Base functionality and abstract base classes for representation, scoring and sampling. More...

Detailed Description

Base functionality and abstract base classes for representation, scoring and sampling.

The contents of the IMP::kernel namespace are hoisted into the IMP namespace for backwards compatibility.

Info

Author(s): Daniel Russel

Maintainer: benmwebb

License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

See main IMP papers list.

Classes
class	AttributeOptimizer
	Base class for optimizers that act on individual attributes. More...

class	CommandDispatcher
	Allow applications to easily implement commmands. More...

class	Configuration
	A class to store a configuration of a model. More...

class	ConfigurationSet
	A class to store a set of configurations of a model. More...

class	Constraint
	Implement a constraint on the Model. More...

class	Container
	Abstract class for containers of particles. More...

class	Decorator

class	DerivativeAccumulator
	Class for adding derivatives from restraints to the model. More...

struct	EvaluationState

struct	FloatIndex

class	Key
	A base class for Keys. More...

class	Model
	Class for storing model, its restraints, constraints, and particles. More...

class	ModelObject

class	Optimizer
	Base class for all optimizers. More...

class	OptimizerState
	Shared optimizer state that is invoked upon commitment of new coordinates. More...

class	OptionParser
	IMP-specific subclass of optparse.OptionParser. More...

class	PairContainer
	A shared container for Pairs. More...

class	PairContainerAdaptor

class	PairModifier
	A base class for modifiers of kernel::ParticlePairsTemp. More...

class	PairPredicate
	Abstract predicate function. More...

class	PairScore
	Abstract class for scoring object(s) of type ParticlePair. More...

class	Particle
	Class to handle individual model particles. More...

class	ParticleAdaptor

class	ParticleIndexAdaptor

class	ParticleIndexesAdaptor

class	ParticleIndexPairsAdaptor

class	ParticleInputs

class	ParticleOutputs

class	PythonDirectedGraph

class	QuadContainer
	A shared container for Quads. More...

class	QuadContainerAdaptor

class	QuadModifier
	A base class for modifiers of kernel::ParticleQuadsTemp. More...

class	QuadPredicate
	Abstract predicate function. More...

class	QuadScore
	Abstract class for scoring object(s) of type ParticleQuad. More...

class	Refiner
	Abstract class to implement hierarchical methods. More...

class	Restraint
	A restraint is a term in an `IMP` ScoringFunction. More...

class	RestraintsAdaptor

class	RestraintSet
	Object used to hold a set of restraints. More...

class	Sampler
	Base class for all samplers. More...

class	SaveToConfigurationSetOptimizerState

class	ScopedAddCacheAttribute

class	ScopedSetAttribute

class	ScoreAccumulator
	Class for adding up scores during ScoringFunction evaluation. More...

class	ScoreState
	ScoreStates maintain invariants in the Model. More...

class	ScoringFunction
	Represents a scoring function on the model. More...

class	ScoringFunctionAdaptor

class	SingletonContainer
	A shared container for Singletons. More...

class	SingletonContainerAdaptor

class	SingletonModifier
	A base class for modifiers of kernel::ParticlesTemp. More...

class	SingletonPredicate
	Abstract predicate function. More...

class	SingletonScore
	Abstract class for scoring object(s) of type Particle. More...

class	TripletContainer
	A shared container for Triplets. More...

class	TripletContainerAdaptor

class	TripletModifier
	A base class for modifiers of kernel::ParticleTripletsTemp. More...

class	TripletPredicate
	Abstract predicate function. More...

class	TripletScore
	Abstract class for scoring object(s) of type ParticleTriplet. More...

class	UnaryFunction
	Abstract single variable functor class for score functions. More...

class	Undecorator

Typedefs
typedef IMP::base::Vector < IMP::base::Pointer < AttributeOptimizer > >	AttributeOptimizers

typedef IMP::base::Vector < IMP::base::WeakPointer < AttributeOptimizer > >	AttributeOptimizersTemp

typedef IMP::base::Vector < IMP::base::Pointer < Configuration > >	Configurations

typedef IMP::base::Vector < IMP::base::Pointer < ConfigurationSet > >	ConfigurationSets

typedef IMP::base::Vector < IMP::base::WeakPointer < ConfigurationSet > >	ConfigurationSetsTemp

typedef IMP::base::Vector < IMP::base::WeakPointer < Configuration > >	ConfigurationsTemp

typedef IMP::base::Vector < IMP::base::Pointer < Constraint > >	Constraints

typedef IMP::base::Vector < IMP::base::WeakPointer < Constraint > >	ConstraintsTemp

typedef IMP::base::Vector < IMP::base::Pointer < Container > >	Containers

typedef IMP::base::Vector < IMP::base::WeakPointer < Container > >	ContainersTemp

typedef boost::graph	DependencyGraph
	A directed graph on the interactions between the various objects in the model. More...

