| Class | Users |
| IMP::Array | IMP::Array::compare(), IMP::PairModifier::apply_index(), IMP::PairPredicate::get_value_index(), IMP::PairPredicate::get_value_index_in_batch(), IMP::PairPredicate::operator()(), IMP::PairScore::create_current_decomposition(), IMP::PairScore::evaluate_if_good_index(), IMP::PairScore::evaluate_index(), IMP::PairScore::do_create_current_decomposition(), IMP::QuadModifier::apply_index(), IMP::QuadPredicate::get_value_index(), IMP::QuadPredicate::get_value_index_in_batch(), IMP::QuadPredicate::operator()(), IMP::QuadScore::create_current_decomposition(), IMP::QuadScore::evaluate_if_good_index(), IMP::QuadScore::evaluate_index(), IMP::QuadScore::do_create_current_decomposition(), IMP::TripletModifier::apply_index(), IMP::TripletPredicate::get_value_index(), IMP::TripletPredicate::get_value_index_in_batch(), IMP::TripletPredicate::operator()(), IMP::TripletScore::create_current_decomposition(), IMP::TripletScore::evaluate_if_good_index(), IMP::TripletScore::evaluate_index(), IMP::TripletScore::do_create_current_decomposition(), IMP::atom::BondedPairFilter::get_value_index(), IMP::atom::CoulombPairScore::evaluate_index(), IMP::atom::LennardJonesPairScore::evaluate_index(), IMP::atom::SameResiduePairFilter::get_value_index(), IMP::atom::SoapPairFilter::get_value_index(), IMP::atom::StereochemistryPairFilter::get_value_index(), IMP::container::ConsecutivePairContainer::get_contains(), IMP::container::ConsecutivePairFilter::get_value_index(), IMP::container::DynamicListPairContainer::add(), IMP::container::DynamicListQuadContainer::add(), IMP::container::DynamicListTripletContainer::add(), IMP::container::ExclusiveConsecutivePairContainer::get_contains(), IMP::container::ExclusiveConsecutivePairFilter::get_value_index(), IMP::container::InContainerPairFilter::get_value_index(), IMP::container::InContainerQuadFilter::get_value_index(), IMP::container::InContainerTripletFilter::get_value_index(), IMP::container::ListPairContainer::add(), IMP::container::ListQuadContainer::add(), IMP::container::ListTripletContainer::add(), IMP::container::MinimumPairScore::do_create_current_decomposition(), IMP::container::MinimumPairScore::evaluate_index(), IMP::container::MinimumQuadScore::do_create_current_decomposition(), IMP::container::MinimumQuadScore::evaluate_index(), IMP::container::MinimumTripletScore::do_create_current_decomposition(), IMP::container::MinimumTripletScore::evaluate_index(), IMP::core::AllSamePairPredicate::get_value_index(), IMP::core::AllSameQuadPredicate::get_value_index(), IMP::core::AllSameTripletPredicate::get_value_index(), IMP::core::AngleTripletScore::evaluate_index(), IMP::core::ClosePairsPairScore::get_close_pairs(), IMP::core::ClosePairsPairScore::create_current_decomposition(), IMP::core::ClosePairsPairScore::evaluate_if_good_index(), IMP::core::ClosePairsPairScore::evaluate_index(), IMP::core::CoinFlipPairPredicate::get_value_index(), IMP::core::CoinFlipQuadPredicate::get_value_index(), IMP::core::CoinFlipTripletPredicate::get_value_index(), IMP::core::ConstantPairPredicate::get_value_index(), IMP::core::ConstantQuadPredicate::get_value_index(), IMP::core::ConstantTripletPredicate::get_value_index(), IMP::core::DirectionAngle::do_setup_particle(), IMP::core::DirectionAngle::setup_particle(), IMP::core::DirectionAngle::setup_particle(), IMP::core::DistancePairScore::evaluate_index(), IMP::core::HarmonicDistancePairScore::evaluate_index(), IMP::core::HarmonicSphereDistancePairScore::evaluate_index(), IMP::core::HarmonicSurfaceDepthPairScore::evaluate_index(), IMP::core::HarmonicSurfaceDistancePairScore::evaluate_index(), IMP::core::HarmonicSurfaceHeightPairScore::evaluate_index(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_index(), IMP::core::HarmonicUpperBoundSphereDistancePairScore::evaluate_index(), IMP::core::IsCollisionPairPredicate::get_value_index(), IMP::core::KClosePairsPairScore::get_close_pairs(), IMP::core::KClosePairsPairScore::create_current_decomposition(), IMP::core::KClosePairsPairScore::evaluate_if_good_index(), IMP::core::KClosePairsPairScore::evaluate_index(), IMP::core::MultipleBinormalRestraint::MultipleBinormalRestraint(), IMP::core::NormalizedSphereDistancePairScore::evaluate_index(), IMP::core::OrderedTypePairPredicate::get_value_index(), IMP::core::OrderedTypePairPredicate::get_value_index_in_batch(), IMP::core::OrderedTypeQuadPredicate::get_value_index(), IMP::core::OrderedTypeQuadPredicate::get_value_index_in_batch(), IMP::core::OrderedTypeTripletPredicate::get_value_index(), IMP::core::OrderedTypeTripletPredicate::get_value_index_in_batch(), IMP::core::PairConstraint::PairConstraint(), IMP::core::PairRestraint::PairRestraint(), IMP::core::QuadConstraint::QuadConstraint(), IMP::core::QuadRestraint::QuadRestraint(), IMP::core::RefinedPairsPairScore::evaluate_index(), IMP::core::RigidBodyAnglePairScore::evaluate_index(), IMP::core::SoftSpherePairScore::evaluate_index(), IMP::core::SoftSubSurfacePairScore::evaluate_index(), IMP::core::SoftSuperSurfacePairScore::evaluate_index(), IMP::core::SphereDistancePairScore::evaluate_index(), IMP::core::SurfaceDepthPairScore::evaluate_index(), IMP::core::SurfaceDistancePairScore::evaluate_index(), IMP::core::SurfaceHeightPairScore::evaluate_index(), IMP::core::SurfaceSymmetryConstraint::SurfaceSymmetryConstraint(), IMP::core::TransformedDistancePairScore::evaluate_index(), IMP::core::TripletConstraint::TripletConstraint(), IMP::core::TripletRestraint::TripletRestraint(), IMP::core::TypedPairScore::evaluate_index(), IMP::core::UnorderedTypePairPredicate::get_value_index(), IMP::core::UnorderedTypeQuadPredicate::get_value_index(), IMP::core::UnorderedTypeTripletPredicate::get_value_index(), IMP::core::WeightedSphereDistancePairScore::evaluate_index(), IMP::example::ExamplePairScore::evaluate_index(), IMP::isd::AtomicCrossLinkMSRestraint::add_contribution(), IMP::isd::CrossLinkMSRestraint::add_contribution(), IMP::isd::RepulsiveDistancePairScore::evaluate_index(), IMP::misc::CommonEndpointPairFilter::get_value_index(), IMP::misc::LogPairScore::evaluate_index(), IMP::misc::LowestRefinedPairScore::evaluate_index(), IMP::misc::SoftCylinderPairScore::evaluate_index(), IMP::npc::MinimumSphereDistancePairScore::evaluate_index(), IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_index(), IMP::npctransport::HarmonicWellPairScore::evaluate_index(), IMP::npctransport::LinearInteraction::get_is_trivially_zero(), IMP::npctransport::LinearInteraction::get_maximum_range(), IMP::npctransport::LinearInteraction::get_score(), IMP::npctransport::LinearInteraction::get_score_and_derivative(), IMP::npctransport::LinearSoftSpherePairScore::evaluate_index(), IMP::npctransport::LinearWellPairScore::evaluate_index(), IMP::npctransport::SitesPairScore::evaluate_index(), IMP::npctransport::SitesPairScore::evaluate_site_contributions(), IMP::npctransport::SitesPairScore::evaluate_site_contributions_with_internal_tables(), IMP::npctransport::SitesPairScore::evaluate_index_with_internal_tables(), IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_index(), IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_index(), 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::evaluate_index(), 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_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::PointToSphereDistance::get_is_trivially_zero(), IMP::score_functor::PointToSphereDistance::get_maximum_range(), IMP::score_functor::PointToSphereDistance::get_score(), IMP::score_functor::PointToSphereDistance::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::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::SurfaceDistancePairScore::evaluate_index(), 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::spb::AttributeDistancePairScore::evaluate_index(), IMP::spb::KinkPairScore::evaluate_index(), IMP::spb::RigidBodyPackingScore::evaluate_index(), IMP::spb::SameParticlePairFilter::get_value_index(), IMP::spb::SameRigidBodyPairFilter::get_value_index(), IMP::npctransport::do_evaluate_index_harmonic(), IMP::npctransport::make_unordered_particle_index_pair() |
| IMP::Configuration | IMP::Configuration::Configuration() |
| IMP::ConfigurationSet | IMP::SaveToConfigurationSetOptimizerState::SaveToConfigurationSetOptimizerState(), IMP::statistics::ConfigurationSetRMSDMetric::ConfigurationSetRMSDMetric(), IMP::statistics::ConfigurationSetXYZEmbedding::ConfigurationSetXYZEmbedding() |
| IMP::ConstVector | IMP::ConstVector::compare(), IMP::swap() |
| IMP::Container | IMP::container::DynamicListPairContainer::DynamicListPairContainer(), IMP::container::DynamicListQuadContainer::DynamicListQuadContainer(), IMP::container::DynamicListSingletonContainer::DynamicListSingletonContainer(), IMP::container::DynamicListTripletContainer::DynamicListTripletContainer(), IMP::create_restraint(), IMP::resize_to_fit(), IMP::container::create_constraint(), IMP::container::create_in_container_filter(), IMP::container::create_restraint() |
| IMP::Decorator | IMP::ParticleAdaptor::ParticleAdaptor(), IMP::ParticleIndexAdaptor::ParticleIndexAdaptor(), IMP::atom::AngularVelocity::IMP_DECORATOR_METHODS(), IMP::atom::LinearVelocity::IMP_DECORATOR_METHODS(), IMP::get_vector_geometry(), IMP::set_vector_geometry() |
| IMP::DerivativeAccumulator | IMP::Constraint::do_after_evaluate(), IMP::Constraint::do_update_derivatives(), IMP::DerivativeAccumulator::DerivativeAccumulator(), IMP::PairScore::evaluate_if_good_index(), IMP::PairScore::evaluate_if_good_indexes(), IMP::PairScore::evaluate_index(), IMP::PairScore::evaluate_indexes(), IMP::QuadScore::evaluate_if_good_index(), IMP::QuadScore::evaluate_if_good_indexes(), IMP::QuadScore::evaluate_index(), IMP::QuadScore::evaluate_indexes(), IMP::RestraintSet::unprotected_evaluate(), IMP::ScoreState::after_evaluate(), IMP::ScoreState::do_after_evaluate(), IMP::SingletonScore::evaluate_if_good_index(), IMP::SingletonScore::evaluate_if_good_indexes(), IMP::SingletonScore::evaluate_index(), IMP::SingletonScore::evaluate_indexes(), IMP::TripletScore::evaluate_if_good_index(), IMP::TripletScore::evaluate_if_good_indexes(), IMP::TripletScore::evaluate_index(), IMP::TripletScore::evaluate_indexes(), IMP::atom::AngleSingletonScore::evaluate_if_good_indexes(), IMP::atom::AngleSingletonScore::evaluate_index(), IMP::atom::AngleSingletonScore::evaluate_indexes(), IMP::atom::BondSingletonScore::evaluate_if_good_indexes(), IMP::atom::BondSingletonScore::evaluate_index(), IMP::atom::BondSingletonScore::evaluate_indexes(), IMP::atom::CAAngleRestraint::unprotected_evaluate(), IMP::atom::CADihedralRestraint::unprotected_evaluate(), IMP::atom::CHARMMStereochemistryRestraint::unprotected_evaluate(), IMP::atom::CoulombPairScore::evaluate_if_good_indexes(), IMP::atom::CoulombPairScore::evaluate_index(), IMP::atom::CoulombPairScore::evaluate_indexes(), IMP::atom::DihedralSingletonScore::evaluate_if_good_indexes(), IMP::atom::DihedralSingletonScore::evaluate_index(), IMP::atom::DihedralSingletonScore::evaluate_indexes(), IMP::atom::EzRestraint::unprotected_evaluate(), IMP::atom::HelixRestraint::unprotected_evaluate(), IMP::atom::ImproperSingletonScore::evaluate_if_good_indexes(), IMP::atom::ImproperSingletonScore::evaluate_index(), IMP::atom::ImproperSingletonScore::evaluate_indexes(), IMP::atom::LennardJonesPairScore::evaluate_if_good_indexes(), IMP::atom::LennardJonesPairScore::evaluate_index(), IMP::atom::LennardJonesPairScore::evaluate_indexes(), IMP::container::DistributePairsScoreState::do_after_evaluate(), IMP::container::DistributeQuadsScoreState::do_after_evaluate(), IMP::container::DistributeSingletonsScoreState::do_after_evaluate(), IMP::container::DistributeTripletsScoreState::do_after_evaluate(), IMP::container::MinimumPairRestraint::unprotected_evaluate(), IMP::container::MinimumPairScore::evaluate_if_good_indexes(), IMP::container::MinimumPairScore::evaluate_index(), IMP::container::MinimumPairScore::evaluate_indexes(), IMP::container::MinimumQuadRestraint::unprotected_evaluate(), IMP::container::MinimumQuadScore::evaluate_if_good_indexes(), IMP::container::MinimumQuadScore::evaluate_index(), IMP::container::MinimumQuadScore::evaluate_indexes(), IMP::container::MinimumSingletonRestraint::unprotected_evaluate(), IMP::container::MinimumSingletonScore::evaluate_if_good_indexes(), IMP::container::MinimumSingletonScore::evaluate_index(), IMP::container::MinimumSingletonScore::evaluate_indexes(), IMP::container::MinimumTripletRestraint::unprotected_evaluate(), IMP::container::MinimumTripletScore::evaluate_if_good_indexes(), IMP::container::MinimumTripletScore::evaluate_index(), IMP::container::MinimumTripletScore::evaluate_indexes(), IMP::container::PairContainerStatistics::do_after_evaluate(), IMP::container::PairsConstraint::do_update_derivatives(), IMP::container::PairsRestraint::unprotected_evaluate(), IMP::container::QuadContainerStatistics::do_after_evaluate(), IMP::container::QuadsConstraint::do_update_derivatives(), IMP::container::QuadsRestraint::unprotected_evaluate(), IMP::container::SingletonContainerStatistics::do_after_evaluate(), IMP::container::SingletonsConstraint::do_update_derivatives(), IMP::container::SingletonsRestraint::unprotected_evaluate(), IMP::container::TripletContainerStatistics::do_after_evaluate(), IMP::container::TripletsConstraint::do_update_derivatives(), IMP::container::TripletsRestraint::unprotected_evaluate(), IMP::core::AngleTripletScore::evaluate_if_good_indexes(), IMP::core::AngleTripletScore::evaluate_index(), IMP::core::AngleTripletScore::evaluate_indexes(), IMP::core::ChecksScoreState::do_after_evaluate(), 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::ConnectivityRestraint::unprotected_evaluate(), IMP::core::ConstantRestraint::unprotected_evaluate(), IMP::core::DiameterRestraint::unprotected_evaluate(), IMP::core::DihedralRestraint::unprotected_evaluate(), IMP::core::Direction::add_to_direction_derivative(), IMP::core::Direction::add_to_direction_derivatives(), IMP::core::DirectionAngle::add_to_angle_derivative(), IMP::core::DistancePairScore::evaluate_index(), IMP::core::ExcludedVolumeRestraint::unprotected_evaluate(), IMP::core::GenericAttributeSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericAttributeSingletonScore::evaluate_index(), IMP::core::GenericAttributeSingletonScore::evaluate_indexes(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_index(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_indexes(), IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_index(), IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_indexes(), IMP::core::GenericDistanceToSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericDistanceToSingletonScore::evaluate_index(), IMP::core::GenericDistanceToSingletonScore::evaluate_indexes(), IMP::core::HarmonicDistancePairScore::evaluate_index(), IMP::core::HarmonicSphereDistancePairScore::evaluate_index(), IMP::core::HarmonicSurfaceDepthPairScore::evaluate_index(), IMP::core::HarmonicSurfaceDistancePairScore::evaluate_index(), IMP::core::HarmonicSurfaceHeightPairScore::evaluate_index(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_if_good_indexes(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_index(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_indexes(), IMP::core::HarmonicUpperBoundSphereDistancePairScore::evaluate_index(), 