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.

For backwards compatibility, the kernel can also be accessed as IMP::kernel.

Graphs

Graphs in IMP are represented in C++ using the Boost.Graph. All graphs used in IMP are VertexAndEdgeListGraphs, have vertex_name properties, are BidirectionalGraphs if they are directed.

The Boost.Graph interface cannot be easily exported to Python so we instead provide a simple wrapper IMP::PythonDirectedGraph. There are methods to translate the graphs into various common python and other formats (eg graphviz).

Values and Objects (C++ only)

As is conventional in C++, IMP classes are divided into broad, exclusive types

Object classes: They inherit from IMP::Object and are always passed by pointer. They are reference counted and so should only be stored using IMP::Pointer (in C++, in Python everything is reference counted). Never allocate these on the stack as very bad things can happen. Objects cannot be duplicated. Equality on objects is defined as identity (eg two different objects are different even if the data they contain is identical).
Value classes which are normal data types. They are passed by value (or const&), never by pointer. Equality is defined based on the data stored in the value. Most value types in IMP are always valid, but a few, mostly geometric types (IMP::algebra::Vector3D) are designed for fast, low-level use and are left in an uninitialized state by their default constructor
RAII classes control some particular resource. They grab control of a resource when created and then free it when they are destroyed. As a result, they cannot be copied. Non-IMP examples include things like files in python, which are automatically closed when the file object is deleted.

All types in IMP, with a few documented exceptions, can be

compared to other objects of the same type
output to a C++ stream or printed in python
meaningfully put into python dictionaries or C++ hash maps

Google Perf Tools

The google perf tools can be used for cpu and memory profiling of IMP. They can be controlled from the command line in many IMP executables.

Info

Author(s): Daniel Russel, Ben Webb

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.

See deprecation support.

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.

	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
	Determine small angle X-ray (SAXS) profiles.

	gsl
	Several general purpose optimizers from the GNU Scientific Library (GSL).

	integrative_docking
	Pairwise docking incorporating additional data.

	isd
	Inferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD).

	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.

	mpi
	Code that uses the MPI parallel library.

	multi_state
	Functionality for handling multi-state models.

	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
	A method for merging SAXS profiles using Gaussian processes.

	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.

Classes
struct	AddBoolFlag

struct	AddFloatFlag

struct	AddIntFlag

struct	AddStringFlag

class	AdvancedFlag
	Use this to add an advanced flag to the program. More...

class	Array
	A class to store an fixed array of same-typed values. More...

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

class	CommandDispatcher
	Allow command line tools to easily implement multiple 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	ConstVector
	Store an array of values of the same type. More...

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

class	CreateLogContext
	Create a new log context. More...

class	Decorator

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

struct	EvaluationState

class	EventException
	An exception that signifies some event occurred. More...

class	Exception
	The general base class for `IMP` exceptions. More...

class	Flag

struct	FloatIndex

class	Index
	A typed index. More...

class	IndexException
	An exception for a request for an invalid member of a container. More...

class	IndexVector

class	InputAdaptor

struct	InternalException
	A general exception for an internal error in IMP. More...

class	IOException
	An input/output exception. More...

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

class	LRUCache

class	Memoizer

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

class	ModelException
	An exception which is thrown when the Model has attributes with invalid values. More...

class	ModelObject

class	NonCopyable

class	Object
	Common base class for heavy weight `IMP` objects. More...

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 ParticlePairsTemp. More...

class	PairPredicate
	Abstract predicate function. More...

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

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

class	ParticleAdaptor

class	ParticleIndexAdaptor

class	ParticleIndexesAdaptor

class	ParticleIndexPairsAdaptor

class	ParticleInputs

class	ParticleOutputs

class	piecewise_linear_distribution

struct	Pointer
	A smart pointer to a reference counted object. More...

struct	PointerMember
	A smart pointer to a ref-counted Object that is a class member. More...

class	PythonDirectedGraph

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

class	QuadContainerAdaptor

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

class	QuadPredicate
	Abstract predicate function. More...

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

class	RAII
	Temporarily change something; undo the change when this object is destroyed. More...

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

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

class	RestraintsAdaptor
	Provide a consistent interface for things that take Restraints as arguments. More...

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	SetCheckState
	A class to change and restore check state. More...

class	SetLogState
	A class to change and restore log state. More...

class	SetLogTarget

class	SetNumberOfThreads

class	Showable

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

class	SingletonContainerAdaptor

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

class	SingletonPredicate
	Abstract predicate function. More...

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

class	SparseSymmetricPairMemoizer

class	TextInput

class	TextOutput

class	Timer

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

class	TripletContainerAdaptor

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

class	TripletPredicate
	Abstract predicate function. More...

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

class	TypeException
	An exception for an invalid type being passed to `IMP`. More...

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

struct	UncheckedWeakPointer
	A weak pointer to an Object or RefCountedObject. More...

class	Undecorator

class	UsageException
	An exception for an invalid usage of `IMP`. More...

class	Value
	Base for a simple primitive-like type. More...

class	ValueException
	An exception for an invalid value being passed to `IMP`. More...

class	Vector

class	VersionInfo
	Version and module information for Objects. More...

struct	WarningContext

struct	WeakPointer
	Smart pointer to Object-derived classes that does not refcount. More...

