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IMP Reference Guide
2.11.0
The Integrative Modeling Platform
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Basic functionality that is expected to be used by a wide variety of IMP users. More...
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.
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:
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 |
| 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 |
| 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 |
| 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 |
| class | CoinFlipQuadPredicate |
| class | CoinFlipSingletonPredicate |
| class | CoinFlipTripletPredicate |
| 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 |
| 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 |
| Set the position and radius of a particle to enclose the refined. More... | |
| class | DataObject |
| 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 |
| 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 |
| Score particles based on how far outside a box they are. More... | |
| 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 |
| 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 |
| class | HarmonicSurfaceDistancePairScore |
| A harmonic score on the distance between a surface and a sphere. More... | |
| class | HarmonicSurfaceHeightPairScore |
| 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 | IncrementalScoringFunction |
| Score the model efficiently when a small number of particles are changed. 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 |
| 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 | 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 |
| 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 below a surface. More... | |
| class | SoftSuperSurfacePairScore |
| A harmonic score that keeps a sphere 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 below a surface. More... | |
| class | SurfaceDistancePairScore |
| A score on the distance between a surface and a sphere. 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 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 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 |
| 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... | |
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 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 functions | |
All | |
| std::string | get_module_version () |
| std::string | get_module_name () |
| std::string | get_data_path (std::string file_name) |
| Return the full path to one of this module's data files. More... | |
| std::string | get_example_path (std::string file_name) |
| Return the full path to one of this module's example files. More... | |
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) |
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 77 of file MultipleBinormalRestraint.h.
A vector of reference-counting object pointers.
Definition at line 23 of file core/DistancePairScore.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 23 of file core/DistancePairScore.h.
Use an IMP::UnaryFunction to score a distance to a point.
Definition at line 82 of file DistanceToSingletonScore.h.
| typedef IMP::Vector<IMP::Pointer< HarmonicDistancePairScore > > IMP::core::HarmonicDistancePairScores |
A vector of reference-counting object pointers.
Definition at line 36 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.
Definition at line 36 of file core/DistancePairScore.h.
| typedef IMP::Vector<IMP::Pointer< HarmonicUpperBoundSphereDiameterPairScore > > IMP::core::HarmonicUpperBoundSphereDiameterPairScores |
A vector of reference-counting object pointers.
Definition at line 82 of file SphereDistancePairScore.h.
| typedef IMP::Vector<IMP::WeakPointer< HarmonicUpperBoundSphereDiameterPairScore > > IMP::core::HarmonicUpperBoundSphereDiameterPairScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 82 of file SphereDistancePairScore.h.
| typedef IMP::Vector<IMP::Pointer< HarmonicWell > > IMP::core::HarmonicWells |
A vector of reference-counting object pointers.
Definition at line 64 of file HarmonicWell.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 64 of file HarmonicWell.h.
Pass or store a set of HierarchyCounter .
Definition at line 423 of file core/Hierarchy.h.
Pass or store a set of HierarchyTraits .
Definition at line 63 of file core/Hierarchy.h.
Pass or store a set of MonteCarloMoverResult .
Definition at line 29 of file MonteCarloMover.h.
A vector of reference-counting object pointers.
Definition at line 109 of file MonteCarloMover.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 109 of file MonteCarloMover.h.
| typedef Key< 34897493 > IMP::core::ParticleType |
| typedef IMP::Vector< ParticleType > IMP::core::ParticleTypes |
A vector of weak (non reference-counting) pointers to specified objects.
| typedef IMP::Vector<IMP::WeakPointer< SurfaceGeometryConstraint > > IMP::core::SurfaceGeometryConstraintsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
| typedef TruncatedHarmonic<BOTH> IMP::core::TruncatedHarmonicBound |
A specialization.
Definition at line 85 of file TruncatedHarmonic.h.
| typedef TruncatedHarmonic<LOWER> IMP::core::TruncatedHarmonicLowerBound |
A specialization for the lower bound.
Definition at line 83 of file TruncatedHarmonic.h.
| typedef TruncatedHarmonic<UPPER> IMP::core::TruncatedHarmonicUpperBound |
A specialization for the upper bound.
Definition at line 81 of file TruncatedHarmonic.h.
| def IMP.core.add_imp_provenance | ( | p | ) |
Tag the given particle as being created by the current version of IMP.
Definition at line 16149 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.
Definition at line 16119 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.
Definition at line 16136 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)
| 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%") |
||
| ) |
| 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.
| 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.
| [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. |
The particles coordinates are optimized.
| GenericHierarchies IMP::core::get_all_descendants | ( | Hierarchy | mhd | ) |
Get all the particles in the subtree.
| 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.
Definition at line 16103 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%" |
||
| ) |
| 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
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.
| double IMP::core::get_depth | ( | const Surface & | s, |
| const XYZR & | d | ||
| ) |
| double IMP::core::get_depth | ( | const Surface & | s, |
| const XYZ & | d | ||
| ) |
| double IMP::core::get_dihedral | ( | XYZ | a, |
| XYZ | b, | ||
| XYZ | c, | ||
| XYZ | d | ||
| ) |
Compute the dihedral angle (in radians) between the four particles.
| double IMP::core::get_distance | ( | XYZR | a, |
| XYZR | b | ||
| ) |
| double IMP::core::get_distance | ( | const Surface & | s, |
| const XYZR & | d | ||
| ) |
| double IMP::core::get_distance | ( | const Surface & | s, |
| const XYZ & | d | ||
| ) |
| double IMP::core::get_distance | ( | XYZ | a, |
| XYZ | b | ||
| ) |
| algebra::Sphere3D IMP::core::get_enclosing_sphere | ( | const XYZs & | v | ) |
Get a sphere enclosing the set of XYZRs.
| [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. |
| 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
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.
| double IMP::core::get_height | ( | const Surface & | s, |
| const XYZR & | d | ||
| ) |
| double IMP::core::get_height | ( | const Surface & | s, |
| const XYZ & | d | ||
| ) |
| 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.
| 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).
| Hierarchy IMP::core::get_root | ( | Hierarchy | h | ) |
Return the root of the hierarchy.
Definition at line 530 of file core/Hierarchy.h.
Here is the call graph for this function:| 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.
| const algebra::Vector3D IMP::core::get_vector_geometry | ( | XYZ | d | ) |
See generic geometry for more information.
Definition at line 135 of file XYZ.h.
Here is the call graph for this function:| void IMP::core::set_enclosing_radius | ( | XYZR | b, |
| const XYZs & | v | ||
| ) |
| 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.
| [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. |
| 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.
Here is the call graph for this function:| 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.
| 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().
Definition at line 830 of file rigid_bodies.h.
Here is the call graph for this function: