Basic functionality that is expected to be used by a wide variety of IMP users. More...

Detailed Description

Basic functionality that is expected to be used by a wide variety of IMP users.

The classes in this module should not directly incorporate experimental data and instead should provide basic building blocks for making restraints and manipulating Particle objects. Typical classes are IMP::core::Harmonic, IMP::core::DistancePairScore, IMP::core::VolumeRestraint etc.

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	AllSamePairPredicate
	Return true (1) if all members of the tuple are the same. More...

class	AllSameQuadPredicate
	Return true (1) if all members of the tuple are the same. More...

class	AllSameSingletonPredicate
	Return true (1) if all members of the tuple are the same. More...

class	AllSameTripletPredicate
	Return true (1) if all members of the tuple are the same. More...

class	AngleRestraint
	Angle restraint between three particles. More...

class	AngleTripletScore
	Apply a function to the angle between three particles. More...

class	AttributeSingletonPredicate
	Return the value of an int attribute as the predicate value. More...

class	BallMover
	Move continuous particle variables by perturbing them within a ball. More...

class	BinormalTerm
	A single binormal term in a MultipleBinormalRestraint. More...

class	BoxSweepClosePairsFinder
	Find all nearby pairs by sweeping the bounding boxes. More...

class	Centroid
	A particle that is the geometric centroid of other particles. More...

class	CentroidOfRefined
	Set a particle to be the centroid of the refined particles. More...

class	ChecksScoreState
	Turn checks on with a given probability each evaluate call. More...

class	ChildrenRefiner
	Return the hierarchy children of a particle. More...

class	ClosedCubicSpline
	Closed cubic spline function. More...

class	ClosePairsFinder
	A base class for algorithms to find spatial proximities. More...

class	ClosePairsPairScore
	Apply the score to all pairs whose spheres are within a distance threshold. More...

class	ClusterProvenance
	Track creation of a system fragment from clustering. More...

class	CoinFlipPairPredicate
	Return true (1) with a fixed probability. More...

class	CoinFlipQuadPredicate
	Return true (1) with a fixed probability. More...

class	CoinFlipSingletonPredicate
	Return true (1) with a fixed probability. More...

class	CoinFlipTripletPredicate
	Return true (1) with a fixed probability. More...

class	CombineProvenance
	Track creation of a system fragment by combination. More...

class	ConjugateGradients
	Simple conjugate gradients optimizer. More...

class	ConnectivityRestraint
	Ensure that a set of particles remains connected with one another. More...

class	ConstantPairPredicate
	Always return a constant value. More...

class	ConstantQuadPredicate
	Always return a constant value. More...

class	ConstantRestraint
	Return a constant value. More...

class	ConstantSingletonPredicate
	Always return a constant value. More...

class	ConstantTripletPredicate
	Always return a constant value. More...

class	Cosine
	Cosine function. More...

class	Cover
	A particle which covers a set of other particles. More...

class	CoverRefined
	Set the position and radius of a particle to enclose the refined. More...

class	DataObject
	Helper class for creating an IMP object storing some data. More...

class	DerivativesFromRefined
	Accumulate the derivatives of the refined particles. More...

class	DerivativesToRefined
	Copy the derivatives from a coarse particle to its refined particles. More...

class	DiameterRestraint
	Restrain the diameter of a set of points. More...

class	DihedralRestraint
	Dihedral restraint between four particles. More...

class	Direction
	A decorator for a particle that represents a direction in 3D. More...

class	DirectionAngle
	A decorator for an angle between two directions. More...

class	DirectionMover
	Modify a direction. More...

class	DistancePairScore
	Score a pair of particles based on the distance between their centers. More...

class	DistanceRestraint
	Distance restraint between two particles. More...

class	EdgePairGeometry
	Display a segment connecting a pair of particles. More...

class	EdgePairsGeometry
	Display a segment for each pair in a IMP::PairContainer. More...

class	ExcludedVolumeRestraint
	Prevent a set of particles and rigid bodies from inter-penetrating. More...

class	FilterProvenance
	Track creation of a system fragment by filtering. More...

class	FixedRefiner
	The refiner can refine any particle by returning a fixed set. More...

class	Gaussian

class	GenericAttributeSingletonScore
	Apply a function to an attribute. More...

class	GenericBoundingBox3DSingletonScore

class	GenericBoundingSphere3DSingletonScore
	Score XYZ or XYZR particles based on how far outside a sphere they are. More...

class	GenericDistanceToSingletonScore
	Apply a function to the distance to a fixed point. More...

class	GridClosePairsFinder
	Find all nearby pairs by testing all pairs. More...

class	Harmonic
	Harmonic function (symmetric about the mean) More...

class	HarmonicDistancePairScore
	Score distance between two particle centers using a harmonic function. More...

class	HarmonicLowerBound
	Lower bound harmonic function (non-zero when feature < mean) More...

class	HarmonicSphereDistancePairScore
	A harmonic score on the distance between two spheres. More...

class	HarmonicSurfaceDepthPairScore
	A harmonic score on the depth of a sphere's surface below a surface. More...

class	HarmonicSurfaceDistancePairScore
	A harmonic score on the distance between a surface and a sphere surface. More...

class	HarmonicSurfaceHeightPairScore
	A harmonic score on the height of a sphere's surface above a surface. More...

class	HarmonicUpperBound
	Upper bound harmonic function (non-zero when feature > mean) More...

