IMP  2.3.1
The Integrative Modeling Platform
IMP Namespace Reference

Synonym for IMP::kernel. More...

Detailed Description

Synonym for IMP::kernel.

See deprecation support.

All IMP code is in the IMP namespace. For convenience and backwards compatibility, the contents of IMP::kernel are hoisted into the IMP namespace itself, in addition to being in the IMP::kernel namespace. For now you should use the IMP namespace versions of the names.

Namespaces

 algebra
 General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP modules.
 
 atom
 Functionality for loading, creating, manipulating and scoring atomic structures.
 
 base
 Low level functionality (logging, error handling, profiling, command line flags etc) that is used by all of IMP.
 
 benchmark
 Support for developing and analyzing benchmarks of IMP code.
 
 cgal
 Make CGAL functionality available to IMP.
 
 cnmultifit
 Generate cyclic atomic structures using cryo-electron microscopy data.
 
 container
 Various classes to hold sets of particles.
 
 core
 Basic functionality that is expected to be used by a wide variety of IMP users.
 
 display
 Output IMP model data in various file formats.
 
 domino
 Divide-and-conquer inferential optimization in discrete space.
 
 em
 Basic utilities for handling cryo-electron microscopy 3D density maps.
 
 em2d
 Restraints using electron microscopy 2D images (class averages).
 
 example
 Example module.
 
 gsl
 Several general purpose optimizers from the GNU Scientific Library (GSL).
 
 isd
 Inferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD).
 
 kernel
 Base functionality and abstract base classes for representation, scoring and sampling.
 
 kinematics
 Functionality for dealing with kinematic mechanical structures.
 
 kmeans
 Interface to the GPL k-means clustering library
 
 misc
 Miscellaneous functionality that is not expected to be used by many IMP users.
 
 modeller
 Interface to the Modeller comparative modeling package.
 
 module_template
 Template for a module that is stored externally to IMP.
 
 mpi
 Code that uses the MPI parallel library.
 
 multifit
 Fitting atomic structures into a cryo-electron microscopy density map.
 
 parallel
 Distribute IMP tasks to multiple processors or machines.
 
 pepdock
 Initial peptide docking.
 
 pmi
 Python classes to represent, score, sample and analyze models.
 
 rmf
 Support for the RMF file format for storing hierarchical molecular data and markup.
 
 rotamer
 Sampling of sidechain rotamers.
 
 saxs
 Support for small angle X-ray scattering (SAXS) data.
 
 score_functor
 Composable functors to implement scores via compile-time composition.
 
 scratch
 A space to add temporary classes while experimenting without forcing you to create your own module.
 
 statistics
 Code to compute statistical measures.
 
 symmetry
 Support for basic symmetry, such as periodic boundary conditions (PBC).
 
 test
 Support for running tests of IMP functionality.
 

Typedefs

typedef
IMP::kernel::CommandDispatcher 
CommandDispatcher
 
typedef IMP::kernel::Configuration Configuration
 
typedef
IMP::kernel::ConfigurationSet 
ConfigurationSet
 
typedef IMP::kernel::Constraint Constraint
 
typedef IMP::kernel::Container Container
 
typedef IMP::kernel::Decorator Decorator
 
typedef
IMP::kernel::DependencyGraph 
DependencyGraph
 
typedef
IMP::kernel::DerivativeAccumulator 
DerivativeAccumulator
 
typedef std::pair< double, double > DerivativePair
 A pair representing a function value with its first derivative. More...
 
typedef IMP::base::Vector
< DerivativePair
DerivativePairs
 
typedef IMP::base::Vector
< DerivativePairs
DerivativePairss
 
typedef
IMP::kernel::EvaluationState 
EvaluationState
 
typedef
IMP::kernel::EvaluationStates 
EvaluationStates
 
typedef double Float
 Basic floating-point value (could be float, double...) More...
 
typedef IMP::kernel::FloatIndex FloatIndex
 
typedef IMP::kernel::FloatIndexes FloatIndexes
 
typedef IMP::kernel::FloatKey FloatKey
 
typedef IMP::kernel::FloatKeys FloatKeys
 
typedef std::pair< double, double > FloatPair
 A generic pair of floats. More...
 
typedef IMP::base::Vector
< FloatPair
FloatPairs
 
typedef IMP::base::Vector
< FloatPairs
FloatPairss
 
typedef std::pair< Float, FloatFloatRange
 A pair representing the allowed range for a Float attribute. More...
 