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

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

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

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

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

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

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

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

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

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

typedef std::pair< double, double >	DerivativePair
	A pair representing a function value with its first derivative. More...

typedef IMP::Vector < DerivativePair >	DerivativePairs

typedef IMP::Vector < DerivativePairs >	DerivativePairss

typedef IMP::Vector < EvaluationState >	EvaluationStates

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

typedef IMP::Vector< FloatIndex >	FloatIndexes

typedef std::pair< double, double >	FloatPair
	A generic pair of floats. More...

typedef IMP::Vector< FloatPair >	FloatPairs

typedef IMP::Vector< FloatPairs >	FloatPairss

typedef std::pair< Float, Float >	FloatRange
	A pair representing the allowed range for a Float attribute. More...

typedef IMP::Vector< FloatRange >	FloatRanges

typedef IMP::Vector< FloatRanges >	FloatRangess

typedef IMP::Vector< Float >	Floats
	Standard way to pass a bunch of Float values. More...

typedef IMP::Vector< Floats >	FloatsList
	Standard way to pass a bunch of Floats values. More...

typedef IMP::Vector< FloatsList >	FloatsLists

typedef IMP::Vector< Floats >	Floatss

typedef int	Int
	Basic integer value. More...

typedef std::pair< Int, Int >	IntPair

typedef IMP::Vector< IntPair >	IntPairs

typedef IMP::Vector< IntPairs >	IntPairss

typedef std::pair< Int, Int >	IntRange

typedef IMP::Vector< IntRange >	IntRanges

typedef IMP::Vector< IntRanges >	IntRangess

typedef IMP::Vector< Int >	Ints
	Standard way to pass a bunch of Int values. More...

typedef IMP::Vector< Ints >	IntsList
	Standard way to pass a bunch of Ints values. More...

typedef IMP::Vector< IntsList >	IntsLists

typedef IMP::Vector< Ints >	Intss

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

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

typedef Vector< ModelObjectsTemp >	ModelObjectsTemps

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

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

typedef IMP::Vector < IMP::Pointer< Object > >	Objects
	A list of objects. More...

typedef IMP::Vector < IMP::WeakPointer< Object > >	ObjectsTemp

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

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

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

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

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

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

typedef PairModifier	PairDerivativeModifier

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

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

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

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

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

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

typedef Index< ParticleIndexTag >	ParticleIndex

typedef Vector< ParticleIndex >	ParticleIndexes

typedef Array< 2, ParticleIndex >	ParticleIndexPair

typedef IMP::Vector < ParticleIndexPair >	ParticleIndexPairs

typedef Array< 4, ParticleIndex >	ParticleIndexQuad

typedef IMP::Vector < ParticleIndexQuad >	ParticleIndexQuads

typedef Array< 3, ParticleIndex >	ParticleIndexTriplet

typedef IMP::Vector < ParticleIndexTriplet >	ParticleIndexTriplets

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

typedef IMP::Vector< ParticlePair >	ParticlePairsTemp

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

typedef IMP::Vector< ParticleQuad >	ParticleQuadsTemp

typedef Vector< Pointer < Particle > >	Particles

typedef Vector< WeakPointer < Particle > >	ParticlesTemp

typedef Vector< ParticlesTemp >	ParticlesTemps

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

typedef IMP::Vector < ParticleTriplet >	ParticleTripletsTemp

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

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

typedef QuadModifier	QuadDerivativeModifier

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

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

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

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

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

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

typedef ::boost::mt19937	RandomNumberGenerator

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

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

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

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

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

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

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

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

typedef ScopedSetAttribute < FloatKey, Float >	ScopedSetFloatAttribute

typedef IMP::Vector < ScoreAccumulator >	ScoreAccumulators

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

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

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

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

typedef IMP::Vector < SetCheckState >	SetCheckStates

typedef IMP::Vector< SetLogState >	SetLogStates

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

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

typedef SingletonModifier	SingletonDerivativeModifier

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

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

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

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

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

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

typedef std::string	String
	Basic string value. More...

typedef IMP::Vector< String >	Strings
	Standard way to pass a bunch of String values. More...

typedef IMP::Vector< Strings >	StringsList
	Standard way to pass a bunch of Strings values. More...

typedef IMP::Vector< StringsList >	StringsLists

typedef IMP::Vector< Strings >	Stringss

typedef IMP::Vector< TextInput >	TextInputs

typedef IMP::Vector< TextOutput >	TextOutputs

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

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

typedef TripletModifier	TripletDerivativeModifier

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

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

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

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

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

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

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

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

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

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

typedef IMP::Vector< VersionInfo >	VersionInfos

Enumerations
enum	CheckLevel { DEFAULT_CHECK = -1, NONE = 0, USAGE = 1, USAGE_AND_INTERNAL = 2 }
	Specify the level of runtime checks performed. More...

enum	LogLevel { DEFAULT = -1, SILENT = 0, WARNING = 0 + 1, PROGRESS = 2, TERSE = 3, VERBOSE = 4, MEMORY = 5 }
	The log levels supported by `IMP`. More...

enum	StatisticsLevel { NO_STATISTICS = 0, ALL_STATISTICS = 1 }
	Specify the level of statistics to record. More...

Functions
def	allow_deprecated
	Context manager to temporarily allow (or disallow) deprecated code. More...

void	clear_statistics ()

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())

TextOutput	create_temporary_file (std::string prefix="imp_temp", std::string suffix="")

std::string	create_temporary_file_name (std::string prefix="imp_temp", std::string suffix="")
	Create a temporary file. More...

def	deprecated_function
	Python decorator to mark a function as deprecated. More...

def	deprecated_method
	Python decorator to mark a method as deprecated. More...

def	deprecated_module
	Mark a Python module as deprecated. More...

def	deprecated_object
	Python decorator to mark a class as deprecated. More...

template<class Tag >
unsigned int	get_as_unsigned_int (Index< Tag > i)

DependencyGraph	get_dependency_graph (Model *m)

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

bool	get_deprecation_exceptions ()
	Get whether an exception is thrown when a deprecated method is used. More...

ParticleIndexes	get_indexes (const ParticlesTemp &ps)

ParticleIndexPairs	get_indexes (const ParticlePairsTemp &ps)

template<class Tag >
Index< Tag >	get_invalid_index ()

bool	get_is_quick_test ()

Strings	get_live_object_names ()
	Return the names of all live objects. More...

Objects	get_live_objects ()
	Return pointers to all live objects. More...