class	HarmonicUpperBoundSphereDiameterPairScore
	A harmonic upper bound on the diameter of the span of two spheres. More...

class	HarmonicUpperBoundSphereDistancePairScore
	A harmonic upper bound on the distance between two spheres. More...

class	HarmonicWell
	A well with harmonic barriers. More...

class	Hierarchy
	A decorator for helping deal with a generalized hierarchy. More...

struct	HierarchyCounter
	A simple functor to count the number of particles in a hierarchy. More...

class	HierarchyTraits
	Define the type for a type of hierarchy. More...

class	HierarchyVisitor
	A visitor for traversal of a hierarchy. More...

class	InBoundingBox3DSingletonPredicate
	Return 1 if the XYZ is in the bounding box, 0 otherwise. More...

class	IsCollisionPairPredicate
	Return 1 if two XYZRs collide. More...

class	KClosePairsPairScore
	Apply a score to a fixed number of close pairs from the two sets. More...

class	LateralSurfaceConstraint
	Constrain the center of a Surface for visualization. More...

class	LeavesRefiner
	Return the hierarchy leaves under a particle. More...

class	Linear
	Linear function More...

class	LogNormalMover
	Modify a set of continuous variables using a log-normal distribution. More...

class	MCCGSampler
	A simple sampler. More...

class	MinimumRestraint
	Score based on the minimum scoring members of a set of restraints. More...

class	ModifierVisitor
	A visitor which applies a modifier to each Particle in a hierarchy. More...

class	MonteCarlo
	A Monte Carlo optimizer. More...

class	MonteCarloMover
	A base class for classes which perturb particles. More...

struct	MonteCarloMoverResult
	Return value of the MonteCarloMover::propose() function. More...

class	MonteCarloWithBasinHopping
	This variant of Monte Carlo uses basis hopping. More...

class	MonteCarloWithLocalOptimization
	This variant of Monte Carlo that relaxes after each move. More...

class	MoveStatisticsScoreState
	Keep track of statistics about how particles move. More...

class	MSConnectivityRestraint
	Ensure that a set of particles remains connected with one another. More...

class	MultipleBinormalRestraint
	Modeller-style multiple binormal (phi/psi) restraint. More...

class	NearestNeighborsClosePairsFinder
	Find all nearby pairs using the algebra::NearestNeighbor code. More...

class	NeighborsTable

class	NonRigidMember
	A decorator for a particle that is part of a rigid body but not rigid. More...

class	NormalizedSphereDistancePairScore
	A score on the normalized distance between the surfaces of two spheres. More...

class	NormalMover
	Modify a set of continuous variables using a normal distribution. More...

class	OpenCubicSpline
	An OpenCubicSpline. More...

class	OrderedTypePairPredicate
	Return a unique predicate value for each ordered set of ParticleTypes. More...

class	OrderedTypeQuadPredicate
	Return a unique predicate value for each ordered set of ParticleTypes. More...

class	OrderedTypeSingletonPredicate
	Return a unique predicate value for each ordered set of ParticleTypes. More...

class	OrderedTypeTripletPredicate
	Return a unique predicate value for each ordered set of ParticleTypes. More...

class	PairConstraint
	Apply a PairFunction to a Pair. More...

class	PairRestraint
	Applies a PairScore to a Pair. More...

class	PredicateSingletonScore

class	Provenance
	Track how parts of the system were created. More...

class	Provenanced
	Tag part of the system to track how it was created. More...

class	QuadConstraint
	Apply a QuadFunction to a Quad. More...

class	QuadraticClosePairsFinder
	Find all nearby pairs by testing all pairs. More...

class	QuadRestraint
	Applies a QuadScore to a Quad. More...

class	Reference
	A particle that has an associated reference particle. More...

class	RefinedPairsPairScore
	Generate pairs to score by applying a Refiner. More...

class	RestraintsScoringFunction
	Create a scoring function on a list of restraints. More...

class	RigidBody
	A decorator for a rigid body. More...

class	RigidBodyAnglePairScore
	Score on the crossing angle between two rigid bodies. More...

class	RigidBodyDerivativeGeometry

class	RigidBodyDerivativesGeometry

class	RigidBodyDistancePairScore
	Accelerated computation of the distance between two rigid bodies. More...

class	RigidBodyFrameGeometry

class	RigidBodyFramesGeometry

class	RigidBodyHierarchyGeometry

class	RigidBodyMember
	A member of a rigid body, it has internal (local) coordinates. More...

class	RigidBodyMover
	Modify the transformation of a rigid body. More...

class	RigidBodyTorque

class	RigidBodyTunneler
	Modify the transformation of a rigid body. More...

class	RigidBodyUmbrella
	Umbrella-like restraint for rigid bodies. More...

class	RigidClosePairsFinder
	Perform more efficient close pair finding when rigid bodies are involved. More...

class	RigidMember

class	SampleProvenance
	Track creation of a system fragment from sampling. More...

class	ScriptProvenance
	Track creation of a system fragment from running a script. More...

class	SerialMover
	Applies a list of movers one at a time. More...

class	SingletonConstraint
	Apply a SingletonFunction to a Singleton. More...

class	SingletonRestraint
	Applies a SingletonScore to a Singleton. More...

class	SoftSpherePairScore

class	SoftSubSurfacePairScore
	A harmonic score that keeps a sphere's surface below a surface. More...

class	SoftSuperSurfacePairScore
	A harmonic score that keeps a sphere's surface above a surface. More...

