IMP Reference Guide
develop.49f026e7cd,2024/12/04
The Integrative Modeling Platform
|
Common base class for heavy weight IMP
objects.
More...
#include <IMP/Object.h>
Inherits IMP::NonCopyable.
Inherited by IMP::algebra::DynamicNearestNeighbor3D, IMP::algebra::NearestNeighborD< D >, IMP::algebra::VectorKDMetric, IMP::atom::CHARMMResidueTopologyBase, IMP::atom::CHARMMSegmentTopology, IMP::atom::CHARMMTopology, IMP::atom::ForceFieldParameters, IMP::atom::Mol2Selector, IMP::atom::PDBSelector, IMP::atom::SmoothingFunction, IMP::bff::DecayLifetimeHandler, IMP::Configuration, IMP::ConfigurationSet, IMP::core::ClosePairsFinder, IMP::core::DataObject< Data >, IMP::display::Geometry, IMP::display::Writer, IMP::domino::AssignmentContainer, IMP::domino::AssignmentsTable, IMP::domino::ParticleStates, IMP::domino::ParticleStatesTable, IMP::domino::RestraintCache, IMP::domino::SubsetFilter, IMP::domino::SubsetFilterTable, IMP::em2d::CollisionCrossSection, IMP::em2d::Image, IMP::em2d::ImageReaderWriter, IMP::em2d::ProjectionFinder, IMP::em2d::ScoreFunction, IMP::em::CoarseCCatIntervals, IMP::em::DensityMap, IMP::em::EnvelopeScore, IMP::em::MapReaderWriter, IMP::em::PCAAligner, IMP::example::ExampleObject, IMP::isd::BivariateFunction, IMP::isd::CrossLinkData, IMP::isd::CysteineCrossLinkData, IMP::isd::Distribution, IMP::isd::FretData, IMP::isd::GaussianProcessInterpolation, IMP::isd::MultivariateFNormalSufficient, IMP::isd::UnivariateFunction, IMP::isd::vonMises, IMP::isd::vonMisesSufficient, IMP::kinematics::DirectionalDOF, IMP::kinematics::DOF, IMP::kinematics::DOFsSampler, IMP::kinematics::Joint, IMP::kinematics::KinematicForest, IMP::kinematics::LocalPlanner, IMP::kinematics::ProteinKinematics, IMP::kmeans::KMeans, IMP::Model, IMP::Model, IMP::ModelObject, IMP::mpi::ReplicaExchange, IMP::multifit::AssemblyHeader, IMP::multifit::ComponentHeader, IMP::multifit::Ensemble, IMP::multifit::FFTFitting, IMP::multifit::FFTFittingOutput, IMP::multifit::ProbabilisticAnchorGraph, IMP::multifit::ProteomicsData, IMP::multifit::ProteomicsEMAlignmentAtomic, IMP::multifit::SettingsData, IMP::npctransport::FGChain, IMP::npctransport::ParticleFactory, IMP::npctransport::Scoring, IMP::npctransport::SimulationData, IMP::npctransport::Statistics, IMP::PairModifier, IMP::PairPredicate, IMP::PairScore, IMP::QuadModifier, IMP::QuadPredicate, IMP::QuadScore, IMP::Refiner, IMP::RestraintInfo, IMP::rmf::LoadLink, IMP::rmf::SaveLink, IMP::rotamer::RotamerCalculator, IMP::rotamer::RotamerLibrary, IMP::Sampler, IMP::saxs::ChiFreeScore, IMP::saxs::ChiScore, IMP::saxs::ChiScoreLog, IMP::saxs::DerivativeCalculator, IMP::saxs::Profile, IMP::saxs::ProfileFitter< ScoringFunctionT >, IMP::saxs::RatioVolatilityScore, IMP::saxs::RigidBodiesProfileHandler, IMP::SingletonModifier, IMP::SingletonPredicate, IMP::SingletonScore, IMP::statistics::Embedding, IMP::statistics::Metric, IMP::statistics::PartitionalClustering, IMP::TripletModifier, IMP::TripletPredicate, IMP::TripletScore, IMP::UnaryFunction, IMP::Undecorator, and log.DummyObject.
Common base class for heavy weight IMP
objects.