TextOutput	get_log_target ()

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

DependencyGraph	get_pruned_dependency_graph (Model *m)

double	get_random_double_uniform ()
	Return a uniformly distributed double number in range [0..1) More...

double	get_random_double_uniform (double min, double max)
	Return a uniformly distributed double number in range [min..max) More...

float	get_random_float_uniform ()
	Return a uniformly distributed float number in range [0..1) More...

float	get_random_float_uniform (float min, float max)
	Return a uniformly distributed float number in range [min..max) More...

template<typename RealType >
void	get_random_numbers_normal (Vector< RealType > &v, unsigned int n, RealType mean=0.0, RealType stddev=1.0)
	Fill the double array with random normally distributed values. More...

template<typename RealType >
void	get_random_numbers_uniform (Vector< RealType > &v, unsigned int n)
	Fill the float array with random normally distributed values. More...

boost::uint64_t	get_random_seed ()
	Return the initial random seed. More...

std::string	get_relative_path (std::string base, std::string relative)
	Return a path to a file relative to another file. More...

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

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

std::string	get_unique_name (std::string templ)
	Return a unique name produced from the string. More...

ScoreStatesTemp	get_update_order (ScoreStatesTemp input)

const algebra::Vector3D	get_vector_geometry (Particle *p)

const algebra::Vector3D	get_vector_geometry (Decorator d)

const algebra::Vector3D	get_vector_geometry (WeakPointer< Particle > d)

const algebra::Vector3D	get_vector_geometry (Pointer< Particle > d)

DependencyGraphVertexIndex	get_vertex_index (const DependencyGraph &g)

void	handle_use_deprecated (std::string message)

template<class T >
std::size_t	hash_value (const T &t)

std::size_t	hash_value (double d)

std::size_t	hash_value (int d)

std::size_t	hash_value (bool d)

std::size_t	hash_value (const std::string &d)

template<class T >
std::size_t	hash_value (const std::vector< T > &t)

template<class T >
std::size_t	hash_value (const __gnu_debug::vector< T > &t)

template<class T >
bool	isinf (const T &a)
	Return true if a number is infinite. More...

template<class T >
bool	isnan (const T &a)
	Return true if a number is NaN. More...

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)

template<class O >
O *	object_cast (Object *o)

std::ostream &	operator<< (std::ostream &out, const Showable &s)

template<class Tag , class Container , class T >
void	resize_to_fit (Container &v, Index< Tag > i, const T &default_value=T())

void	set_deprecation_exceptions (bool tf)
	Toggle whether an exception is thrown when a deprecated method is used. More...

void	set_deprecation_warnings (bool tf)
	Toggle printing of warnings on using deprecated classes. More...

void	set_log_target (TextOutput l)
	Set the target for the log. More...

void	set_show_leaked_objects (bool tf)
	Set whether to complain about objects not being properly cleaned up. More...

void	set_statistics_level (StatisticsLevel l)

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

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

void	set_vector_geometry (WeakPointer< Particle > d, const algebra::Vector3D &v)

void	set_vector_geometry (Pointer< Particle > d, const algebra::Vector3D &v)

void	show_as_graphviz (const DependencyGraph &name, TextOutput out)

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

void	show_timings (TextOutput out)

template<class A >
void	swap (ConstVector< A > &a, ConstVector< A > &b)

void	write_help (std::ostream &out=std::cerr)

Variables
const double	BAD_SCORE

namespace	base = IMP

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

const std::nullptr_t	nullptr

RandomNumberGenerator	random_number_generator
	A shared non-GPU random number generator. 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::Vector< FloatKey >	FloatKeys

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

typedef IMP::Vector< IntKey >	IntKeys

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

typedef IMP::Vector< StringKey >	StringKeys

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

typedef IMP::Vector < ParticleIndexKey >	ParticleIndexKeys

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

typedef IMP::Vector< ObjectKey >	ObjectKeys

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

typedef IMP::Vector < WeakObjectKey >	WeakObjectKeys

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

typedef IMP::Vector< IntsKey >	IntsKeys

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

typedef IMP::Vector < ParticleIndexesKey >	ParticleIndexesKeys

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

typedef IMP::Vector< ObjectsKey >	ObjectsKeys

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

typedef IMP::Vector< ModelKey >	ModelKeys

Error checking and reporting
By default `IMP` performs a variety of runtime error checks. These can be controlled using the IMP::set_check_level function. Call IMP::set_check_level with IMP::NONE to disable all checks when you are performing your optimization as opposed to testing your code. Make sure you run your code with the level set to at least USAGE before running your final optimization to make sure that `IMP` is used correctly. Error handling is provided by IMP/exception.h, Use the `gdbinit` file provided in `tools` to automatically have `gdb` break when `IMP` errors are detected.
void	set_check_level (CheckLevel tf)
	Control runtime checks in the code. More...

CheckLevel	get_check_level ()
	Get the current audit mode. More...

void	handle_error (const char *msg)

Flags
These methods add support for shared command line flags to `IMP`. Programs that use this have access to flags declared in modules which allow users to do things like control log level and turn on and off profiling to see what is going on. These functions are Python accessible. In C++, you can also use the AddFloatFlag, AddStringFlag, AddBoolFlag and AddIntFlag classes to add flags statically.
std::string	get_executable_name ()
	Return the name of the current executable. More...

void	setup_from_argv (int argc, char **argv, std::string description)
	Parse the command line flags and return the positional arguments. More...

Strings	setup_from_argv_allowing_unknown (int argc, char **argv, std::string description)

Strings	setup_from_argv (int argc, char **argv, std::string description, std::string positional_description, int num_positional)

void	setup_from_argv (const Strings &argv, std::string description)

Strings	setup_from_argv (const Strings &argv, std::string description, std::string positional_description, int num_positional)

void	add_string_flag (std::string name, std::string default_value, std::string description)

std::string	get_string_flag (std::string name)

void	add_int_flag (std::string name, size_t default_value, std::string description)

size_t	get_int_flag (std::string name)

void	add_bool_flag (std::string name, std::string description)

bool	get_bool_flag (std::string name)

void	add_float_flag (std::string name, double default_value, std::string description)

double	get_float_flag (std::string name)

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.
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 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 one of this module's data files. More...

std::string	get_example_path (std::string file_name)
	Return the full path to one of this module's example files. More...