class	SoftwareProvenance
	Track creation of a system fragment from running some software. More...

class	SphereDistancePairScore
	A score on the distance between the surfaces of two spheres. More...

class	SphereDistanceToSingletonScore
	Apply a function to the distance to a fixed point. More...

class	StatisticalPairScore

class	SteepestDescent
	A simple steepest descent optimizer. More...

class	StructureProvenance
	Track creation of a system fragment from a PDB file. More...

class	SubsetMover
	Applies a subset of a list of movers. More...

class	Surface
	A decorator for a particle that represents a surface, its coordinates, and orientation. More...

class	SurfaceDepthPairScore
	A score on the depth of a sphere's surface below a surface. More...

class	SurfaceDistancePairScore
	A score on the distance between a surface and a sphere surface. More...

class	SurfaceGeometry
	Display a Surface particle as a cylindrical disk. More...

class	SurfaceGeometryConstraint
	Constrain a SurfaceGeometry to a Surface. More...

class	SurfaceHeightPairScore
	A score on the height of a sphere's surface above a surface. More...

class	SurfaceMover
	Modify a surface orientation. More...

class	SurfaceSymmetryConstraint
	Constrain orientation of surfaces with respect to rigid bodies. More...

class	SurfaceTetheredChain
	Score on surface-to-end distance of chain tethered to impenetrable surface. More...

class	TableRefiner
	A lookup based particle refiner. More...

class	Transform
	Apply a transformation to a passed particle. More...

class	TransformationAndReflectionSymmetry
	Set the coordinates of a particle to be a transformed version of a reference. More...

class	TransformationSymmetry
	Set the coordinates of a particle to be a transformed version of a reference. More...

class	TransformationSymmetryMover
	Modify the given TransformationSymmetry. More...

class	TransformedDistancePairScore
	Apply a function to the distance between two particles after transforming the second. More...

class	TripletConstraint
	Apply a TripletFunction to a Triplet. More...

class	TripletRestraint
	Applies a TripletScore to a Triplet. More...

class	TruncatedHarmonic
	A function that is harmonic over an bounded interval. More...

class	Typed
	A decorator for classifying particles in your system. More...

class	TypedPairScore
	Delegate to another PairScore depending on particle types. More...

class	UnorderedTypePairPredicate
	Return a unique predicate value for each unordered set of ParticleTypes. More...

class	UnorderedTypeQuadPredicate
	Return a unique predicate value for each unordered set of ParticleTypes. More...

class	UnorderedTypeSingletonPredicate
	Return a unique predicate value for each unordered set of ParticleTypes. More...

class	UnorderedTypeTripletPredicate
	Return a unique predicate value for each unordered set of ParticleTypes. More...

class	VolumeRestraint
	A restraint that prevents spheres from inter-penetrating. More...

class	WeightedDerivativesToRefined
	Copy the derivatives from a coarse particle to its refined particles. More...

class	WeightedSphereDistancePairScore
	A score on a weighted distance between the surfaces of two spheres. More...

class	WeightedSum
	Weighted sum of unary functions. More...

class	WeightedSumOfExponential
	Negative logarithm of weighted sum of negative exponential of unary functions. More...

class	WriteRestraintScoresOptimizerState
	Write the scores of the passed restraints to a file during optimization. More...

class	XYZ
	A decorator for a particle with x,y,z coordinates. More...

class	XYZDerivativeGeometry

class	XYZDerivativesGeometry

class	XYZR
	A decorator for a particle with x,y,z coordinates and a radius. More...

class	XYZRGeometry
	Display an IMP::core::XYZR particle as a ball. More...

class	XYZRsGeometry
	Display an IMP::SingletonContainer of IMP::core::XYZR particles as balls. More...

Typedefs
typedef GenericAttributeSingletonScore < UnaryFunction >	AttributeSingletonScore

typedef IMP::Vector< BinormalTerm >	BinormalTermList

typedef GenericBoundingBox3DSingletonScore < UnaryFunction >	BoundingBox3DSingletonScore

typedef GenericBoundingSphere3DSingletonScore < UnaryFunction >	BoundingSphere3DSingletonScore

typedef IMP::Vector< Centroid >	Centroids

typedef IMP::Vector< Cover >	Covers

typedef IMP::Vector < DirectionAngle >	DirectionAngles

typedef IMP::Vector< Direction >	Directions

typedef IMP::Vector < IMP::Pointer < DistancePairScore > >	DistancePairScores

typedef IMP::Vector < IMP::WeakPointer < DistancePairScore > >	DistancePairScoresTemp

typedef GenericDistanceToSingletonScore < UnaryFunction >	DistanceToSingletonScore

typedef IMP::Vector< Gaussian >	Gaussians

typedef IMP::Vector < IMP::Pointer < HarmonicDistancePairScore > >	HarmonicDistancePairScores

typedef IMP::Vector < IMP::WeakPointer < HarmonicDistancePairScore > >	HarmonicDistancePairScoresTemp

typedef score_functor::SphereDistance < score_functor::Shift < score_functor::Harmonic > >	HarmonicSphereDistanceScore

typedef score_functor::PointToSphereDistance < score_functor::Shift < score_functor::Harmonic > >	HarmonicSurfaceDistanceScore

typedef IMP::Vector < IMP::Pointer < HarmonicUpperBoundSphereDiameterPairScore > >	HarmonicUpperBoundSphereDiameterPairScores

typedef IMP::Vector < IMP::WeakPointer < HarmonicUpperBoundSphereDiameterPairScore > >	HarmonicUpperBoundSphereDiameterPairScoresTemp

typedef score_functor::SphereDistance < score_functor::Shift < score_functor::HarmonicUpperBound > >	HarmonicUpperBoundSphereDistanceScore

typedef IMP::Vector < IMP::Pointer< HarmonicWell > >	HarmonicWells

typedef IMP::Vector < IMP::WeakPointer < HarmonicWell > >	HarmonicWellsTemp

typedef IMP::Vector < HierarchyCounter >	HierarchyCounters

typedef IMP::Vector < HierarchyTraits >	HierarchyTraitsList

typedef IMP::Vector < MonteCarloMoverResult >	MonteCarloMoverResults

typedef IMP::Vector < IMP::Pointer < MonteCarloMover > >	MonteCarloMovers

typedef IMP::Vector < IMP::WeakPointer < MonteCarloMover > >	MonteCarloMoversTemp

typedef Key< 34897493 >	ParticleType
	An IMP::Key object for identifying types of particles by strings. More...

typedef IMP::Vector< ParticleType >	ParticleTypes

typedef OptimizerState	PeriodicOptimizerState

typedef score_functor::PointToSphereDistance < score_functor::UnaryFunctionEvaluate >	PointToSphereDistanceScore

typedef IMP::Vector< Reference >	References

typedef IMP::Vector< RigidBody >	RigidBodies

typedef IMP::Vector < RigidBodyMember >	RigidBodyMembers

typedef IMP::Vector< RigidMember >	RigidMembers

typedef score_functor::SphereDistance < score_functor::HarmonicLowerBound >	SoftSphereDistanceScore

typedef score_functor::PointToSphereDistance < score_functor::HarmonicLowerBound >	SoftSurfaceDistanceScore

typedef score_functor::SphereDistance < score_functor::UnaryFunctionEvaluate >	SphereDistanceScore

typedef IMP::Vector < IMP::Pointer < SurfaceGeometry > >	SurfaceGeometries

typedef IMP::Vector < IMP::WeakPointer < SurfaceGeometry > >	SurfaceGeometriesTemp

typedef IMP::Vector < IMP::Pointer < SurfaceGeometryConstraint > >	SurfaceGeometryConstraints

typedef IMP::Vector < IMP::WeakPointer < SurfaceGeometryConstraint > >	SurfaceGeometryConstraintsTemp

typedef IMP::Vector< Surface >	Surfaces

typedef TruncatedHarmonic< BOTH >	TruncatedHarmonicBound

typedef TruncatedHarmonic< LOWER >	TruncatedHarmonicLowerBound

typedef TruncatedHarmonic< UPPER >	TruncatedHarmonicUpperBound

typedef IMP::Vector< Typed >	Typeds

typedef IMP::Vector< XYZR >	XYZRs

typedef IMP::Vector< XYZ >	XYZs

Enumerations
enum	BoundDirection { LOWER, BOTH, UPPER }

Functions
def	add_imp_provenance
	Tag the given particle as being created by the current version of IMP. More...

void	add_provenance (Model *m, ParticleIndex pi, Provenance p)
	Add provenance to part of the model. More...

void	add_rigid_body_cache_key (ObjectKey k)

def	add_script_provenance
	Tag the given particle with the current Python script. More...

def	add_software_provenance
	Tag the given particle with the software used to create it. More...

void	assign_blame (const RestraintsTemp &rs, const ParticlesTemp &ps, FloatKey attribute)

display::Geometries	create_blame_geometries (const RestraintsTemp &rs, const ParticlesTemp &ps, double max=NO_MAX, std::string name=std::string())

template<class UnaryFunction >
GenericBoundingBox3DSingletonScore < UnaryFunction > *	create_bounding_box_3d_singleton_score (UnaryFunction *f, const algebra::BoundingBoxD< 3 > &bb)

template<class UnaryFunction >
GenericBoundingSphere3DSingletonScore < UnaryFunction > *	create_bounding_sphere_3d_singleton_score (UnaryFunction *f, const algebra::Sphere3D &sphere)

Provenance	create_clone (Provenance p)
	Clone provenance (including previous provenance) More...

template<class UnaryFunction >
GenericDistanceToSingletonScore < UnaryFunction > *	create_distance_to_singleton_score (UnaryFunction *f, const algebra::Vector3D &pt)

template<class UF >
GenericAttributeSingletonScore < UF > *	create_generic_attribute_singleton_score (UF *uf, FloatKey k)

SurfaceGeometry *	create_geometry (const Surface s, std::string name=std::string("SurfaceGeometry%1%"))
	Create a geometry from a Surface. More...

template<class Predicate , class Score >
PredicateSingletonScore < Predicate, Score > *	create_predicates_singleton_score (Predicate pred, int val, Score score)

ParticlesTemp	create_rigid_bodies (Model *m, unsigned int n, bool no_members=false)

XYZRs	create_xyzr_particles (Model *m, unsigned int num, Float radius, Float box_side=10)
	Create a set of particles with random coordinates. More...

template<class HD , class F >
HD	find_breadth_first (HD h, F f)
	Find the first node which matches some criteria. More...

template<class H , class Out , class F >
Out	gather (H h, F f, Out out)
	Gather all the particles in the hierarchy that meet some criteria. More...

template<class H , class Out , class K , class V >
Out	gather_by_attribute (H h, K k, V v, Out out)
	Gather all the particles in the hierarchy which match on an attribute. More...

template<class H , class Out , class K0 , class V0 , class K1 , class V1 >
Out	gather_by_attributes (H h, K0 k0, V0 v0, K1 k1, V1 v1, Out out)
	Gather all the particles in the hierarchy which match on two attributes. More...

template<class H , class Out , class F >
Out	gather_slice (H h, F f, Out out)
	Gather all the uppermost particles in the hierarchy that meet some criteria. More...