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::LateralSurfaceConstraint::do_after_evaluate(), IMP::core::LateralSurfaceConstraint::do_update_derivatives(), IMP::core::MSConnectivityRestraint::unprotected_evaluate(), IMP::core::MinimumRestraint::unprotected_evaluate(), IMP::core::MoveStatisticsScoreState::do_after_evaluate(), IMP::core::MultipleBinormalRestraint::unprotected_evaluate(), IMP::core::NeighborsTable::do_after_evaluate(), IMP::core::NonRigidMember::add_to_internal_derivatives(), IMP::core::NonRigidMember::add_to_internal_rotational_derivatives(), IMP::core::NonRigidMember::add_to_internal_rotational_derivatives(), IMP::core::NormalizedSphereDistancePairScore::evaluate_if_good_indexes(), IMP::core::NormalizedSphereDistancePairScore::evaluate_index(), IMP::core::NormalizedSphereDistancePairScore::evaluate_indexes(), IMP::core::PairConstraint::do_update_derivatives(), IMP::core::PairRestraint::unprotected_evaluate(), IMP::core::PredicateSingletonScore::evaluate_if_good_indexes(), IMP::core::PredicateSingletonScore::evaluate_index(), IMP::core::PredicateSingletonScore::evaluate_indexes(), IMP::core::QuadConstraint::do_update_derivatives(), IMP::core::QuadRestraint::unprotected_evaluate(), IMP::core::RefinedPairsPairScore::evaluate_if_good_indexes(), IMP::core::RefinedPairsPairScore::evaluate_index(), IMP::core::RefinedPairsPairScore::evaluate_indexes(), IMP::core::RigidBody::add_to_derivatives(), IMP::core::RigidBody::add_to_derivatives(), IMP::core::RigidBody::add_to_rotational_derivatives(), IMP::core::RigidBody::add_to_rotational_derivatives(), IMP::core::RigidBody::add_to_torque(), IMP::core::RigidBodyAnglePairScore::evaluate_if_good_indexes(), IMP::core::RigidBodyAnglePairScore::evaluate_index(), IMP::core::RigidBodyAnglePairScore::evaluate_indexes(), IMP::core::RigidBodyUmbrella::unprotected_evaluate(), IMP::core::SingletonConstraint::do_update_derivatives(), IMP::core::SingletonRestraint::unprotected_evaluate(), IMP::core::SoftSpherePairScore::evaluate_index(), IMP::core::SoftSubSurfacePairScore::evaluate_index(), IMP::core::SoftSuperSurfacePairScore::evaluate_index(), IMP::core::SphereDistancePairScore::evaluate_index(), IMP::core::SphereDistanceToSingletonScore::evaluate_if_good_indexes(), IMP::core::SphereDistanceToSingletonScore::evaluate_index(), IMP::core::SphereDistanceToSingletonScore::evaluate_indexes(), IMP::core::Surface::add_to_normal_derivative(), IMP::core::Surface::add_to_normal_derivatives(), IMP::core::SurfaceDepthPairScore::evaluate_index(), IMP::core::SurfaceDistancePairScore::evaluate_index(), IMP::core::SurfaceGeometryConstraint::do_after_evaluate(), IMP::core::SurfaceGeometryConstraint::do_update_derivatives(), IMP::core::SurfaceHeightPairScore::evaluate_index(), IMP::core::SurfaceSymmetryConstraint::do_update_derivatives(), IMP::core::TransformedDistancePairScore::evaluate_if_good_indexes(), IMP::core::TransformedDistancePairScore::evaluate_index(), IMP::core::TransformedDistancePairScore::evaluate_indexes(), IMP::core::TripletConstraint::do_update_derivatives(), IMP::core::TripletRestraint::unprotected_evaluate(), IMP::core::TypedPairScore::evaluate_if_good_indexes(), IMP::core::TypedPairScore::evaluate_index(), IMP::core::TypedPairScore::evaluate_indexes(), IMP::core::VolumeRestraint::unprotected_evaluate(), IMP::core::WeightedSphereDistancePairScore::evaluate_if_good_indexes(), IMP::core::WeightedSphereDistancePairScore::evaluate_index(), IMP::core::WeightedSphereDistancePairScore::evaluate_indexes(), IMP::core::XYZ::add_to_derivative(), IMP::core::XYZ::add_to_derivatives(), IMP::core::XYZR::add_to_radius_derivative(), IMP::domino::DependencyScoreState::do_after_evaluate(), IMP::em2d::DummyRestraint::unprotected_evaluate(), IMP::em2d::Em2DRestraint::unprotected_evaluate(), IMP::em2d::Fine2DRegistrationRestraint::unprotected_evaluate(), IMP::em2d::PCAFitRestraint::unprotected_evaluate(), IMP::em2d::ParticlesDummyRestraint::unprotected_evaluate(), IMP::em2d::ProjectionParametersScoreState::do_after_evaluate(), IMP::em2d::RigidBodiesImageFitRestraint::unprotected_evaluate(), IMP::em::DensityFillingRestraint::unprotected_evaluate(), IMP::em::EnvelopeFitRestraint::unprotected_evaluate(), IMP::em::EnvelopePenetrationRestraint::unprotected_evaluate(), IMP::em::FitRestraint::unprotected_evaluate(), IMP::em::PCAFitRestraint::unprotected_evaluate(), IMP::example::ExampleComplexRestraint::unprotected_evaluate(), IMP::example::ExampleConstraint::do_update_derivatives(), IMP::example::ExamplePairScore::evaluate_if_good_indexes(), IMP::example::ExamplePairScore::evaluate_index(), IMP::example::ExamplePairScore::evaluate_indexes(), IMP::isd::AmbiguousNOERestraint::unprotected_evaluate(), IMP::isd::AmbiguousRestraint::unprotected_evaluate(), IMP::isd::AtomicCrossLinkMSRestraint::evaluate_for_contributions(), IMP::isd::AtomicCrossLinkMSRestraint::unprotected_evaluate(), IMP::isd::BivariateFunction::add_to_derivatives(), IMP::isd::BivariateFunction::add_to_particle_derivative(), IMP::isd::Covariance1DFunction::add_to_derivatives(), IMP::isd::Covariance1DFunction::add_to_particle_derivative(), IMP::isd::CrossLinkMSRestraint::unprotected_evaluate(), IMP::isd::CysteineCrossLinkRestraint::unprotected_evaluate(), IMP::isd::FretRestraint::unprotected_evaluate(), IMP::isd::GaussianAnchorEMRestraint::unprotected_evaluate(), IMP::isd::GaussianEMRestraint::unprotected_evaluate(), IMP::isd::GaussianProcessInterpolation::add_to_m_particle_derivative(), IMP::isd::GaussianProcessInterpolation::add_to_Omega_particle_derivative(), IMP::isd::GaussianProcessInterpolationRestraint::unprotected_evaluate(), IMP::isd::GaussianRestraint::unprotected_evaluate(), IMP::isd::GeneralizedGuinierPorodFunction::add_to_derivatives(), IMP::isd::GeneralizedGuinierPorodFunction::add_to_particle_derivative(), IMP::isd::ISDRestraint::unprotected_evaluate(), IMP::isd::JeffreysRestraint::unprotected_evaluate(), IMP::isd::Linear1DFunction::add_to_derivatives(), IMP::isd::Linear1DFunction::add_to_particle_derivative(), IMP::isd::LogWrapper::unprotected_evaluate(), IMP::isd::LognormalAmbiguousRestraint::unprotected_evaluate(), IMP::isd::LognormalRestraint::unprotected_evaluate(), IMP::isd::MarginalHBondRestraint::unprotected_evaluate(), IMP::isd::MarginalNOERestraint::unprotected_evaluate(), IMP::isd::NOERestraint::unprotected_evaluate(), IMP::isd::NormalSigmaPCRestraint::unprotected_evaluate(), IMP::isd::Nuisance::add_to_nuisance_derivative(), IMP::isd::RepulsiveDistancePairScore::evaluate_if_good_indexes(), IMP::isd::RepulsiveDistancePairScore::evaluate_index(), IMP::isd::RepulsiveDistancePairScore::evaluate_indexes(), IMP::isd::Scale::add_to_scale_derivative(), IMP::isd::StudentTRestraint::unprotected_evaluate(), IMP::isd::Switching::add_to_switching_derivative(), IMP::isd::TALOSRestraint::unprotected_evaluate(), IMP::isd::UniformPrior::unprotected_evaluate(), IMP::isd::UnivariateFunction::add_to_derivatives(), IMP::isd::UnivariateFunction::add_to_particle_derivative(), IMP::isd::WeightRestraint::unprotected_evaluate(), IMP::isd::vonMisesKappaConjugateRestraint::unprotected_evaluate(), IMP::isd::vonMisesKappaJeffreysRestraint::unprotected_evaluate(), IMP::kinematics::KinematicForestScoreState::do_after_evaluate(), IMP::misc::CustomXYZR::add_to_radius_derivative(), IMP::misc::LogPairScore::evaluate_index(), IMP::misc::LowestRefinedPairScore::evaluate_if_good_indexes(), IMP::misc::LowestRefinedPairScore::evaluate_index(), IMP::misc::LowestRefinedPairScore::evaluate_indexes(), IMP::misc::SoftCylinderPairScore::evaluate_if_good_indexes(), IMP::misc::SoftCylinderPairScore::evaluate_index(), IMP::misc::SoftCylinderPairScore::evaluate_indexes(), IMP::misc::StateAdaptor::do_after_evaluate(), IMP::multifit::ComplementarityRestraint::unprotected_evaluate(), IMP::multifit::DummyRestraint::unprotected_evaluate(), IMP::multifit::RadiusOfGyrationRestraint::unprotected_evaluate(), IMP::multifit::WeightedExcludedVolumeRestraint::unprotected_evaluate(), IMP::npc::AssemblySymmetryByDihedralRestraint::unprotected_evaluate(), IMP::npc::AssemblySymmetryByDistanceRestraint::unprotected_evaluate(), IMP::npc::CompositeRestraint::unprotected_evaluate(), IMP::npc::MembraneExclusionRestraint::unprotected_evaluate(), IMP::npc::MembraneSurfaceLocationConditionalRestraint::unprotected_evaluate(), IMP::npc::MembraneSurfaceLocationRestraint::unprotected_evaluate(), IMP::npc::MinimumSphereDistancePairScore::evaluate_if_good_indexes(), IMP::npc::MinimumSphereDistancePairScore::evaluate_index(), IMP::npc::MinimumSphereDistancePairScore::evaluate_indexes(), IMP::npc::PerinuclearVolumeLocationRestraint::unprotected_evaluate(), IMP::npc::PoreSideVolumeLocationRestraint::unprotected_evaluate(), IMP::npc::ProteinChainRestraint::unprotected_evaluate(), IMP::npc::ProteinContactRestraint::unprotected_evaluate(), IMP::npc::ProteinProximityRestraint::unprotected_evaluate(), IMP::npc::XYRadialPositionLowerRestraint::unprotected_evaluate(), IMP::npc::XYRadialPositionRestraint::unprotected_evaluate(), IMP::npc::XYRadialPositionUpperRestraint::unprotected_evaluate(), IMP::npc::YAxialPositionLowerRestraint::unprotected_evaluate(), IMP::npc::YAxialPositionRestraint::unprotected_evaluate(), IMP::npc::YAxialPositionUpperRestraint::unprotected_evaluate(), IMP::npc::ZAxialPositionLowerRestraint::unprotected_evaluate(), IMP::npc::ZAxialPositionRestraint::unprotected_evaluate(), IMP::npc::ZAxialPositionUpperRestraint::unprotected_evaluate(), IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_if_good_indexes(), IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_index(), IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_indexes(), IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_if_good_indexes(), IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_index(), IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_indexes(), IMP::npctransport::HarmonicSpringSingletonScore::evaluate_if_good_indexes(), IMP::npctransport::HarmonicSpringSingletonScore::evaluate_index(), IMP::npctransport::HarmonicSpringSingletonScore::evaluate_indexes(), IMP::npctransport::HarmonicWellPairScore::evaluate_if_good_indexes(), IMP::npctransport::HarmonicWellPairScore::evaluate_index(), IMP::npctransport::HarmonicWellPairScore::evaluate_indexes(), IMP::npctransport::LinearInteractionPairScore::evaluate_index(), IMP::npctransport::LinearInteractionPairScore::evaluate_if_good_index(), IMP::npctransport::LinearInteractionPairScore::evaluate_indexes(), IMP::npctransport::LinearSoftSpherePairScore::evaluate_index(), IMP::npctransport::LinearSoftSpherePairScore::evaluate_if_good_indexes(), IMP::npctransport::LinearSoftSpherePairScore::evaluate_index(), IMP::npctransport::LinearSoftSpherePairScore::evaluate_indexes(), IMP::npctransport::LinearWellPairScore::evaluate_if_good_indexes(), IMP::npctransport::LinearWellPairScore::evaluate_index(), IMP::npctransport::LinearWellPairScore::evaluate_indexes(), IMP::npctransport::RelaxingSpring::add_to_rest_length_derivative(), IMP::npctransport::SitesPairScore::evaluate_if_good_indexes(), IMP::npctransport::SitesPairScore::evaluate_index(), IMP::npctransport::SitesPairScore::evaluate_indexes(), IMP::npctransport::SitesPairScore::evaluate_site_contributions(), IMP::npctransport::SitesPairScore::evaluate_site_contributions_with_internal_tables(), IMP::npctransport::SitesPairScore::evaluate_index_with_internal_tables(), IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_if_good_indexes(), IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_index(), IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_indexes(), IMP::npctransport::SlabWithPore::add_to_pore_radius_derivative(), IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_if_good_indexes(), IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_index(), IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_indexes(), IMP::npctransport::ZBiasSingletonScore::evaluate_if_good_indexes(), IMP::npctransport::ZBiasSingletonScore::evaluate_index(), IMP::npctransport::ZBiasSingletonScore::evaluate_indexes(), IMP::pmi1::CompositeRestraint::unprotected_evaluate(), IMP::pmi1::MembraneRestraint::unprotected_evaluate(), IMP::pmi1::SigmoidRestraintSphere::unprotected_evaluate(), IMP::pmi::CompositeRestraint::unprotected_evaluate(), IMP::pmi::MembraneRestraint::unprotected_evaluate(), IMP::pmi::SigmoidRestraintSphere::unprotected_evaluate(), IMP::saxs::RadiusOfGyrationRestraint::unprotected_evaluate(), IMP::saxs::Restraint::unprotected_evaluate(), IMP::saxs::RigidBodiesProfileHandler::compute_derivatives(), IMP::score_functor::DistancePairScore::evaluate_if_good_indexes(), IMP::score_functor::DistancePairScore::evaluate_index(), IMP::score_functor::DistancePairScore::evaluate_indexes(), IMP::score_functor::SurfaceDistancePairScore::evaluate_if_good_indexes(), IMP::score_functor::SurfaceDistancePairScore::evaluate_index(), IMP::score_functor::SurfaceDistancePairScore::evaluate_indexes(), IMP::spb::AttributeDistancePairScore::evaluate_if_good_indexes(), IMP::spb::AttributeDistancePairScore::evaluate_index(), IMP::spb::AttributeDistancePairScore::evaluate_indexes(), IMP::spb::DiameterRgyrRestraint::unprotected_evaluate(), IMP::spb::DistanceTerminiRestraint::unprotected_evaluate(), IMP::spb::EM2DRestraint::unprotected_evaluate(), IMP::spb::KinkPairScore::evaluate_if_good_indexes(), IMP::spb::KinkPairScore::evaluate_index(), IMP::spb::KinkPairScore::evaluate_indexes(), IMP::spb::RigidBodyPackingScore::evaluate_if_good_indexes(), IMP::spb::RigidBodyPackingScore::evaluate_index(), IMP::spb::RigidBodyPackingScore::evaluate_indexes(), IMP::spb::TiltSingletonScore::evaluate_if_good_indexes(), IMP::spb::TiltSingletonScore::evaluate_index(), IMP::spb::TiltSingletonScore::evaluate_indexes(), IMP::spb::TwoStateGoModelRestraint::unprotected_evaluate(), IMP::spb::UniformBoundedRestraint::unprotected_evaluate(), IMP::npctransport::do_evaluate_index(), IMP::npctransport::do_evaluate_index_harmonic() |
| IMP::Index | IMP::Index::IMP_COMPARISONS_1(), IMP::Index::IMP_HASHABLE_INLINE(), IMP::IndexVector::at(), IMP::IndexVector::at(), IMP::IndexVector::operator[](), IMP::IndexVector::operator[](), IMP::get_as_unsigned_int(), IMP::resize_to_fit() |
| IMP::Key | IMP::Key::add_alias(), IMP::ScopedAddCacheAttribute::ScopedAddCacheAttribute(), IMP::ScopedAddCacheAttribute::set(), IMP::ScopedSetAttribute::ScopedSetAttribute(), IMP::ScopedSetAttribute::set(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle() |
| IMP::Model | IMP::AttributeOptimizer::AttributeOptimizer(), IMP::Configuration::Configuration(), IMP::Configuration::Configuration(), IMP::ConfigurationSet::ConfigurationSet(), IMP::Constraint::Constraint(), IMP::Container::Container(), IMP::Decorator::Decorator(), IMP::ModelObject::set_model(), IMP::ModelObject::ModelObject(), IMP::Optimizer::Optimizer(), IMP::OptimizerState::OptimizerState(), IMP::PairContainer::PairContainer(), IMP::PairModifier::apply_index(), IMP::PairModifier::apply_indexes(), IMP::PairPredicate::get_value_index(), IMP::PairPredicate::get_value_index(), IMP::PairPredicate::get_value_index_in_batch(), IMP::PairPredicate::operator()(), IMP::PairPredicate::setup_for_get_value_index_in_batch(), IMP::PairScore::create_current_decomposition(), IMP::PairScore::evaluate_if_good_index(), IMP::PairScore::evaluate_if_good_indexes(), IMP::PairScore::evaluate_index(), IMP::PairScore::evaluate_indexes(), IMP::PairScore::do_create_current_decomposition(), IMP::Particle::Particle(), IMP::Particle::Particle(), IMP::ParticleInputs::get_inputs(), IMP::ParticleInputs::do_get_inputs(), IMP::ParticleOutputs::get_outputs(), IMP::ParticleOutputs::do_get_outputs(), IMP::QuadContainer::QuadContainer(), IMP::QuadModifier::apply_index(), IMP::QuadModifier::apply_indexes(), IMP::QuadPredicate::get_value_index(), IMP::QuadPredicate::get_value_index(), IMP::QuadPredicate::get_value_index_in_batch(), IMP::QuadPredicate::operator()(), IMP::QuadPredicate::setup_for_get_value_index_in_batch(), IMP::QuadScore::create_current_decomposition(), IMP::QuadScore::evaluate_if_good_index(), IMP::QuadScore::evaluate_if_good_indexes(), IMP::QuadScore::evaluate_index(), IMP::QuadScore::evaluate_indexes(), IMP::QuadScore::do_create_current_decomposition(), IMP::Refiner::get_refined_indexes(), IMP::Refiner::get_refined_indexes_by_ref(), IMP::Restraint::Restraint(), IMP::RestraintSet::RestraintSet(), IMP::RestraintSet::RestraintSet(), IMP::Sampler::Sampler(), IMP::ScoreState::ScoreState(), IMP::ScoringFunction::ScoringFunction(), IMP::SingletonContainer::SingletonContainer(), IMP::SingletonModifier::apply_index(), IMP::SingletonModifier::apply_indexes(), IMP::SingletonPredicate::get_value_index(), IMP::SingletonPredicate::get_value_index(), IMP::SingletonPredicate::get_value_index_in_batch(), IMP::SingletonPredicate::operator()(), IMP::SingletonPredicate::setup_for_get_value_index_in_batch(), IMP::SingletonScore::create_current_decomposition(), IMP::SingletonScore::evaluate_if_good_index(), IMP::SingletonScore::evaluate_if_good_indexes(), IMP::SingletonScore::evaluate_index(), IMP::SingletonScore::evaluate_indexes(), IMP::SingletonScore::do_create_current_decomposition(), IMP::TripletContainer::TripletContainer(), IMP::TripletModifier::apply_index(), IMP::TripletModifier::apply_indexes(), IMP::TripletPredicate::get_value_index(), IMP::TripletPredicate::get_value_index(), IMP::TripletPredicate::get_value_index_in_batch(), IMP::TripletPredicate::operator()(), IMP::TripletPredicate::setup_for_get_value_index_in_batch(), IMP::TripletScore::create_current_decomposition(), IMP::TripletScore::evaluate_if_good_index(), IMP::TripletScore::evaluate_if_good_indexes(), IMP::TripletScore::evaluate_index(), IMP::TripletScore::evaluate_indexes(), IMP::TripletScore::do_create_current_decomposition(), IMP::Undecorator::Undecorator(), 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::AngularVelocity::do_setup_particle(), IMP::atom::AngularVelocity::get_is_setup(), 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::BrownianDynamicsTAMD::BrownianDynamicsTAMD(), IMP::atom::CAAngleRestraint::CAAngleRestraint(), IMP::atom::CADihedralRestraint::CADihedralRestraint(), 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::set_constraint(), 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::EzRestraint::EzRestraint(), 