typedef DependencyGraph::EdgeNameMap	DependencyGraphConstEdgeName

typedef DependencyGraph::VertexNameMap	DependencyGraphConstVertexName

typedef DependencyGraph::edge_descriptor	DependencyGraphEdge

typedef boost::graph_traits < DependencyGraph >	DependencyGraphTraits

typedef DependencyGraph::vertex_descriptor	DependencyGraphVertex

typedef IMP::base::Vector < DerivativeAccumulator >	DerivativeAccumulators

typedef IMP::base::Vector < EvaluationState >	EvaluationStates

typedef IMP::base::Vector < FloatIndex >	FloatIndexes

typedef IMP::base::Vector < IMP::base::Pointer < kernel::ModelObject > >	ModelObjects

typedef IMP::base::Vector < IMP::base::WeakPointer < kernel::ModelObject > >	ModelObjectsTemp

typedef base::Vector < ModelObjectsTemp >	ModelObjectsTemps

typedef IMP::base::Vector < IMP::base::Pointer < kernel::Model > >	Models

typedef IMP::base::Vector < IMP::base::WeakPointer < kernel::Model > >	ModelsTemp

typedef IMP::base::Vector < IMP::base::Pointer < Optimizer > >	Optimizers

typedef IMP::base::Vector < IMP::base::Pointer < OptimizerState > >	OptimizerStates

typedef IMP::base::Vector < IMP::base::WeakPointer < OptimizerState > >	OptimizerStatesTemp

typedef IMP::base::Vector < IMP::base::WeakPointer < Optimizer > >	OptimizersTemp

typedef IMP::base::Vector < IMP::base::Pointer < PairContainer > >	PairContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < PairContainer > >	PairContainersTemp

typedef PairModifier	PairDerivativeModifier

typedef IMP::base::Vector < IMP::base::Pointer < PairModifier > >	PairModifiers

typedef IMP::base::Vector < IMP::base::WeakPointer < PairModifier > >	PairModifiersTemp

typedef IMP::base::Vector < IMP::base::Pointer < PairPredicate > >	PairPredicates

typedef IMP::base::Vector < IMP::base::WeakPointer < PairPredicate > >	PairPredicatesTemp

typedef IMP::base::Vector < IMP::base::Pointer < PairScore > >	PairScores

typedef IMP::base::Vector < IMP::base::WeakPointer < PairScore > >	PairScoresTemp

typedef base::Index < ParticleIndexTag >	ParticleIndex

typedef base::Vector < ParticleIndex >	ParticleIndexes

typedef base::Array < 2, ParticleIndex >	ParticleIndexPair

typedef IMP::base::Vector < ParticleIndexPair >	ParticleIndexPairs

typedef base::Array < 4, ParticleIndex >	ParticleIndexQuad

typedef IMP::base::Vector < ParticleIndexQuad >	ParticleIndexQuads

typedef base::Array < 3, ParticleIndex >	ParticleIndexTriplet

typedef IMP::base::Vector < ParticleIndexTriplet >	ParticleIndexTriplets

typedef base::Array < 2, base::WeakPointer < Particle >, Particle * >	ParticlePair

typedef IMP::base::Vector < ParticlePair >	ParticlePairsTemp

typedef base::Array < 4, base::WeakPointer < Particle >, Particle * >	ParticleQuad

typedef IMP::base::Vector < ParticleQuad >	ParticleQuadsTemp

typedef base::Vector < base::Pointer< Particle > >	Particles

typedef base::Vector < base::WeakPointer< Particle > >	ParticlesTemp

typedef base::Vector < ParticlesTemp >	ParticlesTemps

typedef base::Array < 3, base::WeakPointer < Particle >, Particle * >	ParticleTriplet

typedef IMP::base::Vector < ParticleTriplet >	ParticleTripletsTemp

typedef IMP::base::Vector < IMP::base::Pointer < QuadContainer > >	QuadContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < QuadContainer > >	QuadContainersTemp

typedef QuadModifier	QuadDerivativeModifier

typedef IMP::base::Vector < IMP::base::Pointer < QuadModifier > >	QuadModifiers

typedef IMP::base::Vector < IMP::base::WeakPointer < QuadModifier > >	QuadModifiersTemp

typedef IMP::base::Vector < IMP::base::Pointer < QuadPredicate > >	QuadPredicates

typedef IMP::base::Vector < IMP::base::WeakPointer < QuadPredicate > >	QuadPredicatesTemp

typedef IMP::base::Vector < IMP::base::Pointer < QuadScore > >	QuadScores

typedef IMP::base::Vector < IMP::base::WeakPointer < QuadScore > >	QuadScoresTemp

typedef IMP::base::Vector < IMP::base::Pointer< Refiner > >	Refiners
	a collection of Refiner objects More...

typedef IMP::base::Vector < IMP::base::WeakPointer < Refiner > >	RefinersTemp

typedef IMP::base::Vector < IMP::base::Pointer < Restraint > >	Restraints

typedef IMP::base::Vector < IMP::base::Pointer < RestraintSet > >	RestraintSets

typedef IMP::base::Vector < IMP::base::WeakPointer < RestraintSet > >	RestraintSetsTemp

typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > >	RestraintsTemp

typedef IMP::base::Vector < IMP::base::Pointer< Sampler > >	Samplers

typedef IMP::base::Vector < IMP::base::WeakPointer < Sampler > >	SamplersTemp

typedef ScopedSetAttribute < FloatKey, Float >	ScopedSetFloatAttribute

typedef IMP::base::Vector < ScoreAccumulator >	ScoreAccumulators

typedef IMP::base::Vector < IMP::base::Pointer < ScoreState > >	ScoreStates

typedef IMP::base::Vector < IMP::base::WeakPointer < ScoreState > >	ScoreStatesTemp

typedef IMP::base::Vector < IMP::base::Pointer < ScoringFunction > >	ScoringFunctions

typedef IMP::base::Vector < IMP::base::WeakPointer < ScoringFunction > >	ScoringFunctionsTemp

typedef IMP::base::Vector < IMP::base::Pointer < SingletonContainer > >	SingletonContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < SingletonContainer > >	SingletonContainersTemp