The base class for non value-type classes in IMP
. Anything inheriting from Object has the following properties:
Types inheriting from Object should always be created using new
in C++ and passed using pointers and stored using Pointer objects. Note that you have to be careful of cycles and so must use WeakPointer objects to break cycles. IMP_NEW() can help shorten creating a ref counted pointer. See Pointer for more information.
See example::ExampleObject for a simple example.
Reference counting is a technique for managing memory and automatically freeing memory (destroying objects) when it is no longer needed. In reference counting, each object has a reference count, which tracks how many different places are using the object. When this count goes to 0, the object is freed.
Python internally reference counts everything. C++, on the other hand, requires extra steps be taken to ensure that objects are reference counted properly.
In IMP
, reference counting is done through the Pointer, PointerMember and Object classes. The former should be used instead of a raw C++ pointer when storing a pointer to any object inheriting from Object.
Any time one is using reference counting, one needs to be aware of cycles, since if, for example, object A contains an IMP::Pointer to object B and object B contains an Pointer to object A, their reference counts will never go to 0 even if both A and B are no longer used. To avoid this, use an WeakPointer in one of A or B.
Functions that create new objects should follow the following pattern
ObjectType *create_object(arguments) { IMP_NEW(ObjectType, ret, (args)); do_stuff; return ret.release(); }
using Pointer::release() to safely return the new object without freeing it.
Public Member Functions | |
virtual void | clear_caches () |
CheckLevel | get_check_level () const |
LogLevel | get_log_level () const |
virtual VersionInfo | get_version_info () const |
Get information about the module and version of the object. More... | |
void | set_check_level (CheckLevel l) |
void | set_log_level (LogLevel l) |
Set the logging level used in this object. More... | |
void | set_was_used (bool tf) const |
void | show (std::ostream &out=std::cout) const |
Protected Member Functions | |
Object (std::string name) | |
Construct an object with the given name. More... | |
virtual void | do_destroy () |
|
protected |
Construct an object with the given name.
An instance of "%1%" in the string will be replaced by a unique index.
|
virtual |
Objects can have internal caches. This method resets them returning the object to its just-initialized state.
Reimplemented in IMP::core::ExcludedVolumeRestraint, and IMP::core::MinimumRestraint.
|
protectedvirtual |
Override this method to take action on destruction.
Reimplemented in IMP::container::ExclusiveConsecutivePairContainer, and IMP::display::PymolWriter.
|
virtual |
Get information about the module and version of the object.
Reimplemented in