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::LangevinThermostatOptimizerState::LangevinThermostatOptimizerState(), 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::LinearVelocity::do_setup_particle(), IMP::atom::LinearVelocity::get_is_setup(), 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::do_setup_particle(), IMP::atom::Representation::get_is_setup(), IMP::atom::Representation::setup_particle(), 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::do_setup_particle(), IMP::atom::State::get_is_setup(), IMP::atom::State::setup_particle(), 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::StructureSource::do_setup_particle(), IMP::atom::StructureSource::get_is_setup(), IMP::atom::StructureSource::setup_particle(), IMP::atom::StructureSource::StructureSource(), IMP::atom::TAMDCentroid::do_setup_particle(), IMP::atom::TAMDCentroid::do_setup_particle(), IMP::atom::TAMDCentroid::TAMDCentroid(), IMP::atom::TAMDCentroid::get_is_setup(), IMP::atom::TAMDCentroid::setup_particle(), IMP::atom::TAMDCentroid::setup_particle(), IMP::atom::TAMDParticle::do_setup_particle(), IMP::atom::TAMDParticle::do_setup_particle(), IMP::atom::TAMDParticle::TAMDParticle(), IMP::atom::TAMDParticle::get_is_setup(), IMP::atom::TAMDParticle::setup_particle(), IMP::atom::TAMDParticle::setup_particle(), IMP::atom::VelocityScalingOptimizerState::VelocityScalingOptimizerState(), IMP::atom::WritePDBOptimizerState::WritePDBOptimizerState(), IMP::container::ConsecutivePairContainer::ConsecutivePairContainer(), 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::ExclusiveConsecutivePairContainer::ExclusiveConsecutivePairContainer(), 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::AngleRestraint::AngleRestraint(), 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::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::set_constraint(), 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::ClusterProvenance::do_setup_particle(), IMP::core::ClusterProvenance::do_setup_particle(), IMP::core::ClusterProvenance::get_is_setup(), IMP::core::ClusterProvenance::setup_particle(), IMP::core::ClusterProvenance::setup_particle(), IMP::core::ClusterProvenance::ClusterProvenance(), 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::CombineProvenance::do_setup_particle(), IMP::core::CombineProvenance::do_setup_particle(), IMP::core::CombineProvenance::get_is_setup(), IMP::core::CombineProvenance::setup_particle(), IMP::core::CombineProvenance::setup_particle(), IMP::core::CombineProvenance::CombineProvenance(), 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::ConstantRestraint::ConstantRestraint(), 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::set_constraint(), 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::DihedralRestraint::DihedralRestraint(), IMP::core::Direction::do_setup_particle(), IMP::core::Direction::get_is_setup(), IMP::core::Direction::setup_particle(), IMP::core::Direction::Direction(), IMP::core::DirectionAngle::do_setup_particle(), IMP::core::DirectionAngle::do_setup_particle(), IMP::core::DirectionAngle::DirectionAngle(), IMP::core::DirectionAngle::get_is_setup(), IMP::core::DirectionAngle::setup_particle(), IMP::core::DirectionAngle::setup_particle(), IMP::core::DirectionMover::DirectionMover(), IMP::core::DistancePairScore::do_get_inputs(), IMP::core::DistancePairScore::evaluate_index(), IMP::core::DistanceRestraint::DistanceRestraint(), IMP::core::FilterProvenance::do_setup_particle(), IMP::core::FilterProvenance::do_setup_particle(), IMP::core::FilterProvenance::get_is_setup(), IMP::core::FilterProvenance::setup_particle(), IMP::core::FilterProvenance::setup_particle(), IMP::core::FilterProvenance::FilterProvenance(), IMP::core::FixedRefiner::FixedRefiner(), IMP::core::FixedRefiner::do_get_inputs(), IMP::core::FixedRefiner::get_refined_indexes(), IMP::core::FixedRefiner::get_refined_indexes_by_ref(), 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::GenericBoundingSphere3DSingletonScore::do_get_inputs(), IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_index(), IMP::core::GenericBoundingSphere3DSingletonScore::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::HarmonicSurfaceDepthPairScore::do_get_inputs(), IMP::core::HarmonicSurfaceDepthPairScore::evaluate_index(), IMP::core::HarmonicSurfaceDistancePairScore::do_get_inputs(), IMP::core::HarmonicSurfaceDistancePairScore::evaluate_index(), IMP::core::HarmonicSurfaceHeightPairScore::do_get_inputs(), IMP::core::HarmonicSurfaceHeightPairScore::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::IncrementalScoringFunction::IncrementalScoringFunction(), 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::LogNormalMover::LogNormalMover(), IMP::core::LogNormalMover::LogNormalMover(), IMP::core::MCCGSampler::MCCGSampler(), IMP::core::MSConnectivityRestraint::MSConnectivityRestraint(), IMP::core::MonteCarlo::MonteCarlo(), IMP::core::MonteCarloMover::MonteCarloMover(), IMP::core::MultipleBinormalRestraint::MultipleBinormalRestraint(), 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::OrderedTypePairPredicate::get_value_index_in_batch(), IMP::core::OrderedTypePairPredicate::setup_for_get_value_index_in_batch(), IMP::core::OrderedTypeQuadPredicate::do_get_inputs(), IMP::core::OrderedTypeQuadPredicate::get_value_index(), IMP::core::OrderedTypeQuadPredicate::get_value_index(), IMP::core::OrderedTypeQuadPredicate::get_value_index_in_batch(), IMP::core::OrderedTypeQuadPredicate::setup_for_get_value_index_in_batch(), IMP::core::OrderedTypeSingletonPredicate::do_get_inputs(), IMP::core::OrderedTypeSingletonPredicate::get_value_index(), IMP::core::OrderedTypeSingletonPredicate::get_value_index(), IMP::core::OrderedTypeSingletonPredicate::get_value_index_in_batch(), IMP::core::OrderedTypeSingletonPredicate::setup_for_get_value_index_in_batch(), IMP::core::OrderedTypeTripletPredicate::do_get_inputs(), IMP::core::OrderedTypeTripletPredicate::get_value_index(), IMP::core::OrderedTypeTripletPredicate::get_value_index(), IMP::core::OrderedTypeTripletPredicate::get_value_index_in_batch(), IMP::core::OrderedTypeTripletPredicate::setup_for_get_value_index_in_batch(), 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::Provenance::do_setup_particle(), IMP::core::Provenance::get_is_setup(), IMP::core::Provenance::setup_particle(), IMP::core::Provenance::Provenance(), IMP::core::Provenanced::do_setup_particle(), IMP::core::Provenanced::get_is_setup(), IMP::core::Provenanced::setup_particle(), IMP::core::Provenanced::Provenanced(), IMP::core::QuadConstraint::QuadConstraint(), IMP::core::QuadRestraint::QuadRestraint(), IMP::core::QuadraticClosePairsFinder::do_get_inputs(), IMP::core::QuadraticClosePairsFinder::get_are_close_and_filtered(), 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::RigidBodyAnglePairScore::do_get_inputs(), IMP::core::RigidBodyAnglePairScore::evaluate_if_good_indexes(), IMP::core::RigidBodyAnglePairScore::evaluate_index(), IMP::core::RigidBodyAnglePairScore::evaluate_indexes(), 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::SampleProvenance::do_setup_particle(), IMP::core::SampleProvenance::do_setup_particle(), IMP::core::SampleProvenance::get_is_setup(), IMP::core::SampleProvenance::setup_particle(), IMP::core::SampleProvenance::setup_particle(), IMP::core::SampleProvenance::setup_particle(), IMP::core::SampleProvenance::SampleProvenance(), IMP::core::ScriptProvenance::do_setup_particle(), IMP::core::ScriptProvenance::do_setup_particle(), IMP::core::ScriptProvenance::get_is_setup(), IMP::core::ScriptProvenance::setup_particle(), IMP::core::ScriptProvenance::setup_particle(), IMP::core::ScriptProvenance::ScriptProvenance(), IMP::core::SingletonConstraint::SingletonConstraint(), IMP::core::SingletonRestraint::SingletonRestraint(), IMP::core::SoftSpherePairScore::do_get_inputs(), IMP::core::SoftSpherePairScore::evaluate_index(), IMP::core::SoftSubSurfacePairScore::do_get_inputs(), IMP::core::SoftSubSurfacePairScore::evaluate_index(), IMP::core::SoftSuperSurfacePairScore::do_get_inputs(), IMP::core::SoftSuperSurfacePairScore::evaluate_index(), IMP::core::SoftwareProvenance::do_setup_particle(), IMP::core::SoftwareProvenance::do_setup_particle(), IMP::core::SoftwareProvenance::get_is_setup(), IMP::core::SoftwareProvenance::setup_particle(), IMP::core::SoftwareProvenance::setup_particle(), IMP::core::SoftwareProvenance::SoftwareProvenance(), 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::StructureProvenance::do_setup_particle(), IMP::core::StructureProvenance::do_setup_particle(), IMP::core::StructureProvenance::get_is_setup(), IMP::core::StructureProvenance::setup_particle(), IMP::core::StructureProvenance::setup_particle(), IMP::core::StructureProvenance::setup_particle(), IMP::core::StructureProvenance::StructureProvenance(), IMP::core::Surface::do_setup_particle(), IMP::core::Surface::do_setup_particle(), IMP::core::Surface::get_is_setup(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::Surface(), IMP::core::SurfaceDepthPairScore::do_get_inputs(), IMP::core::SurfaceDepthPairScore::evaluate_index(), IMP::core::SurfaceDistancePairScore::do_get_inputs(), IMP::core::SurfaceDistancePairScore::evaluate_index(), IMP::core::SurfaceHeightPairScore::do_get_inputs(), IMP::core::SurfaceHeightPairScore::evaluate_index(), IMP::core::SurfaceMover::SurfaceMover(), IMP::core::SurfaceSymmetryConstraint::SurfaceSymmetryConstraint(), 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::get_internal_transformation(), IMP::core::TransformationSymmetry::apply_index(), IMP::core::TransformationSymmetry::apply_indexes(), IMP::core::TransformationSymmetry::do_get_inputs(), IMP::core::TransformationSymmetry::do_get_outputs(), IMP::core::TransformationSymmetryMover::TransformationSymmetryMover(), 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::DependencyScoreState::DependencyScoreState(), 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::AtomicCrossLinkMSRestraint::AtomicCrossLinkMSRestraint(), IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint(), IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint(), IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint(), IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint(), IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint(), IMP::isd::GaussianEMRestraint::GaussianEMRestraint(), IMP::isd::GaussianProcessInterpolationRestraint::GaussianProcessInterpolationRestraint(), IMP::isd::HybridMonteCarlo::HybridMonteCarlo(), IMP::isd::ISDRestraint::ISDRestraint(), IMP::isd::JeffreysRestraint::JeffreysRestraint(), 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::NormalSigmaPCRestraint::NormalSigmaPCRestraint(), 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::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), 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::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::kinematics::RevoluteJointMover::RevoluteJointMover(), 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::DecayPairContainerOptimizerState::DecayPairContainerOptimizerState(), 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::multifit::RigidLeavesRefiner::do_get_inputs(), IMP::npc::AssemblySymmetryByDihedralRestraint::AssemblySymmetryByDihedralRestraint(), IMP::npc::AssemblySymmetryByDihedralRestraint::AssemblySymmetryByDihedralRestraint(), IMP::npc::AssemblySymmetryByDistanceRestraint::AssemblySymmetryByDistanceRestraint(), IMP::npc::AssemblySymmetryByDistanceRestraint::AssemblySymmetryByDistanceRestraint(), IMP::npc::CompositeRestraint::CompositeRestraint(), IMP::npc::MembraneExclusionRestraint::MembraneExclusionRestraint(), IMP::npc::MembraneExclusionRestraint::MembraneExclusionRestraint(), IMP::npc::MembraneSurfaceLocationConditionalRestraint::MembraneSurfaceLocationConditionalRestraint(), IMP::npc::MembraneSurfaceLocationConditionalRestraint::MembraneSurfaceLocationConditionalRestraint(), IMP::npc::MembraneSurfaceLocationRestraint::MembraneSurfaceLocationRestraint(), IMP::npc::MembraneSurfaceLocationRestraint::MembraneSurfaceLocationRestraint(), IMP::npc::MinimumSphereDistancePairScore::do_get_inputs(), IMP::npc::MinimumSphereDistancePairScore::evaluate_if_good_indexes(), IMP::npc::MinimumSphereDistancePairScore::evaluate_index(), IMP::npc::MinimumSphereDistancePairScore::evaluate_indexes(), IMP::npc::PerinuclearVolumeLocationRestraint::PerinuclearVolumeLocationRestraint(), IMP::npc::PerinuclearVolumeLocationRestraint::PerinuclearVolumeLocationRestraint(), IMP::npc::PoreSideVolumeLocationRestraint::PoreSideVolumeLocationRestraint(), IMP::npc::PoreSideVolumeLocationRestraint::PoreSideVolumeLocationRestraint(), IMP::npc::ProteinChainRestraint::ProteinChainRestraint(), IMP::npc::ProteinChainRestraint::ProteinChainRestraint(), IMP::npc::ProteinContactRestraint::ProteinContactRestraint(), IMP::npc::ProteinContactRestraint::ProteinContactRestraint(), IMP::npc::ProteinProximityRestraint::ProteinProximityRestraint(), IMP::npc::ProteinProximityRestraint::ProteinProximityRestraint(), IMP::npc::XYRadialPositionLowerRestraint::XYRadialPositionLowerRestraint(), IMP::npc::XYRadialPositionLowerRestraint::XYRadialPositionLowerRestraint(), IMP::npc::XYRadialPositionRestraint::XYRadialPositionRestraint(), IMP::npc::XYRadialPositionRestraint::XYRadialPositionRestraint(), IMP::npc::XYRadialPositionUpperRestraint::XYRadialPositionUpperRestraint(), IMP::npc::XYRadialPositionUpperRestraint::XYRadialPositionUpperRestraint(), IMP::npc::YAxialPositionLowerRestraint::YAxialPositionLowerRestraint(), IMP::npc::YAxialPositionLowerRestraint::YAxialPositionLowerRestraint(), IMP::npc::YAxialPositionRestraint::YAxialPositionRestraint(), IMP::npc::YAxialPositionRestraint::YAxialPositionRestraint(), IMP::npc::YAxialPositionUpperRestraint::YAxialPositionUpperRestraint(), IMP::npc::YAxialPositionUpperRestraint::YAxialPositionUpperRestraint(), IMP::npc::ZAxialPositionLowerRestraint::ZAxialPositionLowerRestraint(), IMP::npc::ZAxialPositionLowerRestraint::ZAxialPositionLowerRestraint(), IMP::npc::ZAxialPositionRestraint::ZAxialPositionRestraint(), IMP::npc::ZAxialPositionRestraint::ZAxialPositionRestraint(), IMP::npc::ZAxialPositionUpperRestraint::ZAxialPositionUpperRestraint(), IMP::npc::ZAxialPositionUpperRestraint::ZAxialPositionUpperRestraint(), IMP::npctransport::AnchorToCylidnricalPorePairScore::do_get_inputs(), IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_if_good_indexes(), IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_index(), IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_indexes(), IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport::BrownianDynamicsTAMDWithSlabSupport(), IMP::npctransport::ExcludeZRangeSingletonScore::do_get_inputs(), IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_if_good_indexes(), IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_index(), IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_indexes(), IMP::npctransport::HarmonicSpringSingletonScore::do_get_inputs(), IMP::npctransport::HarmonicSpringSingletonScore::evaluate_if_good_indexes(), IMP::npctransport::HarmonicSpringSingletonScore::evaluate_index(), IMP::npctransport::HarmonicSpringSingletonScore::evaluate_indexes(), IMP::npctransport::HarmonicWellPairScore::do_get_inputs(), IMP::npctransport::HarmonicWellPairScore::evaluate_if_good_indexes(), IMP::npctransport::HarmonicWellPairScore::evaluate_index(), IMP::npctransport::HarmonicWellPairScore::evaluate_indexes(), IMP::npctransport::HierarchyWithSitesLoadLink::do_link_particle(), IMP::npctransport::HierarchyWithSitesLoadLink::do_load_hierarchy(), IMP::npctransport::HierarchyWithSitesLoadLink::do_setup_particle(), IMP::npctransport::HierarchyWithSitesSaveLink::do_save_hierarchy(), IMP::npctransport::HierarchyWithSitesSaveLink::do_setup_node(), IMP::npctransport::LinearInteraction::get_is_trivially_zero(), IMP::npctransport::LinearInteraction::get_maximum_range(), IMP::npctransport::LinearInteraction::get_score(), IMP::npctransport::LinearInteraction::get_score_and_derivative(), IMP::npctransport::LinearInteractionPairScore::do_get_inputs(), IMP::npctransport::LinearInteractionPairScore::evaluate_if_good_index(), IMP::npctransport::LinearInteractionPairScore::evaluate_indexes(), IMP::npctransport::LinearSoftSpherePairScore::do_get_inputs(), IMP::npctransport::LinearSoftSpherePairScore::evaluate_if_good_indexes(), IMP::npctransport::LinearSoftSpherePairScore::evaluate_index(), IMP::npctransport::LinearSoftSpherePairScore::evaluate_indexes(), IMP::npctransport::LinearWellPairScore::do_get_inputs(), IMP::npctransport::LinearWellPairScore::evaluate_if_good_indexes(), IMP::npctransport::LinearWellPairScore::evaluate_index(), IMP::npctransport::LinearWellPairScore::evaluate_indexes(), IMP::npctransport::PoreRadiusSingletonScore::do_get_inputs(), IMP::npctransport::RelaxingSpring::do_setup_particle(), IMP::npctransport::RelaxingSpring::RelaxingSpring(), IMP::npctransport::RelaxingSpring::get_is_setup(), IMP::npctransport::RelaxingSpring::setup_particle(), IMP::npctransport::SitesPairScore::do_get_inputs(), IMP::npctransport::SitesPairScore::evaluate_if_good_indexes(), IMP::npctransport::SitesPairScore::evaluate_index(), IMP::npctransport::SitesPairScore::evaluate_indexes(), IMP::npctransport::SitesPairScore::evaluate_site_contributions(), IMP::npctransport::SitesPairScore::evaluate_index_with_internal_tables(), IMP::npctransport::SlabWithCylindricalPore::do_setup_particle(), IMP::npctransport::SlabWithCylindricalPore::SlabWithCylindricalPore(), IMP::npctransport::SlabWithCylindricalPore::get_is_setup(), IMP::npctransport::SlabWithCylindricalPore::setup_particle(), IMP::npctransport::SlabWithCylindricalPorePairScore::do_get_inputs(), IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_if_good_indexes(), IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_index(), IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_indexes(), IMP::npctransport::SlabWithPore::do_setup_particle(), IMP::npctransport::SlabWithPore::SlabWithPore(), IMP::npctransport::SlabWithPore::get_is_setup(), IMP::npctransport::SlabWithPore::setup_particle(), IMP::npctransport::SlabWithToroidalPore::do_setup_particle(), IMP::npctransport::SlabWithToroidalPore::SlabWithToroidalPore(), IMP::npctransport::SlabWithToroidalPore::get_is_setup(), IMP::npctransport::SlabWithToroidalPore::setup_particle(), IMP::npctransport::SlabWithToroidalPore::setup_particle(), IMP::npctransport::SlabWithToroidalPorePairScore::do_get_inputs(), IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_if_good_indexes(), IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_index(), IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_indexes(), IMP::npctransport::Transporting::do_setup_particle(), IMP::npctransport::Transporting::Transporting(), IMP::npctransport::Transporting::get_is_setup(), IMP::npctransport::Transporting::setup_particle(), IMP::npctransport::ZBiasSingletonScore::do_get_inputs(), IMP::npctransport::ZBiasSingletonScore::evaluate_if_good_indexes(), IMP::npctransport::ZBiasSingletonScore::evaluate_index(), IMP::npctransport::ZBiasSingletonScore::evaluate_indexes(), IMP::pmi1::CompositeRestraint::CompositeRestraint(), IMP::pmi1::InternalCoordinatesConstraint::apply_index(), IMP::pmi1::InternalCoordinatesConstraint::apply_indexes(), IMP::pmi1::InternalCoordinatesConstraint::do_get_inputs(), IMP::pmi1::InternalCoordinatesConstraint::do_get_outputs(), IMP::pmi1::MembraneRestraint::MembraneRestraint(), IMP::pmi1::Resolution::do_setup_particle(), IMP::pmi1::Resolution::get_is_setup(), IMP::pmi1::Resolution::setup_particle(), IMP::pmi1::Resolution::Resolution(), IMP::pmi1::SigmoidRestraintSphere::SigmoidRestraintSphere(), IMP::pmi1::Symmetric::do_setup_particle(), IMP::pmi1::Symmetric::get_is_setup(), IMP::pmi1::Symmetric::setup_particle(), IMP::pmi1::Symmetric::Symmetric(), IMP::pmi1::TransformMover::TransformMover(), IMP::pmi1::TransformMover::TransformMover(), IMP::pmi1::TransformMover::TransformMover(), IMP::pmi1::Uncertainty::do_setup_particle(), IMP::pmi1::Uncertainty::get_is_setup(), IMP::pmi1::Uncertainty::setup_particle(), IMP::pmi1::Uncertainty::Uncertainty(), IMP::pmi::CompositeRestraint::CompositeRestraint(), IMP::pmi::InternalCoordinatesConstraint::apply_index(), IMP::pmi::InternalCoordinatesConstraint::apply_indexes(), IMP::pmi::InternalCoordinatesConstraint::do_get_inputs(), IMP::pmi::InternalCoordinatesConstraint::do_get_outputs(), IMP::pmi::MembraneRestraint::MembraneRestraint(), IMP::pmi::Resolution::do_setup_particle(), IMP::pmi::Resolution::get_is_setup(), IMP::pmi::Resolution::setup_particle(), IMP::pmi::Resolution::Resolution(), IMP::pmi::SigmoidRestraintSphere::SigmoidRestraintSphere(), IMP::pmi::Symmetric::do_setup_particle(), IMP::pmi::Symmetric::get_is_setup(), IMP::pmi::Symmetric::setup_particle(), IMP::pmi::Symmetric::Symmetric(), IMP::pmi::TransformMover::TransformMover(), IMP::pmi::TransformMover::TransformMover(), IMP::pmi::TransformMover::TransformMover(), IMP::pmi::Uncertainty::do_setup_particle(), IMP::pmi::Uncertainty::get_is_setup(), IMP::pmi::Uncertainty::setup_particle(), IMP::pmi::Uncertainty::Uncertainty(), IMP::rmf::HierarchyLoadLink::add_link_recursive(), IMP::rmf::HierarchyLoadLink::create_one_provenance(), IMP::rmf::HierarchyLoadLink::create_provenance(), 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::HierarchySaveLink::add_provenance(), IMP::rmf::HierarchySaveLink::add_recursive(), IMP::rmf::HierarchySaveLink::do_save_hierarchy(), IMP::rmf::HierarchySaveLink::do_setup_node(), 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::PointToSphereDistance::get_radius(), IMP::score_functor::PointToSphereDistance::get_is_trivially_zero(), IMP::score_functor::PointToSphereDistance::get_maximum_range(), IMP::score_functor::PointToSphereDistance::get_score(), IMP::score_functor::PointToSphereDistance::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::SurfaceDistancePairScore::do_get_inputs(), IMP::score_functor::SurfaceDistancePairScore::evaluate_if_good_indexes(), IMP::score_functor::SurfaceDistancePairScore::evaluate_index(), IMP::score_functor::SurfaceDistancePairScore::evaluate_indexes(), 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::spb::AttributeDistancePairScore::do_get_inputs(), IMP::spb::AttributeDistancePairScore::evaluate_if_good_indexes(), IMP::spb::AttributeDistancePairScore::evaluate_index(), IMP::spb::AttributeDistancePairScore::evaluate_indexes(), IMP::spb::HelixDecorator::HelixDecorator(), IMP::spb::HelixDecorator::get_is_setup(), IMP::spb::ISDRestraint::ISDRestraint(), IMP::spb::KinkPairScore::do_get_inputs(), IMP::spb::KinkPairScore::evaluate_if_good_indexes(), IMP::spb::KinkPairScore::evaluate_index(), IMP::spb::KinkPairScore::evaluate_indexes(), IMP::spb::MolecularDynamicsWithWte::MolecularDynamicsWithWte(), IMP::spb::MonteCarloWithWte::MonteCarloWithWte(), IMP::spb::MonteCarloWithWte::MonteCarloWithWte(), IMP::spb::NuisanceRangeModifier::apply_index(), IMP::spb::NuisanceRangeModifier::apply_indexes(), IMP::spb::NuisanceRangeModifier::do_get_inputs(), IMP::spb::NuisanceRangeModifier::do_get_outputs(), IMP::spb::RigidBodyPackingScore::do_get_inputs(), IMP::spb::RigidBodyPackingScore::evaluate_if_good_indexes(), IMP::spb::RigidBodyPackingScore::evaluate_index(), IMP::spb::RigidBodyPackingScore::evaluate_indexes(), IMP::spb::SameParticlePairFilter::do_get_inputs(), IMP::spb::SameParticlePairFilter::get_value_index(), IMP::spb::SameParticlePairFilter::get_value_index(), IMP::spb::SameRigidBodyPairFilter::do_get_inputs(), IMP::spb::SameRigidBodyPairFilter::get_value_index(), IMP::spb::SameRigidBodyPairFilter::get_value_index(), IMP::spb::TiltSingletonScore::do_get_inputs(), IMP::spb::TiltSingletonScore::evaluate_if_good_indexes(), IMP::spb::TiltSingletonScore::evaluate_index(), IMP::spb::TiltSingletonScore::evaluate_indexes(), IMP::spb::TransformationSymmetry::apply_index(), IMP::spb::TransformationSymmetry::apply_indexes(), IMP::spb::TransformationSymmetry::do_get_inputs(), IMP::spb::TransformationSymmetry::do_get_outputs(), IMP::get_dependency_graph(), IMP::get_particles(), IMP::get_pruned_dependency_graph(), IMP::make_predicate_equal(), IMP::make_predicate_not_equal(), 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::read_mmcif(), IMP::atom::read_multimodel_mmcif(), IMP::atom::setup_coarse_secondary_structure_residue(), IMP::atom::setup_coarse_secondary_structure_residues(), IMP::core::add_provenance(), IMP::core::create_rigid_bodies(), IMP::core::create_xyzr_particles(), IMP::core::get_initial_reference_frame(), IMP::em::density2particles(), IMP::example::create_chain_restraint(), IMP::example::create_excluded_volume(), IMP::example::create_serial_mover(), IMP::example::optimize_assembly(), IMP::example::optimize_balls(), IMP::multifit::create_coarse_molecule_from_density(), IMP::multifit::load_ensemble(), IMP::npctransport::create_hierarchies_with_sites(), IMP::npctransport::do_evaluate_index_harmonic(), IMP::rmf::create_hierarchies(), IMP::rmf::create_particles(), IMP::rmf::create_restraints(), IMP::saxs::read_files(), IMP::saxs::read_pdb(), IMP::spb::add_GFP_restraint(), IMP::spb::add_internal_restraint(), IMP::spb::add_ISD_particles(), IMP::spb::add_link(), IMP::spb::add_link(), IMP::spb::add_my_connectivity(), IMP::spb::add_restrain_coiledcoil_to_cterm(), IMP::spb::add_SPBexcluded_volume(), IMP::spb::add_stay_close_restraint(), IMP::spb::add_stay_close_restraint(), IMP::spb::add_stay_on_plane_restraint(), IMP::spb::add_symmetry_restraint(), IMP::spb::add_tilt(), IMP::spb::add_tilt_restraint(), IMP::spb::create_coiled_coil(), IMP::spb::create_GFP(), IMP::spb::create_merged_protein(), IMP::spb::create_protein(), IMP::spb::create_protein(), IMP::spb::create_representation(), IMP::spb::do_bipartite_mindist(), IMP::spb::do_bipartite_mindist(), IMP::spb::setup_SPBMonteCarlo(), IMP::spb::spb_assemble_restraints(), IMP::spb::y2h_restraint(), IMP::spb::y2h_restraint(), IMP::spb::y2h_restraint(), IMP::spb::y2h_restraint() |
| IMP::ModelObject | IMP::Model::check_dependency_invariants(), IMP::Model::do_add_dependencies(), IMP::Model::do_add_model_object(), IMP::Model::do_check_inputs_and_outputs(), IMP::Model::do_check_not_in_readers_and_writers(), IMP::Model::do_check_readers_and_writers(), IMP::Model::do_check_required_score_states(), IMP::Model::do_clear_dependencies(), IMP::Model::do_clear_required_score_states(), IMP::Model::do_get_has_dependencies(), IMP::Model::do_get_has_required_score_states(), IMP::Model::do_get_required_score_states(), IMP::Model::do_remove_model_object(), IMP::Model::do_set_has_dependencies(), IMP::Model::do_set_has_required_score_states(), IMP::Model::get_ancestor_score_states(), IMP::Model::get_dependency_graph_inputs(), IMP::Model::get_dependency_graph_outputs(), IMP::Model::get_descendent_score_states(), IMP::get_dependent_particles(), IMP::get_required_score_states() |
| IMP::Object | IMP::CreateLogContext::CreateLogContext(), IMP::CreateLogContext::CreateLogContext(), IMP::CreateLogContext::set(), IMP::Decorator::compare(), IMP::Model::add_data(), IMP::Object::add_live_object(), IMP::Object::remove_live_object(), IMP::Object::compare(), IMP::SetCheckState::do_set(), IMP::SetCheckState::SetCheckState(), IMP::SetCheckState::set(), IMP::SetLogState::do_set(), IMP::SetLogState::SetLogState(), IMP::SetLogState::set(), IMP::object_cast(), IMP::rmf::get_node_from_association(), IMP::rmf::get_node_from_association(), IMP::rmf::get_has_associated_node(), IMP::rmf::set_association() |
| IMP::Optimizer | IMP::Optimizer::set_optimizer_state_optimizer(), IMP::OptimizerState::set_optimizer(), IMP::core::MCCGSampler::set_local_optimizer(), IMP::core::MonteCarloWithBasinHopping::MonteCarloWithBasinHopping(), IMP::core::MonteCarloWithLocalOptimization::MonteCarloWithLocalOptimization(), IMP::npctransport::Statistics::add_optimizer_states(), IMP::container::get_slack_estimate() |
| IMP::OptimizerState | IMP::Optimizer::remove_optimizer_state(), IMP::Optimizer::add_optimizer_state(), IMP::Optimizer::set_optimizer_state_optimizer(), IMP::core::MCCGSampler::remove_optimizer_state(), IMP::core::MCCGSampler::add_optimizer_state(), IMP::misc::StateAdaptor::StateAdaptor() |
| IMP::PairContainer | IMP::PairContainerAdaptor::PairContainerAdaptor(), IMP::container::InContainerPairFilter::InContainerPairFilter(), IMP::container::InContainerPairFilter::InContainerPairFilter(), IMP::container::PairContainerSet::remove_pair_container(), IMP::container::PairContainerSet::add_pair_container(), IMP::container::PairContainerSet::get_set(), IMP::core::EdgePairsGeometry::EdgePairsGeometry(), IMP::core::NeighborsTable::NeighborsTable(), IMP::display::PairsGeometry::PairsGeometry(), IMP::display::PairsGeometry::PairsGeometry(), IMP::isd::AmbiguousNOERestraint::AmbiguousNOERestraint(), IMP::isd::MarginalHBondRestraint::add_contribution(), IMP::isd::MarginalNOERestraint::add_contribution(), IMP::npctransport::Scoring::create_predicates_pair_restraint() |
| IMP::PairContainerAdaptor | IMP::container::DistributePairsScoreState::DistributePairsScoreState(), IMP::container::EventPairsOptimizerState::EventPairsOptimizerState(), IMP::container::MinimumPairRestraint::MinimumPairRestraint(), IMP::container::PairContainerStatistics::PairContainerStatistics(), IMP::container::PairsConstraint::PairsConstraint(), IMP::container::PairsOptimizerState::PairsOptimizerState(), IMP::container::PairsRestraint::PairsRestraint(), IMP::container::PredicatePairsRestraint::PredicatePairsRestraint() |
| IMP::PairModifier | IMP::PairContainer::apply(), IMP::PairContainer::apply_generic(), IMP::PairContainer::do_apply(), IMP::atom::BondPairContainer::do_apply(), IMP::container::AllBipartitePairContainer::do_apply(), IMP::container::AllPairContainer::do_apply(), IMP::container::CloseBipartitePairContainer::do_apply(), IMP::container::ClosePairContainer::do_apply(), IMP::container::ConnectingPairContainer::do_apply(), IMP::container::ConsecutivePairContainer::do_apply(), IMP::container::ExclusiveConsecutivePairContainer::do_apply(), IMP::container::PairsConstraint::PairsConstraint(), IMP::container::PairsOptimizerState::PairsOptimizerState(), IMP::core::PairConstraint::PairConstraint(), IMP::core::PairConstraint::PairConstraint() |
| IMP::PairPredicate | IMP::container::CloseBipartitePairContainer::remove_pair_filter(), IMP::container::CloseBipartitePairContainer::add_pair_filter(), IMP::container::ClosePairContainer::remove_pair_filter(), IMP::container::ClosePairContainer::add_pair_filter(), IMP::container::DistributePairsScoreState::add_predicate(), IMP::container::EventPairsOptimizerState::EventPairsOptimizerState(), IMP::container::PredicatePairsRestraint::PredicatePairsRestraint(), IMP::core::ClosePairsFinder::remove_pair_filter(), IMP::core::ClosePairsFinder::add_pair_filter(), IMP::core::ExcludedVolumeRestraint::add_pair_filter(), IMP::core::ExcludedVolumeRestraint::remove_pair_filter(), IMP::misc::DecayPairContainerOptimizerState::DecayPairContainerOptimizerState() |
| IMP::PairScore | IMP::container::MinimumPairRestraint::MinimumPairRestraint(), IMP::container::PairsRestraint::PairsRestraint(), IMP::container::PredicatePairsRestraint::set_score(), IMP::container::PredicatePairsRestraint::set_unknown_score(), IMP::core::ClosePairsPairScore::ClosePairsPairScore(), IMP::core::ConnectivityRestraint::ConnectivityRestraint(), IMP::core::IncrementalScoringFunction::add_close_pair_score(), IMP::core::IncrementalScoringFunction::add_close_pair_score(), IMP::core::KClosePairsPairScore::KClosePairsPairScore(), IMP::core::MSConnectivityRestraint::MSConnectivityRestraint(), IMP::core::PairRestraint::PairRestraint(), IMP::core::RefinedPairsPairScore::RefinedPairsPairScore(), IMP::core::RigidBodyDistancePairScore::RigidBodyDistancePairScore(), IMP::core::TypedPairScore::set_pair_score(), IMP::misc::LowestRefinedPairScore::LowestRefinedPairScore(), IMP::npc::CompositeRestraint::CompositeRestraint(), IMP::rotamer::RotamerCalculator::transform(), IMP::example::optimize_assembly() |
