(), IMP::atom::State::do_setup_particle(), IMP::atom::State::get_is_setup(), IMP::atom::State::setup_particle(), IMP::atom::State::State(), IMP::atom::StereochemistryPairFilter::do_get_inputs(), IMP::atom::StereochemistryPairFilter::get_value_index(), IMP::atom::StereochemistryPairFilter::get_value_index(), IMP::atom::VelocityScalingOptimizerState::VelocityScalingOptimizerState(), IMP::atom::WritePDBOptimizerState::WritePDBOptimizerState(), IMP::container::ConsecutivePairFilter::do_get_inputs(), IMP::container::ConsecutivePairFilter::get_value_index(), IMP::container::ConsecutivePairFilter::get_value_index(), IMP::container::ExclusiveConsecutivePairContainer::get_contains(), IMP::container::ExclusiveConsecutivePairFilter::do_get_inputs(), IMP::container::ExclusiveConsecutivePairFilter::get_value_index(), IMP::container::ExclusiveConsecutivePairFilter::get_value_index(), IMP::container::InContainerPairFilter::do_get_inputs(), IMP::container::InContainerPairFilter::get_value_index(), IMP::container::InContainerPairFilter::get_value_index(), IMP::container::InContainerQuadFilter::do_get_inputs(), IMP::container::InContainerQuadFilter::get_value_index(), IMP::container::InContainerQuadFilter::get_value_index(), IMP::container::InContainerSingletonFilter::do_get_inputs(), IMP::container::InContainerSingletonFilter::get_value_index(), IMP::container::InContainerSingletonFilter::get_value_index(), IMP::container::InContainerTripletFilter::do_get_inputs(), IMP::container::InContainerTripletFilter::get_value_index(), IMP::container::InContainerTripletFilter::get_value_index(), IMP::container::ListPairContainer::ListPairContainer(), IMP::container::ListQuadContainer::ListQuadContainer(), IMP::container::ListSingletonContainer::ListSingletonContainer(), IMP::container::ListTripletContainer::ListTripletContainer(), IMP::container::MinimumPairScore::do_create_current_decomposition(), IMP::container::MinimumPairScore::do_get_inputs(), IMP::container::MinimumPairScore::evaluate_if_good_indexes(), IMP::container::MinimumPairScore::evaluate_index(), IMP::container::MinimumPairScore::evaluate_indexes(), IMP::container::MinimumQuadScore::do_create_current_decomposition(), IMP::container::MinimumQuadScore::do_get_inputs(), IMP::container::MinimumQuadScore::evaluate_if_good_indexes(), IMP::container::MinimumQuadScore::evaluate_index(), IMP::container::MinimumQuadScore::evaluate_indexes(), IMP::container::MinimumSingletonScore::do_create_current_decomposition(), IMP::container::MinimumSingletonScore::do_get_inputs(), IMP::container::MinimumSingletonScore::evaluate_if_good_indexes(), IMP::container::MinimumSingletonScore::evaluate_index(), IMP::container::MinimumSingletonScore::evaluate_indexes(), IMP::container::MinimumTripletScore::do_create_current_decomposition(), IMP::container::MinimumTripletScore::do_get_inputs(), IMP::container::MinimumTripletScore::evaluate_if_good_indexes(), IMP::container::MinimumTripletScore::evaluate_index(), IMP::container::MinimumTripletScore::evaluate_indexes(), IMP::container::PairContainerSet::PairContainerSet(), IMP::container::QuadContainerSet::QuadContainerSet(), IMP::container::SingletonContainerSet::SingletonContainerSet(), IMP::container::TripletContainerSet::TripletContainerSet(), IMP::core::AllSamePairPredicate::do_get_inputs(), IMP::core::AllSamePairPredicate::get_value_index(), IMP::core::AllSamePairPredicate::get_value_index(), IMP::core::AllSameQuadPredicate::do_get_inputs(), IMP::core::AllSameQuadPredicate::get_value_index(), IMP::core::AllSameQuadPredicate::get_value_index(), IMP::core::AllSameSingletonPredicate::do_get_inputs(), IMP::core::AllSameSingletonPredicate::get_value_index(), IMP::core::AllSameSingletonPredicate::get_value_index(), IMP::core::AllSameTripletPredicate::do_get_inputs(), IMP::core::AllSameTripletPredicate::get_value_index(), IMP::core::AllSameTripletPredicate::get_value_