typedef IMP::base::Vector
< FloatRange
FloatRanges
 
typedef IMP::base::Vector
< FloatRanges
FloatRangess
 
typedef IMP::base::Vector< FloatFloats
 Standard way to pass a bunch of Float values. More...
 
typedef IMP::base::Vector< FloatsFloatsList
 Standard way to pass a bunch of Floats values. More...
 
typedef IMP::base::Vector
< FloatsList
FloatsLists
 
typedef IMP::base::Vector< FloatsFloatss
 
typedef int Int
 Basic integer value. More...
 
typedef IMP::kernel::IntKey IntKey
 
typedef IMP::kernel::IntKeys IntKeys
 
typedef std::pair< Int, IntIntPair
 
typedef IMP::base::Vector
< IntPair > 
IntPairs
 
typedef IMP::base::Vector
< IntPairs
IntPairss
 
typedef std::pair< Int, IntIntRange
 
typedef IMP::base::Vector
< IntRange > 
IntRanges
 
typedef IMP::base::Vector
< IntRanges
IntRangess
 
typedef IMP::base::Vector< IntInts
 Standard way to pass a bunch of Int values. More...
 
typedef IMP::base::Vector< IntsIntsList
 Standard way to pass a bunch of Ints values. More...
 
typedef IMP::base::Vector
< IntsList
IntsLists
 
typedef IMP::base::Vector< IntsIntss
 
typedef IMP::kernel::Model Model
 
typedef IMP::kernel::ModelObject ModelObject
 
typedef IMP::kernel::ObjectKey ObjectKey
 
typedef IMP::kernel::ObjectKeys ObjectKeys
 
typedef IMP::kernel::Optimizer Optimizer
 
typedef IMP::kernel::OptimizerState OptimizerState
 
typedef IMP::kernel::OptionParser OptionParser
 
typedef IMP::kernel::PairContainer PairContainer
 
typedef IMP::kernel::PairModifier PairModifier
 
typedef IMP::kernel::PairPredicate PairPredicate
 
typedef IMP::kernel::PairScore PairScore
 
typedef IMP::kernel::Particle Particle
 
typedef IMP::kernel::ParticleIndex ParticleIndex
 
typedef
IMP::kernel::ParticleIndexes 
ParticleIndexes
 
typedef
IMP::kernel::ParticleIndexesKey 
ParticleIndexesKey
 
typedef
IMP::kernel::ParticleIndexesKeys 
ParticleIndexesKeys
 
typedef
IMP::kernel::ParticleIndexKey 
ParticleIndexKey
 
typedef
IMP::kernel::ParticleIndexKeys 
ParticleIndexKeys
 
typedef
IMP::kernel::ParticleIndexPairs 
ParticleIndexPairs
 
typedef
IMP::kernel::ParticleIndexQuads 
ParticleIndexQuads
 
typedef
IMP::kernel::ParticleIndexTriplets 
ParticleIndexTriplets
 
typedef IMP::kernel::ParticlePair ParticlePair
 
typedef
IMP::kernel::ParticlePairsTemp 
ParticlePairsTemp
 
typedef IMP::kernel::ParticleQuad ParticleQuad
 
typedef
IMP::kernel::ParticleQuadsTemp 
ParticleQuadsTemp
 
typedef
IMP::kernel::ParticleTriplet 
ParticleTriplet
 
typedef
IMP::kernel::ParticleTripletsTemp 
ParticleTripletsTemp
 
typedef
IMP::kernel::PythonRestraint 
PythonRestraint
 
typedef
IMP::kernel::PythonScoreState 
PythonScoreState
 
typedef IMP::kernel::QuadContainer QuadContainer
 
typedef IMP::kernel::QuadModifier QuadModifier
 
typedef IMP::kernel::QuadPredicate QuadPredicate
 
typedef IMP::kernel::QuadScore QuadScore
 
typedef IMP::kernel::Refiner Refiner
 
typedef IMP::kernel::Restraint Restraint
 
typedef IMP::kernel::RestraintBase RestraintBase
 
typedef IMP::kernel::RestraintSet RestraintSet
 
typedef
IMP::kernel::RestraintStatistics 
RestraintStatistics
 
typedef
IMP::kernel::RestraintStatisticsList 
RestraintStatisticsList
 
typedef IMP::kernel::Sampler Sampler
 
typedef
IMP::kernel::SaveToConfigurationSetOptimizerState 
SaveToConfigurationSetOptimizerState
 