| IMP::Particle | IMP::Model::add_particle_internal(), IMP::ParticleAdaptor::ParticleAdaptor(), IMP::ParticleAdaptor::ParticleAdaptor(), IMP::ParticleAdaptor::ParticleAdaptor(), IMP::ParticleAdaptor::ParticleAdaptor(), IMP::ParticleIndexAdaptor::ParticleIndexAdaptor(), IMP::Refiner::refined_begin(), IMP::Refiner::refined_end(), IMP::Refiner::get_can_refine(), IMP::Refiner::get_number_of_refined(), IMP::Refiner::get_refined(), IMP::Refiner::get_refined(), IMP::ScopedAddCacheAttribute::ScopedAddCacheAttribute(), IMP::ScopedAddCacheAttribute::set(), IMP::ScopedSetAttribute::ScopedSetAttribute(), IMP::ScopedSetAttribute::set(), IMP::SingletonPredicate::get_value(), IMP::atom::BondEndpointsRefiner::get_can_refine(), IMP::atom::BondEndpointsRefiner::get_refined(), IMP::atom::BondGeometry::BondGeometry(), IMP::atom::CHARMMParameters::add_angle(), IMP::atom::CHARMMParameters::add_dihedral(), IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::Selection::Selection(), IMP::atom::Simulator::remove_particle(), IMP::atom::Simulator::add_particle(), IMP::atom::TAMDParticle::do_setup_particle(), IMP::atom::TAMDParticle::setup_particle(), IMP::atom::TAMDParticle::setup_particle(), IMP::container::InContainerSingletonFilter::get_value(), IMP::core::AllSameSingletonPredicate::get_value(), IMP::core::AttributeSingletonPredicate::get_value(), IMP::core::ChildrenRefiner::get_can_refine(), IMP::core::ChildrenRefiner::get_refined(), IMP::core::CoinFlipSingletonPredicate::get_value(), IMP::core::ConstantSingletonPredicate::get_value(), IMP::core::FixedRefiner::get_can_refine(), IMP::core::FixedRefiner::get_refined(), IMP::core::InBoundingBox3DSingletonPredicate::get_value(), IMP::core::LeavesRefiner::get_can_refine(), IMP::core::LeavesRefiner::get_refined(), IMP::core::OrderedTypeSingletonPredicate::get_value(), IMP::core::QuadraticClosePairsFinder::get_are_close_and_filtered(), IMP::core::RigidBody::add_member_internal(), IMP::core::RigidBody::teardown_constraints(), IMP::core::RigidBodyDerivativeGeometry::RigidBodyDerivativeGeometry(), IMP::core::RigidBodyFrameGeometry::RigidBodyFrameGeometry(), IMP::core::RigidBodyTorque::extract_geometry(), IMP::core::RigidBodyTorque::RigidBodyTorque(), IMP::core::SingletonConstraint::SingletonConstraint(), IMP::core::TableRefiner::add_particle(), IMP::core::TableRefiner::get_can_refine(), IMP::core::TableRefiner::get_refined(), IMP::core::TableRefiner::remove_particle(), IMP::core::TableRefiner::set_particle(), IMP::core::TypedPairScore::set_particle_type(), IMP::core::UnorderedTypeSingletonPredicate::get_value(), IMP::core::XYZDerivativeGeometry::XYZDerivativeGeometry(), IMP::core::XYZRGeometry::XYZRGeometry(), IMP::display::SingletonGeometry::SingletonGeometry(), IMP::domino::CompoundStates::load_particle_state(), IMP::domino::DiscreteSampler::set_particle_states(), IMP::domino::DisjointSetsSubsetFilterTable::get_index(), IMP::domino::IndexStates::load_particle_state(), IMP::domino::ListSubsetFilterTable::get_number_of_particle_states(), IMP::domino::ListSubsetFilterTable::set_allowed_states(), IMP::domino::NestedRigidBodyStates::load_particle_state(), IMP::domino::ParticleStates::load_particle_state(), IMP::domino::ParticleStatesTable::get_has_particle(), IMP::domino::ParticleStatesTable::get_particle_states(), IMP::domino::ParticleStatesTable::set_particle_states(), IMP::domino::PermutationStates::load_particle_state(), IMP::domino::RecursiveStates::RecursiveStates(), IMP::domino::RecursiveStates::load_particle_state(), IMP::domino::RigidBodyStates::load_particle_state(), IMP::domino::XYZStates::load_particle_state(), IMP::em2d::DummyRestraint::DummyRestraint(), IMP::em2d::GridStates::load_particle_state(), IMP::em2d::ProjectionParametersScoreState::ProjectionParametersScoreState(), IMP::em2d::ProjectionStates::load_particle_state(), IMP::em::DensityFillingRestraint::add_particle(), IMP::em::DensityFillingRestraint::remove_particle(), IMP::em::EnvelopePenetrationRestraint::add_particle(), IMP::em::EnvelopePenetrationRestraint::remove_particle(), IMP::em::FitRestraint::add_particle(), IMP::em::FitRestraint::remove_particle(), IMP::em::PCAFitRestraint::add_particle(), IMP::em::PCAFitRestraint::remove_particle(), IMP::example::ExampleConstraint::ExampleConstraint(), IMP::isd::Covariance1DFunction::Covariance1DFunction(), IMP::isd::FretRestraint::get_current_center(), IMP::isd::FretRestraint::get_current_centers(), IMP::isd::FretRestraint::FretRestraint(), IMP::isd::FretRestraint::FretRestraint(), IMP::isd::FretRestraint::FretRestraint(), IMP::isd::GaussianAnchorEMRestraint::GaussianAnchorEMRestraint(), IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GeneralizedGuinierPorodFunction::GeneralizedGuinierPorodFunction(), IMP::isd::JeffreysRestraint::JeffreysRestraint(), IMP::isd::Linear1DFunction::Linear1DFunction(), IMP::isd::LognormalAmbiguousRestraint::LognormalAmbiguousRestraint(), IMP::isd::LognormalAmbiguousRestraint::add_contribution(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::MarginalHBondRestraint::add_contribution(), IMP::isd::MarginalNOERestraint::add_contribution(), IMP::isd::NOERestraint::NOERestraint(), IMP::isd::Nuisance::set_lower(), IMP::isd::Nuisance::set_upper(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::UniformPrior::UniformPrior(), IMP::isd::WeightMover::WeightMover(), IMP::isd::WeightRestraint::WeightRestraint(), IMP::isd::vonMisesKappaConjugateRestraint::vonMisesKappaConjugateRestraint(), IMP::isd::vonMisesKappaJeffreysRestraint::vonMisesKappaJeffreysRestraint(), IMP::kinematics::KinematicForest::reset_root(), IMP::kinematics::KinematicForest::get_children(), IMP::kinematics::KinematicForest::get_parent(), IMP::multifit::DummyRestraint::DummyRestraint(), IMP::multifit::FittingStates::load_particle_state(), IMP::multifit::ProbabilisticAnchorGraph::get_are_probabilities_for_particle_set(), IMP::multifit::ProbabilisticAnchorGraph::get_particle_anchors(), IMP::multifit::ProbabilisticAnchorGraph::get_particle_probabilities(), IMP::multifit::ProbabilisticAnchorGraph::set_particle_probabilities_on_anchors(), IMP::multifit::RadiusOfGyrationRestraint::add_particle(), IMP::multifit::RadiusOfGyrationRestraint::remove_particle(), IMP::multifit::RigidLeavesRefiner::get_can_refine(), IMP::multifit::RigidLeavesRefiner::get_refined(), IMP::multifit::WeightedExcludedVolumeRestraint::add_particle(), IMP::multifit::WeightedExcludedVolumeRestraint::remove_particle(), IMP::npctransport::BodyStatisticsOptimizerState::BodyStatisticsOptimizerState(), IMP::npctransport::FGChain::FGChain(), IMP::npctransport::FGChain::set_root(), IMP::npctransport::ParticleTransportStatisticsOptimizerState::ParticleTransportStatisticsOptimizerState(), IMP::npctransport::Scoring::add_restrained_anchor_bead(), IMP::npctransport::Scoring::add_z_bias_restraint(), IMP::npctransport::Scoring::get_site_interactions_statistics(), IMP::npctransport::SitesGeometry::SitesGeometry(), IMP::npctransport::Statistics::add_floater_stats(), IMP::npctransport::Statistics::update_particle_type_xyz_distribution_map(), IMP::npctransport::Statistics::update_particle_type_zr_distribution_map(), IMP::rmf::HierarchyLoadLink::do_add_link(), IMP::rmf::HierarchyLoadLink::do_load_one(), IMP::rmf::HierarchySaveLink::do_add(), IMP::rmf::HierarchySaveLink::do_save_one(), IMP::rmf::HierarchySaveLink::get_type(), IMP::saxs::DeltaDistributionFunction::calculate_derivative_distribution(), IMP::saxs::FormFactorTable::get_dummy_form_factor(), IMP::saxs::FormFactorTable::get_dummy_form_factors(), IMP::saxs::FormFactorTable::get_form_factor(), IMP::saxs::FormFactorTable::get_form_factors(), IMP::saxs::FormFactorTable::get_radius(), IMP::saxs::FormFactorTable::get_vacuum_form_factor(), IMP::saxs::FormFactorTable::get_vacuum_form_factors(), IMP::saxs::FormFactorTable::get_volume(), IMP::saxs::FormFactorTable::get_form_factor_atom_type(), IMP::spb::BoxedMover::BoxedMover(), IMP::spb::CellMover::CellMover(), IMP::spb::DistanceRMSDMetric::DistanceRMSDMetric(), IMP::spb::DistanceTerminiRestraint::DistanceTerminiRestraint(), IMP::spb::EM2DRestraint::EM2DRestraint(), IMP::spb::HelixDecorator::setup_particle(), IMP::spb::PbcBoxedMover::PbcBoxedMover(), IMP::spb::PbcBoxedRigidBodyMover::PbcBoxedRigidBodyMover(), IMP::spb::TransformationSymmetry::TransformationSymmetry(), IMP::spb::UniformBoundedRestraint::UniformBoundedRestraint(), IMP::symmetry::BallMover::BallMover(), IMP::get_vector_geometry(), IMP::get_vector_geometry(), IMP::get_vector_geometry(), IMP::set_vector_geometry(), IMP::set_vector_geometry(), IMP::set_vector_geometry(), IMP::atom::setup_as_approximation(), IMP::em::local_rigid_fitting(), IMP::em::local_rigid_fitting_around_point(), IMP::em::local_rigid_fitting_around_points(), IMP::multifit::get_close_to_point(), IMP::npctransport::copy_hierarchy_reference_frame_recursive(), IMP::npctransport::copy_particle_reference_frame_if_applicable(), IMP::npctransport::get_fg_chain(), IMP::npctransport::get_global_from_local_v3(), IMP::rmf::add_particle(), IMP::spb::add_bayesian_layer_restraint(), IMP::spb::add_NuisanceMover(), IMP::spb::add_PbcBoxedMover(), IMP::spb::add_PbcBoxedRigidBodyMover(), IMP::spb::add_restrain_coiledcoil_to_cterm(), IMP::spb::add_restrain_protein_length(), IMP::spb::add_symmetry_restraint(), IMP::spb::add_tilt_restraint(), IMP::spb::create_GFP(), IMP::spb::create_representation(), IMP::spb::em2d_restraint(), IMP::spb::fret_restraint(), IMP::spb::fret_restraint(), IMP::spb::fret_restraint(), IMP::spb::spb_assemble_restraints() |
| IMP::ParticleAdaptor | IMP::Decorator::Decorator(), IMP::atom::Angle::Angle(), IMP::atom::Angle::get_is_setup(), IMP::atom::Angle::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::Bonded::Bonded(), IMP::atom::Bonded::get_is_setup(), IMP::atom::Bonded::setup_particle(), IMP::atom::CHARMMAtom::CHARMMAtom(), IMP::atom::CHARMMAtom::get_is_setup(), IMP::atom::CHARMMAtom::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::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::Charged(), IMP::atom::Charged::get_is_setup(), IMP::atom::Charged::setup_particle(), IMP::atom::Charged::setup_particle(), IMP::atom::Copy::get_is_setup(), IMP::atom::Copy::setup_particle(), IMP::atom::Copy::Copy(), 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::Dihedral(), IMP::atom::Dihedral::get_is_setup(), IMP::atom::Dihedral::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::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::LennardJones::LennardJones(), IMP::atom::LennardJones::get_is_setup(), IMP::atom::LennardJones::setup_particle(), IMP::atom::LennardJones::setup_particle(), IMP::atom::Mass::get_is_setup(), IMP::atom::Mass::setup_particle(), IMP::atom::Mass::Mass(), IMP::atom::Molecule::Molecule(), IMP::atom::Molecule::get_is_setup(), IMP::atom::Molecule::setup_particle(), IMP::atom::Molecule::setup_particle(), IMP::atom::Representation::get_is_setup(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::Representation(), 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::RigidBodyDiffusion(), IMP::atom::RigidBodyDiffusion::get_is_setup(), IMP::atom::RigidBodyDiffusion::setup_particle(), IMP::atom::SecondaryStructureResidue::SecondaryStructureResidue(), IMP::atom::SecondaryStructureResidue::get_is_setup(), IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::State::get_is_setup(), IMP::atom::State::setup_particle(), IMP::atom::State::setup_particle(), IMP::atom::State::State(), IMP::atom::StructureSource::get_is_setup(), IMP::atom::StructureSource::setup_particle(), IMP::atom::StructureSource::StructureSource(), IMP::atom::TAMDCentroid::TAMDCentroid(), IMP::atom::TAMDCentroid::get_is_setup(), IMP::atom::TAMDCentroid::setup_particle(), IMP::atom::TAMDCentroid::setup_particle(), IMP::atom::TAMDParticle::TAMDParticle(), IMP::atom::TAMDParticle::get_is_setup(), IMP::atom::TAMDParticle::setup_particle(), IMP::atom::TAMDParticle::setup_particle(), IMP::core::Centroid::Centroid(), IMP::core::Centroid::get_is_setup(), IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle(), IMP::core::ClusterProvenance::get_is_setup(), IMP::core::ClusterProvenance::setup_particle(), IMP::core::ClusterProvenance::setup_particle(), IMP::core::ClusterProvenance::ClusterProvenance(), IMP::core::CombineProvenance::get_is_setup(), IMP::core::CombineProvenance::setup_particle(), IMP::core::CombineProvenance::setup_particle(), IMP::core::CombineProvenance::CombineProvenance(), IMP::core::Cover::Cover(), IMP::core::Cover::get_is_setup(), IMP::core::Cover::setup_particle(), IMP::core::Cover::setup_particle(), IMP::core::Direction::get_is_setup(), IMP::core::Direction::setup_particle(), IMP::core::Direction::Direction(), IMP::core::DirectionAngle::DirectionAngle(), IMP::core::DirectionAngle::get_is_setup(), IMP::core::DirectionAngle::setup_particle(), IMP::core::DirectionAngle::setup_particle(), IMP::core::FilterProvenance::get_is_setup(), IMP::core::FilterProvenance::setup_particle(), IMP::core::FilterProvenance::setup_particle(), IMP::core::FilterProvenance::FilterProvenance(), IMP::core::Gaussian::Gaussian(), IMP::core::Gaussian::get_is_setup(), IMP::core::Gaussian::setup_particle(), IMP::core::Gaussian::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::NonRigidMember::NonRigidMember(), IMP::core::NonRigidMember::get_is_setup(), IMP::core::Provenance::get_is_setup(), IMP::core::Provenance::setup_particle(), IMP::core::Provenance::Provenance(), IMP::core::Provenanced::get_is_setup(), IMP::core::Provenanced::setup_particle(), IMP::core::Provenanced::Provenanced(), IMP::core::Reference::Reference(), IMP::core::Reference::get_is_setup(), IMP::core::Reference::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::RigidMember::RigidMember(), IMP::core::RigidMember::get_is_setup(), IMP::core::SampleProvenance::get_is_setup(), IMP::core::SampleProvenance::setup_particle(), IMP::core::SampleProvenance::setup_particle(), IMP::core::SampleProvenance::setup_particle(), IMP::core::SampleProvenance::SampleProvenance(), IMP::core::ScriptProvenance::get_is_setup(), IMP::core::ScriptProvenance::setup_particle(), IMP::core::ScriptProvenance::setup_particle(), IMP::core::ScriptProvenance::ScriptProvenance(), IMP::core::SoftwareProvenance::get_is_setup(), IMP::core::SoftwareProvenance::setup_particle(), IMP::core::SoftwareProvenance::setup_particle(), IMP::core::SoftwareProvenance::SoftwareProvenance(), IMP::core::StructureProvenance::get_is_setup(), IMP::core::StructureProvenance::setup_particle(), IMP::core::StructureProvenance::setup_particle(), IMP::core::StructureProvenance::setup_particle(), IMP::core::StructureProvenance::StructureProvenance(), IMP::core::Surface::get_is_setup(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::Surface(), IMP::core::Typed::get_is_setup(), IMP::core::Typed::setup_particle(), IMP::core::Typed::Typed(), IMP::core::XYZ::get_is_setup(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::XYZ(), 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::Colored(), IMP::display::Colored::get_is_setup(), IMP::display::Colored::setup_particle(), IMP::em2d::ProjectionParameters::ProjectionParameters(), IMP::em2d::ProjectionParameters::get_is_setup(), IMP::em2d::ProjectionParameters::setup_particle(), IMP::em::Voxel::get_is_setup(), IMP::em::Voxel::setup_particle(), IMP::em::Voxel::Voxel(), IMP::example::ExampleDecorator::get_is_setup(), IMP::example::ExampleDecorator::setup_particle(), IMP::example::ExampleDecorator::ExampleDecorator(), IMP::isd::Nuisance::Nuisance(), IMP::isd::Nuisance::get_is_setup(), IMP::isd::Nuisance::setup_particle(), IMP::isd::Nuisance::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::Switching(), IMP::isd::Switching::get_is_setup(), IMP::isd::Switching::setup_particle(), IMP::isd::Switching::setup_particle(), IMP::isd::Weight::Weight(), IMP::isd::Weight::get_is_setup(), IMP::isd::Weight::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::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::npctransport::RelaxingSpring::RelaxingSpring(), IMP::npctransport::RelaxingSpring::get_is_setup(), IMP::npctransport::RelaxingSpring::setup_particle(), IMP::npctransport::SlabWithCylindricalPore::SlabWithCylindricalPore(), IMP::npctransport::SlabWithCylindricalPore::get_is_setup(), IMP::npctransport::SlabWithCylindricalPore::setup_particle(), IMP::npctransport::SlabWithPore::SlabWithPore(), IMP::npctransport::SlabWithPore::get_is_setup(), IMP::npctransport::SlabWithPore::setup_particle(), IMP::npctransport::SlabWithToroidalPore::SlabWithToroidalPore(), IMP::npctransport::SlabWithToroidalPore::get_is_setup(), IMP::npctransport::SlabWithToroidalPore::setup_particle(), IMP::npctransport::SlabWithToroidalPore::setup_particle(), IMP::npctransport::Transporting::Transporting(), IMP::npctransport::Transporting::get_is_setup(), IMP::npctransport::Transporting::setup_particle(), IMP::pmi1::Resolution::get_is_setup(), IMP::pmi1::Resolution::setup_particle(), IMP::pmi1::Resolution::Resolution(), IMP::pmi1::Symmetric::get_is_setup(), IMP::pmi1::Symmetric::setup_particle(), IMP::pmi1::Symmetric::Symmetric(), IMP::pmi1::Uncertainty::get_is_setup(), IMP::pmi1::Uncertainty::setup_particle(), IMP::pmi1::Uncertainty::Uncertainty(), IMP::pmi::Resolution::get_is_setup(), IMP::pmi::Resolution::setup_particle(), IMP::pmi::Resolution::Resolution(), IMP::pmi::Symmetric::get_is_setup(), IMP::pmi::Symmetric::setup_particle(), IMP::pmi::Symmetric::Symmetric(), IMP::pmi::Uncertainty::get_is_setup(), IMP::pmi::Uncertainty::setup_particle(), IMP::pmi::Uncertainty::Uncertainty(), IMP::spb::HelixDecorator::HelixDecorator(), IMP::spb::HelixDecorator::get_is_setup() |
| IMP::ParticleIndexAdaptor | IMP::atom::CAAngleRestraint::CAAngleRestraint(), IMP::atom::CADihedralRestraint::CADihedralRestraint(), IMP::atom::Representation::add_representation(), IMP::core::AngleRestraint::AngleRestraint(), IMP::core::DihedralRestraint::DihedralRestraint(), IMP::core::DirectionAngle::do_setup_particle(), IMP::core::DirectionAngle::setup_particle(), IMP::core::DirectionAngle::setup_particle(), IMP::core::DistanceRestraint::DistanceRestraint(), IMP::core::Reference::setup_particle(), IMP::core::Reference::setup_particle(), IMP::core::RigidBody::add_member(), IMP::core::RigidBody::add_non_rigid_member(), IMP::core::RigidBodyMember::get_is_setup(), IMP::core::RigidMember::get_is_setup(), IMP::isd::AmbiguousNOERestraint::AmbiguousNOERestraint(), IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint(), IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint(), IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint(), IMP::isd::CysteineCrossLinkRestraint::add_contribution(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::isd::StudentTRestraint::StudentTRestraint(), IMP::pmi1::SigmoidRestraintSphere::SigmoidRestraintSphere(), IMP::pmi1::TransformMover::TransformMover(), IMP::pmi1::TransformMover::add_rigid_body_particle(), IMP::pmi1::TransformMover::add_xyz_particle(), IMP::pmi::SigmoidRestraintSphere::SigmoidRestraintSphere(), IMP::pmi::TransformMover::TransformMover(), IMP::pmi::TransformMover::add_rigid_body_particle(), IMP::pmi::TransformMover::add_xyz_particle() |