index(), IMP::core::AngleTripletScore::do_get_inputs(), IMP::core::AngleTripletScore::evaluate_if_good_indexes(), IMP::core::AngleTripletScore::evaluate_index(), IMP::core::AngleTripletScore::evaluate_indexes(), IMP::core::AttributeSingletonPredicate::do_get_inputs(), IMP::core::AttributeSingletonPredicate::get_value_index(), IMP::core::AttributeSingletonPredicate::get_value_index(), IMP::core::BallMover::BallMover(), IMP::core::BallMover::BallMover(), IMP::core::BoxSweepClosePairsFinder::do_get_inputs(), IMP::core::BoxSweepClosePairsFinder::get_close_pairs(), IMP::core::BoxSweepClosePairsFinder::get_close_pairs(), IMP::core::Centroid::do_setup_particle(), IMP::core::Centroid::do_setup_particle(), IMP::core::Centroid::Centroid(), IMP::core::Centroid::get_is_setup(), IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle(), IMP::core::CentroidOfRefined::apply_index(), IMP::core::CentroidOfRefined::apply_indexes(), IMP::core::CentroidOfRefined::do_get_inputs(), IMP::core::CentroidOfRefined::do_get_outputs(), IMP::core::ChecksScoreState::ChecksScoreState(), IMP::core::ChildrenRefiner::do_get_inputs(), IMP::core::ClosePairsFinder::get_close_pairs(), IMP::core::ClosePairsFinder::get_close_pairs(), IMP::core::ClosePairsPairScore::get_close_pairs(), IMP::core::ClosePairsPairScore::create_current_decomposition(), IMP::core::ClosePairsPairScore::do_get_inputs(), IMP::core::ClosePairsPairScore::evaluate_if_good_index(), IMP::core::ClosePairsPairScore::evaluate_if_good_indexes(), IMP::core::ClosePairsPairScore::evaluate_index(), IMP::core::ClosePairsPairScore::evaluate_indexes(), IMP::core::CoinFlipPairPredicate::do_get_inputs(), IMP::core::CoinFlipPairPredicate::get_value_index(), IMP::core::CoinFlipPairPredicate::get_value_index(), IMP::core::CoinFlipQuadPredicate::do_get_inputs(), IMP::core::CoinFlipQuadPredicate::get_value_index(), IMP::core::CoinFlipQuadPredicate::get_value_index(), IMP::core::CoinFlipSingletonPredicate::do_get_inputs(), IMP::core::CoinFlipSingletonPredicate::get_value_index(), IMP::core::CoinFlipSingletonPredicate::get_value_index(), IMP::core::CoinFlipTripletPredicate::do_get_inputs(), IMP::core::CoinFlipTripletPredicate::get_value_index(), IMP::core::CoinFlipTripletPredicate::get_value_index(), IMP::core::ConjugateGradients::ConjugateGradients(), IMP::core::ConstantPairPredicate::do_get_inputs(), IMP::core::ConstantPairPredicate::get_value_index(), IMP::core::ConstantPairPredicate::get_value_index(), IMP::core::ConstantQuadPredicate::do_get_inputs(), IMP::core::ConstantQuadPredicate::get_value_index(), IMP::core::ConstantQuadPredicate::get_value_index(), IMP::core::ConstantSingletonPredicate::do_get_inputs(), IMP::core::ConstantSingletonPredicate::get_value_index(), IMP::core::ConstantSingletonPredicate::get_value_index(), IMP::core::ConstantTripletPredicate::do_get_inputs(), IMP::core::ConstantTripletPredicate::get_value_index(), IMP::core::ConstantTripletPredicate::get_value_index(), IMP::core::Cover::do_setup_particle(), IMP::core::Cover::do_setup_particle(), IMP::core::Cover::Cover(), IMP::core::Cover::get_is_setup(), IMP::core::Cover::setup_particle(), IMP::core::Cover::setup_particle(), IMP::core::CoverRefined::apply_index(), IMP::core::CoverRefined::apply_indexes(), IMP::core::CoverRefined::do_get_inputs(), IMP::core::CoverRefined::do_get_outputs(), IMP::core::DerivativesFromRefined::apply_index(), IMP::core::DerivativesFromRefined::apply_indexes(), IMP::core::DerivativesFromRefined::do_get_inputs(), IMP::core::DerivativesFromRefined::do_get_outputs(), IMP::core::DerivativesToRefined::apply_index(), IMP::core::DerivativesToRefined::apply_indexes(), IMP::core::DerivativesToRefined::do_get_inputs(), IMP::core::DerivativesToRefined::do_get_outputs(), IMP::core::DistancePairScore::do_get_inputs(), IMP::core::DistancePairScore::evaluate_index(), IMP::core::FixedRefiner::do_get_inputs(), IMP::core::Gaussian::do_setup_particle(), IMP::core::Gaussian::do_setup_particle(), IMP::core::Gaussian::Gaussian(), IMP::core::Gaussian::get_is_setup(), IMP::core::Gaussian::setup_particle(), IMP::core::Gaussian::setup_particle(), IMP::core::GenericAttributeSingletonScore::do_get_inputs(), IMP::core::GenericAttributeSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericAttributeSingletonScore::evaluate_index(), IMP::core::GenericAttributeSingletonScore::evaluate_indexes(), IMP::core::GenericBoundingBox3DSingletonScore::do_get_inputs(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_index(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_indexes(), IMP::core::GenericDistanceToSingletonScore::do_get_inputs(), IMP::core::GenericDistanceToSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericDistanceToSingletonScore::evaluate_index(), IMP::core::GenericDistanceToSingletonScore::evaluate_indexes(), IMP::core::GridClosePairsFinder::do_get_inputs(), IMP::core::GridClosePairsFinder::get_close_pairs(), IMP::core::GridClosePairsFinder::get_close_pairs(), IMP::core::HarmonicDistancePairScore::do_get_inputs(), IMP::core::HarmonicDistancePairScore::evaluate_index(), IMP::core::HarmonicSphereDistancePairScore::do_get_inputs(), IMP::core::HarmonicSphereDistancePairScore::evaluate_index(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::do_get_inputs(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_if_good_indexes(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_index(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_indexes(), IMP::core::HarmonicUpperBoundSphereDistancePairScore::do_get_inputs(), IMP::core::HarmonicUpperBoundSphereDistancePairScore::evaluate_index(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::Hierarchy(), IMP::core::Hierarchy::get_is_setup(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::InBoundingBox3DSingletonPredicate::do_get_inputs(), IMP::core::InBoundingBox3DSingletonPredicate::get_value_index(), IMP::core::InBoundingBox3DSingletonPredicate::get_value_index(), IMP::core::IsCollisionPairPredicate::do_get_inputs(), IMP::core::IsCollisionPairPredicate::get_value_index(), IMP::core::KClosePairsPairScore::get_close_pairs(), IMP::core::KClosePairsPairScore::create_current_decomposition(), IMP::core::KClosePairsPairScore::do_get_inputs(), IMP::core::KClosePairsPairScore::evaluate_if_good_index(), IMP::core::KClosePairsPairScore::evaluate_if_good_indexes(), IMP::core::KClosePairsPairScore::evaluate_index(), IMP::core::KClosePairsPairScore::evaluate_indexes(), IMP::core::LeavesRefiner::do_get_inputs(), IMP::core::MCCGSampler::MCCGSampler(), IMP::core::MonteCarlo::MonteCarlo(), IMP::core::MonteCarloMover::MonteCarloMover(), IMP::core::NearestNeighborsClosePairsFinder::do_get_inputs(), IMP::core::NearestNeighborsClosePairsFinder::get_close_pairs(), IMP::core::NearestNeighborsClosePairsFinder::get_close_pairs(), IMP::core::NonRigidMember::NonRigidMember(), IMP::core::NonRigidMember::get_is_setup(), IMP::core::NormalMover::NormalMover(), IMP::core::NormalMover::NormalMover(), IMP::core::NormalizedSphereDistancePairScore::do_get_inputs(), IMP::core::NormalizedSphereDistancePairScore::evaluate_if_good_indexes(), IMP::core::NormalizedSphereDistancePairScore::evaluate_index(), IMP::core::NormalizedSphereDistancePairScore::evaluate_indexes(), IMP::core::OrderedTypePairPredicate::do_get_inputs(), IMP::core::OrderedTypePairPredicate::get_value_index(), IMP::core::OrderedTypePairPredicate::get_value_index(), IMP::core::OrderedTypeQuadPredicate::do_get_inputs(), IMP::core::OrderedTypeQuadPredicate::get_value_index(), IMP::core::OrderedTypeQuadPredicate::get_value_index(), IMP::core::OrderedTypeSingletonPredicate::do_get_inputs(), IMP::core::OrderedTypeSingletonPredicate::get_value_index(), IMP::core::OrderedTypeSingletonPredicate::get_value_index(), IMP::core::OrderedTypeTripletPredicate::do_get_inputs(), IMP::core::OrderedTypeTripletPredicate::get_value_index(), IMP::core::OrderedTypeTripletPredicate::get_value_index(), IMP::core::PairConstraint::PairConstraint(), IMP::core::PairRestraint::PairRestraint(), IMP::core::PredicateSingletonScore::do_get_inputs(), IMP::core::PredicateSingletonScore::evaluate_if_good_indexes(), IMP::core::PredicateSingletonScore::evaluate_index(), IMP::core::PredicateSingletonScore::evaluate_indexes(), IMP::core::QuadConstraint::QuadConstraint(), IMP::core::QuadRestraint::QuadRestraint(), IMP::core::QuadraticClosePairsFinder::do_get_inputs(), IMP::core::QuadraticClosePairsFinder::get_are_close(), IMP::core::QuadraticClosePairsFinder::get_close_pairs(), IMP::core::QuadraticClosePairsFinder::get_close_pairs(), IMP::core::Reference::do_setup_particle(), IMP::core::Reference::Reference(), IMP::core::Reference::get_is_setup(), IMP::core::Reference::setup_particle(), IMP::core::RefinedPairsPairScore::do_get_inputs(), IMP::core::RefinedPairsPairScore::evaluate_if_good_indexes(), IMP::core::RefinedPairsPairScore::evaluate_index(), IMP::core::RefinedPairsPairScore::evaluate_indexes(), IMP::core::RigidBody::do_setup_particle(), IMP::core::RigidBody::do_setup_particle(), IMP::core::RigidBody::RigidBody(), IMP::core::RigidBody::get_is_setup(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBodyMember::RigidBodyMember(), IMP::core::RigidBodyMember::get_is_setup(), IMP::core::RigidBodyMover::RigidBodyMover(), IMP::core::RigidBodyTunneler::RigidBodyTunneler(), IMP::core::RigidBodyTunneler::get_reduced_coordinates(), IMP::core::RigidBodyTunneler::get_reduced_coordinates(), IMP::core::RigidBodyTunneler::set_reduced_coordinates(), IMP::core::RigidBodyUmbrella::RigidBodyUmbrella(), IMP::core::RigidBodyUmbrella::RigidBodyUmbrella(), IMP::core::RigidClosePairsFinder::do_get_inputs(), IMP::core::RigidClosePairsFinder::get_close_pairs(), IMP::core::RigidClosePairsFinder::get_close_pairs(), IMP::core::RigidClosePairsFinder::get_close_pairs(), IMP::core::RigidMember::RigidMember(), IMP::core::RigidMember::get_is_setup(), IMP::core::SingletonConstraint::SingletonConstraint(), IMP::core::SingletonRestraint::SingletonRestraint(), IMP::core::SoftSpherePairScore::do_get_inputs(), IMP::core::SoftSpherePairScore::evaluate_index(), IMP::core::SphereDistancePairScore::do_get_inputs(), IMP::core::SphereDistancePairScore::evaluate_index(), IMP::core::SphereDistanceToSingletonScore::do_get_inputs(), IMP::core::SphereDistanceToSingletonScore::evaluate_if_good_indexes(), IMP::core::SphereDistanceToSingletonScore::evaluate_index(), IMP::core::SphereDistanceToSingletonScore::evaluate_indexes(), IMP::core::SteepestDescent::SteepestDescent(), IMP::core::TableRefiner::do_get_inputs(), IMP::core::Transform::apply_index(), IMP::core::Transform::apply_indexes(), IMP::core::Transform::do_get_inputs(), IMP::core::Transform::do_get_outputs(), IMP::core::TransformationAndReflectionSymmetry::apply_index(), IMP::core::TransformationAndReflectionSymmetry::apply_indexes(), IMP::core::TransformationAndReflectionSymmetry::do_get_inputs(), IMP::core::TransformationAndReflectionSymmetry::do_get_outputs(), IMP::core::TransformationSymmetry::apply_index(), IMP::core::TransformationSymmetry::apply_indexes(), IMP::core::TransformationSymmetry::do_get_inputs(), IMP::core::TransformationSymmetry::do_get_outputs(), IMP::core::TransformedDistancePairScore::do_get_inputs(), IMP::core::TransformedDistancePairScore::evaluate_if_good_indexes(), IMP::core::TransformedDistancePairScore::evaluate_index(), IMP::core::TransformedDistancePairScore::evaluate_indexes(), IMP::core::TripletConstraint::TripletConstraint(), IMP::core::TripletRestraint::TripletRestraint(), IMP::core::Typed::do_setup_particle(), IMP::core::Typed::get_is_setup(), IMP::core::Typed::setup_particle(), IMP::core::Typed::Typed(), IMP::core::TypedPairScore::do_get_inputs(), IMP::core::TypedPairScore::evaluate_if_good_indexes(), IMP::core::TypedPairScore::evaluate_index(), IMP::core::TypedPairScore::evaluate_indexes(), IMP::core::UnorderedTypePairPredicate::do_get_inputs(), IMP::core::UnorderedTypePairPredicate::get_value_index(), IMP::core::UnorderedTypePairPredicate::get_value_index(), IMP::core::UnorderedTypeQuadPredicate::do_get_inputs(), IMP::core::UnorderedTypeQuadPredicate::get_value_index(), IMP::core::UnorderedTypeQuadPredicate::get_value_index(), IMP::core::UnorderedTypeSingletonPredicate::do_get_inputs(), IMP::core::UnorderedTypeSingletonPredicate::get_value_index(), IMP::core::UnorderedTypeSingletonPredicate::get_value_index(), IMP::core::UnorderedTypeTripletPredicate::do_get_inputs(), IMP::core::UnorderedTypeTripletPredicate::get_value_index(), IMP::core::UnorderedTypeTripletPredicate::get_value_index(), IMP::core::WeightedDerivativesToRefined::apply_index(), IMP::core::WeightedDerivativesToRefined::apply_indexes(), IMP::core::WeightedDerivativesToRefined::do_get_inputs(), IMP::core::WeightedDerivativesToRefined::do_get_outputs(), IMP::core::WeightedSphereDistancePairScore::do_get_inputs(), IMP::core::WeightedSphereDistancePairScore::evaluate_if_good_indexes(), IMP::core::WeightedSphereDistancePairScore::evaluate_index(), IMP::core::WeightedSphereDistancePairScore::evaluate_indexes(), IMP::core::XYZ::do_setup_particle(), IMP::core::XYZ::get_is_setup(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::XYZ(), IMP::core::XYZR::do_setup_particle(), IMP::core::XYZR::do_setup_particle(), IMP::core::XYZR::do_setup_particle(), IMP::core::XYZR::XYZR(), IMP::core::XYZR::get_is_setup(), IMP::core::XYZR::setup_particle(), IMP::core::XYZR::setup_particle(), IMP::core::XYZR::setup_particle(), IMP::display::Colored::do_setup_particle(), IMP::display::Colored::Colored(), IMP::display::Colored::get_is_setup(), IMP::display::Colored::setup_particle(), IMP::display::RestraintGeometry::RestraintGeometry(), IMP::display::WriteOptimizerState::WriteOptimizerState(), IMP::domino::BranchAndBoundSampler::BranchAndBoundSampler(), IMP::domino::BranchAndBoundSampler::BranchAndBoundSampler(), IMP::domino::DiscreteSampler::DiscreteSampler(), IMP::domino::DominoSampler::DominoSampler(), IMP::domino::DominoSampler::DominoSampler(), IMP::em2d::Em2DRestraint::Em2DRestraint(), IMP::em2d::Fine2DRegistrationRestraint::Fine2DRegistrationRestraint(), IMP::em2d::Fine2DRegistrationRestraint::setup(), IMP::em2d::ProjectionParameters::do_setup_particle(), IMP::em2d::ProjectionParameters::ProjectionParameters(), IMP::em2d::ProjectionParameters::set_proper_ranges_for_keys(), IMP::em2d::ProjectionParameters::get_is_setup(), IMP::em2d::ProjectionParameters::setup_particle(), IMP::em::Voxel::do_setup_particle(), IMP::em::Voxel::get_is_setup(), IMP::em::Voxel::setup_particle(), IMP::em::Voxel::Voxel(), IMP::example::ExampleDecorator::do_setup_particle(), IMP::example::ExampleDecorator::get_is_setup(), IMP::example::ExampleDecorator::setup_particle(), IMP::example::ExampleDecorator::ExampleDecorator(), IMP::example::ExamplePairScore::do_get_inputs(), IMP::example::ExamplePairScore::evaluate_if_good_indexes(), IMP::example::ExamplePairScore::evaluate_index(), IMP::example::ExamplePairScore::evaluate_indexes(), IMP::example::ExampleRestraint::ExampleRestraint(), IMP::example::ExampleSingletonModifier::apply_index(), IMP::example::ExampleSingletonModifier::apply_indexes(), IMP::example::ExampleSingletonModifier::do_get_inputs(), IMP::example::ExampleSingletonModifier::do_get_outputs(), IMP::gsl::ConjugateGradients::ConjugateGradients(), IMP::gsl::GSLOptimizer::GSLOptimizer(), IMP::gsl::QuasiNewton::QuasiNewton(), IMP::gsl::Simplex::Simplex(), IMP::isd::AmbiguousNOERestraint::AmbiguousNOERestraint(), IMP::isd::AmbiguousRestraint::AmbiguousRestraint(), IMP::isd::AmbiguousRestraint::AmbiguousRestraint(), IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint(), IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint(), IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint(), IMP::isd::GaussianProcessInterpolationRestraint::GaussianProcessInterpolationRestraint(), IMP::isd::HybridMonteCarlo::HybridMonteCarlo(), IMP::isd::LogWrapper::LogWrapper(), IMP::isd::LogWrapper::LogWrapper(), IMP::isd::MarginalHBondRestraint::MarginalHBondRestraint(), IMP::isd::MarginalNOERestraint::MarginalNOERestraint(), IMP::isd::MolecularDynamics::MolecularDynamics(), IMP::isd::MolecularDynamicsMover::MolecularDynamicsMover(), IMP::isd::NOERestraint::NOERestraint(), IMP::isd::Nuisance::do_setup_particle(), IMP::isd::Nuisance::Nuisance(), IMP::isd::Nuisance::get_is_setup(), IMP::isd::Nuisance::setup_particle(), IMP::isd::Nuisance::setup_particle(), IMP::isd::RepulsiveDistancePairScore::do_get_inputs(), IMP::isd::RepulsiveDistancePairScore::evaluate_if_good_indexes(), IMP::isd::RepulsiveDistancePairScore::evaluate_index(), IMP::isd::RepulsiveDistancePairScore::evaluate_indexes(), IMP::isd::Scale::do_setup_particle(), IMP::isd::Scale::Scale(), IMP::isd::Scale::get_is_setup(), IMP::isd::Scale::setup_particle(), IMP::isd::Scale::setup_particle(), IMP::isd::Switching::do_setup_particle(), IMP::isd::Switching::Switching(), IMP::isd::Switching::get_is_setup(), IMP::isd::Switching::setup_particle(), IMP::isd::Switching::setup_particle(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::UniformPrior::UniformPrior(), IMP::isd::Weight::do_setup_particle(), IMP::isd::Weight::Weight(), IMP::isd::Weight::get_is_setup(), IMP::isd::Weight::setup_particle(), IMP::isd::vonMisesKappaConjugateRestraint::vonMisesKappaConjugateRestraint(), IMP::isd::vonMisesKappaJeffreysRestraint::vonMisesKappaJeffreysRestraint(), IMP::kernel::AttributeOptimizer::AttributeOptimizer(), IMP::kernel::Configuration::Configuration(), IMP::kernel::Configuration::Configuration(), IMP::kernel::ConfigurationSet::ConfigurationSet(), IMP::kernel::Constraint::Constraint(), IMP::kernel::Container::Container(), IMP::kernel::Decorator::Decorator(), IMP::kernel::ModelObject::set_model(), IMP::kernel::ModelObject::ModelObject(), IMP::kernel::Optimizer::Optimizer(), IMP::kernel::OptimizerState::OptimizerState(), IMP::kernel::PairContainer::PairContainer(), IMP::kernel::PairModifier::apply_index(), IMP::kernel::PairModifier::apply_indexes(), IMP::kernel::PairPredicate::get_value_index(), IMP::kernel::PairPredicate::get_value_index(), IMP::kernel::PairPredicate::operator()(), IMP::kernel::PairScore::create_current_decomposition(), IMP::kernel::PairScore::evaluate_if_good_index(), IMP::kernel::PairScore::evaluate_if_good_indexes(), IMP::kernel::PairScore::evaluate_index(), IMP::kernel::PairScore::evaluate_indexes(), IMP::kernel::PairScore::do_create_current_decomposition(), IMP::kernel::Particle::Particle(), IMP::kernel::Particle::Particle(), IMP::kernel::ParticleInputs::get_inputs(), IMP::kernel::ParticleInputs::do_get_inputs(), IMP::kernel::ParticleOutputs::get_outputs(), IMP::kernel::ParticleOutputs::do_get_outputs(), IMP::kernel::QuadContainer::QuadContainer(), IMP::kernel::QuadModifier::apply_index(), IMP::kernel::QuadModifier::apply_indexes(), IMP::kernel::QuadPredicate::get_value_index(), IMP::kernel::QuadPredicate::get_value_index(), IMP::kernel::QuadPredicate::operator()(), IMP::kernel::QuadScore::create_current_decomposition(), IMP::kernel::QuadScore::evaluate_if_good_index(), IMP::kernel::QuadScore::evaluate_if_good_indexes(), IMP::kernel::QuadScore::evaluate_index(), IMP::kernel::QuadScore::evaluate_indexes(), IMP::kernel::QuadScore::do_create_current_decomposition(), IMP::kernel::Refiner::get_refined_indexes(), IMP::kernel::Refiner::get_refined_indexes_by_ref(), IMP::kernel::Restraint::Restraint(), IMP::kernel::RestraintSet::RestraintSet(), IMP::kernel::RestraintSet::RestraintSet(), IMP::kernel::RestraintsAdaptor::get