typedef
IMP::kernel::ScopedRemoveRestraint 
ScopedRemoveRestraint
 
typedef
IMP::kernel::ScopedRemoveScoreState 
ScopedRemoveScoreState
 
typedef
IMP::kernel::ScopedRestraint 
ScopedRestraint
 
typedef
IMP::kernel::ScopedScoreState 
ScopedScoreState
 
typedef
IMP::kernel::ScopedSetFloatAttribute 
ScopedSetFloatAttribute
 
typedef
IMP::kernel::ScoreAccumulator 
ScoreAccumulator
 
typedef
IMP::kernel::ScoreAccumulators 
ScoreAccumulators
 
typedef IMP::kernel::ScoreState ScoreState
 
typedef IMP::kernel::ScoreStateBase ScoreStateBase
 
typedef
IMP::kernel::ScoringFunction 
ScoringFunction
 
typedef
IMP::kernel::SingletonContainer 
SingletonContainer
 
typedef
IMP::kernel::SingletonModifier 
SingletonModifier
 
typedef
IMP::kernel::SingletonPredicate 
SingletonPredicate
 
typedef IMP::kernel::SingletonScore SingletonScore
 
typedef std::string String
 Basic string value. More...
 
typedef IMP::kernel::StringKey StringKey
 
typedef IMP::kernel::StringKeys StringKeys
 
typedef IMP::base::Vector< StringStrings
 Standard way to pass a bunch of String values. More...
 
typedef IMP::base::Vector
< Strings
StringsList
 Standard way to pass a bunch of Strings values. More...
 
typedef IMP::base::Vector
< StringsList
StringsLists
 
typedef IMP::base::Vector
< Strings
Stringss
 
typedef
IMP::kernel::TripletContainer 
TripletContainer
 
typedef
IMP::kernel::TripletModifier 
TripletModifier
 
typedef
IMP::kernel::TripletPredicate 
TripletPredicate
 
typedef IMP::kernel::TripletScore TripletScore
 
typedef IMP::kernel::UnaryFunction UnaryFunction
 

Variables

const std::nullptr_t nullptr
 

Typedef Documentation

Import IMP::kernel::Configuration in the IMP namespace.

Definition at line 22 of file kernel/doxygen.h.

Import IMP::kernel::ConfigurationSet in the IMP namespace.

Definition at line 25 of file kernel/doxygen.h.

Import IMP::kernel::Constraint in the IMP namespace.

Definition at line 28 of file kernel/doxygen.h.

Import IMP::kernel::Container in the IMP namespace.

Definition at line 31 of file kernel/doxygen.h.

Import IMP::kernel::Decorator in the IMP namespace.

Definition at line 34 of file kernel/doxygen.h.

Import IMP::kernel::DependencyGraph in the IMP namespace.

Definition at line 37 of file kernel/doxygen.h.

typedef std::pair<double, double> IMP::DerivativePair

A pair representing a function value with its first derivative.

Definition at line 23 of file types.h.

Pass or store a set of DerivativePair .

Definition at line 24 of file types.h.

Pass or store a set of DerivativePairs .

Definition at line 24 of file types.h.

Import IMP::kernel::EvaluationState in the IMP namespace.

Definition at line 43 of file kernel/doxygen.h.

Import IMP::kernel::EvaluationStates in the IMP namespace.

Definition at line 46 of file kernel/doxygen.h.

typedef double IMP::Float

Basic floating-point value (could be float, double...)

Definition at line 20 of file types.h.

Import IMP::kernel::FloatIndex in the IMP namespace.

Definition at line 49 of file kernel/doxygen.h.

Import IMP::kernel::FloatIndexes in the IMP namespace.

Definition at line 52 of file kernel/doxygen.h.

Import IMP::kernel::FloatKey in the IMP namespace.

Definition at line 55 of file kernel/doxygen.h.

Import IMP::kernel::FloatKeys in the IMP namespace.

Definition at line 58 of file kernel/doxygen.h.

typedef std::pair<double, double> IMP::FloatPair

A generic pair of floats.

Definition at line 27 of file types.h.

Pass or store a set of FloatPair .

Definition at line 28 of file types.h.

Pass or store a set of FloatPairs .

Definition at line 28 of file types.h.

typedef std::pair<Float, Float> IMP::FloatRange

A pair representing the allowed range for a Float attribute.

Definition at line 31 of file types.h.

Pass or store a set of FloatRange .

Definition at line 32 of file types.h.

Pass or store a set of FloatRanges .

Definition at line 32 of file types.h.

Standard way to pass a bunch of Float values.

Pass or store a set of Float .

Definition at line 47 of file types.h.

Standard way to pass a bunch of Floats values.

Pass or store a set of Floats .