IMP::npc::OverallPositionRestraint, IMP::npc::XAxialPositionUpperRestraint, IMP::npc::XAxialPositionLowerRestraint, IMP::npc::XAxialPositionRestraint, IMP::npc::ProteinProximityRestraint, IMP::isd::GeneralizedGuinierPorodFunction, IMP::npc::AssemblySymmetryByDihedralRestraint, IMP::npctransport::SimulationData, IMP::npctransport::Scoring, IMP::npc::AssemblySymmetryByDistanceRestraint, IMP::npc::PerinuclearVolumeLocationRestraint, IMP::atom::WritePDBOptimizerState, IMP::Model, IMP::npc::PoreSideVolumeLocationRestraint, IMP::npc::MembraneExclusionRestraint, IMP::npc::MembraneSurfaceLocationConditionalRestraint, IMP::npc::MembraneSurfaceLocationRestraint, IMP::atom::NotPDBSelector, IMP::atom::CHARMMResidueTopology, IMP::atom::XorPDBSelector, IMP::npc::ProteinChainRestraint, IMP::atom::OrPDBSelector, IMP::npctransport::LinearWellPairScore, IMP::em::DensityMap, IMP::npc::ProteinContactRestraint, IMP::atom::CHARMMPatch, IMP::atom::AndPDBSelector, IMP::isd::Covariance1DFunction, IMP::atom::PPDBSelector, IMP::npc::XYRadialPositionUpperRestraint, IMP::atom::BackbonePDBSelector, IMP::atom::CHARMMIdealResidueTopology, IMP::atom::NonWaterPDBSelector, IMP::domino::CappedAssignmentContainer, IMP::atom::SelectionGeometry, IMP::npctransport::Statistics, IMP::npc::XYRadialPositionLowerRestraint, IMP::atom::NonHydrogenPDBSelector, IMP::domino::HeapAssignmentContainer, IMP::atom::CHARMMParameters, IMP::domino::ProbabilisticSubsetFilterTable, IMP::atom::CHARMMResidueTopologyBase, IMP::atom::NonWaterNonHydrogenPDBSelector, IMP::domino::RangeViewAssignmentContainer, IMP::npctransport::LinearInteractionPairScore, IMP::npc::XYRadialPositionRestraint, IMP::domino::PairListSubsetFilterTable, IMP::atom::HydrogenPDBSelector, IMP::domino::ReadAssignmentContainer, IMP::atom::BondGeometry, IMP::atom::BondsGeometry, IMP::atom::WaterPDBSelector, IMP::domino::ListSubsetFilterTable, IMP::core::LateralSurfaceConstraint, IMP::domino::PermutationStates, IMP::isd::Linear1DFunction, IMP::npctransport::BipartitePairsStatisticsOptimizerState, IMP::domino::WriteAssignmentContainer, IMP::npc::YAxialPositionUpperRestraint, IMP::atom::ChainPDBSelector, IMP::atom::CHARMMTopology, IMP::saxs::Profile, IMP::npctransport::SitesPairScore, IMP::atom::AllPDBSelector, IMP::core::MonteCarloWithBasinHopping, IMP::domino::RecursiveStates, IMP::domino::EquivalenceAndExclusionSubsetFilterTable, IMP::domino::EquivalenceSubsetFilterTable, IMP::atom::NPDBSelector, IMP::domino::ReadHDF5AssignmentContainer, IMP::core::SurfaceGeometryConstraint, IMP::domino::RestraintCache, IMP::core::MonteCarloWithLocalOptimization, IMP::npc::YAxialPositionLowerRestraint, IMP::domino::EqualitySubsetFilterTable, IMP::domino::CompoundStates, IMP::atom::HierarchiesGeometry, IMP::isd::MultivariateFNormalSufficient, IMP::atom::CPDBSelector, IMP::domino::ExclusionSubsetFilterTable, IMP::kinematics::ProteinKinematics, IMP::domino::WriteHDF5AssignmentContainer, IMP::domino::NestedRigidBodyStates, IMP::atom::ResidueTypePDBSelector, IMP::RestraintInfo, IMP::atom::HierarchyGeometry, IMP::algebra::DynamicNearestNeighbor3D, IMP::multifit::ProteomicsData, IMP::misc::MetricClosePairsFinder< LowerBound, UpperBound >, IMP::core::SoftSpherePairScore, IMP::core::SurfaceGeometry, IMP::npc::YAxialPositionRestraint, IMP::atom::AtomTypePDBSelector, IMP::container::ExclusiveConsecutivePairFilter, IMP::npctransport::FGChain, IMP::bff::AVNetworkRestraint, IMP::domino::RigidBodyStates, IMP::core::CoinFlipPairPredicate, IMP::core::CoinFlipQuadPredicate, IMP::core::CoinFlipSingletonPredicate, IMP::core::CoinFlipTripletPredicate, IMP::core::WeightedSphereDistancePairScore, IMP::em2d::ProjectionFinder, IMP::core::EdgePairGeometry, IMP::core::EdgePairsGeometry, IMP::atom::CBetaPDBSelector, IMP::domino::SampleAssignmentContainer, IMP::container::ExclusiveConsecutivePairContainer, IMP::multifit::SettingsData, IMP::algebra::NearestNeighborD< D >, IMP::domino::XYZStates, IMP::isd::CrossLinkMSRestraint, IMP::core::XYZDerivativeGeometry, IMP::core::XYZDerivativesGeometry, IMP::core::TransformationSymmetryMover, IMP::core::AllSamePairPredicate, IMP::core::AllSameQuadPredicate, IMP::core::AllSameSingletonPredicate, IMP::core::AllSameTripletPredicate, IMP::em2d::Image, IMP::em2d::SpiderImageReaderWriter, IMP::atom::CAlphaPDBSelector, IMP::core::SoftSubSurfacePairScore, IMP::isd::GaussianAnchorEMRestraint, IMP::core::NormalizedSphereDistancePairScore, IMP::core::XYZRGeometry, IMP::core::XYZRsGeometry, IMP::domino::MinimumRestraintScoreSubsetFilterTable, IMP::isd::FStudentT, IMP::bayesianem::GaussianEMRestraint, IMP::isd::GaussianProcessInterpolation, IMP::npc::ZAxialPositionUpperRestraint, IMP::atom::MolecularDynamics, IMP::isd::vonMisesSufficient, IMP::atom::ATOMPDBSelector, IMP::em2d::Em2DRestraint, IMP::container::ClosePairContainer, IMP::core::SoftSuperSurfacePairScore, IMP::pmi::TransformMover, IMP::core::PredicateSingletonScore< Predicate, Score >, IMP::rmf::HierarchyLoadLink, IMP::core::OrderedTypePairPredicate, IMP::core::OrderedTypeQuadPredicate, IMP::core::OrderedTypeSingletonPredicate, IMP::core::OrderedTypeTripletPredicate, IMP::domino::ListAssignmentsTable, IMP::domino::IndexStates, IMP::container::PredicatePairsRestraint, IMP::container::PredicateQuadsRestraint, IMP::container::PredicateSingletonsRestraint, IMP::container::PredicateTripletsRestraint, IMP::domino::ListAssignmentContainer, IMP::core::SphereDistanceToSingletonScore, IMP::atom::NonAlternativePDBSelector, IMP::rotamer::RotamerLibrary, IMP::atom::ForceSwitch, IMP::core::MCCGSampler, IMP::domino::RestraintScoreSubsetFilterTable, IMP::npctransport::LinearSoftSpherePairScore, IMP::isd::GaussianEMRestraint, IMP::core::HarmonicSurfaceDepthPairScore, IMP::bff::DecayLifetimeHandler, IMP::em2d::ProjectionParametersScoreState, IMP::atom::BrownianDynamics, IMP::display::PlaneGeometry, IMP::multifit::AssemblyHeader, IMP::npctransport::ParticleTransportStatisticsOptimizerState, IMP::npctransport::ChainStatisticsOptimizerState, IMP::core::TransformationSymmetry, IMP::isd::CysteineCrossLinkRestraint, IMP::isd::FretRestraint, IMP::domino::BranchAndBoundAssignmentsTable, IMP::domino::ParticleStatesTable, IMP::npctransport::SlabWithCylindricalPorePairScore, IMP::rotamer::RotamerCalculator, IMP::core::ClosePairsPairScore, IMP::core::RigidClosePairsFinder, IMP::em2d::JPGImageReaderWriter, IMP::isd::OneDimensionalSufficientDistribution, IMP::core::RigidBodyTunneler, IMP::em2d::ProjectionStates, IMP::isd::PenalizedComplexityPrior, IMP::npctransport::ParticleFactory, IMP::core::HarmonicSphereDistancePairScore, IMP::em2d::TIFFImageReaderWriter, IMP::npc::ZAxialPositionLowerRestraint, IMP::rmf::HierarchySaveLink, IMP::core::HarmonicSurfaceHeightPairScore, IMP::core::IsCollisionPairPredicate, IMP::core::WeightedSumOfExponential, IMP::kmeans::KMeans, IMP::statistics::VectorDEmbedding, IMP::core::MSConnectivityRestraint, IMP::display::SurfaceMeshGeometry, IMP::core::ExcludedVolumeRestraint, IMP::em2d::PCAFitRestraint, IMP::npctransport::SlabWithToroidalPorePairScore, IMP::container::ConsecutivePairFilter, IMP::core::RigidBodyUmbrella, IMP::npctransport::HarmonicWellPairScore, IMP::pmi::CompositeRestraint, IMP::container::CloseBipartitePairContainer, IMP::core::GenericBoundingBox3DSingletonScore< UF >, IMP::isd::TALOSRestraint, IMP::isd::FNormal, IMP::core::BallMover, IMP::em::MRCReaderWriter, IMP::core::SurfaceMover, IMP::em2d::ParticlesDummyRestraint, IMP::core::TruncatedHarmonic< DIRECTION >, IMP::em::SpiderMapReaderWriter, IMP::npctransport::AnchorToCylidnricalPorePairScore, IMP::npctransport::HarmonicSpringSingletonScore, IMP::npctransport::ZBiasSingletonScore, IMP::core::HarmonicSurfaceDistancePairScore, IMP::atom::LennardJonesPairScore, IMP::multifit::ComplementarityRestraint, IMP::container::ListPairContainer, IMP::container::ListQuadContainer, IMP::container::ListSingletonContainer, IMP::container::ListTripletContainer, IMP::core::HarmonicUpperBoundSphereDiameterPairScore, IMP::core::UnorderedTypePairPredicate, IMP::core::UnorderedTypeQuadPredicate, IMP::core::UnorderedTypeSingletonPredicate, IMP::core::UnorderedTypeTripletPredicate, IMP::display::LabelGeometry, IMP::isd::StudentTRestraint, IMP::mpi::ReplicaExchange, IMP::container::PairsConstraint, IMP::container::QuadsConstraint, IMP::container::SingletonsConstraint, IMP::container::TripletsConstraint, IMP::domino::PackedAssignmentContainer, IMP::isd::LognormalAmbiguousRestraint, IMP::container::DynamicListPairContainer, IMP::container::DynamicListQuadContainer, IMP::container::DynamicListSingletonContainer, IMP::container::DynamicListTripletContainer, IMP::core::DirectionMover, IMP::core::SurfaceTetheredChain, IMP::domino::RecursiveAssignmentsTable, IMP::spb::EM2DRestraint, IMP::algebra::MaxVectorKDMetric, IMP::atom::SoapPairFilter, IMP::isd::GaussianProcessInterpolationRestraint, IMP::misc::FreelyJointedChain, IMP::npc::CompositeRestraint, IMP::core::FixedRefiner, IMP::core::WeightedSum, IMP::atom::CHARMMStereochemistryRestraint, IMP::core::WeightedDerivativesToRefined, IMP::statistics::ParticleEmbedding, IMP::core::LogNormalMover, IMP::core::RigidBodyMover, IMP::core::TypedPairScore, IMP::isd::AtomicCrossLinkMSRestraint, IMP::kinematics::DirectionalDOF, IMP::core::CentroidOfRefined, IMP::em::FitRestraint, IMP::multifit::ProteomicsEMAlignmentAtomic, IMP::spb::MonteCarloWithWte, IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >, IMP::score_functor::DistancePairScoreWithCache< score_functor::OrientedSoap >, IMP::container::PairsRestraint, IMP::container::QuadsRestraint, IMP::container::SingletonsRestraint, IMP::container::TripletsRestraint, IMP::core::NormalMover, IMP::core::PairConstraint, IMP::core::QuadConstraint, IMP::core::SingletonConstraint, IMP::core::TripletConstraint, IMP::saxs::Restraint, IMP::container::ConsecutivePairContainer, IMP::core::TransformationAndReflectionSymmetry, IMP::em::EMReaderWriter, IMP::isd::ResidueProteinProximityRestraint, IMP::npctransport::BodyStatisticsOptimizerState, IMP::RestraintSet, IMP::container::ConnectingPairContainer, IMP::em2d::ScoreFunction, IMP::gsl::Simplex, IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >, IMP::core::GenericDistanceToSingletonScore< UF >, IMP::core::SurfaceDepthPairScore, IMP::display::ReferenceFrameGeometry, IMP::display::PymolWriter, IMP::isd::NormalSigmaPCRestraint, IMP::em2d::GridStates, IMP::npctransport::FunctorLinearInteractionPairScore, IMP::core::KClosePairsPairScore, IMP::isd::CrossLinkData, IMP::isd::MarginalNOERestraint, IMP::isd::vonMises, IMP::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< LinearInteractionScore >, IMP::score_functor::DistancePairScore< LinearSoftSphereScore >, IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >, IMP::score_functor::DistancePairScore< score_functor::LoopStatistical >, IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > >, IMP::score_functor::DistancePairScore< score_functor::Dope >, IMP::container::PairContainerSet, IMP::container::QuadContainerSet, IMP::container::SingletonContainerSet, IMP::container::TripletContainerSet, IMP::core::ConnectivityRestraint, IMP::em::EnvelopeScore, IMP::em2d::RelativePositionMover, IMP::npc::ZAxialPositionRestraint, IMP::container::AllBipartitePairContainer, IMP::container::DistributePairsScoreState, IMP::container::DistributeQuadsScoreState, IMP::container::DistributeSingletonsScoreState, IMP::container::DistributeTripletsScoreState, IMP::isd::GaussianRestraint, IMP::isd::LognormalRestraint, IMP::core::CoverRefined, IMP::core::HarmonicWell, IMP::core::SurfaceSymmetryConstraint, IMP::em::EnvelopeFitRestraint, IMP::pmi::CrossLinkRestraintSet, IMP::statistics::ChiSquareMetric, IMP::core::PairRestraint, IMP::core::QuadRestraint, IMP::core::SingletonRestraint, IMP::core::TripletRestraint, IMP::display::BoundingBoxGeometry, IMP::em::CoarseCCatIntervals, IMP::em2d::DistanceFilter, IMP::em2d::DummyRestraint, IMP::isd::OneDimensionalDistribution, IMP::core::AttributeSingletonPredicate, IMP::core::SubsetMover, IMP::isd::MarginalHBondRestraint, IMP::atom::BondPairContainer, IMP::SaveToConfigurationSetOptimizerState, IMP::core::HarmonicUpperBoundSphereDistancePairScore, IMP::domino::SimpleAssignmentsTable, IMP::isd::CysteineCrossLinkData, IMP::isd::FretData, IMP::multifit::ProbabilisticAnchorGraph, IMP::atom::CADihedralRestraint, IMP::statistics::ConfigurationSetRMSDMetric, IMP::atom::StereochemistryPairFilter, IMP::display::TriangleGeometry, IMP::domino::DependencyScoreState, IMP::example::ExampleSingletonModifier, IMP::isd::AmbiguousNOERestraint, IMP::isd::LogWrapper, IMP::multifit::ComponentHeader, IMP::rmf::SaveOptimizerState, IMP::atom::BerendsenThermostatOptimizerState, IMP::isd::AmbiguousRestraint, IMP::isd::HybridMonteCarlo, IMP::npc::MinimumSphereDistancePairScore, IMP::algebra::EuclideanVectorKDMetric, IMP::atom::CoulombPairScore, IMP::core::HarmonicDistancePairScore, IMP::em2d::CollisionCrossSection, IMP::container::InContainerPairFilter, IMP::container::InContainerQuadFilter, IMP::container::InContainerSingletonFilter, IMP::container::InContainerTripletFilter, IMP::core::SerialMover, IMP::em::PCAFitRestraint, IMP::statistics::PartitionalClusteringWithCenter, IMP::core::MultipleBinormalRestraint, IMP::core::NeighborsTable, IMP::core::SurfaceHeightPairScore, IMP::display::PolygonGeometry, IMP::em::FitRestraintBayesEM3D, IMP::example::ExampleComplexRestraint, IMP::multifit::DummyRestraint, IMP::npctransport::TypedSitesGeometry, IMP::pmi::MembraneRestraint, IMP::container::AllPairContainer, IMP::core::MonteCarlo, IMP::core::ConstantPairPredicate, IMP::core::ConstantQuadPredicate, IMP::core::ConstantSingletonPredicate, IMP::core::ConstantTripletPredicate, IMP::core::DiameterRestraint, IMP::example::ExampleObject, IMP::npc::SlabWithSphericalIndentMBMScore, IMP::npc::SphericalIndentSurfaceDepthPairScore, IMP::npctransport::GlobalStatisticsOptimizerState, IMP::Particle, IMP::spb::TransformationSymmetry, IMP::atom::CAAngleRestraint, IMP::core::ConjugateGradients, IMP::display::FilterGeometry, IMP::em::EnvelopePenetrationRestraint, IMP::em::PCAAligner, IMP::em2d::DistanceFilterTable, IMP::gsl::QuasiNewton, IMP::npc::SlabWithToroidalPoreGoPairScore, IMP::npc::SlabWithToroidalPoreMBMScore, IMP::npc::ToroidalPoreSurfaceDepthPairScore, IMP::spb::Gaussian, IMP::core::AngleRestraint, IMP::display::RestraintSetGeometry, IMP::example::