typedef SingletonModifier	SingletonDerivativeModifier

typedef IMP::base::Vector < IMP::base::Pointer < SingletonModifier > >	SingletonModifiers

typedef IMP::base::Vector < IMP::base::WeakPointer < SingletonModifier > >	SingletonModifiersTemp

typedef IMP::base::Vector < IMP::base::Pointer < SingletonPredicate > >	SingletonPredicates

typedef IMP::base::Vector < IMP::base::WeakPointer < SingletonPredicate > >	SingletonPredicatesTemp

typedef IMP::base::Vector < IMP::base::Pointer < SingletonScore > >	SingletonScores

typedef IMP::base::Vector < IMP::base::WeakPointer < SingletonScore > >	SingletonScoresTemp

typedef IMP::base::Vector < IMP::base::Pointer < TripletContainer > >	TripletContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < TripletContainer > >	TripletContainersTemp

typedef TripletModifier	TripletDerivativeModifier

typedef IMP::base::Vector < IMP::base::Pointer < TripletModifier > >	TripletModifiers

typedef IMP::base::Vector < IMP::base::WeakPointer < TripletModifier > >	TripletModifiersTemp

typedef IMP::base::Vector < IMP::base::Pointer < TripletPredicate > >	TripletPredicates

typedef IMP::base::Vector < IMP::base::WeakPointer < TripletPredicate > >	TripletPredicatesTemp

typedef IMP::base::Vector < IMP::base::Pointer < TripletScore > >	TripletScores

typedef IMP::base::Vector < IMP::base::WeakPointer < TripletScore > >	TripletScoresTemp

typedef IMP::base::Vector < IMP::base::Pointer < UnaryFunction > >	UnaryFunctions

typedef IMP::base::Vector < IMP::base::WeakPointer < UnaryFunction > >	UnaryFunctionsTemp

typedef IMP::base::Vector < IMP::base::Pointer < Undecorator > >	Undecorators

typedef IMP::base::Vector < IMP::base::WeakPointer < Undecorator > >	UndecoratorsTemp

Functions
template<class Before , class After >
Constraint *	create_constraint (Before b, After a, const typename Before::Argument &t, std::string name=std::string())

ScoringFunctions	create_decomposition (ScoringFunction *sf)

Restraints	create_decomposition (const RestraintsTemp &rs)
	Return the decomposition of a list of restraints. More...

template<class Score >
Restraint *	create_restraint (Score *s, const typename Score::Argument &t, std::string name=std::string())

template<class Score >
Restraint *	create_restraint (const Score *s, const typename Score::Argument &t, std::string name=std::string())

template<class Score , class Container >
Restraint *	create_restraint (const Score s, Container t, std::string name=std::string())

template<class RestraintType >
ScoringFunction *	create_scoring_function (RestraintType *rs, double weight=1.0, double max=NO_MAX, std::string name=std::string())

DependencyGraph	get_dependency_graph (kernel::Model *m)

ParticlesTemp	get_dependent_particles (ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)

RestraintsTemp	get_dependent_restraints (ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)

ScoreStatesTemp	get_dependent_score_states (ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)

ParticleIndexes	get_indexes (const ParticlesTemp &ps)

ParticleIndexPairs	get_indexes (const ParticlePairsTemp &ps)

ParticlesTemp	get_particles (kernel::Model *m, const ParticleIndexes &ps)

DependencyGraph	get_pruned_dependency_graph (kernel::Model *m)

ScoreStatesTemp	get_required_score_states (ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)

ScoreStatesTemp	get_required_score_states (const ModelObjectsTemp &mos, ScoreStatesTemp exclude=ScoreStatesTemp())

ScoreStatesTemp	get_update_order (ScoreStatesTemp input)

const algebra::Vector3D	get_vector_geometry (Particle *p)

const algebra::Vector3D	get_vector_geometry (Decorator d)

DependencyGraphVertexIndex	get_vertex_index (const DependencyGraph &g)

template<class Pred >
internal::PredicateEquals < Pred, true >	make_predicate_equal (const Pred p, Model m, int value)
	Return a functor that returns true when the predicate has a certain value. More...

template<class Pred >
internal::PredicateEquals < Pred, false >	make_predicate_not_equal (const Pred p, Model m, int value)

void	set_vector_geometry (Particle *p, const algebra::Vector3D &v)

void	set_vector_geometry (Decorator d, const algebra::Vector3D &v)

void	show_as_graphviz (const DependencyGraph &name, base::TextOutput out)

void	show_restraint_hierarchy (ScoringFunctionAdaptor rs, std::ostream &out=std::cout)
	Print the hierarchy of restraints. More...

Variables
const double	BAD_SCORE

const double	NO_MAX
	Use this value when you want to turn off maximum for restraint evaluation. More...

