See IMP.core for more information.

Classes
class	AllSamePairPredicate

class	AllSameQuadPredicate

class	AllSameSingletonPredicate

class	AllSameTripletPredicate

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

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

class	AttributeSingletonPredicate

class	BallMover
	Modify a set of continuous variables by perturbing them within a ball. More...

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

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

class	CentroidOfRefined
	Set the coordinates of the particle to be the centoid of the particles. More...

class	ChecksScoreState

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

class	CoinFlipPairPredicate

class	CoinFlipQuadPredicate

class	CoinFlipSingletonPredicate

class	CoinFlipTripletPredicate

class	ConjugateGradients
	Simple conjugate gradients optimizer. More...

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

class	ConstantPairPredicate

class	ConstantQuadPredicate

class	ConstantRestraint
	Return a constant value. More...

class	ConstantSingletonPredicate

class	ConstantTripletPredicate

class	Cosine
	Cosine function. More...

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

class	CoverRefined
	This class sets the position and radius of each particle to enclose the refined. More...

class	DataObject

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

class	DerivativesToRefined
	Copy the derivatives from the 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	DistancePairScore

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::kernel::PairContainer. More...

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

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

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

class	GenericBoundingBox3DSingletonScore
	Score particles based on how far outside a box 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

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	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 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

class	IncrementalScoringFunction

class	IsCollisionPairPredicate

class	KClosePairsPairScore

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

class	Linear
	Linear function 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 which applies a singleton modifier to each kernel::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

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	Mover

class	MoverBase

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	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

class	OrderedTypeQuadPredicate

class	OrderedTypeSingletonPredicate

class	OrderedTypeTripletPredicate

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

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

class	PredicateSingletonScore

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 a decorator for a particle with an associated reference particle. More...

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

class	RestraintsScoringFunction

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

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

class	RigidBodyTorque

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

class	RigidMember
	A decorator for a particle that is part of a rigid body. More...

class	SerialMover
	Apply 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	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	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	TransformedDistancePairScore
	Apply a function to the distance between two particles after transforming the first. 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 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

class	UnorderedTypeQuadPredicate

class	UnorderedTypeSingletonPredicate

class	UnorderedTypeTripletPredicate

class	VolumeRestraint
	kernel::Restraint the volume of a set of spheres More...

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

class	WriteRestraintScoresOptimizerState

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 GenericBoundingBox3DSingletonScore < UnaryFunction >	BoundingBox3DSingletonScore

typedef IMP::base::Vector < Centroid >	Centroids

typedef IMP::base::Vector< Cover >	Covers

typedef GenericDistanceToSingletonScore < UnaryFunction >	DistanceToSingletonScore

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

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

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

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

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

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

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

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

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

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

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

typedef IMP::base::Vector < IMP::base::Pointer < MoverBase > >	MoverBases

typedef IMP::base::Vector < IMP::base::WeakPointer < MoverBase > >	MoverBasesTemp

typedef MonteCarloMovers	Movers

typedef MonteCarloMoversTemp	MoversTemp

typedef Key< 34897493, true >	ParticleType

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

typedef kernel::OptimizerState	PeriodicOptimizerState

typedef IMP::base::Vector < Reference >	References

typedef IMP::base::Vector < RigidBody >	RigidBodies

typedef IMP::base::Vector < RigidMember >	RigidMembers

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

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

typedef TruncatedHarmonic< BOTH >	TruncatedHarmonicBound
	A specialization.

typedef TruncatedHarmonic< LOWER >	TruncatedHarmonicLowerBound
	A specialization for the lower bound.

typedef TruncatedHarmonic< UPPER >	TruncatedHarmonicUpperBound
	A specialization for the upper bound.

typedef IMP::base::Vector< Typed >	Typeds

typedef IMP::base::Vector< XYZR >	XYZRs

typedef IMP::base::Vector< XYZ >	XYZs

Enumerations
enum	BoundDirection { LOWER, BOTH, UPPER }

Functions
void	add_rigid_body_cache_key (ObjectKey k)

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

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

display::Geometries	create_blame_geometries (const kernel::RestraintsTemp &rs, const kernel::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 >
GenericDistanceToSingletonScore < UnaryFunction > *	create_distance_to_singleton_score (UnaryFunction *f, const algebra::Vector3D &pt)

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

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

XYZRs	create_xyzr_particles (kernel::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 which 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 particles in the hierarchy which meet some criteria. More...

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

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

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

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

algebra::ReferenceFrame3D	get_initial_reference_frame (const kernel::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...

const algebra::Sphere3D	get_sphere_d_geometry (XYZR d)

const algebra::Vector3D	get_vector_d_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_sphere_d_geometry (XYZR d, const algebra::Sphere3D &v)

void	set_vector_d_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 as to display each node. More...

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 i)
	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 i)
	Apply functor F to each particle, traversing the hierarchy depth first. More...

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

std::string	get_module_name ()

Python Only
The following functions are only availale 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 63 of file AttributeSingletonScore.h.

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

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

Definition at line 82 of file DistanceToSingletonScore.h.

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

Store a set of objects.

Definition at line 82 of file SphereDistancePairScore.h.

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

Pass a \ set of \ objects. \ See \ HarmonicUpperBoundSphereDiameterPairScore

Definition at line 82 of file SphereDistancePairScore.h.

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

Store a set of objects.

Definition at line 64 of file HarmonicWell.h.

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

Pass a \ set of \ objects. \ See \ HarmonicWell

Definition at line 64 of file HarmonicWell.h.

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

Pass or store a set of HierarchyCounter .

Definition at line 418 of file core/Hierarchy.h.

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

Pass or store a set of HierarchyTraits .

Definition at line 64 of file core/Hierarchy.h.

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

Pass or store a set of MonteCarloMoverResult .

Definition at line 29 of file MonteCarloMover.h.

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

Store a set of objects.

Definition at line 108 of file MonteCarloMover.h.

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

Pass a \ set of \ objects. \ See \ MonteCarloMover

Definition at line 108 of file MonteCarloMover.h.

typedef IMP::base::Vector<IMP::base::Pointer< MoverBase > > IMP::core::MoverBases

Store a set of objects.

Definition at line 68 of file MoverBase.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< MoverBase > > IMP::core::MoverBasesTemp

Pass a \ set of \ objects. \ See \ MoverBase

Definition at line 68 of file MoverBase.h.

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

A kernel::ParticleType is an IMP::kernel::Key object for identifying types of particles by strings. The kernel::ParticleType key is used to type particles within the Typed decorator

Definition at line 31 of file Typed.h.

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

Pass or store a set of ParticleType .

Definition at line 32 of file Typed.h.

Function Documentation

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.

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

Assign blame to the passed particles by dividing up the scores of the passed restraints over the particles they add 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.

template<class UF >

GenericAttributeSingletonScore<UF>* IMP::core::create_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 69 of file AttributeSingletonScore.h.

display::Geometries IMP::core::create_blame_geometries	(	const kernel::RestraintsTemp &	rs,
		const kernel::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.

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 151 of file predicates.h.

kernel::ParticlesTemp IMP::core::create_rigid_bodies	(	kernel::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 amongst 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	(	kernel::Model *	m,
		unsigned int	num,
		Float	radius,
		Float	box_side = `10`
	)

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 XYZR

The particles coordinates are optimized.

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

See Hierarchy

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

Compute the boudning box of a set of particles

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

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

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

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

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

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

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

See XYZ

Definition at line 143 of file XYZ.h.

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

Compute the spere distance between a and b See XYZR

Definition at line 88 of file XYZR.h.

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

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

See XYZ

Definition at line 135 of file XYZ.h.

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

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 XYZR

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

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

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

model));

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

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

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

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

See Hierarchy

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

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

See Hierarchy

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

See Hierarchy

Definition at line 515 of file core/Hierarchy.h.

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const algebra::Sphere3D IMP::core::get_sphere_d_geometry ( XYZR d )

See generic geometry for more information.

Definition at line 141 of file XYZR.h.

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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_d_geometry ( XYZ d )

See generic geometry for more information.

Definition at line 154 of file XYZ.h.

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

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 XYZR

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

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 XYZR

void IMP::core::set_sphere_d_geometry	(	XYZR	d,
		const algebra::Sphere3D &	v
	)

See generic geometry for more information.

Definition at line 146 of file XYZR.h.

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

See generic geometry for more information.

Definition at line 158 of file XYZ.h.

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

See XYZ See algebra::Transformation3D

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

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

See RigidBody algebra::Transformation3D

Definition at line 413 of file rigid_bodies.h.

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