ExampleUnaryFunction, IMP::isd::NOERestraint, IMP::multifit::WeightedExcludedVolumeRestraint, IMP::spb::DistanceRMSDMetric, IMP::core::QuadraticClosePairsFinder, IMP::core::TransformedDistancePairScore, IMP::display::SegmentGeometry, IMP::em::DensityFillingRestraint, IMP::em2d::RigidBodiesImageFitRestraint, IMP::spb::UniformBoundedRestraint, IMP::atom::ImproperSingletonScore, IMP::Configuration, IMP::container::PairContainerStatistics, IMP::container::PairsOptimizerState, IMP::container::QuadContainerStatistics, IMP::container::QuadsOptimizerState, IMP::container::SingletonContainerStatistics, IMP::container::SingletonsOptimizerState, IMP::container::TripletContainerStatistics, IMP::container::TripletsOptimizerState, IMP::domino::DominoSampler, IMP::isd::UniformPrior, IMP::npctransport::ExcludeZRangeSingletonScore, IMP::saxs::RigidBodiesProfileHandler, IMP::spb::ChiSquareMetric, IMP::core::GenericBoundingSphere3DSingletonScore< UF >, IMP::core::ConstantRestraint, IMP::core::DerivativesFromRefined, IMP::core::TableRefiner, IMP::spb::TiltSingletonScore, IMP::atom::LangevinThermostatOptimizerState, IMP::container::MinimumPairRestraint, IMP::container::MinimumQuadRestraint, IMP::container::MinimumSingletonRestraint, IMP::container::MinimumTripletRestraint, IMP::core::AngleTripletScore, IMP::core::Cosine, IMP::core::DerivativesToRefined, IMP::core::GridClosePairsFinder, IMP::multifit::FFTFitting, IMP::npc::SlabWithToroidalPoreWireGeometry, IMP::spb::RigidBodyNewMover, IMP::ConfigurationSet, IMP::core::ChildrenRefiner, IMP::core::Harmonic, IMP::display::PointGeometry, IMP::em::MapReaderWriter, IMP::example::ExampleRestraint, IMP::kinematics::KinematicForest, IMP::kinematics::KinematicForestScoreState, IMP::kinematics::RevoluteJointMover, IMP::npctransport::SlabWithToroidalPoreWireGeometry, IMP::saxs::ChiScoreLog, IMP::spb::DistanceTerminiRestraint, IMP::core::SphereDistancePairScore, IMP::core::Transform, IMP::isd::JeffreysRestraint, IMP::misc::DecayPairContainerOptimizerState, IMP::misc::WormLikeChain, IMP::saxs::RadiusOfGyrationRestraint, IMP::spb::ContactMapMetric, IMP::spb::PbcBoxedRigidBodyMover, IMP::spb::TwoStateGoModelRestraint, IMP::statistics::ConfigurationSetXYZEmbedding, IMP::atom::AngleSingletonScore, IMP::atom::DihedralSingletonScore, IMP::core::DihedralRestraint, IMP::core::HarmonicLowerBound, IMP::core::HarmonicUpperBound, IMP::core::Linear, IMP::core::MoveStatisticsScoreState, IMP::example::ExampleSubsetFilterTable, IMP::isd::RepulsiveDistancePairScore, IMP::multifit::RadiusOfGyrationRestraint, IMP::spb::AttributeDistancePairScore, IMP::symmetry::RigidBodyMover, IMP::atom::EzRestraint, IMP::atom::HelixRestraint, IMP::atom::VelocityScalingOptimizerState, IMP::container::EventPairsOptimizerState, IMP::container::EventQuadsOptimizerState, IMP::container::EventSingletonsOptimizerState, IMP::container::EventTripletsOptimizerState, IMP::core::BoxSweepClosePairsFinder, IMP::core::ChecksScoreState, IMP::core::GenericAttributeSingletonScore< UF >, IMP::core::LeavesRefiner, IMP::core::RigidBodyFrameGeometry, IMP::core::RigidBodyFramesGeometry, IMP::display::EllipsoidGeometry, IMP::em2d::ImageReaderWriter, IMP::isd::MolecularDynamicsMover, IMP::npctransport::FunctorLinearSoftSpherePairScore, IMP::saxs::RatioVolatilityScore, IMP::core::GenericAttributeSingletonScore< core::Harmonic >, IMP::atom::BondSingletonScore, IMP::core::MinimumRestraint, IMP::isd::vonMisesKappaJeffreysRestraint, IMP::spb::BoxedMover, IMP::spb::PbcBoxedMover, IMP::core::RefinedPairsPairScore, IMP::core::SurfaceDistancePairScore, IMP::example::ExampleConstraint, IMP::example::ExamplePairScore, IMP::isd::vonMisesKappaConjugateRestraint, IMP::multifit::Ensemble, IMP::score_functor::ScoreUnaryFunction< Score, D >, IMP::spb::DiameterRgyrRestraint, IMP::score_functor::ScoreUnaryFunction< score_functor::OpenCubicSpline >, IMP::container::MinimumPairScore, IMP::container::MinimumQuadScore, IMP::container::MinimumSingletonScore, IMP::container::MinimumTripletScore, IMP::core::NearestNeighborsClosePairsFinder, IMP::core::InBoundingBox3DSingletonPredicate, IMP::display::RestraintGeometry, IMP::em::XplorReaderWriter, IMP::misc::LowestRefinedPairScore, IMP::core::RigidBodyDerivativeGeometry, IMP::core::RigidBodyDerivativesGeometry, IMP::display::CylinderGeometry, IMP::isd::GammaPrior, IMP::kinematics::DihedralMover, IMP::npctransport::SitesGeometry, IMP::spb::KinkPairScore, IMP::statistics::RecursivePartitionalClusteringEmbedding, IMP::statistics::RecursivePartitionalClusteringMetric, IMP::symmetry::BallMover, IMP::atom::CHARMMSegmentTopology, IMP::atom::CoverBond, IMP::core::ClosedCubicSpline, IMP::core::WriteRestraintScoresOptimizerState, IMP::display::WriteOptimizerState, IMP::domino::BranchAndBoundSampler, IMP::misc::LogPairScore, IMP::spb::CellMover, IMP::atom::BondedPairFilter, IMP::atom::RemoveTranslationOptimizerState, IMP::isd::ISDRestraint, IMP::isd::WeightMover, IMP::misc::SoftCylinderPairScore, IMP::multifit::FittingStates, IMP::saxs::ChiScore, IMP::spb::RMSDMetric, IMP::atom::BondEndpointsRefiner, IMP::core::RigidBodyAnglePairScore, IMP::kinematics::Joint, IMP::core::VolumeRestraint, IMP::display::SphereGeometry, IMP::isd::WeightRestraint, IMP::kinematics::DOF, IMP::multifit::FFTFittingOutput, IMP::npctransport::SlabWithCylindricalPoreWireGeometry, IMP::spb::NuisanceRangeModifier, IMP::atom::RemoveRigidMotionOptimizerState, IMP::atom::SameResiduePairFilter, IMP::core::DistancePairScore, IMP::kinematics::RRT, IMP::misc::StateAdaptor, IMP::spb::SameParticlePairFilter, IMP::spb::SameRigidBodyPairFilter, IMP::core::RigidBodyHierarchyGeometry, IMP::gsl::ConjugateGradients, IMP::statistics::EuclideanMetric, IMP::display::GeometrySet, IMP::multifit::RigidLeavesRefiner, IMP::npc::SlabWithSphericalIndentGeometry, IMP::core::SteepestDescent, IMP::em::HighDensityEmbedding, IMP::isd::Distribution, IMP::misc::CommonEndpointPairFilter, IMP::kinematics::LocalPlanner, and IMP::kinematics::DOFsSampler.
void IMP::Object::set_check_level | ( | CheckLevel | l | ) |
Each object can be assigned a different check level too.
void IMP::Object::set_log_level | ( | LogLevel | l | ) |
Set the logging level used in this object.
Each object can be assigned a different log level in order to, for example, suppress messages for verbose and uninteresting objects. If set to DEFAULT, the global level as returned by IMP::get_log_level() is used, otherwise the local one is used. Methods in classes inheriting from Object should start with IMP_OBJECT_LOG to change the log level to the local one for this object and increase the current indent.
void IMP::Object::set_was_used | ( | bool | tf | ) | const |
IMP
provides warnings when objects are never used before they are destroyed. Examples of use include adding an IMP::Restraint to an IMP::Model. If an object is not properly marked as used, or your code is the one using it, call set_was_used(true) on the object.