Attribute Keys
Each type of attribute has an associated type of key. The keys can be constructed from a string. Such construction can be expensive and so the resulting keys should be cached.
typedef Key< 0, true >	FloatKey
	The type used to identify float attributes in the Particles. More...

typedef IMP::base::Vector < FloatKey >	FloatKeys

typedef Key< 1, true >	IntKey
	The type used to identify int attributes in the Particles. More...

typedef IMP::base::Vector< IntKey >	IntKeys

typedef Key< 2, true >	StringKey
	The type used to identify string attributes in the Particles. More...

typedef IMP::base::Vector < StringKey >	StringKeys

typedef Key< 3, true >	ParticleIndexKey
	The type used to identify a particle attribute in the Particles. More...

typedef IMP::base::Vector < ParticleIndexKey >	ParticleIndexKeys

typedef Key< 4, true >	ObjectKey
	The type used to identify an Object attribute. More...

typedef IMP::base::Vector < ObjectKey >	ObjectKeys

typedef Key< 9, true >	WeakObjectKey
	The type used to identify a non-ref counted Object attribute. More...

typedef IMP::base::Vector < WeakObjectKey >	WeakObjectKeys

typedef Key< 5, true >	IntsKey
	The type used to identify int attributes in the Particles. More...

typedef IMP::base::Vector < IntsKey >	IntsKeys

typedef Key< 6, true >	ParticleIndexesKey
	The type used to identify a particle attribute in the Particles. More...

typedef IMP::base::Vector < ParticleIndexesKey >	ParticleIndexesKeys

typedef Key< 7, true >	ObjectsKey
	The type used to identify a particle attribute in the Particles. More...

typedef IMP::base::Vector < ObjectsKey >	ObjectsKeys

typedef Key< 8, true >	ModelKey
	The type used to identify data stored directly in the model. More...

typedef IMP::base::Vector < kernel::ModelKey >	ModelKeys

Inputs and outputs
These methods recursively find all inputs or outputs of a given type. If you don't want recursive, use the non input/output variants.
ParticlesTemp	get_input_particles (const ModelObjectsTemp &mos)
	Return all the input particles for a given ModelObject. More...

ContainersTemp	get_input_containers (const ModelObjectsTemp &mos)
	Return all the input particles for a given ModelObject. More...

ParticlesTemp	get_output_particles (const ModelObjectsTemp &mos)
	Return all the output particles for a given ModelObject. More...

ContainersTemp	get_output_containers (const ModelObjectsTemp &mos)
	Return all the output particles for a given ModelObject. More...

Buffer I/O
Write/read the state of the particles to/from a buffer in memory. Note Not all particles need to have all the attributes, missing attributes will be skipped. However, the set of attributes must match on the write and read particles. There is no handling of architectural issues. That is, this is only guaranteed to work if it is read and written on the same operating system and system bit length. We could probably fix this. both these methods should be considered unstable.
base::Vector< char >	write_particles_to_buffer (const ParticlesTemp &particles, const FloatKeys &keys)
	return a binary buffer with the data More...

void	read_particles_from_buffer (const base::Vector< char > &buffer, const ParticlesTemp &particles, const FloatKeys &keys)
	load found attributes into the particles More...

Standard module functions
All `IMP` modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()

std::string	get_module_name ()

std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...

std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...

Python Only
The following functions are only available in Python.
void	show_altgraph (Graph g)

networkx::DiGraph	get_networkx_graph (Graph g)

std::string	show_graphviz (Graph g)

Gathering restraints
It is sometimes useful to extract all the non-RestraintSet restraints from a hierarchy involving RestraintSets mixed with Restraints.
RestraintsTemp	get_restraints (const RestraintsTemp &rs)

template<class It >
RestraintsTemp	get_restraints (It b, It e)

Typedef Documentation

typedef IMP::base::Vector<IMP::base::Pointer< AttributeOptimizer > > IMP::kernel::AttributeOptimizers

Store a set of objects.

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

typedef IMP::base::Vector<IMP::base::WeakPointer< AttributeOptimizer > > IMP::kernel::AttributeOptimizersTemp

Pass a set of objects.

See Also: AttributeOptimizer

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

typedef IMP::base::Vector<IMP::base::Pointer< Configuration > > IMP::kernel::Configurations

Store a set of objects.

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

typedef IMP::base::Vector<IMP::base::Pointer< ConfigurationSet > > IMP::kernel::ConfigurationSets

Store a set of objects.

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

typedef IMP::base::Vector<IMP::base::WeakPointer< ConfigurationSet > > IMP::kernel::ConfigurationSetsTemp

Pass a set of objects.

See Also: ConfigurationSet

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

typedef IMP::base::Vector<IMP::base::WeakPointer< Configuration > > IMP::kernel::ConfigurationsTemp

Pass a set of objects.

See Also: Configuration

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

typedef IMP::base::Vector<IMP::base::Pointer< Constraint > > IMP::kernel::Constraints

Store a set of objects.

Definition at line 62 of file kernel/Constraint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< Constraint > > IMP::kernel::ConstraintsTemp

Pass a set of objects.

See Also: Constraint

Definition at line 62 of file kernel/Constraint.h.

typedef IMP::base::Vector<IMP::base::Pointer< Container > > IMP::kernel::Containers

Store a set of objects.

Definition at line 93 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< Container > > IMP::kernel::ContainersTemp

Pass a set of objects.

See Also: Container

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

typedef boost::graph IMP::kernel::DependencyGraph

A directed graph on the interactions between the various objects in the model.

The vertices are named by the associated Object*. There is an edge from a to b, if a is an input to b. For example, there is an edge from a particle to a restraint if the restraint directly reads the particle.

See Dependencies for more information about dependencies.See Graphs in IMP for more information.

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

typedef IMP::base::Vector< DerivativeAccumulator > IMP::kernel::DerivativeAccumulators

Pass or store a set of DerivativeAccumulator .

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

typedef IMP::base::Vector< EvaluationState > IMP::kernel::EvaluationStates

Pass or store a set of EvaluationState .