| IMP::ParticleIndexesAdaptor | IMP::atom::CenterOfMass::setup_particle(), IMP::atom::CenterOfMass::setup_particle(), IMP::atom::EzRestraint::EzRestraint(), IMP::atom::Hierarchy::setup_particle(), IMP::atom::LangevinThermostatOptimizerState::LangevinThermostatOptimizerState(), IMP::atom::RemoveRigidMotionOptimizerState::RemoveRigidMotionOptimizerState(), IMP::atom::RemoveTranslationOptimizerState::RemoveTranslationOptimizerState(), IMP::atom::TAMDCentroid::setup_particle(), IMP::atom::TAMDCentroid::setup_particle(), IMP::atom::VelocityScalingOptimizerState::VelocityScalingOptimizerState(), IMP::atom::WritePDBOptimizerState::WritePDBOptimizerState(), IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle(), IMP::core::Cover::setup_particle(), IMP::core::Cover::setup_particle(), IMP::core::RigidBody::do_setup_particle(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBody::setup_particle(), IMP::pmi1::CompositeRestraint::CompositeRestraint(), IMP::pmi1::CompositeRestraint::add_composite_particle(), IMP::pmi::CompositeRestraint::CompositeRestraint(), IMP::pmi::CompositeRestraint::add_composite_particle() |
| IMP::QuadContainer | IMP::QuadContainerAdaptor::QuadContainerAdaptor(), IMP::container::InContainerQuadFilter::InContainerQuadFilter(), IMP::container::InContainerQuadFilter::InContainerQuadFilter(), IMP::container::QuadContainerSet::remove_quad_container(), IMP::container::QuadContainerSet::add_quad_container(), IMP::container::QuadContainerSet::get_set() |
| IMP::QuadContainerAdaptor | IMP::container::DistributeQuadsScoreState::DistributeQuadsScoreState(), IMP::container::EventQuadsOptimizerState::EventQuadsOptimizerState(), IMP::container::MinimumQuadRestraint::MinimumQuadRestraint(), IMP::container::PredicateQuadsRestraint::PredicateQuadsRestraint(), IMP::container::QuadContainerStatistics::QuadContainerStatistics(), IMP::container::QuadsConstraint::QuadsConstraint(), IMP::container::QuadsOptimizerState::QuadsOptimizerState(), IMP::container::QuadsRestraint::QuadsRestraint() |
| IMP::QuadModifier | IMP::QuadContainer::apply(), IMP::QuadContainer::apply_generic(), IMP::QuadContainer::do_apply(), IMP::container::QuadsConstraint::QuadsConstraint(), IMP::container::QuadsOptimizerState::QuadsOptimizerState(), IMP::core::QuadConstraint::QuadConstraint(), IMP::core::QuadConstraint::QuadConstraint() |
| IMP::QuadPredicate | IMP::container::DistributeQuadsScoreState::add_predicate(), IMP::container::EventQuadsOptimizerState::EventQuadsOptimizerState(), IMP::container::PredicateQuadsRestraint::PredicateQuadsRestraint() |
| IMP::QuadScore | IMP::container::MinimumQuadRestraint::MinimumQuadRestraint(), IMP::container::PredicateQuadsRestraint::set_score(), IMP::container::PredicateQuadsRestraint::set_unknown_score(), IMP::container::QuadsRestraint::QuadsRestraint(), IMP::core::QuadRestraint::QuadRestraint() |
| IMP::Refiner | IMP::atom::CenterOfMass::do_setup_particle(), IMP::atom::CenterOfMass::setup_particle(), IMP::atom::CenterOfMass::setup_particle(), IMP::atom::TAMDCentroid::do_setup_particle(), IMP::atom::TAMDCentroid::setup_particle(), IMP::atom::TAMDCentroid::setup_particle(), IMP::core::Centroid::do_setup_particle(), IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle(), IMP::core::CentroidOfRefined::CentroidOfRefined(), IMP::core::ClosePairsPairScore::ClosePairsPairScore(), IMP::core::Cover::do_setup_particle(), IMP::core::Cover::setup_particle(), IMP::core::Cover::setup_particle(), IMP::core::CoverRefined::CoverRefined(), IMP::core::DerivativesFromRefined::DerivativesFromRefined(), IMP::core::DerivativesToRefined::DerivativesToRefined(), IMP::core::KClosePairsPairScore::KClosePairsPairScore(), IMP::core::RefinedPairsPairScore::RefinedPairsPairScore(), IMP::core::RigidBodyDistancePairScore::RigidBodyDistancePairScore(), IMP::core::WeightedDerivativesToRefined::WeightedDerivativesToRefined(), IMP::misc::LowestRefinedPairScore::LowestRefinedPairScore(), IMP::multifit::WeightedExcludedVolumeRestraint::WeightedExcludedVolumeRestraint(), IMP::em::compute_fitting_scores(), IMP::em::local_rigid_fitting(), IMP::em::local_rigid_fitting_around_point(), IMP::em::local_rigid_fitting_around_points(), IMP::multifit::create_hit_map(), IMP::multifit::pca_based_rigid_fitting() |
| IMP::Restraint | IMP::RestraintSet::remove_restraint(), IMP::RestraintSet::add_restraint(), IMP::RestraintSet::on_add(), IMP::RestraintSet::on_remove(), IMP::RestraintsAdaptor::get(), IMP::RestraintsAdaptor::RestraintsAdaptor(), IMP::ScoreAccumulator::ScoreAccumulator(), IMP::ScoringFunctionAdaptor::get(), IMP::ScoringFunctionAdaptor::ScoringFunctionAdaptor(), IMP::core::IncrementalScoringFunction::create_data(), IMP::core::MinimumRestraint::add_restraint(), IMP::core::MinimumRestraint::remove_restraint(), IMP::display::RestraintGeometry::RestraintGeometry(), IMP::display::RestraintGeometry::RestraintGeometry(), IMP::domino::RestraintCache::add_restraint_internal(), IMP::domino::RestraintCache::add_restraint_set_child_internal(), IMP::domino::RestraintCache::get_subset(), IMP::domino::RestraintCache::get_score(), IMP::domino::RestraintCache::get_score(), IMP::domino::RestraintCache::get_slice(), IMP::domino::RestraintCache::load_last_score(), IMP::isd::AmbiguousRestraint::AmbiguousRestraint(), IMP::npctransport::Scoring::add_custom_restraint(), IMP::rmf::add_restraint() |
| IMP::RestraintSet | IMP::RestraintSet::on_remove(), IMP::display::RestraintSetGeometry::RestraintSetGeometry(), IMP::domino::RestraintCache::add_restraint_internal(), IMP::domino::RestraintCache::add_restraint_set_child_internal(), IMP::domino::RestraintCache::add_restraint_set_internal(), IMP::spb::MonteCarloWithWte::MonteCarloWithWte(), IMP::domino::get_restraints(), IMP::spb::add_bayesian_layer_restraint(), IMP::spb::add_diameter_rgyr_restraint(), IMP::spb::add_GFP_restraint(), IMP::spb::add_internal_restraint(), IMP::spb::add_ISD_particles(), IMP::spb::add_layer_restraint(), IMP::spb::add_link(), IMP::spb::add_link(), IMP::spb::add_my_connectivity(), IMP::spb::add_restrain_coiledcoil_to_cterm(), IMP::spb::add_restrain_protein_length(), IMP::spb::add_SPBexcluded_volume(), IMP::spb::add_stay_close_restraint(), IMP::spb::add_stay_close_restraint(), IMP::spb::add_stay_on_plane_restraint(), IMP::spb::add_tilt(), IMP::spb::add_tilt_restraint(), IMP::spb::create_merged_protein(), IMP::spb::create_protein(), IMP::spb::create_representation(), IMP::spb::spb_assemble_restraints() |
| IMP::RestraintsAdaptor | IMP::core::RestraintsScoringFunction::RestraintsScoringFunction(), IMP::core::RestraintsScoringFunction::RestraintsScoringFunction(), IMP::domino::DiscreteSampler::set_restraints(), IMP::domino::RestraintCache::add_restraints(), IMP::domino::RestraintScoreSubsetFilterTable::RestraintScoreSubsetFilterTable() |
| IMP::Sampler | IMP::core::MCCGSampler::MCCGSampler() |
| IMP::ScoreAccumulator | IMP::Restraint::add_score_and_derivatives(), IMP::Restraint::do_add_score_and_derivatives(), IMP::ScoreAccumulator::ScoreAccumulator(), IMP::ScoreAccumulator::ScoreAccumulator(), IMP::ScoringFunction::do_add_score_and_derivatives(), IMP::container::PredicatePairsRestraint::do_add_score_and_derivatives(), IMP::container::PredicateQuadsRestraint::do_add_score_and_derivatives(), IMP::container::PredicateSingletonsRestraint::do_add_score_and_derivatives(), IMP::container::PredicateTripletsRestraint::do_add_score_and_derivatives(), IMP::core::IncrementalScoringFunction::do_add_score_and_derivatives(), IMP::example::ExampleRestraint::do_add_score_and_derivatives(), IMP::isd::LogWrapper::do_add_score_and_derivatives() |
| IMP::ScoreState | IMP::Model::remove_score_state(), IMP::Model::add_score_state(), IMP::Model::do_add_score_state(), IMP::Model::do_check_update_order(), IMP::Model::do_remove_score_state() |
| IMP::ScoringFunction | IMP::ScoringFunctionAdaptor::get(), IMP::ScoringFunctionAdaptor::ScoringFunctionAdaptor(), IMP::kinematics::LocalPlanner::is_valid(), IMP::kinematics::LocalPlanner::plan(), IMP::kinematics::PathLocalPlanner::plan(), IMP::kinematics::RRT::check_initial_configuration(), IMP::create_decomposition() |
| IMP::ScoringFunctionAdaptor | IMP::Optimizer::set_scoring_function(), IMP::Sampler::set_scoring_function(), IMP::show_restraint_hierarchy(), IMP::domino::get_interaction_graph(), IMP::domino::get_interaction_graph(), IMP::domino::get_merge_tree(), IMP::domino::get_restraint_graph() |
| IMP::SingletonContainer | IMP::SingletonContainerAdaptor::SingletonContainerAdaptor(), IMP::atom::BondPairContainer::BondPairContainer(), IMP::atom::BondsGeometry::BondsGeometry(), IMP::atom::HierarchiesGeometry::HierarchiesGeometry(), IMP::container::ConnectingPairContainer::initialize(), IMP::container::ConnectingPairContainer::ConnectingPairContainer(), IMP::container::InContainerSingletonFilter::InContainerSingletonFilter(), IMP::container::InContainerSingletonFilter::InContainerSingletonFilter(), IMP::container::SingletonContainerSet::remove_singleton_container(), IMP::container::SingletonContainerSet::add_singleton_container(), IMP::container::SingletonContainerSet::get_set(), IMP::core::DiameterRestraint::DiameterRestraint(), IMP::core::RigidBodyDerivativesGeometry::RigidBodyDerivativesGeometry(), IMP::core::RigidBodyFramesGeometry::RigidBodyFramesGeometry(), IMP::core::VolumeRestraint::VolumeRestraint(), IMP::core::XYZDerivativesGeometry::XYZDerivativesGeometry(), IMP::core::XYZRsGeometry::XYZRsGeometry(), IMP::em2d::Em2DRestraint::set_particles(), IMP::em2d::ParticlesDummyRestraint::ParticlesDummyRestraint(), IMP::example::ExampleComplexRestraint::ExampleComplexRestraint(), IMP::statistics::ConfigurationSetRMSDMetric::ConfigurationSetRMSDMetric() |
| IMP::SingletonContainerAdaptor | IMP::container::AllBipartitePairContainer::AllBipartitePairContainer(), IMP::container::AllPairContainer::AllPairContainer(), IMP::container::CloseBipartitePairContainer::CloseBipartitePairContainer(), IMP::container::ClosePairContainer::ClosePairContainer(), IMP::container::ClosePairContainer::ClosePairContainer(), IMP::container::DistributeSingletonsScoreState::DistributeSingletonsScoreState(), IMP::container::EventSingletonsOptimizerState::EventSingletonsOptimizerState(), IMP::container::MinimumSingletonRestraint::MinimumSingletonRestraint(), IMP::container::PredicateSingletonsRestraint::PredicateSingletonsRestraint(), IMP::container::SingletonContainerStatistics::SingletonContainerStatistics(), IMP::container::SingletonsConstraint::SingletonsConstraint(), IMP::container::SingletonsOptimizerState::SingletonsOptimizerState(), IMP::container::SingletonsRestraint::SingletonsRestraint(), IMP::core::ConnectivityRestraint::ConnectivityRestraint(), IMP::core::ExcludedVolumeRestraint::ExcludedVolumeRestraint(), IMP::core::ExcludedVolumeRestraint::ExcludedVolumeRestraint(), IMP::display::SingletonsGeometry::SingletonsGeometry(), IMP::display::SingletonsGeometry::SingletonsGeometry(), IMP::npc::AssemblySymmetryByDihedralRestraint::AssemblySymmetryByDihedralRestraint(), IMP::npc::AssemblySymmetryByDistanceRestraint::AssemblySymmetryByDistanceRestraint(), IMP::npc::MembraneExclusionRestraint::MembraneExclusionRestraint(), IMP::npc::MembraneSurfaceLocationConditionalRestraint::MembraneSurfaceLocationConditionalRestraint(), IMP::npc::MembraneSurfaceLocationRestraint::MembraneSurfaceLocationRestraint(), IMP::npc::PerinuclearVolumeLocationRestraint::PerinuclearVolumeLocationRestraint(), IMP::npc::PoreSideVolumeLocationRestraint::PoreSideVolumeLocationRestraint(), IMP::npc::ProteinChainRestraint::ProteinChainRestraint(), IMP::npc::ProteinContactRestraint::ProteinContactRestraint(), IMP::npc::ProteinProximityRestraint::ProteinProximityRestraint(), IMP::npc::XYRadialPositionLowerRestraint::XYRadialPositionLowerRestraint(), IMP::npc::XYRadialPositionRestraint::XYRadialPositionRestraint(), IMP::npc::XYRadialPositionUpperRestraint::XYRadialPositionUpperRestraint(), IMP::npc::YAxialPositionLowerRestraint::YAxialPositionLowerRestraint(), IMP::npc::YAxialPositionRestraint::YAxialPositionRestraint(), IMP::npc::YAxialPositionUpperRestraint::YAxialPositionUpperRestraint(), IMP::npc::ZAxialPositionLowerRestraint::ZAxialPositionLowerRestraint(), IMP::npc::ZAxialPositionRestraint::ZAxialPositionRestraint(), IMP::npc::ZAxialPositionUpperRestraint::ZAxialPositionUpperRestraint(), IMP::npctransport::Scoring::add_z_bias_restraint(), IMP::npctransport::Scoring::create_bounding_box_restraint(), IMP::npctransport::Scoring::create_close_beads_container(), IMP::npctransport::Scoring::create_close_beads_container(), IMP::npctransport::Scoring::create_slab_restraint(), IMP::npctransport::Scoring::create_z_bias_restraint(), IMP::npctransport::Scoring::get_chain_restraints_on(), IMP::npctransport::Scoring::get_custom_scoring_function(), IMP::npctransport::Scoring::get_custom_scoring_function(), IMP::npctransport::TypedSitesGeometry::TypedSitesGeometry(), IMP::statistics::ConfigurationSetXYZEmbedding::ConfigurationSetXYZEmbedding(), IMP::npctransport::load_pb_conformation(), IMP::npctransport::save_pb_conformation() |
| IMP::SingletonModifier | IMP::SingletonContainer::apply(), IMP::SingletonContainer::apply_generic(), IMP::SingletonContainer::do_apply(), IMP::atom::CenterOfMass::set_constraint(), IMP::container::SingletonsConstraint::SingletonsConstraint(), IMP::container::SingletonsOptimizerState::SingletonsOptimizerState(), IMP::core::Centroid::set_constraint(), IMP::core::Cover::set_constraint(), IMP::core::ModifierVisitor::ModifierVisitor(), IMP::core::SingletonConstraint::SingletonConstraint(), IMP::core::SingletonConstraint::SingletonConstraint() |
| IMP::SingletonPredicate | IMP::container::DistributeSingletonsScoreState::add_predicate(), IMP::container::EventSingletonsOptimizerState::EventSingletonsOptimizerState(), IMP::container::PredicateSingletonsRestraint::PredicateSingletonsRestraint() |
| IMP::SingletonScore | IMP::container::MinimumSingletonRestraint::MinimumSingletonRestraint(), IMP::container::PredicateSingletonsRestraint::set_score(), IMP::container::PredicateSingletonsRestraint::set_unknown_score(), IMP::container::SingletonsRestraint::SingletonsRestraint(), IMP::core::SingletonRestraint::SingletonRestraint() |
| IMP::TextInput | IMP::atom::CHARMMParameters::read_parameter_file(), IMP::atom::CHARMMParameters::read_topology_file(), IMP::atom::CHARMMParameters::CHARMMParameters(), IMP::atom::DopePairScore::DopePairScore(), IMP::atom::ProteinLigandAtomPairScore::ProteinLigandAtomPairScore(), IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint(), IMP::core::StatisticalPairScore::StatisticalPairScore(), IMP::core::StatisticalPairScore::StatisticalPairScore(), IMP::score_functor::Dope::Dope(), IMP::score_functor::SingletonStatistical::SingletonStatistical(), IMP::score_functor::Soap::Soap(), IMP::score_functor::Statistical::Statistical(), IMP::score_functor::Statistical::Statistical(), IMP::algebra::read_pts(), IMP::algebra::read_spheres(), IMP::atom::read_mol2(), IMP::atom::read_pdb(), IMP::atom::read_pdb(), IMP::atom::read_multimodel_pdb(), IMP::atom::read_psipred(), IMP::atom::read_psipred(), IMP::atom::read_mmcif(), IMP::atom::read_multimodel_mmcif(), IMP::spb::get_SPBParameters() |
| IMP::TextOutput | IMP::SetLogTarget::SetLogTarget(), IMP::SetLogTarget::set(), IMP::core::WriteRestraintScoresOptimizerState::WriteRestraintScoresOptimizerState(), IMP::display::PymolWriter::PymolWriter(), IMP::display::TextWriter::TextWriter(), IMP::set_log_target(), IMP::show_as_graphviz(), IMP::algebra::write_pts(), IMP::algebra::write_spheres(), IMP::atom::write_mol2(), IMP::atom::write_pdb(), IMP::atom::write_pdb_of_c_alphas(), IMP::atom::write_multimodel_pdb(), IMP::atom::show_as_graphviz(), IMP::core::show_rigid_body_hierarchy(), IMP::domino::show_as_graphviz(), IMP::multifit::write_connolly_surface() |
| IMP::TripletContainer | IMP::TripletContainerAdaptor::TripletContainerAdaptor(), IMP::container::InContainerTripletFilter::InContainerTripletFilter(), IMP::container::InContainerTripletFilter::InContainerTripletFilter(), IMP::container::TripletContainerSet::remove_triplet_container(), IMP::container::TripletContainerSet::add_triplet_container(), IMP::container::TripletContainerSet::get_set() |
| IMP::TripletContainerAdaptor | IMP::container::DistributeTripletsScoreState::DistributeTripletsScoreState(), IMP::container::EventTripletsOptimizerState::EventTripletsOptimizerState(), IMP::container::MinimumTripletRestraint::MinimumTripletRestraint(), IMP::container::PredicateTripletsRestraint::PredicateTripletsRestraint(), IMP::container::TripletContainerStatistics::TripletContainerStatistics(), IMP::container::TripletsConstraint::TripletsConstraint(), IMP::container::TripletsOptimizerState::TripletsOptimizerState(), IMP::container::TripletsRestraint::TripletsRestraint() |
| IMP::TripletModifier | IMP::TripletContainer::apply(), IMP::TripletContainer::apply_generic(), IMP::TripletContainer::do_apply(), IMP::container::TripletsConstraint::TripletsConstraint(), IMP::container::TripletsOptimizerState::TripletsOptimizerState(), IMP::core::TripletConstraint::TripletConstraint(), IMP::core::TripletConstraint::TripletConstraint() |
| IMP::TripletPredicate | IMP::container::DistributeTripletsScoreState::add_predicate(), IMP::container::EventTripletsOptimizerState::EventTripletsOptimizerState(), IMP::container::PredicateTripletsRestraint::PredicateTripletsRestraint() |
| IMP::TripletScore | IMP::container::MinimumTripletRestraint::MinimumTripletRestraint(), IMP::container::PredicateTripletsRestraint::set_score(), IMP::container::PredicateTripletsRestraint::set_unknown_score(), IMP::container::TripletsRestraint::TripletsRestraint(), IMP::core::TripletRestraint::TripletRestraint() |
| IMP::UnaryFunction | IMP::atom::AngleSingletonScore::AngleSingletonScore(), IMP::atom::BondSingletonScore::BondSingletonScore(), IMP::atom::ImproperSingletonScore::ImproperSingletonScore(), IMP::core::AngleRestraint::AngleRestraint(), IMP::core::AngleTripletScore::AngleTripletScore(), IMP::core::DiameterRestraint::DiameterRestraint(), IMP::core::DihedralRestraint::DihedralRestraint(), IMP::core::DistancePairScore::DistancePairScore(), IMP::core::DistanceRestraint::DistanceRestraint(), IMP::core::NormalizedSphereDistancePairScore::NormalizedSphereDistancePairScore(), IMP::core::RigidBodyAnglePairScore::RigidBodyAnglePairScore(), IMP::core::SphereDistancePairScore::SphereDistancePairScore(), IMP::core::SphereDistanceToSingletonScore::SphereDistanceToSingletonScore(), IMP::core::SurfaceDepthPairScore::SurfaceDepthPairScore(), IMP::core::SurfaceDistancePairScore::SurfaceDistancePairScore(), IMP::core::SurfaceHeightPairScore::SurfaceHeightPairScore(), IMP::core::TransformedDistancePairScore::TransformedDistancePairScore(), IMP::core::VolumeRestraint::VolumeRestraint(), IMP::core::WeightedSphereDistancePairScore::WeightedSphereDistancePairScore(), IMP::example::ExampleComplexRestraint::ExampleComplexRestraint(), IMP::npc::MinimumSphereDistancePairScore::MinimumSphereDistancePairScore(), IMP::score_functor::UnaryFunctionEvaluate::UnaryFunctionEvaluate(), IMP::spb::AttributeDistancePairScore::AttributeDistancePairScore(), IMP::spb::KinkPairScore::KinkPairScore(), IMP::spb::TiltSingletonScore::TiltSingletonScore(), IMP::core::create_bounding_box_3d_singleton_score(), IMP::core::create_bounding_sphere_3d_singleton_score(), IMP::core::create_distance_to_singleton_score() |
| IMP::Undecorator | IMP::Model::add_undecorator() |
| IMP::Value | IMP::ScopedAddCacheAttribute::ScopedAddCacheAttribute(), IMP::ScopedAddCacheAttribute::set(), IMP::ScopedSetAttribute::ScopedSetAttribute(), IMP::ScopedSetAttribute::set(), IMP::algebra::GridD::GridD(), IMP::algebra::GridD::GridD(), IMP::algebra::GridD::GridD(), IMP::algebra::GridD::GridD(), IMP::algebra::GridD::GridD(), IMP::algebra::GridD::add_voxel(), IMP::display::IsosurfaceGeometry::IsosurfaceGeometry(), IMP::algebra::get_bounding_box(), IMP::algebra::get_linearly_interpolated() |
| IMP::Vector | IMP::ConstVector::ConstVector(), IMP::ParticleIndexesAdaptor::ParticleIndexesAdaptor(), IMP::ParticleIndexesAdaptor::ParticleIndexesAdaptor(), IMP::ParticleIndexesAdaptor::ParticleIndexesAdaptor(), IMP::ParticleInputs::get_inputs(), IMP::ParticleInputs::do_get_inputs(), IMP::ParticleOutputs::get_outputs(), IMP::ParticleOutputs::do_get_outputs(), IMP::SingletonContainerAdaptor::SingletonContainerAdaptor(), IMP::SingletonModifier::apply_indexes(), IMP::SingletonPredicate::get_value(), IMP::SingletonPredicate::get_value_index(), IMP::SingletonScore::evaluate_if_good_indexes(), IMP::SingletonScore::evaluate_indexes(), IMP::SparseSymmetricPairMemoizer::SparseSymmetricPairMemoizer(), IMP::algebra::BoundingBoxD::BoundingBoxD(), IMP::algebra::NearestNeighborD::NearestNeighborD(), IMP::algebra::PrincipalComponentAnalysisD::PrincipalComponentAnalysisD(), IMP::atom::AngleSingletonScore::do_get_inputs(), IMP::atom::AngleSingletonScore::evaluate_if_good_indexes(), IMP::atom::AngleSingletonScore::evaluate_indexes(), IMP::atom::BerendsenThermostatOptimizerState::BerendsenThermostatOptimizerState(), IMP::atom::BerendsenThermostatOptimizerState::set_particles(), IMP::atom::BondEndpointsRefiner::do_get_inputs(), IMP::atom::BondSingletonScore::do_get_inputs(), IMP::atom::BondSingletonScore::evaluate_if_good_indexes(), IMP::atom::BondSingletonScore::evaluate_indexes(), IMP::atom::BondedPairFilter::do_get_inputs(), IMP::atom::BrownianDynamics::do_advance_chunk(), IMP::atom::BrownianDynamics::do_step(), IMP::atom::BrownianDynamics::setup(), IMP::atom::BrownianDynamicsTAMD::do_advance_chunk(), IMP::atom::CHARMMConnection::CHARMMConnection(), IMP::atom::CHARMMInternalCoordinate::CHARMMInternalCoordinate(), IMP::atom::CHARMMParameters::add_angle(), IMP::atom::CHARMMParameters::add_dihedral(), IMP::atom::CHARMMParameters::parse_dihedrals_parameters_line(), IMP::atom::CHARMMParameters::create_angles(), IMP::atom::CHARMMParameters::create_dihedrals(), IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint(), IMP::atom::CenterOfMass::do_setup_particle(), IMP::atom::CoulombPairScore::do_get_inputs(), IMP::atom::CoverBond::apply_indexes(), IMP::atom::CoverBond::do_get_inputs(), IMP::atom::CoverBond::do_get_outputs(), IMP::atom::DihedralSingletonScore::do_get_inputs(), IMP::atom::DihedralSingletonScore::evaluate_if_good_indexes(), IMP::atom::DihedralSingletonScore::evaluate_indexes(), IMP::atom::HelixRestraint::HelixRestraint(), IMP::atom::Hierarchy::create_fragment(), IMP::atom::Hierarchy::get_leaves(), IMP::atom::ImproperSingletonScore::do_get_inputs(), IMP::atom::ImproperSingletonScore::evaluate_if_good_indexes(), IMP::atom::ImproperSingletonScore::evaluate_indexes(), IMP::atom::LangevinThermostatOptimizerState::set_particles(), IMP::atom::LennardJonesPairScore::do_get_inputs(), IMP::atom::MolecularDynamics::do_step(), IMP::atom::MolecularDynamics::setup(), IMP::atom::MolecularDynamics::propagate_coordinates(), IMP::atom::MolecularDynamics::propagate_velocities(), IMP::atom::MolecularDynamics::setup_degrees_of_freedom(), IMP::atom::RemoveRigidMotionOptimizerState::set_particles(), IMP::atom::RemoveTranslationOptimizerState::set_particles(), IMP::atom::SameResiduePairFilter::do_get_inputs(), IMP::atom::Selection::set_hierarchies(), IMP::atom::Selection::Selection(), IMP::atom::Selection::Selection(), IMP::atom::Selection::Selection(), IMP::atom::Selection::Selection(), IMP::atom::Simulator::remove_particles(), IMP::atom::Simulator::set_particles(), IMP::atom::Simulator::set_particles_order(), IMP::atom::Simulator::add_particles(), IMP::atom::Simulator::do_step(), IMP::atom::Simulator::setup(), IMP::atom::SoapPairFilter::do_get_inputs(), IMP::atom::StereochemistryPairFilter::do_get_inputs(), IMP::atom::StereochemistryPairFilter::set_angles(), IMP::atom::StereochemistryPairFilter::set_bonds(), IMP::atom::StereochemistryPairFilter::set_dihedrals(), IMP::atom::TAMDCentroid::do_setup_particle(), IMP::atom::VelocityScalingOptimizerState::set_particles(), IMP::atom::WritePDBOptimizerState::WritePDBOptimizerState(), IMP::cnmultifit::AlignSymmetric::get_symm_axis_alignments_from_model_to_density(), IMP::cnmultifit::AlignSymmetric::score_alignment(), IMP::cnmultifit::CnSymmAxisDetector::CnSymmAxisDetector(), IMP::cnmultifit::MolCnSymmAxisDetector::MolCnSymmAxisDetector(), IMP::container::ConsecutivePairContainer::ConsecutivePairContainer(), IMP::container::ConsecutivePairFilter::do_get_inputs(), IMP::container::DynamicListSingletonContainer::add(), IMP::container::DynamicListSingletonContainer::set(), IMP::container::ExclusiveConsecutivePairContainer::ExclusiveConsecutivePairContainer(), IMP::container::ExclusiveConsecutivePairFilter::do_get_inputs(), IMP::container::InContainerPairFilter::do_get_inputs(), IMP::container::InContainerQuadFilter::do_get_inputs(), IMP::container::InContainerSingletonFilter::do_get_inputs(), IMP::container::InContainerSingletonFilter::get_value(), IMP::container::InContainerSingletonFilter::get_value_index(), IMP::container::InContainerTripletFilter::do_get_inputs(), IMP::container::ListSingletonContainer::ListSingletonContainer(), IMP::container::ListSingletonContainer::add(), IMP::container::ListSingletonContainer::set(), IMP::container::MinimumPairScore::do_get_inputs(), IMP::container::MinimumQuadScore::do_get_inputs(), IMP::container::MinimumSingletonScore::do_get_inputs(), IMP::container::MinimumSingletonScore::evaluate_if_good_indexes(), IMP::container::MinimumSingletonScore::evaluate_indexes(), IMP::container::MinimumTripletScore::do_get_inputs(), IMP::container::SingletonContainerSet::get_indexes_in_place(), IMP::core::AllSamePairPredicate::do_get_inputs(), IMP::core::AllSameQuadPredicate::do_get_inputs(), IMP::core::AllSameSingletonPredicate::do_get_inputs(), IMP::core::AllSameSingletonPredicate::get_value(), IMP::core::AllSameSingletonPredicate::get_value_index(), IMP::core::AllSameTripletPredicate::do_get_inputs(), IMP::core::AngleTripletScore::do_get_inputs(), IMP::core::AttributeSingletonPredicate::do_get_inputs(), IMP::core::AttributeSingletonPredicate::get_value(), IMP::core::AttributeSingletonPredicate::get_value_index(), IMP::core::BallMover::initialize(), 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::CentroidOfRefined::apply_indexes(), IMP::core::CentroidOfRefined::do_get_inputs(), IMP::core::CentroidOfRefined::do_get_outputs(), IMP::core::ChildrenRefiner::do_get_inputs(), IMP::core::ClosePairsFinder::get_close_pairs(), IMP::core::ClosePairsFinder::get_close_pairs(), IMP::core::ClosePairsPairScore::do_get_inputs(), IMP::core::CoinFlipPairPredicate::do_get_inputs(), IMP::core::CoinFlipQuadPredicate::do_get_inputs(), IMP::core::CoinFlipSingletonPredicate::do_get_inputs(), IMP::core::CoinFlipSingletonPredicate::get_value(), IMP::core::CoinFlipSingletonPredicate::get_value_index(), IMP::core::CoinFlipTripletPredicate::do_get_inputs(), IMP::core::ConjugateGradients::get_score(), IMP::core::ConjugateGradients::line_search(), IMP::core::ConstantPairPredicate::do_get_inputs(), IMP::core::ConstantQuadPredicate::do_get_inputs(), IMP::core::ConstantSingletonPredicate::do_get_inputs(), IMP::core::ConstantSingletonPredicate::get_value(), IMP::core::ConstantSingletonPredicate::get_value_index(), IMP::core::ConstantTripletPredicate::do_get_inputs(), IMP::core::Cover::do_setup_particle(), IMP::core::CoverRefined::apply_indexes(), IMP::core::CoverRefined::do_get_inputs(), IMP::core::CoverRefined::do_get_outputs(), IMP::core::DerivativesFromRefined::apply_indexes(), IMP::core::DerivativesFromRefined::do_get_inputs(), IMP::core::DerivativesFromRefined::do_get_outputs(), 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::FixedRefiner::FixedRefiner(), IMP::core::FixedRefiner::FixedRefiner(), IMP::core::FixedRefiner::do_get_inputs(), IMP::core::GenericAttributeSingletonScore::do_get_inputs(), IMP::core::GenericAttributeSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericAttributeSingletonScore::evaluate_indexes(), IMP::core::GenericBoundingBox3DSingletonScore::do_get_inputs(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_indexes(), IMP::core::GenericBoundingSphere3DSingletonScore::do_get_inputs(), IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_indexes(), IMP::core::GenericDistanceToSingletonScore::do_get_inputs(), IMP::core::GenericDistanceToSingletonScore::evaluate_if_good_indexes(), 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::HarmonicSphereDistancePairScore::do_get_inputs(), IMP::core::HarmonicSurfaceDepthPairScore::do_get_inputs(), IMP::core::HarmonicSurfaceDistancePairScore::do_get_inputs(), IMP::core::HarmonicSurfaceHeightPairScore::do_get_inputs(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::do_get_inputs(), IMP::core::HarmonicUpperBoundSphereDistancePairScore::do_get_inputs(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::setup_particle(), 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(), IMP::core::InBoundingBox3DSingletonPredicate::get_value_index(), IMP::core::IncrementalScoringFunction::IncrementalScoringFunction(), IMP::core::IncrementalScoringFunction::add_close_pair_score(), IMP::core::IncrementalScoringFunction::add_close_pair_score(), IMP::core::IncrementalScoringFunction::set_moved_particles(), IMP::core::IsCollisionPairPredicate::do_get_inputs(), IMP::core::KClosePairsPairScore::do_get_inputs(), IMP::core::LeavesRefiner::do_get_inputs(), IMP::core::LogNormalMover::initialize(), IMP::core::MSConnectivityRestraint::add_type(), IMP::core::MonteCarlo::do_evaluate(), IMP::core::MoveStatisticsScoreState::MoveStatisticsScoreState(), IMP::core::NearestNeighborsClosePairsFinder::do_get_inputs(), IMP::core::NearestNeighborsClosePairsFinder::get_close_pairs(), IMP::core::NearestNeighborsClosePairsFinder::get_close_pairs(), IMP::core::NormalMover::initialize(), IMP::core::NormalizedSphereDistancePairScore::do_get_inputs(), IMP::core::OrderedTypePairPredicate::do_get_inputs(), IMP::core::OrderedTypeQuadPredicate::do_get_inputs(), IMP::core::OrderedTypeSingletonPredicate::do_get_inputs(), IMP::core::OrderedTypeSingletonPredicate::get_value(), IMP::core::OrderedTypeSingletonPredicate::get_value_index(), IMP::core::OrderedTypeTripletPredicate::do_get_inputs(), IMP::core::PredicateSingletonScore::do_get_inputs(), IMP::core::PredicateSingletonScore::evaluate_if_good_indexes(), IMP::core::PredicateSingletonScore::evaluate_indexes(), IMP::core::QuadraticClosePairsFinder::do_get_inputs(), IMP::core::QuadraticClosePairsFinder::get_close_pairs(), IMP::core::QuadraticClosePairsFinder::get_close_pairs(), IMP::core::RefinedPairsPairScore::do_get_inputs(), IMP::core::RigidBody::set_reference_frame_from_members(), IMP::core::RigidBodyAnglePairScore::do_get_inputs(), IMP::core::RigidBodyHierarchyGeometry::RigidBodyHierarchyGeometry(), IMP::core::RigidBodyTunneler::RigidBodyTunneler(), 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::SoftSpherePairScore::do_get_inputs(), IMP::core::SoftSubSurfacePairScore::do_get_inputs(), IMP::core::SoftSuperSurfacePairScore::do_get_inputs(), IMP::core::SphereDistancePairScore::do_get_inputs(), IMP::core::SphereDistanceToSingletonScore::do_get_inputs(), IMP::core::SphereDistanceToSingletonScore::evaluate_if_good_indexes(), IMP::core::SphereDistanceToSingletonScore::evaluate_indexes(), IMP::core::SurfaceDepthPairScore::do_get_inputs(), IMP::core::SurfaceDistancePairScore::do_get_inputs(), IMP::core::SurfaceHeightPairScore::do_get_inputs(), IMP::core::TableRefiner::add_particle(), IMP::core::TableRefiner::do_get_inputs(), IMP::core::TableRefiner::set_particle(), IMP::core::Transform::apply_indexes(), IMP::core::Transform::do_get_inputs(), IMP::core::Transform::do_get_outputs(), IMP::core::TransformationAndReflectionSymmetry::apply_indexes(), IMP::core::TransformationAndReflectionSymmetry::do_get_inputs(), IMP::core::TransformationAndReflectionSymmetry::do_get_outputs(), 