Logging
`IMP` provides tools for controlling the amount of log output produced and directing it to the terminal or a file. Only log messages tagged with a lower level than the current LogLevel are emitted. In addition to a global log level (get_log_level(), set_log_level()), each IMP::Object has an internal log level (IMP::Object::get_log_level(), IMP::Object::set_log_level()) which is used when executing code on that object. Logging is provided by IMP/log.h. People implementing IMP::Object classes should also see IMP_OBJECT_LOG() and IMP::SetLogState. All logging is disabled when `IMP` is built using `build='fast'`.
void	add_to_log (LogLevel level, std::string to_write)
	Write a string to the log, for Python. More...

void	set_log_level (LogLevel l)
	Set the current global log level. More...

void	set_log_timer (bool tb)
	Set whether log messages are tagged with the current log time. More...

void	reset_log_timer ()
	Reset the log timer. More...

LogLevel	get_log_level ()
	Get the currently active global log level. More...

Create a progress bar in the terminal
void	set_progress_display (std::string description, unsigned int steps)
	Set up the progress bar with the passed description. More...

void	add_to_progress_display (unsigned int step=1)
	Set the current progress. 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)

Number of threads
Get and set the default number of threads to use in `IMP`.
unsigned int	get_number_of_threads ()

void	set_number_of_threads (unsigned int n)

Typedef Documentation

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

Store a set of objects.

Definition at line 100 of file AttributeOptimizer.h.

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

Pass a set of objects.

See Also: AttributeOptimizer

Definition at line 100 of file AttributeOptimizer.h.

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

Store a set of objects.

Definition at line 49 of file Configuration.h.

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

Store a set of objects.

Definition at line 46 of file ConfigurationSet.h.

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

Pass a set of objects.

See Also: ConfigurationSet

Definition at line 46 of file ConfigurationSet.h.

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

Pass a set of objects.

See Also: Configuration

Definition at line 49 of file Configuration.h.

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

Store a set of objects.

Definition at line 62 of file Constraint.h.

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

Pass a set of objects.

See Also: Constraint

Definition at line 62 of file Constraint.h.

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

Store a set of objects.

Definition at line 93 of file base_types.h.

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

Pass a set of objects.

See Also: Container

Definition at line 94 of file base_types.h.

typedef boost::graph IMP::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 dependency_graph.h.

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

Pass or store a set of DerivativeAccumulator .

Definition at line 49 of file DerivativeAccumulator.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.

typedef IMP::Vector< DerivativePair > IMP::DerivativePairs

Pass or store a set of DerivativePair .

Definition at line 24 of file types.h.

typedef IMP::Vector< DerivativePairs > IMP::DerivativePairss

Pass or store a set of DerivativePairs .

Definition at line 24 of file types.h.

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

Pass or store a set of EvaluationState .

Definition at line 36 of file ScoreAccumulator.h.

typedef double IMP::Float

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

Definition at line 20 of file types.h.

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

Pass or store a set of FloatIndex .

Definition at line 22 of file FloatIndex.h.

typedef Key<0, true> IMP::FloatKey

The type used to identify float attributes in the Particles.

Definition at line 32 of file base_types.h.

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

Pass or store a set of FloatKey .

Definition at line 33 of file base_types.h.

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

A generic pair of floats.

Definition at line 27 of file types.h.

typedef IMP::Vector< FloatPair > IMP::FloatPairs

Pass or store a set of FloatPair .

Definition at line 28 of file types.h.

typedef IMP::Vector< FloatPairs > IMP::FloatPairss

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.

typedef IMP::Vector< FloatRange > IMP::FloatRanges

Pass or store a set of FloatRange .

Definition at line 32 of file types.h.

typedef IMP::Vector< FloatRanges > IMP::FloatRangess

Pass or store a set of FloatRanges .

Definition at line 32 of file types.h.

typedef IMP::Vector< Float > IMP::Floats

Standard way to pass a bunch of Float values.

Pass or store a set of Float .

Definition at line 47 of file types.h.

typedef IMP::Vector< Floats > IMP::FloatsList

Standard way to pass a bunch of Floats values.

Pass or store a set of Floats .

Definition at line 54 of file types.h.

typedef IMP::Vector< FloatsList > IMP::FloatsLists

Pass or store a set of FloatsList .

Definition at line 54 of file types.h.

typedef IMP::Vector< Floats > IMP::Floatss

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.

typedef Key<1, true> IMP::IntKey

The type used to identify int attributes in the Particles.

Definition at line 36 of file base_types.h.

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

Pass or store a set of IntKey .

Definition at line 37 of file base_types.h.

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

Pass or store a set of IntPair .

Definition at line 41 of file types.h.

typedef IMP::Vector< IntPairs > IMP::IntPairss

Pass or store a set of IntPairs .

Definition at line 41 of file types.h.

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

Pass or store a set of IntRange .

Definition at line 38 of file types.h.

typedef IMP::Vector< IntRanges > IMP::IntRangess

Pass or store a set of IntRanges .

Definition at line 38 of file types.h.

typedef IMP::Vector< Int > IMP::Ints

Standard way to pass a bunch of Int values.

Pass or store a set of Int .

Definition at line 49 of file types.h.

typedef Key<5, true> IMP::IntsKey

The type used to identify int attributes in the Particles.

Definition at line 56 of file base_types.h.

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

Pass or store a set of IntsKey .

Definition at line 57 of file base_types.h.

typedef IMP::Vector< Ints > IMP::IntsList

Standard way to pass a bunch of Ints values.

Pass or store a set of Ints .

Definition at line 56 of file types.h.

typedef IMP::Vector< IntsList > IMP::IntsLists

Pass or store a set of IntsList .

Definition at line 56 of file types.h.

typedef IMP::Vector< Ints > IMP::Intss

Pass or store a set of Ints .

Definition at line 49 of file types.h.

typedef Key<8, true> IMP::ModelKey

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

Definition at line 74 of file base_types.h.

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

Pass or store a set of ModelKey .

Definition at line 75 of file base_types.h.

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

Store a set of objects.

Definition at line 81 of file base_types.h.

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

Pass a set of objects.

See Also: ModelObject

Definition at line 82 of file base_types.h.

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

Store a set of objects.

Definition at line 85 of file base_types.h.

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

Pass a set of objects.