GenericHierarchies	get_all_descendants (Hierarchy mhd)
	Get all the particles in the subtree. More...

def	get_all_provenance
	Yield all provenance decorators of the given types for the particle. More...

double	get_angle (Direction a, Direction b)
	Get angle between directions. More...

algebra::BoundingBoxD< 3 >	get_bounding_box (const XYZRs &ps)
	Get the bounding box. More...

algebra::Vector3D	get_centroid (const XYZs &ps)
	Get the centroid. More...

SurfaceGeometry *	get_constrained_surface_geometry (const Surface s, std::string name="SurfaceGeometry%1%")
	Get surface geometry constrained to the surface. More...

double	get_depth (const Surface &s, const XYZR &d)
	Get depth of sphere below surface. More...

double	get_depth (const Surface &s, const XYZ &d)
	Get depth of point below surface. More...

double	get_dihedral (XYZ a, XYZ b, XYZ c, XYZ d)
	Compute the dihedral angle (in radians) between the four particles. More...

double	get_distance (XYZR a, XYZR b)
	Compute the sphere distance between a and b. More...

double	get_distance (const Surface &s, const XYZR &d)
	Get distance from sphere to surface. More...

double	get_distance (const Surface &s, const XYZ &d)
	Get distance from point to surface. More...

double	get_distance (XYZ a, XYZ b)
	Compute the distance between a pair of particles. More...

algebra::Sphere3D	get_enclosing_sphere (const XYZs &v)
	Get a sphere enclosing the set of XYZRs. More...

double	get_height (const Surface &s, const XYZR &d)
	Get height of sphere above surface. More...

double	get_height (const Surface &s, const XYZ &d)
	Get height of point above surface. More...

algebra::ReferenceFrame3D	get_initial_reference_frame (Model *m, const ParticleIndexes &pis)

algebra::ReferenceFrame3D	get_initial_reference_frame (const ParticlesTemp &ps)

GenericHierarchies	get_internal (Hierarchy mhd)
	Get all the non-leaves of the bit of hierarchy. More...

GenericHierarchies	get_leaves (Hierarchy mhd)
	Get all the leaves of the bit of hierarchy. More...

Hierarchy	get_root (Hierarchy h)
	Return the root of the hierarchy. More...

ParticleIndex	get_root_rigid_body (RigidMember m)
	Return the index of the outer-most rigid body containing the member. More...

const algebra::Vector3D &	get_vector_geometry (XYZ d)

void	set_enclosing_radius (XYZR b, const XYZs &v)
	Set the radius of the first to enclose the list. More...

void	set_enclosing_sphere (XYZR b, const XYZs &v, double slack=0)
	Set the coordinates and radius of the first to enclose the list. More...

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

template<class ND >
std::ostream &	show (Hierarchy h, std::ostream &out=std::cout)
	Print the hierarchy using a given decorator to display each node. More...

void	show_rigid_body_hierarchy (RigidBody rb, TextOutput out=TextOutput(std::cout))

void	transform (XYZ a, const algebra::Transformation3D &tr)
	Apply a transformation to the particle. More...

void	transform (RigidBody a, const algebra::Transformation3D &tr)
	Transform a rigid body. More...

template<class HD , class F >
F	visit_breadth_first (HD d, F f)
	Apply the visitor to each particle, breadth first. More...

template<class HD , class F >
F	visit_breadth_first_with_data (HD d, F f, typename F::result_type data)
	Apply functor F to each particle, traversing the hierarchy breadth first. More...

template<class HD , class F >
F	visit_depth_first (HD d, F &f)
	Apply functor F to each particle, traversing the hierarchy depth first. More...

template<class HD , class F >
F	visit_depth_first_with_data (HD d, F f, typename F::result_type data)
	Apply functor F to each particle, traversing the hierarchy depth first. 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 ()
	Return the version of this module, as a string. More...

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...

Python Only
The following functions are only available in Python as the equivalent C++ functionality is provided via template functions or in other ways that don't directly map to Python.
algebra::Transformation3D	get_transformation_aligning_first_to_second (XYZsOrVector3ds a, XYZsOrVector3ds b)

Typedef Documentation

typedef GenericAttributeSingletonScore<UnaryFunction> IMP::core::AttributeSingletonScore

For Python users. C++ users should use create_attribute_singleton_score().

Definition at line 65 of file GenericAttributeSingletonScore.h.

typedef IMP::Vector< BinormalTerm > IMP::core::BinormalTermList

Pass or store a set of BinormalTerm .

Definition at line 85 of file MultipleBinormalRestraint.h.

typedef GenericBoundingBox3DSingletonScore< UnaryFunction > IMP::core::BoundingBox3DSingletonScore

Score particles based on how far outside a box they are by applying f to the distance.

