IMP  2.1.1
The Integrative Modeling Platform
IMP::core Namespace Reference

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< CoverCovers
 
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< TypedTypeds
 
typedef IMP::base::Vector< XYZRXYZRs
 
typedef IMP::base::Vector< XYZXYZs
 

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

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

Definition at line 82 of file DistanceToSingletonScore.h.

Store a set of objects.

Definition at line 64 of file HarmonicWell.h.

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

Definition at line 64 of file HarmonicWell.h.

Pass or store a set of HierarchyCounter .

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

Pass or store a set of HierarchyTraits .

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

Store a set of objects.

Definition at line 108 of file MonteCarloMover.h.

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

Definition at line 108 of file MonteCarloMover.h.

Store a set of objects.

Definition at line 68 of file MoverBase.h.

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.

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]mThe model to add them to.
[in]numThe number of particles to create.
[in]radiusThe radius to give them.
[in]box_sideThe 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]vThe 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

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.
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]vThe vector of XYZ or XYZR particles to enclose
[out]bThe 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]vThe vector of XYZ or XYZR particles to enclose
[out]bThe one whose values should be set
[in]slackAn 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 
)
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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