Definition at line 54 of file types.h.

Pass or store a set of FloatsList .

Definition at line 54 of file types.h.

Pass or store a set of Floats .

Definition at line 47 of file types.h.

typedef int IMP::Int

Basic integer value.

Definition at line 35 of file types.h.

Import IMP::kernel::IntKey in the IMP namespace.

Definition at line 61 of file kernel/doxygen.h.

Import IMP::kernel::IntKeys in the IMP namespace.

Definition at line 64 of file kernel/doxygen.h.

typedef IMP::base::Vector< IntPair > IMP::IntPairs

Pass or store a set of IntPair .

Definition at line 41 of file types.h.

Pass or store a set of IntPairs .

Definition at line 41 of file types.h.

typedef IMP::base::Vector< IntRange > IMP::IntRanges

Pass or store a set of IntRange .

Definition at line 38 of file types.h.

Pass or store a set of IntRanges .

Definition at line 38 of file types.h.

Standard way to pass a bunch of Int values.

Pass or store a set of Int .

Definition at line 49 of file types.h.

Standard way to pass a bunch of Ints values.

Pass or store a set of Ints .

Definition at line 56 of file types.h.

Pass or store a set of IntsList .

Definition at line 56 of file types.h.

Pass or store a set of Ints .

Definition at line 49 of file types.h.

Import IMP::kernel::Model in the IMP namespace.

Examples:
atom/dope_and_excluded_volume.cpp.

Definition at line 67 of file kernel/doxygen.h.

Import IMP::kernel::ModelObject in the IMP namespace.

Definition at line 70 of file kernel/doxygen.h.

Import IMP::kernel::ObjectKey in the IMP namespace.

Definition at line 73 of file kernel/doxygen.h.

Import IMP::kernel::ObjectKeys in the IMP namespace.

Definition at line 76 of file kernel/doxygen.h.

Import IMP::kernel::Optimizer in the IMP namespace.

Definition at line 79 of file kernel/doxygen.h.

Import IMP::kernel::OptimizerState in the IMP namespace.

Definition at line 82 of file kernel/doxygen.h.

Import IMP::kernel::OptionParser in the IMP namespace.

Definition at line 85 of file kernel/doxygen.h.

Import IMP::kernel::PairContainer in the IMP namespace.

Definition at line 88 of file kernel/doxygen.h.

Import IMP::kernel::PairModifier in the IMP namespace.

Definition at line 91 of file kernel/doxygen.h.

Import IMP::kernel::PairPredicate in the IMP namespace.

Definition at line 94 of file kernel/doxygen.h.

Import IMP::kernel::PairScore in the IMP namespace.

Definition at line 97 of file kernel/doxygen.h.

Import IMP::kernel::Particle in the IMP namespace.

Definition at line 100 of file kernel/doxygen.h.

Import IMP::kernel::ParticleIndex in the IMP namespace.

Definition at line 103 of file kernel/doxygen.h.

Import IMP::kernel::ParticleIndexes in the IMP namespace.

Definition at line 121 of file kernel/doxygen.h.

Import IMP::kernel::ParticleIndexKey in the IMP namespace.

Definition at line 106 of file kernel/doxygen.h.

Import IMP::kernel::ParticlePair in the IMP namespace.

Definition at line 130 of file kernel/doxygen.h.

Import IMP::kernel::ParticleQuad in the IMP namespace.

Definition at line 136 of file kernel/doxygen.h.

Import IMP::kernel::ParticleTriplet in the IMP namespace.

Definition at line 142 of file kernel/doxygen.h.

typedef IMP::kernel::PythonRestraint IMP::PythonRestraint

Import IMP::kernel::PythonRestraint in the IMP namespace.

Definition at line 148 of file kernel/doxygen.h.

typedef IMP::kernel::PythonScoreState IMP::PythonScoreState

Import IMP::kernel::PythonScoreState in the IMP namespace.

Definition at line 151 of file kernel/doxygen.h.

Import IMP::kernel::QuadContainer in the IMP namespace.

Definition at line 154 of file kernel/doxygen.h.

Import IMP::kernel::QuadModifier in the IMP namespace.

Definition at line 157 of file kernel/doxygen.h.

Import IMP::kernel::QuadPredicate in the IMP namespace.

Definition at line 160 of file kernel/doxygen.h.

Import IMP::kernel::QuadScore in the IMP namespace.

Definition at line 163 of file kernel/doxygen.h.

Import IMP::kernel::Refiner in the IMP namespace.

Definition at line 166 of file kernel/doxygen.h.