See Also: GenericBoundingBox3DSingletonScore Example usage is provided in GenericBoundingBox3DSingletonScore

Definition at line 151 of file BoundingBox3DSingletonScore.h.

typedef GenericBoundingSphere3DSingletonScore< UnaryFunction > IMP::core::BoundingSphere3DSingletonScore

Score particles based on how far outside a sphere they are by applying f to the distance.

See Also: GenericBoundingSphere3DSingletonScore

Definition at line 99 of file BoundingSphere3DSingletonScore.h.

typedef IMP::Vector<IMP::Pointer< DistancePairScore > > IMP::core::DistancePairScores

A vector of reference-counting object pointers.

Definition at line 32 of file core/DistancePairScore.h.

typedef IMP::Vector<IMP::WeakPointer< DistancePairScore > > IMP::core::DistancePairScoresTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: DistancePairScore

Definition at line 32 of file core/DistancePairScore.h.

typedef GenericDistanceToSingletonScore< UnaryFunction > IMP::core::DistanceToSingletonScore

Use an IMP::UnaryFunction to score a distance to a point.

Definition at line 92 of file DistanceToSingletonScore.h.

typedef IMP::Vector<IMP::Pointer< HarmonicDistancePairScore > > IMP::core::HarmonicDistancePairScores

A vector of reference-counting object pointers.

Definition at line 55 of file core/DistancePairScore.h.

typedef IMP::Vector<IMP::WeakPointer< HarmonicDistancePairScore > > IMP::core::HarmonicDistancePairScoresTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: HarmonicDistancePairScore

Definition at line 55 of file core/DistancePairScore.h.

typedef IMP::Vector<IMP::Pointer< HarmonicUpperBoundSphereDiameterPairScore > > IMP::core::HarmonicUpperBoundSphereDiameterPairScores

A vector of reference-counting object pointers.

Definition at line 86 of file SphereDistancePairScore.h.

typedef IMP::Vector<IMP::WeakPointer< HarmonicUpperBoundSphereDiameterPairScore > > IMP::core::HarmonicUpperBoundSphereDiameterPairScoresTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: HarmonicUpperBoundSphereDiameterPairScore

Definition at line 86 of file SphereDistancePairScore.h.

typedef IMP::Vector<IMP::Pointer< HarmonicWell > > IMP::core::HarmonicWells

A vector of reference-counting object pointers.

Definition at line 67 of file HarmonicWell.h.

typedef IMP::Vector<IMP::WeakPointer< HarmonicWell > > IMP::core::HarmonicWellsTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: HarmonicWell

Definition at line 67 of file HarmonicWell.h.

typedef IMP::Vector< HierarchyCounter > IMP::core::HierarchyCounters

Pass or store a set of HierarchyCounter .

Definition at line 455 of file core/Hierarchy.h.

typedef IMP::Vector< HierarchyTraits > IMP::core::HierarchyTraitsList

Pass or store a set of HierarchyTraits .

Definition at line 71 of file core/Hierarchy.h.

typedef IMP::Vector< MonteCarloMoverResult > IMP::core::MonteCarloMoverResults

Pass or store a set of MonteCarloMoverResult .

Definition at line 31 of file MonteCarloMover.h.

typedef IMP::Vector<IMP::Pointer< MonteCarloMover > > IMP::core::MonteCarloMovers

A vector of reference-counting object pointers.

Definition at line 119 of file MonteCarloMover.h.

typedef IMP::Vector<IMP::WeakPointer< MonteCarloMover > > IMP::core::MonteCarloMoversTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: MonteCarloMover

Definition at line 119 of file MonteCarloMover.h.

typedef Key< 34897493 > IMP::core::ParticleType

An IMP::Key object for identifying types of particles by strings.

The ParticleType key is used to type particles within the Typed decorator

Definition at line 28 of file Typed.h.

typedef IMP::Vector< ParticleType > IMP::core::ParticleTypes

Pass or store a set of ParticleType .

Definition at line 29 of file Typed.h.

typedef IMP::Vector<IMP::Pointer< SurfaceGeometry > > IMP::core::SurfaceGeometries

A vector of reference-counting object pointers.

Definition at line 196 of file Surface.h.

typedef IMP::Vector<IMP::WeakPointer< SurfaceGeometry > > IMP::core::SurfaceGeometriesTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: SurfaceGeometry

Definition at line 196 of file Surface.h.

typedef IMP::Vector<IMP::Pointer< SurfaceGeometryConstraint > > IMP::core::SurfaceGeometryConstraints

A vector of reference-counting object pointers.

Definition at line 243 of file Surface.h.

typedef IMP::Vector<IMP::WeakPointer< SurfaceGeometryConstraint > > IMP::core::SurfaceGeometryConstraintsTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: SurfaceGeometryConstraint

Definition at line 243 of file Surface.h.

typedef TruncatedHarmonic<BOTH> IMP::core::TruncatedHarmonicBound

A specialization of TruncatedHarmonic that returns non-zero value for any input values other than center value

Definition at line 104 of file TruncatedHarmonic.h.

typedef TruncatedHarmonic<LOWER> IMP::core::TruncatedHarmonicLowerBound

A specialization of TruncatedHarmonic that returns a non-zero value only for input values that are lower than the center value

Definition at line 100 of file TruncatedHarmonic.h.

typedef TruncatedHarmonic<UPPER> IMP::core::TruncatedHarmonicUpperBound

A specialization of TruncatedHarmonic that returns a non-zero value only for input values that are greater than the center value

Definition at line 96 of file TruncatedHarmonic.h.