(), IMP::kernel::Sampler::Sampler(), IMP::kernel::ScoreState::ScoreState(), IMP::kernel::ScoringFunction::ScoringFunction(), IMP::kernel::ScoringFunctionAdaptor::get(), IMP::kernel::SingletonContainer::SingletonContainer(), IMP::kernel::SingletonModifier::apply_index(), IMP::kernel::SingletonModifier::apply_indexes(), IMP::kernel::SingletonPredicate::get_value_index(), IMP::kernel::SingletonPredicate::get_value_index(), IMP::kernel::SingletonPredicate::operator()(), IMP::kernel::SingletonScore::create_current_decomposition(), IMP::kernel::SingletonScore::evaluate_if_good_index(), IMP::kernel::SingletonScore::evaluate_if_good_indexes(), IMP::kernel::SingletonScore::evaluate_index(), IMP::kernel::SingletonScore::evaluate_indexes(), IMP::kernel::SingletonScore::do_create_current_decomposition(), IMP::kernel::TripletContainer::TripletContainer(), IMP::kernel::TripletModifier::apply_index(), IMP::kernel::TripletModifier::apply_indexes(), IMP::kernel::TripletPredicate::get_value_index(), IMP::kernel::TripletPredicate::get_value_index(), IMP::kernel::TripletPredicate::operator()(), IMP::kernel::TripletScore::create_current_decomposition(), IMP::kernel::TripletScore::evaluate_if_good_index(), IMP::kernel::TripletScore::evaluate_if_good_indexes(), IMP::kernel::TripletScore::evaluate_index(), IMP::kernel::TripletScore::evaluate_indexes(), IMP::kernel::TripletScore::do_create_current_decomposition(), IMP::kernel::Undecorator::Undecorator(), IMP::kinematics::KinematicForest::KinematicForest(), IMP::kinematics::KinematicForest::KinematicForest(), IMP::kinematics::KinematicNode::do_setup_particle(), IMP::kinematics::KinematicNode::KinematicNode(), IMP::kinematics::KinematicNode::get_is_setup(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::LocalPlanner::LocalPlanner(), IMP::kinematics::PathLocalPlanner::PathLocalPlanner(), IMP::kinematics::RRT::RRT(), IMP::misc::CommonEndpointPairFilter::do_get_inputs(), IMP::misc::CommonEndpointPairFilter::get_value_index(), IMP::misc::CommonEndpointPairFilter::get_value_index(), IMP::misc::CustomXYZR::do_setup_particle(), IMP::misc::CustomXYZR::do_setup_particle(), IMP::misc::CustomXYZR::do_setup_particle(), IMP::misc::CustomXYZR::CustomXYZR(), IMP::misc::CustomXYZR::get_is_setup(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::LogPairScore::do_get_inputs(), IMP::misc::LogPairScore::evaluate_index(), IMP::misc::LowestRefinedPairScore::do_get_inputs(), IMP::misc::LowestRefinedPairScore::evaluate_if_good_indexes(), IMP::misc::LowestRefinedPairScore::evaluate_index(), IMP::misc::LowestRefinedPairScore::evaluate_indexes(), IMP::misc::MetricClosePairsFinder::get_close_pairs_internal(), IMP::misc::MetricClosePairsFinder::get_close_pairs_internal(), IMP::misc::MetricClosePairsFinder::get_close_pairs_internal(), IMP::misc::MetricClosePairsFinder::get_index(), IMP::misc::MetricClosePairsFinder::do_get_inputs(), IMP::misc::MetricClosePairsFinder::get_close_pairs(), IMP::misc::MetricClosePairsFinder::get_close_pairs(), IMP::misc::SoftCylinderPairScore::do_get_inputs(), IMP::misc::SoftCylinderPairScore::evaluate_if_good_indexes(), IMP::misc::SoftCylinderPairScore::evaluate_index(), IMP::misc::SoftCylinderPairScore::evaluate_indexes(), IMP::misc::StateAdaptor::StateAdaptor(), IMP::multifit::AnchorsData::setup_secondary_structure(), IMP::pmi::CompositeRestraint::CompositeRestraint(), IMP::pmi::Resolution::setup_particle(), IMP::pmi::Resolution::Resolution(), IMP::pmi::SigmoidRestraintSphere::SigmoidRestraintSphere(), IMP::pmi::Symmetric::setup_particle(), IMP::pmi::Symmetric::Symmetric(), IMP::pmi::TransformMover::TransformMover(), IMP::pmi::TransformMover::TransformMover(), IMP::pmi::Uncertainty::setup_particle(), IMP::pmi::Uncertainty::Uncertainty(), IMP::rmf::HierarchyLoadLink::add_link_recursive(), IMP::rmf::HierarchyLoadLink::create_recursive(), IMP::rmf::HierarchyLoadLink::do_create(), IMP::rmf::HierarchyLoadLink::do_link_particle(), IMP::rmf::HierarchyLoadLink::do_load_hierarchy(), IMP::rmf::HierarchyLoadLink::do_setup_particle(), IMP::rmf::SaveOptimizerState::SaveOptimizerState(), IMP::rmf::SimpleLoadLink::do_create(), IMP::rmf::SimpleLoadLink::create(), IMP::score_functor::AddScores::get_inputs(), IMP::score_functor::AddScores::get_is_trivially_zero(), IMP::score_functor::AddScores::get_maximum_range(), IMP::score_functor::AddScores::get_score(), IMP::score_functor::AddScores::get_score_and_derivative(), IMP::score_functor::DistancePairScore::do_get_inputs(), IMP::score_functor::DistancePairScore::evaluate_if_good_indexes(), IMP::score_functor::DistancePairScore::evaluate_index(), IMP::score_functor::DistancePairScore::evaluate_indexes(), IMP::score_functor::Harmonic::get_score(), IMP::score_functor::Harmonic::get_score_and_derivative(), IMP::score_functor::HarmonicLowerBound::get_is_trivially_zero(), IMP::score_functor::HarmonicLowerBound::get_maximum_range(), IMP::score_functor::HarmonicLowerBound::get_score(), IMP::score_functor::HarmonicLowerBound::get_score_and_derivative(), IMP::score_functor::HarmonicUpperBound::get_score(), IMP::score_functor::HarmonicUpperBound::get_score_and_derivative(), IMP::score_functor::LinearLowerBound::get_is_trivially_zero(), IMP::score_functor::LinearLowerBound::get_maximum_range(), IMP::score_functor::LinearLowerBound::get_score(), IMP::score_functor::LinearLowerBound::get_score_and_derivative(), IMP::score_functor::OpenCubicSpline::get_is_trivially_zero(), IMP::score_functor::OpenCubicSpline::get_maximum_range(), IMP::score_functor::OpenCubicSpline::get_score(), IMP::score_functor::OpenCubicSpline::get_score_and_derivative(), IMP::score_functor::OrientedSoap::get_inputs(), IMP::score_functor::OrientedSoap::get_is_trivially_zero(), IMP::score_functor::OrientedSoap::get_maximum_range(), IMP::score_functor::OrientedSoap::get_score(), IMP::score_functor::OrientedSoap::get_score_and_derivative(), IMP::score_functor::Shift::get_is_trivially_zero(), IMP::score_functor::Shift::get_maximum_range(), IMP::score_functor::Shift::get_score(), IMP::score_functor::Shift::get_score_and_derivative(), IMP::score_functor::SingletonStatistical::get_score(), IMP::score_functor::SphereDistance::get_rsum(), IMP::score_functor::SphereDistance::get_is_trivially_zero(), IMP::score_functor::SphereDistance::get_maximum_range(), IMP::score_functor::SphereDistance::get_score(), IMP::score_functor::SphereDistance::get_score_and_derivative(), IMP::score_functor::Statistical::get_is_trivially_zero(), IMP::score_functor::Statistical::get_maximum_range(), IMP::score_functor::Statistical::get_score(), IMP::score_functor::Statistical::get_score_and_derivative(), IMP::score_functor::UnaryFunctionEvaluate::get_score(), IMP::score_functor::UnaryFunctionEvaluate::get_score_and_derivative(), IMP::score_functor::WeightScore::get_score(), IMP::score_functor::WeightScore::get_score_and_derivative(), IMP::atom::read_mol2(), IMP::atom::read_pdb(), IMP::atom::read_multimodel_pdb(), IMP::atom::read_psipred(), IMP::atom::create_protein(), IMP::atom::create_protein(), IMP::atom::get_resolution(), IMP::atom::setup_coarse_secondary_structure_residue(), IMP::atom::setup_coarse_secondary_structure_residues(), IMP::core::create_rigid_bodies(), IMP::core::create_xyzr_particles(), IMP::core::get_initial_reference_frame(), IMP::em::density2particles(), IMP::example::optimize_assembly(), IMP::kernel::get_dependency_graph(), IMP::kernel::get_particles(), IMP::kernel::get_pruned_dependency_graph(), IMP::kernel::make_predicate_equal(), IMP::kernel::make_predicate_not_equal(), IMP::multifit::create_coarse_molecule_from_density(), IMP::multifit::create_coarse_molecule_from_molecule(), IMP::multifit::create_coarse_molecules_from_molecules(), IMP::rmf::create_hierarchies(), IMP::rmf::create_particles(), IMP::rmf::create_restraints() |