Import IMP::kernel::Restraint in the IMP namespace.

Definition at line 169 of file kernel/doxygen.h.

typedef IMP::kernel::RestraintBase IMP::RestraintBase

Import IMP::kernel::RestraintBase in the IMP namespace.

Definition at line 172 of file kernel/doxygen.h.

Import IMP::kernel::RestraintSet in the IMP namespace.

Definition at line 175 of file kernel/doxygen.h.

typedef IMP::kernel::RestraintStatistics IMP::RestraintStatistics

Import IMP::kernel::RestraintStatistics in the IMP namespace.

Definition at line 178 of file kernel/doxygen.h.

typedef IMP::kernel::RestraintStatisticsList IMP::RestraintStatisticsList

Import IMP::kernel::RestraintStatisticsList in the IMP namespace.

Definition at line 181 of file kernel/doxygen.h.

Import IMP::kernel::Sampler in the IMP namespace.

Definition at line 184 of file kernel/doxygen.h.

typedef IMP::kernel::ScopedRemoveRestraint IMP::ScopedRemoveRestraint

Import IMP::kernel::ScopedRemoveRestraint in the IMP namespace.

Definition at line 191 of file kernel/doxygen.h.

typedef IMP::kernel::ScopedRemoveScoreState IMP::ScopedRemoveScoreState

Import IMP::kernel::ScopedRemoveScoreState in the IMP namespace.

Definition at line 194 of file kernel/doxygen.h.

typedef IMP::kernel::ScopedRestraint IMP::ScopedRestraint

Import IMP::kernel::ScopedRestraint in the IMP namespace.

Definition at line 197 of file kernel/doxygen.h.

typedef IMP::kernel::ScopedScoreState IMP::ScopedScoreState

Import IMP::kernel::ScopedScoreState in the IMP namespace.

Definition at line 200 of file kernel/doxygen.h.

Import IMP::kernel::ScopedSetFloatAttribute in the IMP namespace.

Definition at line 203 of file kernel/doxygen.h.

Import IMP::kernel::ScoreAccumulator in the IMP namespace.

Definition at line 206 of file kernel/doxygen.h.

Import IMP::kernel::ScoreState in the IMP namespace.

Definition at line 212 of file kernel/doxygen.h.

typedef IMP::kernel::ScoreStateBase IMP::ScoreStateBase

Import IMP::kernel::ScoreStateBase in the IMP namespace.

Definition at line 215 of file kernel/doxygen.h.

Import IMP::kernel::ScoringFunction in the IMP namespace.

Definition at line 218 of file kernel/doxygen.h.

Import IMP::kernel::SingletonScore in the IMP namespace.

Definition at line 230 of file kernel/doxygen.h.

typedef std::string IMP::String

Basic string value.

Definition at line 44 of file types.h.

Import IMP::kernel::StringKey in the IMP namespace.

Definition at line 233 of file kernel/doxygen.h.

Import IMP::kernel::StringKeys in the IMP namespace.

Definition at line 236 of file kernel/doxygen.h.

Standard way to pass a bunch of String values.

Pass or store a set of String .

Definition at line 51 of file types.h.

Standard way to pass a bunch of Strings values.

Pass or store a set of Strings .

Definition at line 58 of file types.h.

Pass or store a set of StringsList .

Definition at line 58 of file types.h.

Pass or store a set of Strings .

Definition at line 51 of file types.h.

Import IMP::kernel::TripletContainer in the IMP namespace.

Definition at line 239 of file kernel/doxygen.h.

Import IMP::kernel::TripletModifier in the IMP namespace.

Definition at line 242 of file kernel/doxygen.h.

Import IMP::kernel::TripletPredicate in the IMP namespace.

Definition at line 245 of file kernel/doxygen.h.

Import IMP::kernel::TripletScore in the IMP namespace.

Definition at line 248 of file kernel/doxygen.h.

Import IMP::kernel::UnaryFunction in the IMP namespace.

Definition at line 251 of file kernel/doxygen.h.

Variable Documentation

const std::nullptr_t IMP::nullptr

The C++0x standard adds the nullptr keyword to get around a variety of problems with NULL. We provide an emulation within the IMP namespace when it is not available.

Use "nullptr" in code; the compiler will use our IMP::nullptr emulation automatically on systems that don't provide a native nullptr implementation.

If you are not in the IMP namespace, use the IMP_NULLPTR macro rather than asking for "IMP::nullptr". The latter does not work with some compilers (e.g. MSVC, which gets confused because nullptr is a keyword).

Definition at line 27 of file nullptr.h.