Function Documentation

def IMP.core.add_imp_provenance ( p )

Tag the given particle as being created by the current version of IMP.

Note: This function is only available in Python.

Definition at line 15833 of file core/__init__.py.

void IMP::core::add_provenance	(	Model *	m,
		ParticleIndex	pi,
		Provenance	p
	)

Add provenance to part of the model.

void IMP::core::add_rigid_body_cache_key ( ObjectKey k )

It is often useful to store precalculated properties of the rigid body for later use. These need to be cleared out when the rigid body changes. To make sure this happens, register the key here.

def IMP.core.add_script_provenance ( p )

Tag the given particle with the current Python script.

This is a noop if the particle is already so tagged.

Note: This function is only available in Python.

Definition at line 15803 of file core/__init__.py.

def IMP.core.add_software_provenance	(	p,
		name,
		version,
		location
	)

Tag the given particle with the software used to create it.

This is a noop if the particle is already so tagged.

Note: This function is only available in Python.

Definition at line 15820 of file core/__init__.py.

void IMP::core::assign_blame	(	const RestraintsTemp &	rs,
		const ParticlesTemp &	ps,
		FloatKey	attribute
	)

Assign blame to the passed particles by dividing up the scores of the passed restraints over the particles they act on. The restraints will be decomposed first in order to make sure that the assignment is as fine grained as possible.

The main cost is evaluating the restraints.

display::Geometries IMP::core::create_blame_geometries	(	const RestraintsTemp &	rs,
		const ParticlesTemp &	ps,
		double	max = `NO_MAX`,
		std::string	name = `std::string()`
	)

Create a set of geometry objects colored by the blame as described in the docs of the assign_blame() function.

All particles must be XYZR particles.

If max is NO_MAX, then the max is found automatically.

Provenance IMP::core::create_clone ( Provenance p )

Clone provenance (including previous provenance)

template<class UF >

GenericAttributeSingletonScore<UF>* IMP::core::create_generic_attribute_singleton_score	(	UF *	uf,
		FloatKey	k
	)

Provide a compile time binding version of AttributeSingletonScore, which runs faster than the runtime bound version. UF should be a subclass of UnaryFunction (and not pointer to a generic UnaryFunction).

Definition at line 71 of file GenericAttributeSingletonScore.h.

SurfaceGeometry* IMP::core::create_geometry	(	const Surface	s,
		std::string	name = `std::string("SurfaceGeometry%1%")`
	)

Create a geometry from a Surface.

Definition at line 191 of file Surface.h.

template<class Predicate , class Score >

PredicateSingletonScore<Predicate, Score>* IMP::core::create_predicates_singleton_score	(	Predicate *	pred,
		int	val,
		Score *	score
	)

Other overloads can be created as needed.

Definition at line 152 of file predicates.h.

ParticlesTemp IMP::core::create_rigid_bodies	(	Model *	m,
		unsigned int	n,
		bool	no_members = `false`
	)

Create a set of rigid bodies that are bound together for efficiency. These rigid bodies cannot nest or have other dependencies among them.

All rigid bodies have the default reference frame.

Note: Do not use this with DOMINO as all the rigid bodies use the same ScoreState and so will be considered inter-dependent.

XYZRs IMP::core::create_xyzr_particles	(	Model *	m,
		unsigned int	num,
		Float	radius,
		Float	box_side = `10`
	)

Create a set of particles with random coordinates.

This function is mostly to be used to keep demo code brief.

Parameters

[in]	m	The model to add them to.
[in]	num	The number of particles to create.
[in]	radius	The radius to give them.
[in]	box_side	The particles have coordinates from -box_side to box_side.

See Also: XYZR

The particles coordinates are optimized.

GenericHierarchies IMP::core::get_all_descendants ( Hierarchy mhd )

Get all the particles in the subtree.

See Also: Hierarchy

def IMP.core.get_all_provenance	(	p,
		types = `[StructureProvenance`,
		SampleProvenance,
		CombineProvenance,
		FilterProvenance,
		ClusterProvenance,
		ScriptProvenance,
		SoftwareProvenance
	)

Yield all provenance decorators of the given types for the particle.

By default, all provenance types are returned. Provenance is returned in order, most recent first. If the particle has no provenance information, an empty generator is returned.

Note: This function is only available in Python.

Definition at line 15787 of file core/__init__.py.

double IMP::core::get_angle	(	Direction	a,
		Direction	b
	)

Get angle between directions.

algebra::BoundingBoxD<3> IMP::core::get_bounding_box ( const XYZRs & ps )

Get the bounding box.

Compute the bounding box of a set of particles

algebra::Vector3D IMP::core::get_centroid ( const XYZs & ps )

Get the centroid.

Compute the centroid (mean) of a set of particles.

SurfaceGeometry* IMP::core::get_constrained_surface_geometry	(	const Surface	s,
		std::string	name = `"SurfaceGeometry%1%"`
	)

Get surface geometry constrained to the surface.

Definition at line 236 of file Surface.h.

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std::string IMP::core::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::core::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.

double IMP::core::get_depth	(	const Surface &	s,
		const XYZR &	d
	)

Get depth of sphere below surface.

Note: If sphere crosses or is above surface, depth is negative the distance from the surface to the furthest point of the sphere.

Definition at line 143 of file Surface.h.