See Also: Model

Definition at line 86 of file base_types.h.

typedef Key<4, true> IMP::ObjectKey

The type used to identify an Object attribute.

Definition at line 48 of file base_types.h.

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

Pass or store a set of ObjectKey .

Definition at line 49 of file base_types.h.

typedef IMP::Vector<IMP::Pointer< Object > > IMP::Objects

A list of objects.

Store a set of objects.

Definition at line 60 of file types.h.

typedef Key<7, true> IMP::ObjectsKey

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

Definition at line 70 of file base_types.h.

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

Pass or store a set of ObjectsKey .

Definition at line 71 of file base_types.h.

typedef IMP::Vector<IMP::WeakPointer< Object > > IMP::ObjectsTemp

Pass a set of objects.

See Also: Object

Definition at line 62 of file types.h.

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

Store a set of objects.

Definition at line 137 of file Optimizer.h.

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

Store a set of objects.

Definition at line 99 of file base_types.h.

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

Pass a set of objects.

See Also: OptimizerState

Definition at line 100 of file base_types.h.

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

Pass a set of objects.

See Also: Optimizer

Definition at line 137 of file Optimizer.h.

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

Store a set of objects.

Definition at line 103 of file base_types.h.

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

Pass a set of objects.

See Also: PairContainer

Definition at line 104 of file base_types.h.

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

Store a set of objects.

Definition at line 130 of file base_types.h.

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

Pass a set of objects.

See Also: PairModifier

Definition at line 131 of file base_types.h.

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

Store a set of objects.

Definition at line 121 of file base_types.h.

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

Pass a set of objects.

See Also: PairPredicate

Definition at line 122 of file base_types.h.

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

Store a set of objects.

Definition at line 112 of file base_types.h.

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

Pass a set of objects.

See Also: PairScore

Definition at line 113 of file base_types.h.

typedef Index<ParticleIndexTag> IMP::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 base_types.h.

typedef Key<6, true> IMP::ParticleIndexesKey

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

Definition at line 60 of file base_types.h.

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

Pass or store a set of ParticleIndexesKey .

Definition at line 61 of file base_types.h.

typedef Key<3, true> IMP::ParticleIndexKey

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

Definition at line 44 of file base_types.h.

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

Pass or store a set of ParticleIndexKey .

Definition at line 45 of file base_types.h.

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

Pass or store a set of ParticleIndexPair .

Definition at line 161 of file base_types.h.

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

Pass or store a set of ParticleIndexQuad .

Definition at line 163 of file base_types.h.

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

Pass or store a set of ParticleIndexTriplet .

Definition at line 162 of file base_types.h.

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

An ordered pair of particles.

Definition at line 135 of file base_types.h.

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

Pass or store a set of ParticlePair .

Definition at line 139 of file base_types.h.

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

An ordered quad of particles.

Definition at line 144 of file base_types.h.

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

Pass or store a set of ParticleQuad .

Definition at line 145 of file base_types.h.

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

An ordered triplet of particles.

Definition at line 141 of file base_types.h.

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

Pass or store a set of ParticleTriplet .

Definition at line 142 of file base_types.h.

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

Store a set of objects.

Definition at line 107 of file base_types.h.

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

Pass a set of objects.

See Also: QuadContainer

Definition at line 108 of file base_types.h.

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

Store a set of objects.

Definition at line 134 of file base_types.h.

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

Pass a set of objects.

See Also: QuadModifier

Definition at line 135 of file base_types.h.

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

Store a set of objects.

Definition at line 125 of file base_types.h.

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

Pass a set of objects.

See Also: QuadPredicate

Definition at line 126 of file base_types.h.

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

Store a set of objects.

Definition at line 116 of file base_types.h.

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

Pass a set of objects.

See Also: QuadScore

Definition at line 117 of file base_types.h.

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

a collection of Refiner objects

Store a set of objects.

Definition at line 122 of file Refiner.h.

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

Pass a set of objects.

See Also: Refiner

Definition at line 122 of file Refiner.h.

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

Store a set of objects.

Definition at line 79 of file base_types.h.

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

Store a set of objects.

Definition at line 87 of file base_types.h.

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

Pass a set of objects.

See Also: RestraintSet

Definition at line 88 of file base_types.h.

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

Pass a set of objects.

See Also: Restraint

Definition at line 80 of file base_types.h.

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

Store a set of objects.

Definition at line 69 of file Sampler.h.

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

Pass a set of objects.

See Also: Sampler

Definition at line 69 of file Sampler.h.

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

Pass or store a set of ScoreAccumulator .

Definition at line 137 of file ScoreAccumulator.h.

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

Store a set of objects.

Definition at line 89 of file base_types.h.

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

Pass a set of objects.

See Also: ScoreState

Definition at line 90 of file base_types.h.

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

Store a set of objects.

Definition at line 91 of file base_types.h.

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

Pass a set of objects.

See Also: ScoringFunction

Definition at line 92 of file base_types.h.

typedef IMP::Vector< SetCheckState > IMP::SetCheckStates

Pass or store a set of SetCheckState .

Definition at line 54 of file SetCheckState.h.

typedef IMP::Vector< SetLogState > IMP::SetLogStates

Pass or store a set of SetLogState .

Definition at line 50 of file SetLogState.h.

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

Store a set of objects.

Definition at line 101 of file base_types.h.

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

Pass a set of objects.

See Also: SingletonContainer

Definition at line 102 of file base_types.h.

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

Store a set of objects.

Definition at line 128 of file base_types.h.

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

Pass a set of objects.

See Also: SingletonModifier

Definition at line 129 of file base_types.h.

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

Store a set of objects.

Definition at line 119 of file base_types.h.

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

Pass a set of objects.

See Also: SingletonPredicate

Definition at line 120 of file base_types.h.

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

Store a set of objects.

Definition at line 110 of file base_types.h.

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

Pass a set of objects.

See Also: SingletonScore

Definition at line 111 of file base_types.h.

typedef std::string IMP::String

Basic string value.

Definition at line 44 of file types.h.

typedef Key<2, true> IMP::StringKey

The type used to identify string attributes in the Particles.