Definition at line 36 of file kernel/ScoreAccumulator.h.

typedef IMP::base::Vector< FloatIndex > IMP::kernel::FloatIndexes

Pass or store a set of FloatIndex .

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

typedef Key<0, true> IMP::kernel::FloatKey

The type used to identify float attributes in the Particles.

Definition at line 32 of file kernel/base_types.h.

typedef IMP::base::Vector< FloatKey > IMP::kernel::FloatKeys

Pass or store a set of FloatKey .

Definition at line 33 of file kernel/base_types.h.

typedef Key<1, true> IMP::kernel::IntKey

The type used to identify int attributes in the Particles.

Definition at line 36 of file kernel/base_types.h.

typedef IMP::base::Vector< IntKey > IMP::kernel::IntKeys

Pass or store a set of IntKey .

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

typedef Key<5, true> IMP::kernel::IntsKey

The type used to identify int attributes in the Particles.

Definition at line 56 of file kernel/base_types.h.

typedef IMP::base::Vector< IntsKey > IMP::kernel::IntsKeys

Pass or store a set of IntsKey .

Definition at line 57 of file kernel/base_types.h.

typedef Key<8, true> IMP::kernel::ModelKey

The type used to identify data stored directly in the model.

Definition at line 74 of file kernel/base_types.h.

typedef IMP::base::Vector< kernel::ModelKey > IMP::kernel::ModelKeys

Pass or store a set of kernel::ModelKey .

Definition at line 75 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< kernel::ModelObject > > IMP::kernel::ModelObjects

Store a set of objects.

Definition at line 81 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< kernel::ModelObject > > IMP::kernel::ModelObjectsTemp

Pass a set of objects.

See Also: kernel::ModelObject

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

typedef IMP::base::Vector<IMP::base::Pointer< kernel::Model > > IMP::kernel::Models

Store a set of objects.

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

typedef IMP::base::Vector<IMP::base::WeakPointer< kernel::Model > > IMP::kernel::ModelsTemp

Pass a set of objects.

See Also: kernel::Model

Definition at line 86 of file kernel/base_types.h.

typedef Key<4, true> IMP::kernel::ObjectKey

The type used to identify an Object attribute.

Definition at line 48 of file kernel/base_types.h.

typedef IMP::base::Vector< ObjectKey > IMP::kernel::ObjectKeys

Pass or store a set of ObjectKey .

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

typedef Key<7, true> IMP::kernel::ObjectsKey

The type used to identify a particle attribute in the Particles.

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

typedef IMP::base::Vector< ObjectsKey > IMP::kernel::ObjectsKeys

Pass or store a set of ObjectsKey .

Definition at line 71 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< Optimizer > > IMP::kernel::Optimizers

Store a set of objects.

Definition at line 127 of file kernel/Optimizer.h.

typedef IMP::base::Vector<IMP::base::Pointer< OptimizerState > > IMP::kernel::OptimizerStates

Store a set of objects.

Definition at line 99 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< OptimizerState > > IMP::kernel::OptimizerStatesTemp

Pass a set of objects.

See Also: OptimizerState

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

typedef IMP::base::Vector<IMP::base::WeakPointer< Optimizer > > IMP::kernel::OptimizersTemp

Pass a set of objects.

See Also: Optimizer

Definition at line 127 of file kernel/Optimizer.h.

typedef IMP::base::Vector<IMP::base::Pointer< PairContainer > > IMP::kernel::PairContainers

Store a set of objects.

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

typedef IMP::base::Vector<IMP::base::WeakPointer< PairContainer > > IMP::kernel::PairContainersTemp

Pass a set of objects.

See Also: PairContainer

Definition at line 104 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< PairModifier > > IMP::kernel::PairModifiers

Store a set of objects.

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

typedef IMP::base::Vector<IMP::base::WeakPointer< PairModifier > > IMP::kernel::PairModifiersTemp

Pass a set of objects.

See Also: PairModifier

Definition at line 131 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< PairPredicate > > IMP::kernel::PairPredicates

Store a set of objects.

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

typedef IMP::base::Vector<IMP::base::WeakPointer< PairPredicate > > IMP::kernel::PairPredicatesTemp

Pass a set of objects.

See Also: PairPredicate

Definition at line 122 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< PairScore > > IMP::kernel::PairScores

Store a set of objects.

Definition at line 112 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< PairScore > > IMP::kernel::PairScoresTemp

Pass a set of objects.

See Also: PairScore

Definition at line 113 of file kernel/base_types.h.

typedef base::Index<ParticleIndexTag> IMP::kernel::ParticleIndex

A unique identifier for a particle within a Model. Use it to identify particles when getting and setting attributes and constructing decorators.

See for example, Model attributes, Decorator, and Model::get_particle().

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

typedef Key<6, true> IMP::kernel::ParticleIndexesKey

The type used to identify a particle attribute in the Particles.

Definition at line 60 of file kernel/base_types.h.

typedef IMP::base::Vector< ParticleIndexesKey > IMP::kernel::ParticleIndexesKeys

Pass or store a set of ParticleIndexesKey .

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

typedef Key<3, true> IMP::kernel::ParticleIndexKey

The type used to identify a particle attribute in the Particles.

Definition at line 44 of file kernel/base_types.h.

typedef IMP::base::Vector< ParticleIndexKey > IMP::kernel::ParticleIndexKeys

Pass or store a set of ParticleIndexKey .

Definition at line 45 of file kernel/base_types.h.

typedef IMP::base::Vector< ParticleIndexPair > IMP::kernel::ParticleIndexPairs

Pass or store a set of ParticleIndexPair .