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double IMP::core::get_depth	(	const Surface &	s,
		const XYZ &	d
	)

Get depth of point below surface.

Definition at line 148 of file Surface.h.

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double IMP::core::get_dihedral	(	XYZ	a,
		XYZ	b,
		XYZ	c,
		XYZ	d
	)

Compute the dihedral angle (in radians) between the four particles.

See Also: XYZ

double IMP::core::get_distance	(	XYZR	a,
		XYZR	b
	)

Compute the sphere distance between a and b.

See Also: XYZR

Definition at line 89 of file XYZR.h.

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double IMP::core::get_distance	(	const Surface &	s,
		const XYZR &	d
	)

Get distance from sphere to surface.

Definition at line 153 of file Surface.h.

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double IMP::core::get_distance	(	const Surface &	s,
		const XYZ &	d
	)

Get distance from point to surface.

Definition at line 158 of file Surface.h.

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double IMP::core::get_distance	(	XYZ	a,
		XYZ	b
	)

Compute the distance between a pair of particles.

compute the distance between the x,y,z coordinates of a and b

See Also: XYZ

Definition at line 192 of file XYZ.h.

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algebra::Sphere3D IMP::core::get_enclosing_sphere ( const XYZs & v )

Get a sphere enclosing the set of XYZRs.

Parameters

[in] v The one whose radius should be set Any particle which does not have the attribute b.get_radius() is assumed to have a radius of 0.

See Also: XYZR

std::string IMP::core::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::core::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.

double IMP::core::get_height	(	const Surface &	s,
		const XYZR &	d
	)

Get height of sphere above surface.

Note: If sphere crosses or is below surface, height is negative the distance from the surface to the furthest point of the sphere.

Definition at line 129 of file Surface.h.

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double IMP::core::get_height	(	const Surface &	s,
		const XYZ &	d
	)

Get height of point above surface.

Definition at line 134 of file Surface.h.

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algebra::ReferenceFrame3D IMP::core::get_initial_reference_frame	(	Model *	m,
		const ParticleIndexes &	pis
	)

Compute the rigid body reference frame given a set of input particles.

GenericHierarchies IMP::core::get_internal ( Hierarchy mhd )

Get all the non-leaves of the bit of hierarchy.

See Also: Hierarchy

GenericHierarchies IMP::core::get_leaves ( Hierarchy mhd )

Get all the leaves of the bit of hierarchy.

The leaves are returned in the obvious order (first child before second child).

See Also: Hierarchy

std::string IMP::core::get_module_version ( )

Return the version of this module, as a string.

Note: This function is only available in Python.

Definition at line 5 of file EMageFit/__init__.py.

Hierarchy IMP::core::get_root ( Hierarchy h )

Return the root of the hierarchy.

See Also: Hierarchy

Definition at line 562 of file core/Hierarchy.h.

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ParticleIndex IMP::core::get_root_rigid_body ( RigidMember m )

Return the index of the outer-most rigid body containing the member.

Use this to, for example, group particles into rigid bodies.

algebra::Transformation3D IMP::core::get_transformation_aligning_first_to_second	(	XYZsOrVector3ds	a,
		XYZsOrVector3ds	b
	)

Align any combination of XYZ objects and algebra::Vector3D objects to one another.

Note: each of the two lists must all have the same type. That is, list "a" cannot be a mix of algebra::Vector3D objects and XYZ objects.
IMP::algebra::get_transformation_aligning_first_to_second(a,b);

const algebra::Vector3D& IMP::core::get_vector_geometry ( XYZ d )

See generic geometry for more information.

Definition at line 135 of file XYZ.h.

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void IMP::core::set_enclosing_radius	(	XYZR	b,
		const XYZs &	v
	)

Set the radius of the first to enclose the list.

Parameters

[in]	v	The vector of XYZ or XYZR particles to enclose
[out]	b	The one whose radius should be set Any particle which does not have the attribute b.get_radius() is assumed to have a radius of 0.

See Also: XYZR

void IMP::core::set_enclosing_sphere	(	XYZR	b,
		const XYZs &	v,
		double	slack = `0`
	)

Set the coordinates and radius of the first to enclose the list.

Parameters

[in]	v	The vector of XYZ or XYZR particles to enclose
[out]	b	The one whose values should be set
[in]	slack	An amount to add to the radius. Any particle which does not have the attribute b.get_radius() is assumed to have a radius of 0.

Note: This function produces tighter bounds if the CGAL library is available.

See Also: XYZR

void IMP::core::set_vector_geometry	(	XYZ	d,
		const algebra::Vector3D &	v
	)

See generic geometry for more information.

Definition at line 131 of file XYZ.h.

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void IMP::core::show_rigid_body_hierarchy	(	RigidBody	rb,
		TextOutput	out = `TextOutput(std::cout)`
	)

Show the rigid body hierarchy rooted at passed body.

void IMP::core::transform	(	XYZ	a,
		const algebra::Transformation3D &	tr
	)

Apply a transformation to the particle.

See Also: XYZ; algebra::Transformation3D

void IMP::core::transform	(	RigidBody	a,
		const algebra::Transformation3D &	tr
	)

Transform a rigid body.

The transformation is applied current conformation of the rigid body, as opposed to replacing the current conformation, as in RigidBody::set_reference_frame().

See Also: RigidBody; algebra::Transformation3D

Definition at line 882 of file rigid_bodies.h.

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Detailed Description

Info

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Typedef Documentation

Function Documentation