Definition at line 40 of file base_types.h.

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

Pass or store a set of StringKey .

Definition at line 41 of file base_types.h.

typedef IMP::Vector< String > IMP::Strings

Standard way to pass a bunch of String values.

Pass or store a set of String .

Definition at line 51 of file types.h.

typedef IMP::Vector< Strings > IMP::StringsList

Standard way to pass a bunch of Strings values.

Pass or store a set of Strings .

Definition at line 58 of file types.h.

typedef IMP::Vector< StringsList > IMP::StringsLists

Pass or store a set of StringsList .

Definition at line 58 of file types.h.

typedef IMP::Vector< Strings > IMP::Stringss

Pass or store a set of Strings .

Definition at line 51 of file types.h.

typedef IMP::Vector< TextInput > IMP::TextInputs

Pass or store a set of TextInput .

Definition at line 150 of file file.h.

typedef IMP::Vector< TextOutput > IMP::TextOutputs

Pass or store a set of TextOutput .

Definition at line 151 of file file.h.

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

Store a set of objects.

Definition at line 105 of file base_types.h.

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

Pass a set of objects.

See Also: TripletContainer

Definition at line 106 of file base_types.h.

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

Store a set of objects.

Definition at line 132 of file base_types.h.

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

Pass a set of objects.

See Also: TripletModifier

Definition at line 133 of file base_types.h.

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

Store a set of objects.

Definition at line 123 of file base_types.h.

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

Pass a set of objects.

See Also: TripletPredicate

Definition at line 124 of file base_types.h.

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

Store a set of objects.

Definition at line 114 of file base_types.h.

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

Pass a set of objects.

See Also: TripletScore

Definition at line 115 of file base_types.h.

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

Store a set of objects.

Definition at line 56 of file UnaryFunction.h.

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

Pass a set of objects.

See Also: UnaryFunction

Definition at line 56 of file UnaryFunction.h.

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

Store a set of objects.

Definition at line 33 of file Undecorator.h.

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

Pass a set of objects.

See Also: Undecorator

Definition at line 33 of file Undecorator.h.

typedef IMP::Vector< VersionInfo > IMP::VersionInfos

Pass or store a set of VersionInfo .

Definition at line 48 of file VersionInfo.h.

typedef Key<9, true> IMP::WeakObjectKey

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

Definition at line 52 of file base_types.h.

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

Pass or store a set of WeakObjectKey .

Definition at line 53 of file base_types.h.

Enumeration Type Documentation

enum IMP::CheckLevel

Specify the level of runtime checks performed.

Enumerator
DEFAULT_CHECK	Use the default check level (eg IMP::Object::set_check_level()).
NONE	Perform no runtime checks.
USAGE	Perform checks that `IMP` is being called correctly.
USAGE_AND_INTERNAL	Check internal `IMP` invariants. This is to be used for debugging `IMP`.

Definition at line 53 of file enums.h.

enum IMP::LogLevel

The log levels supported by IMP.

Enumerator
DEFAULT	Use to specify that the global log level should be used (eg in IMP::Object::set_log_level())
SILENT	Do not output any text.
WARNING	Output only warnings.
PROGRESS	Output only progress meter style displays and occasional printouts when switching phases of work.
TERSE	Output a line or two per evaluation call.
VERBOSE	Produce copious output to allow someone to trace through the computation.
MEMORY	Log memory allocations and frees.

Definition at line 19 of file enums.h.

enum IMP::StatisticsLevel

Specify the level of statistics to record.

See Also: show_timings().

Definition at line 72 of file enums.h.

Function Documentation

void IMP::add_bool_flag	(	std::string	name,
		std::string	description
	)

For Python use. Default is always false.

void IMP::add_float_flag	(	std::string	name,
		double	default_value,
		std::string	description
	)

For Python use.

void IMP::add_int_flag	(	std::string	name,
		size_t	default_value,
		std::string	description
	)

For Python use.

void IMP::add_string_flag	(	std::string	name,
		std::string	default_value,
		std::string	description
	)

For Python use.

void IMP::add_to_log	(	LogLevel	level,
		std::string	to_write
	)

Write a string to the log, for Python.

void IMP::add_to_progress_display ( unsigned int step = 1 )

Set the current progress.

When it equals the number of steps, the bar is done.

def IMP.allow_deprecated ( allow = True )

Context manager to temporarily allow (or disallow) deprecated code.

See Also: deprecation support.

Note: This function is only available in Python.

Definition at line 9407 of file __init__.py.

void IMP::clear_statistics ( )

Reset all the statistics for IMP.

template<class Before , class After >

Constraint* IMP::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 generic.h.

ScoringFunctions IMP::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::create_decomposition ( const RestraintsTemp & rs )

Return the decomposition of a list of restraints.

template<class Score >

Restraint* IMP::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 generic.h.

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template<class RestraintType >

ScoringFunction* IMP::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 generic.h.

TextOutput IMP::create_temporary_file	(	std::string	prefix = `"imp_temp"`,
		std::string	suffix = `""`
	)

Create a temporary file. The path can be extracted from the TextOutput.

If suffix is non-empty, there is some small chance of a collision on non-BSD systems as a unique temporary file is first created, and then a file with that suffix appended is created.

std::string IMP::create_temporary_file_name	(	std::string	prefix = `"imp_temp"`,
		std::string	suffix = `""`
	)

Create a temporary file.

If suffix is non-empty, there is some small chance of a collision on non-BSD systems as a unique temporary file is first created, and then a file with that suffix appended is created.

def IMP.deprecated_function	(	version,
		help_message
	)

Python decorator to mark a function as deprecated.

See Also: deprecation support.

Note: This function is only available in Python.

Definition at line 9395 of file __init__.py.

def IMP.deprecated_method	(	version,
		help_message
	)

Python decorator to mark a method as deprecated.

See Also: deprecation support.

Note: This function is only available in Python.

Definition at line 9383 of file __init__.py.

def IMP.deprecated_module	(	version,
		module,
		help_message
	)

Mark a Python module as deprecated.

Note: The module argument would normally be __name__.