Definition at line 161 of file kernel/base_types.h.

typedef IMP::base::Vector< ParticleIndexQuad > IMP::kernel::ParticleIndexQuads

Pass or store a set of ParticleIndexQuad .

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

typedef IMP::base::Vector< ParticleIndexTriplet > IMP::kernel::ParticleIndexTriplets

Pass or store a set of ParticleIndexTriplet .

Definition at line 162 of file kernel/base_types.h.

typedef base::Array<2, base::WeakPointer<Particle>, Particle*> IMP::kernel::ParticlePair

An ordered pair of particles.

Definition at line 135 of file kernel/base_types.h.

typedef IMP::base::Vector< ParticlePair > IMP::kernel::ParticlePairsTemp

Pass or store a set of ParticlePair .

Definition at line 139 of file kernel/base_types.h.

typedef base::Array<4, base::WeakPointer<Particle>, Particle*> IMP::kernel::ParticleQuad

An ordered quad of particles.

Definition at line 144 of file kernel/base_types.h.

typedef IMP::base::Vector< ParticleQuad > IMP::kernel::ParticleQuadsTemp

Pass or store a set of ParticleQuad .

Definition at line 145 of file kernel/base_types.h.

typedef base::Array<3, base::WeakPointer<Particle>, Particle*> IMP::kernel::ParticleTriplet

An ordered triplet of particles.

Definition at line 141 of file kernel/base_types.h.

typedef IMP::base::Vector< ParticleTriplet > IMP::kernel::ParticleTripletsTemp

Pass or store a set of ParticleTriplet .

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

typedef IMP::base::Vector<IMP::base::Pointer< QuadContainer > > IMP::kernel::QuadContainers

Store a set of objects.

Definition at line 107 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< QuadContainer > > IMP::kernel::QuadContainersTemp

Pass a set of objects.

See Also: QuadContainer

Definition at line 108 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< QuadModifier > > IMP::kernel::QuadModifiers

Store a set of objects.

Definition at line 134 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< QuadModifier > > IMP::kernel::QuadModifiersTemp

Pass a set of objects.

See Also: QuadModifier

Definition at line 135 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< QuadPredicate > > IMP::kernel::QuadPredicates

Store a set of objects.

Definition at line 125 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< QuadPredicate > > IMP::kernel::QuadPredicatesTemp

Pass a set of objects.

See Also: QuadPredicate

Definition at line 126 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< QuadScore > > IMP::kernel::QuadScores

Store a set of objects.

Definition at line 116 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< QuadScore > > IMP::kernel::QuadScoresTemp

Pass a set of objects.

See Also: QuadScore

Definition at line 117 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< Refiner > > IMP::kernel::Refiners

a collection of Refiner objects

Store a set of objects.

Definition at line 122 of file kernel/Refiner.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< Refiner > > IMP::kernel::RefinersTemp

Pass a set of objects.

See Also: Refiner

Definition at line 122 of file kernel/Refiner.h.

typedef IMP::base::Vector<IMP::base::Pointer< Restraint > > IMP::kernel::Restraints

Store a set of objects.

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

typedef IMP::base::Vector<IMP::base::Pointer< RestraintSet > > IMP::kernel::RestraintSets

Store a set of objects.

Definition at line 87 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< RestraintSet > > IMP::kernel::RestraintSetsTemp

Pass a set of objects.

See Also: RestraintSet

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

typedef IMP::base::Vector<IMP::base::WeakPointer< Restraint > > IMP::kernel::RestraintsTemp

Pass a set of objects.

See Also: Restraint

Definition at line 80 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< Sampler > > IMP::kernel::Samplers

Store a set of objects.

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

typedef IMP::base::Vector<IMP::base::WeakPointer< Sampler > > IMP::kernel::SamplersTemp

Pass a set of objects.

See Also: Sampler

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

typedef IMP::base::Vector< ScoreAccumulator > IMP::kernel::ScoreAccumulators

Pass or store a set of ScoreAccumulator .

Definition at line 137 of file kernel/ScoreAccumulator.h.

typedef IMP::base::Vector<IMP::base::Pointer< ScoreState > > IMP::kernel::ScoreStates

Store a set of objects.

Definition at line 89 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< ScoreState > > IMP::kernel::ScoreStatesTemp

Pass a set of objects.

See Also: ScoreState

Definition at line 90 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< ScoringFunction > > IMP::kernel::ScoringFunctions

Store a set of objects.

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

typedef IMP::base::Vector<IMP::base::WeakPointer< ScoringFunction > > IMP::kernel::ScoringFunctionsTemp

Pass a set of objects.

See Also: ScoringFunction

Definition at line 92 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< SingletonContainer > > IMP::kernel::SingletonContainers

Store a set of objects.

Definition at line 101 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< SingletonContainer > > IMP::kernel::SingletonContainersTemp

Pass a set of objects.

See Also: SingletonContainer

Definition at line 102 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< SingletonModifier > > IMP::kernel::SingletonModifiers

Store a set of objects.

Definition at line 128 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< SingletonModifier > > IMP::kernel::SingletonModifiersTemp

Pass a set of objects.

See Also: SingletonModifier

Definition at line 129 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< SingletonPredicate > > IMP::kernel::SingletonPredicates

Store a set of objects.

Definition at line 119 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< SingletonPredicate > > IMP::kernel::SingletonPredicatesTemp

Pass a set of objects.

See Also: SingletonPredicate

Definition at line 120 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< SingletonScore > > IMP::kernel::SingletonScores

Store a set of objects.

Definition at line 110 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< SingletonScore > > IMP::kernel::SingletonScoresTemp

Pass a set of objects.

See Also: SingletonScore

Definition at line 111 of file kernel/base_types.h.

typedef Key<2, true> IMP::kernel::StringKey

The type used to identify string attributes in the Particles.

Definition at line 40 of file kernel/base_types.h.

typedef IMP::base::Vector< StringKey > IMP::kernel::StringKeys

Pass or store a set of StringKey .

Definition at line 41 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< TripletContainer > > IMP::kernel::TripletContainers

Store a set of objects.

Definition at line 105 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< TripletContainer > > IMP::kernel::TripletContainersTemp

Pass a set of objects.

See Also: TripletContainer

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

typedef IMP::base::Vector<IMP::base::Pointer< TripletModifier > > IMP::kernel::TripletModifiers

Store a set of objects.

Definition at line 132 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< TripletModifier > > IMP::kernel::TripletModifiersTemp

Pass a set of objects.

See Also: TripletModifier

Definition at line 133 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< TripletPredicate > > IMP::kernel::TripletPredicates

Store a set of objects.

Definition at line 123 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< TripletPredicate > > IMP::kernel::TripletPredicatesTemp

Pass a set of objects.

See Also: TripletPredicate

Definition at line 124 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< TripletScore > > IMP::kernel::TripletScores

Store a set of objects.

Definition at line 114 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< TripletScore > > IMP::kernel::TripletScoresTemp

Pass a set of objects.

See Also: TripletScore

Definition at line 115 of file kernel/base_types.h.

typedef IMP::base::Vector<IMP::base::Pointer< UnaryFunction > > IMP::kernel::UnaryFunctions

Store a set of objects.

Definition at line 56 of file kernel/UnaryFunction.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< UnaryFunction > > IMP::kernel::UnaryFunctionsTemp

Pass a set of objects.

See Also: UnaryFunction

Definition at line 56 of file kernel/UnaryFunction.h.

typedef IMP::base::Vector<IMP::base::Pointer< Undecorator > > IMP::kernel::Undecorators

Store a set of objects.

Definition at line 33 of file kernel/Undecorator.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< Undecorator > > IMP::kernel::UndecoratorsTemp

Pass a set of objects.

See Also: Undecorator

Definition at line 33 of file kernel/Undecorator.h.

typedef Key<9, true> IMP::kernel::WeakObjectKey

The type used to identify a non-ref counted Object attribute.

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

typedef IMP::base::Vector< WeakObjectKey > IMP::kernel::WeakObjectKeys

Pass or store a set of WeakObjectKey .

Definition at line 53 of file kernel/base_types.h.

Function Documentation

template<class Before , class After >

Constraint* IMP::kernel::create_constraint	(	Before *	b,
		After *	a,
		const typename Before::Argument &	t,
		std::string	name = `std::string()`
	)

When programming in C++, you can use generic constraint instead of a SingletonConstraint, PairConstraint, etc. The result is somewhat faster (20% or so).

Definition at line 63 of file kernel/generic.h.

ScoringFunctions IMP::kernel::create_decomposition ( ScoringFunction * sf )

Return a list of ScoringFunction objects where each is as simple as possible and evaluating the sum (and anding the good score bits) is exactly like evaluating the one ScoringFunction.

Restraints IMP::kernel::create_decomposition ( const RestraintsTemp & rs )

Return the decomposition of a list of restraints.

template<class Score >

Restraint* IMP::kernel::create_restraint	(	Score *	s,
		const typename Score::Argument &	t,
		std::string	name = `std::string()`
	)

When programming in C++, you can use generic restraint instead of a SingletonRestraint, PairRestraint, etc. The result is somewhat faster (20% or so).

Definition at line 36 of file kernel/generic.h.

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template<class RestraintType >

ScoringFunction* IMP::kernel::create_scoring_function	(	RestraintType *	rs,
		double	weight = `1.0`,
		double	max = `NO_MAX`,
		std::string	name = `std::string()`
	)

Create a ScoringFunction on a single restraints. This can be faster than using a RestraintsScoringFunction.

Definition at line 23 of file kernel/generic.h.

std::string IMP::kernel::get_data_path ( std::string file_name )

Return the full path to installed data.

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.

DependencyGraph IMP::kernel::get_dependency_graph ( kernel::Model * m )

The dependency graph captures the interactions between Restraint, ScoreState and Particle objects. The graph has a directed edge if the source of the edge is an input for the target of the edge or the target of the edge is an output for the source. eg, there is an edge connecting a Container to the Restraint which gets its particles from the Container.

See Also: get_pruned_dependency_graph()

ParticlesTemp IMP::kernel::get_dependent_particles	(	ModelObject *	p,
		const ModelObjectsTemp &	all,
		const DependencyGraph &	dg,
		const DependencyGraphVertexIndex &	index
	)

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should act directly on the ModelObjects instead.

RestraintsTemp IMP::kernel::get_dependent_restraints	(	ModelObject *	p,
		const ModelObjectsTemp &	all,
		const DependencyGraph &	dg,
		const DependencyGraphVertexIndex &	index
	)

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should act directly on the ModelObjects instead.

ScoreStatesTemp IMP::kernel::get_dependent_score_states	(	ModelObject *	p,
		const ModelObjectsTemp &	all,
		const DependencyGraph &	dg,
		const DependencyGraphVertexIndex &	index
	)

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should act directly on the ModelObjects instead.

std::string IMP::kernel::get_example_path ( std::string file_name )

Return the path to installed example data for this module.

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb",

model));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.

ParticleIndexes IMP::kernel::get_indexes ( const ParticlesTemp & ps )

Get the indexes from a list of particles.

ParticleIndexPairs IMP::kernel::get_indexes ( const ParticlePairsTemp & ps )

Get the indexes from a list of particle pairs.

ContainersTemp IMP::kernel::get_input_containers ( const ModelObjectsTemp & mos )

Return all the input particles for a given ModelObject.

ParticlesTemp IMP::kernel::get_input_particles ( const ModelObjectsTemp & mos )

Return all the input particles for a given ModelObject.

networkx::DiGraph IMP::kernel::get_networkx_graph ( Graph g )

Export an IMP graph to a networkx graph. The resulting graph can be analyzed and displayed, although the graph layout algorithms in networkx seem to be quite poor compared to graphviz.

On a Mac, such graphs can be displayed by

import matplotlib
# the engine to be used must be selected before pyplot is imported
matplotlib.use("macosx")
import matplotlib.pyplot as plt
import networkx
networkx.draw_spring(xg)
plt.show()

ContainersTemp IMP::kernel::get_output_containers ( const ModelObjectsTemp & mos )

Return all the output particles for a given ModelObject.

ParticlesTemp IMP::kernel::get_output_particles ( const ModelObjectsTemp & mos )

Return all the output particles for a given ModelObject.

ParticlesTemp IMP::kernel::get_particles	(	kernel::Model *	m,
		const ParticleIndexes &	ps
	)

Get the particles from a list of indexes.

DependencyGraph IMP::kernel::get_pruned_dependency_graph ( kernel::Model * m )

The pruned dependency graph merges all particles which have the same dependencies to produce a simpler graph.

ScoreStatesTemp IMP::kernel::get_required_score_states	(	ModelObject *	p,
		const ModelObjectsTemp &	all,
		const DependencyGraph &	dg,
		const DependencyGraphVertexIndex &	index
	)

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should act directly on the ModelObjects instead.

ScoreStatesTemp IMP::kernel::get_required_score_states	(	const ModelObjectsTemp &	mos,
		ScoreStatesTemp	exclude = `ScoreStatesTemp()`
	)

Compute the set of score states required by the passed list of ModelObjects. This will compute dependencies if needed.

ScoreStatesTemp IMP::kernel::get_update_order ( ScoreStatesTemp input )

Return an appropriate (topologically sorted) order to update the score states in.

const algebra::Vector3D IMP::kernel::get_vector_geometry ( Particle * p )

See generic geometry for more information.

Definition at line 145 of file XYZ.h.

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template<class Pred >

internal::PredicateEquals<Pred, true> IMP::kernel::make_predicate_equal	(	const Pred *	p,
		Model *	m,
		int	value
	)

Return a functor that returns true when the predicate has a certain value.

Definition at line 19 of file kernel/functor.h.

template<class Pred >

internal::PredicateEquals<Pred, false> IMP::kernel::make_predicate_not_equal	(	const Pred *	p,
		Model *	m,
		int	value
	)

Return a functor that returns true when the predicate doesn't have a certain value.

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

void IMP::kernel::read_particles_from_buffer	(	const base::Vector< char > &	buffer,
		const ParticlesTemp &	particles,
		const FloatKeys &	keys
	)

load found attributes into the particles

void IMP::kernel::set_vector_geometry	(	Particle *	p,
		const algebra::Vector3D &	v
	)

See generic geometry for more information.

Definition at line 149 of file XYZ.h.

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void IMP::kernel::set_vector_geometry	(	Decorator	d,
		const algebra::Vector3D &	v
	)

See generic geometry for more information.

Definition at line 157 of file XYZ.h.

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void IMP::kernel::show_altgraph ( Graph g )

Use the Python altgraph package to graphically display a graph. Note that is requires X11 to be running (you can find it in your Utilities folder in MacOS) and the window produced is shockingly retro.

An alterntative is to write the graph to a dot file

g.show_graphviz(open("graph.dot", "w"));

then turn it to pdf with dot

dot -Tpdf graph.dot > graph.pdf

and finally view the pdf.

std::string IMP::kernel::show_graphviz ( Graph g )

Generate a nice pdf of the graph and attempt to open the pdf. The name of the pdf will be returned in case the attempt to open it fails.

void IMP::kernel::show_restraint_hierarchy	(	ScoringFunctionAdaptor	rs,
		std::ostream &	out = `std::cout`
	)

Print the hierarchy of restraints.

The maximum accepted score (Restraint::get_maximum_score()) and the weight (Restraint::get_weight()) are printed for each restraint.

base::Vector<char> IMP::kernel::write_particles_to_buffer	(	const ParticlesTemp &	particles,
		const FloatKeys &	keys
	)

return a binary buffer with the data

Variable Documentation

const double IMP::kernel::BAD_SCORE

Evaluation can return this value if limits are exceeded and it is a ScoringFunction::evaluate_if_below() or ScoringFunction::evaluate_if_good

const double IMP::kernel::NO_MAX

Use this value when you want to turn off maximum for restraint evaluation.

Detailed Description

Info

Classes

Typedefs

Functions

Variables

Attribute Keys

Inputs and outputs

Buffer I/O

Standard module functions

Python Only

Gathering restraints

Typedef Documentation

Function Documentation

Variable Documentation