IMP
2.4.0
The Integrative Modeling Platform
|
Synonym for IMP::kernel. More...
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). | |
EMageFit | |
Build assembly models consistent with EM images (class averages). | |
example | |
Example module. | |
foxs | |
gsl | |
Several general purpose optimizers from the GNU Scientific Library (GSL). | |
integrative_docking | |
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. | |
multi_state | |
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. | |
saxs_merge | |
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. | |
Variables | |
const std::nullptr_t | nullptr |
Import IMP::kernel::CommandDispatcher in the IMP namespace.
Definition at line 19 of file kernel/doxygen.h.
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.
typedef IMP::kernel::Container IMP::Container |
Import IMP::kernel::Container in the IMP namespace.
Definition at line 31 of file kernel/doxygen.h.
typedef IMP::kernel::Decorator IMP::Decorator |
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.
Import IMP::kernel::DerivativeAccumulator in the IMP namespace.
Definition at line 40 of file kernel/doxygen.h.
typedef std::pair<double, double> IMP::DerivativePair |
typedef IMP::base::Vector< DerivativePair > IMP::DerivativePairs |
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 |
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.
typedef IMP::kernel::FloatKey IMP::FloatKey |
Import IMP::kernel::FloatKey in the IMP namespace.
Definition at line 55 of file kernel/doxygen.h.
typedef IMP::kernel::FloatKeys IMP::FloatKeys |
Import IMP::kernel::FloatKeys in the IMP namespace.
Definition at line 58 of file kernel/doxygen.h.
typedef std::pair<double, double> IMP::FloatPair |
typedef IMP::base::Vector< FloatPair > IMP::FloatPairs |
typedef IMP::base::Vector< FloatPairs > IMP::FloatPairss |
typedef std::pair<Float, Float> IMP::FloatRange |
typedef IMP::base::Vector< FloatRange > IMP::FloatRanges |
typedef IMP::base::Vector< FloatRanges > IMP::FloatRangess |
typedef IMP::base::Vector< Float > IMP::Floats |
typedef IMP::base::Vector< Floats > IMP::FloatsList |
typedef IMP::base::Vector< FloatsList > IMP::FloatsLists |
typedef IMP::base::Vector< Floats > IMP::Floatss |
typedef IMP::kernel::IntKey IMP::IntKey |
Import IMP::kernel::IntKey in the IMP namespace.
Definition at line 61 of file kernel/doxygen.h.
typedef IMP::kernel::IntKeys IMP::IntKeys |
Import IMP::kernel::IntKeys in the IMP namespace.
Definition at line 64 of file kernel/doxygen.h.
typedef IMP::base::Vector< IntPair > IMP::IntPairs |
typedef IMP::base::Vector< IntPairs > IMP::IntPairss |
typedef IMP::base::Vector< IntRange > IMP::IntRanges |
typedef IMP::base::Vector< IntRanges > IMP::IntRangess |
typedef IMP::base::Vector< Int > IMP::Ints |
typedef IMP::base::Vector< Ints > IMP::IntsList |
typedef IMP::base::Vector< IntsList > IMP::IntsLists |
typedef IMP::base::Vector< Ints > IMP::Intss |
typedef IMP::kernel::Model IMP::Model |
Import IMP::kernel::Model in the IMP namespace.
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.
typedef IMP::kernel::ObjectKey IMP::ObjectKey |
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.
typedef IMP::kernel::Optimizer IMP::Optimizer |
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.
typedef IMP::kernel::PairScore IMP::PairScore |
Import IMP::kernel::PairScore in the IMP namespace.
Definition at line 97 of file kernel/doxygen.h.
typedef IMP::kernel::Particle IMP::Particle |
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::ParticleIndexesKey in the IMP namespace.
Definition at line 124 of file kernel/doxygen.h.
Import IMP::kernel::ParticleIndexesKeys in the IMP namespace.
Definition at line 127 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::ParticleIndexKeys in the IMP namespace.
Definition at line 109 of file kernel/doxygen.h.
Import IMP::kernel::ParticleIndexPairs in the IMP namespace.
Definition at line 112 of file kernel/doxygen.h.
Import IMP::kernel::ParticleIndexQuads in the IMP namespace.
Definition at line 115 of file kernel/doxygen.h.
Import IMP::kernel::ParticleIndexTriplets in the IMP namespace.
Definition at line 118 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::ParticlePairsTemp in the IMP namespace.
Definition at line 133 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::ParticleQuadsTemp in the IMP namespace.
Definition at line 139 of file kernel/doxygen.h.
Import IMP::kernel::ParticleTriplet in the IMP namespace.
Definition at line 142 of file kernel/doxygen.h.
Import IMP::kernel::ParticleTripletsTemp in the IMP namespace.
Definition at line 145 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.
typedef IMP::kernel::QuadScore IMP::QuadScore |
Import IMP::kernel::QuadScore in the IMP namespace.
Definition at line 163 of file kernel/doxygen.h.
typedef IMP::kernel::Refiner IMP::Refiner |
Import IMP::kernel::Refiner in the IMP namespace.
Definition at line 166 of file kernel/doxygen.h.
typedef IMP::kernel::Restraint IMP::Restraint |
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.
typedef IMP::kernel::Sampler IMP::Sampler |
Import IMP::kernel::Sampler in the IMP namespace.
Definition at line 184 of file kernel/doxygen.h.
Import IMP::kernel::SaveToConfigurationSetOptimizerState in the IMP namespace.
Definition at line 188 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::ScoreAccumulators in the IMP namespace.
Definition at line 209 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::SingletonContainer in the IMP namespace.
Definition at line 221 of file kernel/doxygen.h.
Import IMP::kernel::SingletonModifier in the IMP namespace.
Definition at line 224 of file kernel/doxygen.h.
Import IMP::kernel::SingletonPredicate in the IMP namespace.
Definition at line 227 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 |
typedef IMP::kernel::StringKey IMP::StringKey |
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.
typedef IMP::base::Vector< String > IMP::Strings |
typedef IMP::base::Vector< Strings > IMP::StringsList |
typedef IMP::base::Vector< StringsList > IMP::StringsLists |
typedef IMP::base::Vector< Strings > IMP::Stringss |
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.
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).