See Also: deprecation support.

Note: This function is only available in Python.

Definition at line 9360 of file __init__.py.

def IMP.deprecated_object	(	version,
		help_message
	)

Python decorator to mark a class as deprecated.

See Also: deprecation support.

Note: This function is only available in Python.

Definition at line 9367 of file __init__.py.

bool IMP::get_bool_flag ( std::string name )

For Python use.

CheckLevel IMP::get_check_level ( )

Get the current audit mode.

Definition at line 81 of file exception.h.

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

Return the full path to one of this module's data files.

To read the data file "data_library" that was placed in the data directory of this module, do something like

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

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

Note: Each module has its own data directory, so be sure to use this function from the correct module.

DependencyGraph IMP::get_dependency_graph ( 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::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.

bool IMP::get_deprecation_exceptions ( )

Get whether an exception is thrown when a deprecated method is used.

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

Return the full path to one of this module's example files.

To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like

std::ifstream in(IMP::get_example_path("example_protein.pdb"));

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

Note: Each module has its own example directory, so be sure to use this function from the correct module.

std::string IMP::get_executable_name ( )

Return the name of the current executable.

double IMP::get_float_flag ( std::string name )

For Python use.

ParticleIndexes IMP::get_indexes ( const ParticlesTemp & ps )

Get the indexes from a list of particles.

ParticleIndexPairs IMP::get_indexes ( const ParticlePairsTemp & ps )

Get the indexes from a list of particle pairs.

ContainersTemp IMP::get_input_containers ( const ModelObjectsTemp & mos )

Return all the input particles for a given ModelObject.

ParticlesTemp IMP::get_input_particles ( const ModelObjectsTemp & mos )

Return all the input particles for a given ModelObject.

size_t IMP::get_int_flag ( std::string name )

For Python use.

bool IMP::get_is_quick_test ( )

Executables can inspect this flag and when it is true, run a shorter, simpler version of their code to just make sure things work.

Definition at line 178 of file flags.h.

Strings IMP::get_live_object_names ( )

Return the names of all live objects.

Use this to check for memory leaks.

Objects IMP::get_live_objects ( )

Return pointers to all live objects.

Use this to check for memory leaks.

LogLevel IMP::get_log_level ( )

Get the currently active global log level.

Get the currently active global log level

Note: This may not always match the value passed to set_log_level() as objects can temporarily override the global level while they are evaluating.

See Also: set_log_level(); IMP::Object::set_log_level()

Definition at line 94 of file log.h.

networkx::DiGraph IMP::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()

unsigned int IMP::get_number_of_threads ( )

Get the current number of threads requested. The default is the number of cores/hardware threads in the machine if there is OpenMP support, or 1 otherwise.

ContainersTemp IMP::get_output_containers ( const ModelObjectsTemp & mos )

Return all the output particles for a given ModelObject.

ParticlesTemp IMP::get_output_particles ( const ModelObjectsTemp & mos )

Return all the output particles for a given ModelObject.

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

Get the particles from a list of indexes.

DependencyGraph IMP::get_pruned_dependency_graph ( Model * m )

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

double IMP::get_random_double_uniform ( )

Return a uniformly distributed double number in range [0..1)

Note: the random number is retrieved from a cache of random numbers generated using GPU if compiled with CUDA, or from boost without a cache otherwise.

Definition at line 149 of file random_utils.h.

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double IMP::get_random_double_uniform	(	double	min,
		double	max
	)

Return a uniformly distributed double number in range [min..max)

Note: the random number is retrieved from a cache of random numbers generated using GPU if compiled with CUDA, or from boost without a cache otherwise.

Definition at line 167 of file random_utils.h.

float IMP::get_random_float_uniform ( )

Return a uniformly distributed float number in range [0..1)

Note: the random number is retrieved from a cache of random numbers generated using GPU if compiled with CUDA, or from boost without a cache otherwise.

Definition at line 117 of file random_utils.h.

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float IMP::get_random_float_uniform	(	float	min,
		float	max
	)

Return a uniformly distributed float number in range [min..max)

Note: the random number is retrieved from a cache of random numbers generated using GPU if compiled with CUDA, or from boost without a cache otherwise.

Definition at line 136 of file random_utils.h.

template<typename RealType >

void IMP::get_random_numbers_normal	(	Vector< RealType > &	v,
		unsigned int	n,
		RealType	mean = `0.0`,
		RealType	stddev = `1.0`
	)

Fill the double array with random normally distributed values.

The pre-allocated array is filled with n double numbers with random normally distributed values with specified mean and standard deviation.

Parameters

v	vector array that will be resized to n
n	size of array
mean	mean of normal distribution
stddev	standard deviation

Note: Implementation relies on random_number_generator (a boost random number generator), or on the CUDA random number generator if kernel is built with IMP_KERNEL_CUDA_LIB cmake flag. Either is initially seeded with get_random_seed().

Definition at line 44 of file random_utils.h.

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template<typename RealType >

void IMP::get_random_numbers_uniform	(	Vector< RealType > &	v,
		unsigned int	n
	)

Fill the float array with random normally distributed values.

Fill a pre-allocated array of n float numbers with random normally distributed values with specified mean and standard deviation.

Parameters

v	vector array that will be resized to n
n	size of array

Note: Implementation relies on random_number_generator (a boost random number generator), or on the CUDA random number generator if kernel is built with CUDA flag. Either is initially seeded with get_random_seed().

Definition at line 73 of file random_utils.h.

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boost::uint64_t IMP::get_random_seed ( )

Return the initial random seed.

std::string IMP::get_relative_path	(	std::string	base,
		std::string	relative
	)

Return a path to a file relative to another file.

For example if base is path/to/config.file and relative is data/image0.jpg then the return value would be path/to/data/image0.jpg. This function should be used when processing configuration files so that the meaning of the configuration file does not change if current working directory changes.

ScoreStatesTemp IMP::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::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.

std::string IMP::get_string_flag ( std::string name )

For Python use.

std::string IMP::get_unique_name ( std::string templ )

Return a unique name produced from the string.

This is done by replacing %1% with a sequential number.