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::TypedPairScore::do_get_inputs(), IMP::core::UnorderedTypePairPredicate::do_get_inputs(), IMP::core::UnorderedTypeQuadPredicate::do_get_inputs(), IMP::core::UnorderedTypeSingletonPredicate::do_get_inputs(), IMP::core::UnorderedTypeSingletonPredicate::get_value(), IMP::core::UnorderedTypeSingletonPredicate::get_value_index(), IMP::core::UnorderedTypeTripletPredicate::do_get_inputs(), IMP::core::WeightedDerivativesToRefined::apply_indexes(), IMP::core::WeightedDerivativesToRefined::do_get_inputs(), IMP::core::WeightedDerivativesToRefined::do_get_outputs(), IMP::core::WeightedSphereDistancePairScore::do_get_inputs(), IMP::domino::DependencyScoreState::set_input_particles(), IMP::domino::DependencyScoreState::set_output_particles(), IMP::domino::DisjointSetsSubsetFilterTable::add_set(), IMP::domino::Order::Order(), IMP::domino::PairListSubsetFilterTable::fill(), IMP::domino::ParticlesAdaptor::ParticlesAdaptor(), IMP::domino::ReadAssignmentContainer::ReadAssignmentContainer(), IMP::domino::ReadHDF5AssignmentContainer::ReadHDF5AssignmentContainer(), IMP::domino::RestraintCache::load_cache(), IMP::domino::RestraintCache::save_cache(), IMP::domino::Subset::get_sorted(), IMP::domino::Subset::Subset(), IMP::domino::WriteAssignmentContainer::WriteAssignmentContainer(), IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer(), IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer(), IMP::em2d::CollisionCrossSection::set_model_particles(), IMP::em2d::Fine2DRegistrationRestraint::setup(), IMP::em2d::MasksManager::create_masks(), IMP::em2d::PCAFitRestraint::PCAFitRestraint(), IMP::em2d::ProjectionFinder::set_model_particles(), IMP::em2d::RigidBodiesImageFitRestraint::RigidBodiesImageFitRestraint(), IMP::em::DensityFillingRestraint::DensityFillingRestraint(), IMP::em::DensityFillingRestraint::add_particles(), IMP::em::DensityFillingRestraint::remove_particles(), IMP::em::DensityFillingRestraint::set_particles(), IMP::em::DensityFillingRestraint::set_particles_order(), IMP::em::DensityMap::add_to_map(), IMP::em::EnvelopeFitRestraint::EnvelopeFitRestraint(), IMP::em::EnvelopePenetrationRestraint::EnvelopePenetrationRestraint(), IMP::em::EnvelopePenetrationRestraint::add_particles(), IMP::em::EnvelopePenetrationRestraint::remove_particles(), IMP::em::EnvelopePenetrationRestraint::set_particles(), IMP::em::EnvelopePenetrationRestraint::set_particles_order(), IMP::em::FitRestraint::FitRestraint(), IMP::em::FitRestraint::add_particles(), IMP::em::FitRestraint::remove_particles(), IMP::em::FitRestraint::set_particles(), IMP::em::FitRestraint::set_particles_order(), IMP::em::FitRestraint::store_particles(), IMP::em::PCAFitRestraint::PCAFitRestraint(), IMP::em::PCAFitRestraint::add_particles(), IMP::em::PCAFitRestraint::remove_particles(), IMP::em::PCAFitRestraint::set_particles(), IMP::em::PCAFitRestraint::set_particles_order(), IMP::em::PCAFitRestraint::store_particles(), IMP::em::SampledDensityMap::SampledDensityMap(), IMP::em::SampledDensityMap::project(), IMP::em::SampledDensityMap::set_particles(), IMP::em::SampledDensityMap::calculate_particles_bounding_box(), IMP::em::SurfaceShellDensityMap::SurfaceShellDensityMap(), IMP::example::ExamplePairScore::do_get_inputs(), IMP::example::ExampleSingletonModifier::apply_indexes(), IMP::example::ExampleSingletonModifier::do_get_inputs(), IMP::example::ExampleSingletonModifier::do_get_outputs(), IMP::example::ExampleSubsetFilterTable::ExampleSubsetFilterTable(), IMP::isd::CysteineCrossLinkRestraint::add_contribution(), IMP::isd::CysteineCrossLinkRestraint::get_CB_coordinates(), IMP::isd::FretRestraint::FretRestraint(), IMP::isd::GaussianAnchorEMRestraint::GaussianAnchorEMRestraint(), IMP::isd::GaussianEMRestraint::GaussianEMRestraint(), IMP::isd::HybridMonteCarlo::do_evaluate(), IMP::isd::MolecularDynamics::propagate_coordinates(), IMP::isd::MolecularDynamics::propagate_velocities(), IMP::isd::MolecularDynamics::setup_degrees_of_freedom(), IMP::isd::RepulsiveDistancePairScore::do_get_inputs(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::kinematics::KinematicForest::add_rigid_bodies_in_chain(), IMP::kinematics::KinematicForestScoreState::KinematicForestScoreState(), IMP::kinematics::ProteinKinematics::ProteinKinematics(), IMP::kinematics::ProteinKinematics::add_dihedral_joint(), IMP::kinematics::ProteinKinematics::add_dihedral_joints(), IMP::kinematics::ProteinKinematics::add_dihedral_joints(), IMP::kinematics::ProteinKinematics::add_edges_to_rb_graph(), IMP::kinematics::ProteinKinematics::init(), IMP::kinematics::ProteinKinematics::mark_rotatable_angles(), IMP::kinematics::ProteinKinematics::open_loop(), IMP::kinematics::ProteinKinematics::order_rigid_bodies(), IMP::misc::CommonEndpointPairFilter::do_get_inputs(), IMP::misc::LogPairScore::do_get_inputs(), IMP::misc::LowestRefinedPairScore::do_get_inputs(), 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::multi_state::EnsembleGenerator::EnsembleGenerator(), IMP::multi_state::EnsembleGenerator::add_one_state(), IMP::multi_state::EnsembleGenerator::get_state_probabilities(), IMP::multi_state::EnsembleGenerator::get_weights_average_and_std(), IMP::multi_state::EnsembleGenerator::output(), IMP::multi_state::EnsembleGenerator::rescore(), IMP::multi_state::MultiStateModelScore::get_score(), IMP::multi_state::SAXSMultiStateModelScore::get_score(), IMP::multi_state::SAXSMultiStateModelScore::set_average_c1_c2(), IMP::multifit::AnchorsData::set_secondary_structure_probabilities(), IMP::multifit::ComplementarityRestraint::ComplementarityRestraint(), IMP::multifit::ComplementarityRestraint::get_grid(), IMP::multifit::ComplementarityRestraint::get_grid_object(), IMP::multifit::Ensemble::get_rmsd(), IMP::multifit::GeometricHash::neighbors(), IMP::multifit::MergeTreeBuilder::MergeTreeBuilder(), IMP::multifit::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(), IMP::multifit::RadiusOfGyrationRestraint::add_particles(), IMP::multifit::RadiusOfGyrationRestraint::remove_particles(), IMP::multifit::RadiusOfGyrationRestraint::set_particles(), IMP::multifit::RadiusOfGyrationRestraint::set_particles_order(), IMP::multifit::RigidLeavesRefiner::do_get_inputs(), IMP::multifit::WeightedExcludedVolumeRestraint::WeightedExcludedVolumeRestraint(), IMP::multifit::WeightedExcludedVolumeRestraint::add_particles(), IMP::multifit::WeightedExcludedVolumeRestraint::remove_particles(), IMP::multifit::WeightedExcludedVolumeRestraint::set_particles(), IMP::multifit::WeightedExcludedVolumeRestraint::set_particles_order(), IMP::npc::CompositeRestraint::add_type(), IMP::npc::MinimumSphereDistancePairScore::do_get_inputs(), IMP::npctransport::AnchorToCylidnricalPorePairScore::do_get_inputs(), IMP::npctransport::BipartitePairsStatisticsOptimizerState::BipartitePairsStatisticsOptimizerState(), IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport::do_advance_chunk(), IMP::npctransport::ChainStatisticsOptimizerState::ChainStatisticsOptimizerState(), IMP::npctransport::ExcludeZRangeSingletonScore::do_get_inputs(), IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_if_good_indexes(), IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_indexes(), IMP::npctransport::HarmonicSpringSingletonScore::do_get_inputs(), IMP::npctransport::HarmonicSpringSingletonScore::evaluate_if_good_indexes(), IMP::npctransport::HarmonicSpringSingletonScore::evaluate_indexes(), IMP::npctransport::HarmonicWellPairScore::do_get_inputs(), IMP::npctransport::LinearInteractionPairScore::do_get_inputs(), IMP::npctransport::LinearSoftSpherePairScore::do_get_inputs(), IMP::npctransport::LinearWellPairScore::do_get_inputs(), IMP::npctransport::PoreRadiusSingletonScore::do_get_inputs(), IMP::npctransport::Scoring::create_backbone_restraint(), IMP::npctransport::Scoring::create_close_beads_container(), IMP::npctransport::Scoring::get_custom_scoring_function(), IMP::npctransport::SitesPairScore::do_get_inputs(), IMP::npctransport::SlabWithCylindricalPorePairScore::do_get_inputs(), IMP::npctransport::SlabWithToroidalPorePairScore::do_get_inputs(), IMP::npctransport::Statistics::fill_in_zr_hist(), IMP::npctransport::Statistics::get_interactions_and_interacting(), IMP::npctransport::Statistics::get_z_distribution(), IMP::npctransport::ZBiasSingletonScore::do_get_inputs(), IMP::npctransport::ZBiasSingletonScore::evaluate_if_good_indexes(), IMP::npctransport::ZBiasSingletonScore::evaluate_indexes(), IMP::pmi1::InternalCoordinatesConstraint::apply_indexes(), IMP::pmi1::InternalCoordinatesConstraint::do_get_inputs(), IMP::pmi1::InternalCoordinatesConstraint::do_get_outputs(), IMP::pmi1::MembraneRestraint::add_particles_above(), IMP::pmi1::MembraneRestraint::add_particles_below(), IMP::pmi1::MembraneRestraint::add_particles_inside(), IMP::pmi::InternalCoordinatesConstraint::apply_indexes(), IMP::pmi::InternalCoordinatesConstraint::do_get_inputs(), IMP::pmi::InternalCoordinatesConstraint::do_get_outputs(), IMP::pmi::MembraneRestraint::add_particles_above(), IMP::pmi::MembraneRestraint::add_particles_below(), IMP::pmi::MembraneRestraint::add_particles_inside(), IMP::rmf::HierarchyLoadLink::add_link_recursive(), IMP::rmf::HierarchyLoadLink::create_recursive(), IMP::rmf::HierarchySaveLink::add_recursive(), IMP::rmf::SimpleLoadLink::link(), IMP::rmf::SimpleSaveLink::add(), IMP::saxs::DeltaDistributionFunction::DeltaDistributionFunction(), IMP::saxs::DerivativeCalculator::compute_chisquare_derivative(), IMP::saxs::DerivativeCalculator::compute_chisquare_derivative(), IMP::saxs::DerivativeCalculator::compute_gaussian_effect_size(), IMP::saxs::DerivativeCalculator::compute_intensity_derivatives(), IMP::saxs::DerivativeCalculator::precompute_derivative_helpers(), IMP::saxs::DerivativeCalculator::compute_sinc_cos(), IMP::saxs::Profile::add(), IMP::saxs::Profile::add_partial_profiles(), IMP::saxs::Profile::calculate_I0(), IMP::saxs::Profile::calculate_profile(), IMP::saxs::Profile::calculate_profile(), IMP::saxs::Profile::calculate_profile_constant_form_factor(), IMP::saxs::Profile::calculate_profile_partial(), IMP::saxs::Profile::calculate_profile_partial(), IMP::saxs::Profile::calculate_profile_reciprocal_partial(), IMP::saxs::Profile::calculate_profile_symmetric(), IMP::saxs::Profile::calculate_profile_real(), IMP::saxs::Profile::calculate_profile_real(), IMP::saxs::Profile::calculate_profile_reciprocal(), IMP::saxs::Profile::calculate_profile_reciprocal(), IMP::saxs::Profile::squared_distributions_2_partial_profiles(), IMP::saxs::ProfileClustering::ProfileClustering(), IMP::saxs::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(), IMP::saxs::Restraint::Restraint(), IMP::saxs::RigidBodiesProfileHandler::RigidBodiesProfileHandler(), IMP::saxs::RigidBodiesProfileHandler::compute_derivatives(), IMP::saxs::SolventAccessibleSurface::get_solvent_accessibility(), IMP::saxs::SolventAccessibleSurface::create_sphere_dots(), IMP::saxs::WeightedFitParameters::WeightedFitParameters(), IMP::saxs::WeightedFitParameters::set_weights(), IMP::saxs::WeightedProfileFitter::compute_score(), IMP::saxs::WeightedProfileFitter::search_fit_parameters(), IMP::score_functor::AddScores::get_inputs(), IMP::score_functor::DistancePairScore::do_get_inputs(), IMP::score_functor::OrientedSoap::get_inputs(), IMP::score_functor::SurfaceDistancePairScore::do_get_inputs(), IMP::spb::AttributeDistancePairScore::do_get_inputs(), IMP::spb::CellMover::CellMover(), IMP::spb::CellMover::get_particles(), IMP::spb::CellMover::get_rigid_bodies(), IMP::spb::ContactMapMetric::ContactMapMetric(), IMP::spb::DiameterRgyrRestraint::DiameterRgyrRestraint(), IMP::spb::DistanceRMSDMetric::DistanceRMSDMetric(), IMP::spb::EM2DRestraint::EM2DRestraint(), IMP::spb::EM2DRestraint::EM2DRestraint(), IMP::spb::EM2DRestraint::set_particles(), IMP::spb::KinkPairScore::do_get_inputs(), IMP::spb::MolecularDynamicsWithWte::do_step(), IMP::spb::MolecularDynamicsWithWte::setup(), IMP::spb::MolecularDynamicsWithWte::propagate_coordinates(), IMP::spb::MolecularDynamicsWithWte::propagate_velocities(), IMP::spb::MolecularDynamicsWithWte::setup_degrees_of_freedom(), IMP::spb::MonteCarloWithWte::do_evaluate(), IMP::spb::NuisanceRangeModifier::apply_indexes(), IMP::spb::NuisanceRangeModifier::do_get_inputs(), IMP::spb::NuisanceRangeModifier::do_get_outputs(), IMP::spb::PbcBoxedMover::PbcBoxedMover(), IMP::spb::PbcBoxedRigidBodyMover::PbcBoxedRigidBodyMover(), IMP::spb::PbcBoxedRigidBodyMover::get_particles(), IMP::spb::PbcBoxedRigidBodyMover::get_rigid_bodies(), IMP::spb::RMSDMetric::RMSDMetric(), IMP::spb::RigidBodyPackingScore::do_get_inputs(), IMP::spb::SameParticlePairFilter::do_get_inputs(), IMP::spb::SameRigidBodyPairFilter::do_get_inputs(), IMP::spb::TiltSingletonScore::do_get_inputs(), IMP::spb::TiltSingletonScore::evaluate_if_good_indexes(), IMP::spb::TiltSingletonScore::evaluate_indexes(), IMP::spb::TransformationSymmetry::apply_indexes(), IMP::spb::TransformationSymmetry::do_get_inputs(), IMP::spb::TransformationSymmetry::do_get_outputs(), IMP::spb::TwoStateGoModelRestraint::set_parameters(), IMP::spb::TwoStateGoModelRestraint::TwoStateGoModelRestraint(), IMP::statistics::ParticleEmbedding::ParticleEmbedding(), IMP::symmetry::BallMover::BallMover(), IMP::symmetry::RigidBodyMover::RigidBodyMover(), IMP::symmetry::RigidBodyMover::get_particles(), IMP::symmetry::RigidBodyMover::get_rigid_bodies(), IMP::write_particles_to_buffer(), IMP::read_particles_from_buffer(), IMP::get_indexes(), IMP::get_particles(), IMP::get_random_numbers_normal(), IMP::get_random_numbers_uniform(), IMP::algebra::get_principal_components(), IMP::atom::write_multimodel_pdb(), IMP::atom::read_psipred(), IMP::atom::create_excluded_volume_restraint(), IMP::atom::create_rigid_body(), IMP::atom::get_component_placement_score(), IMP::atom::get_pairwise_rmsd_score(), IMP::atom::get_placement_score(), IMP::atom::get_radius_of_gyration(), IMP::atom::get_rmsd(), IMP::atom::get_rmsd_transforming_first(), IMP::atom::setup_as_approximation(), IMP::atom::setup_coarse_secondary_structure_residue(), IMP::atom::setup_coarse_secondary_structure_residues(), IMP::cnmultifit::cn_symm_score(), IMP::cnmultifit::fit_cn_assembly(), IMP::cnmultifit::generate_cn_transformations(), IMP::cnmultifit::generate_translations_along_symm_axis(), IMP::cnmultifit::get_cn_rmsd(), IMP::cnmultifit::symmetry_local_fitting(), IMP::cnmultifit::transform_cn_assembly(), IMP::container::get_slack_estimate(), IMP::core::assign_blame(), IMP::core::create_blame_geometries(), IMP::core::get_bounding_box(), IMP::core::get_centroid(), IMP::core::get_enclosing_sphere(), IMP::core::get_initial_reference_frame(), IMP::core::get_initial_reference_frame(), IMP::core::set_enclosing_radius(), IMP::core::set_enclosing_sphere(), IMP::domino::get_interaction_graph(), IMP::domino::write_merge_tree(), IMP::domino::read_merge_tree(), IMP::domino::get_index(), IMP::domino::get_partial_index(), IMP::domino::get_possible_interactions(), IMP::em::compute_fitting_score(), IMP::em::compute_fitting_scores(), IMP::em::get_number_of_particles_outside_of_the_density(), IMP::em::get_numbers_of_particles_outside_of_the_density(), IMP::em::get_percentage_of_voxels_covered_by_particles(), IMP::em::local_rigid_fitting_grid_search(), IMP::em::particles2binarized_density(), IMP::em::particles2density(), IMP::em::particles2surface(), IMP::em2d::create_evenly_distributed_projections(), IMP::em2d::do_project_particles(), IMP::em2d::get_enclosing_image_size(), IMP::em2d::get_projection(), IMP::em2d::get_projections(), IMP::em2d::get_projections(), IMP::example::create_chain_restraint(), IMP::example::create_excluded_volume(), IMP::example::create_serial_mover(), IMP::example::get_number_of_incidences(), IMP::example::optimize_assembly(), IMP::example::optimize_balls(), IMP::kinematics::add_missing_bonds(), IMP::kinematics::create_bond(), IMP::kinematics::find_atom(), IMP::kinematics::find_residue(), IMP::kinematics::get_ca_atom(), IMP::kinematics::read_angle_file(), IMP::kinematics::read_connect_chains_file(), IMP::multifit::get_actual_radius_of_gyration(), IMP::multifit::get_anchor_indices_matching_secondary_structure(), IMP::multifit::pca_based_rigid_fitting(), IMP::multifit::write_connolly_surface(), IMP::npctransport::add_hierarchies_with_sites(), IMP::npctransport::add_hierarchies_with_sites(), IMP::npctransport::get_maximal_number_of_unordered_pairs(), IMP::npctransport::get_non_optimizable_particles(), IMP::npctransport::get_optimizable_particles(), IMP::npctransport::get_particle_indexes(), IMP::npctransport::link_hierarchies_with_sites(), IMP::npctransport::write_geometry(), IMP::pmi::create_elastic_network(), IMP::pmi::get_bipartite_minimum_sphere_distance(), IMP::pmi::get_list_of_bipartite_minimum_sphere_distance(), IMP::pmi1::create_elastic_network(), IMP::pmi1::get_bipartite_minimum_sphere_distance(), IMP::pmi1::get_list_of_bipartite_minimum_sphere_distance(), IMP::rmf::add_hierarchies(), IMP::rmf::add_hierarchies(), IMP::rmf::link_hierarchies(), IMP::rmf::add_particles(), IMP::rmf::add_particles(), IMP::rmf::link_particles(), IMP::saxs::compute_max_distance(), IMP::saxs::compute_max_distance(), IMP::saxs::compute_profile(), IMP::saxs::get_coordinates(), IMP::saxs::get_form_factors(), IMP::saxs::radius_of_gyration(), IMP::saxs::read_files(), IMP::saxs::read_pdb(), IMP::spb::add_BallMover(), IMP::spb::add_link(), IMP::spb::add_link(), IMP::spb::add_PbcBoxedMover(), IMP::spb::add_PbcBoxedRigidBodyMover(), IMP::spb::add_SPBexcluded_volume(), IMP::spb::add_symmetry_restraint(), IMP::spb::create_merged_protein(), IMP::spb::do_bipartite_mindist(), IMP::spb::do_bipartite_mindist(), IMP::spb::em2d_restraint(), IMP::spb::em2d_restraint(), IMP::spb::fret_restraint(), IMP::spb::fret_restraint(), IMP::spb::fret_restraint(), IMP::spb::get_rigid_bodies(), IMP::spb::load_restart(), IMP::spb::recenter_rb(), IMP::spb::spb_assemble_restraints(), IMP::spb::y2h_restraint(), IMP::spb::y2h_restraint(), IMP::spb::y2h_restraint(), IMP::spb::y2h_restraint() |