ScoreStatesTemp IMP::get_update_order ( ScoreStatesTemp input )

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

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

See generic geometry for more information.

Definition at line 145 of file XYZ.h.

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void IMP::handle_error ( const char * msg )

This function is called whenever IMP detects an error. It can be useful to add a breakpoint in the function when using a debugger.

void IMP::handle_use_deprecated ( std::string message )

Break in this method in gdb to find deprecated uses at runtime.

template<class T >

bool IMP::isinf ( const T & a )

Return true if a number is infinite.

Definition at line 35 of file math.h.

template<class T >

bool IMP::isnan ( const T & a )

Return true if a number is NaN.

With certain compiler settings the compiler can optimize out a!=a (and certain Intel chips had issues with it too).

Definition at line 24 of file math.h.

template<class Pred >

internal::PredicateEquals<Pred, true> IMP::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 functor.h.

template<class Pred >

internal::PredicateEquals<Pred, false> IMP::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 functor.h.

template<class O >

O* IMP::object_cast ( Object * o )

Up (or down) cast an IMP Object-derived class. If the cast does not succeed a ValueException will be thrown. Use a dynamic_cast if you prefer to have a nullptr returned.

Definition at line 24 of file object_cast.h.

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

load found attributes into the particles

void IMP::reset_log_timer ( )

Reset the log timer.

void IMP::set_check_level ( CheckLevel tf )

Control runtime checks in the code.

The default level of checks is USAGE for release builds and USAGE_AND_INTERNAL for debug builds.

Definition at line 73 of file exception.h.

void IMP::set_deprecation_exceptions ( bool tf )

Toggle whether an exception is thrown when a deprecated method is used.

void IMP::set_deprecation_warnings ( bool tf )

Toggle printing of warnings on using deprecated classes.

If set to true (the default) a warning is printed every time a class marked as deprecated is used.

void IMP::set_log_level ( LogLevel l )

Set the current global log level.

Note: may be overridden by set_log_level of specific objects that inherit from IMP::Object; this global method should not, currently, be used directly during Model::evaluate() calls.

See Also: get_log_level(); IMP::Object::set_log_level()

void IMP::set_log_target ( TextOutput l )

Set the target for the log.

See TextOutput for options. Python users should use SetLogTarget instead.

void IMP::set_log_timer ( bool tb )

Set whether log messages are tagged with the current log time.

void IMP::set_number_of_threads ( unsigned int n )

Set the current number of threads to a number greater or equal to 1. Setting it to 1 disables multithreaded evaluation.

void IMP::set_progress_display	(	std::string	description,
		unsigned int	steps
	)

Set up the progress bar with the passed description.

See Also: IMP_PROGRESS_DISPLAY().

void IMP::set_show_leaked_objects ( bool tf )

Set whether to complain about objects not being properly cleaned up.

void IMP::set_statistics_level ( StatisticsLevel l )

Set the level of statistics to be gathered.

void IMP::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::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::set_vector_geometry	(	WeakPointer< Particle >	d,
		const algebra::Vector3D &	v
	)

See generic geometry for more information.

Definition at line 166 of file XYZ.h.

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void IMP::set_vector_geometry	(	Pointer< Particle >	d,
		const algebra::Vector3D &	v
	)

See generic geometry for more information.

Definition at line 175 of file XYZ.h.

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void IMP::setup_from_argv	(	int	argc,
		char **	argv,
		std::string	description
	)

Parse the command line flags and return the positional arguments.

Parameters

[in]	argc	argc
[in]	argv	argv
[in]	description	A message describing what the program does.

Examples:: atom/dope_and_excluded_volume.cpp, core/simple.cpp, flags.cpp, and grid.cpp.

Strings IMP::setup_from_argv	(	int	argc,
		char **	argv,
		std::string	description,
		std::string	positional_description,
		int	num_positional
	)

Parse the command line flags and return the positional arguments.

Parameters

[in]	argc	argc
[in]	argv	argv
[in]	description	A message describing what the program does.
[in]	positional_description	A message describing the the positional arguments
[in]	num_positional	A positive integer to require that many positional arguments, or a negative integer to require at least that many.

void IMP::setup_from_argv	(	const Strings &	argv,
		std::string	description
	)

Parse the command line flags and return the positional arguments. For Python.

Parameters

[in]	argv	sys.argv
[in]	description	A message describing what the program does.

Strings IMP::setup_from_argv	(	const Strings &	argv,
		std::string	description,
		std::string	positional_description,
		int	num_positional
	)

Parse the command line flags and return the positional arguments. For Python.

Parameters

[in]	argv	sys.argv
[in]	description	A message describing what the program does.
[in]	positional_description	A message describing the positional arguments, eg "input.pdb output.pdb"
[in]	num_positional	A positive integer to require that many positional arguments, or a negative integer to require at least that many.

Strings IMP::setup_from_argv_allowing_unknown	(	int	argc,
		char **	argv,
		std::string	description
	)

Parse the command line flags and return the positional arguments returning unknown flags in a list. Use this version if some arguments are to be parsed by a different system.

Parameters

[in]	argc	argc
[in]	argv	argv
[in]	description	A message describing what the program does.

void IMP::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::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::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.

void IMP::show_timings ( TextOutput out )

Show all captured timings.

void IMP::write_help ( std::ostream & out = std::cerr )

Prints out the help message, useful if you have extra error checking and the flags don't pass it.

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

return a binary buffer with the data

Variable Documentation

const double IMP::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::NO_MAX

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

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.

RandomNumberGenerator IMP::random_number_generator

A shared non-GPU random number generator.

The random number generator is seeded based on command line specified flag. Otherwise, the default seed is retrieved from among either boost::random_device, /dev/urandom, or the system clock, based on which method is available in this priority order.

This generator can be used by the Boost.Random distributions.

Detailed Description

Graphs

Values and Objects (C++ only)

Google Perf Tools

Info

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Attribute Keys

Error checking and reporting

Flags

Inputs and outputs

Buffer I/O

Standard module functions

Logging

Create a progress bar in the terminal

Python Only

Gathering restraints

Number of threads

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation