IMP  2.1.0
The Integrative Modeling Platform
Public Member Functions | List of all members
IMP::core::SphereDistanceToSingletonScore Class Reference

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

#include <IMP/core/DistanceToSingletonScore.h>

+ Inheritance diagram for IMP::core::SphereDistanceToSingletonScore:

Public Member Functions

 SphereDistanceToSingletonScore (UnaryFunction *f, const algebra::Vector3D &pt)
 
virtual kernel::ModelObjectsTemp do_get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const
 
double evaluate_if_good_indexes (kernel::Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual double evaluate_index (kernel::Model *m, kernel::ParticleIndex p, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed.
 
double evaluate_indexes (kernel::Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual std::string get_type_name () const
 
virtual ::IMP::base::VersionInfo get_version_info () const
 Get information about the module and version of the object.
 
- Public Member Functions inherited from IMP::kernel::SingletonScore
 SingletonScore (std::string name="SingletonScore %1%")
 
Restraints create_current_decomposition (kernel::Model *m, ParticleIndex vt) const
 
virtual double evaluate (Particle *vt, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed. More...
 
virtual double evaluate_if_good_index (kernel::Model *m, ParticleIndex vt, DerivativeAccumulator *da, double max) const
 Compute the score and the derivative if needed.
 
- Public Member Functions inherited from IMP::kernel::ParticleInputs
virtual ContainersTemp get_input_containers (Particle *p) const
 
virtual ParticlesTemp get_input_particles (Particle *p) const
 
ModelObjectsTemp get_inputs (kernel::Model *m, const ParticleIndexes &pis) const
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
virtual void do_destroy ()
 
CheckLevel get_check_level () const
 
LogLevel get_log_level () const
 
void set_check_level (CheckLevel l)
 
void set_log_level (LogLevel l)
 Set the logging level used in this object. More...
 
void set_was_used (bool tf) const
 
void show (std::ostream &out=std::cout) const
 
const std::string & get_name () const
 
void set_name (std::string name)
 

Additional Inherited Members

- Public Types inherited from IMP::kernel::SingletonScore
typedef Particle * Argument
 
typedef ParticleIndex IndexArgument
 
typedef SingletonModifier Modifier
 
typedef Particle * PassArgument
 
typedef ParticleIndex PassIndexArgument
 
- Protected Member Functions inherited from IMP::kernel::SingletonScore
virtual Restraints do_create_current_decomposition (kernel::Model *m, ParticleIndex vt) const
 
- Protected Member Functions inherited from IMP::base::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
 Object ()
 

Detailed Description

A particle is scored based on the distance between it and a constant point as passed to a UnaryFunction. This is useful for anchoring constraining particles within a sphere.

To restrain a set of particles store in SingletonContainer pc in a sphere do the following:

1 ## \example core/restrain_in_sphere.py
2 # This fragment shows how to restrain a set of points stored in a
3 # SingletonContainer in a sphere of radius 'radius' centered around
4 # 'center'.
5 
6 import IMP
7 import IMP.core
8 radius = 10
9 stiffness = 2
10 center = IMP.algebra.Vector3D(1, 2, 3)
11 m = IMP.kernel.Model()
12 p = m.add_particle("particle")
13 IMP.core.XYZR.setup_particle(
14  m, p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(100, 0, 0), 1))
15 
16 ub = IMP.core.HarmonicUpperBound(radius, stiffness)
17 
18 # Restrain based on the distance to a single point (hence a ball
19 ss = IMP.core.DistanceToSingletonScore(ub, center)
20 
21 r = IMP.core.SingletonRestraint(ss, m.get_particle(p))
22 r.evaluate(False)

Definition at line 93 of file DistanceToSingletonScore.h.

Member Function Documentation

virtual kernel::ModelObjectsTemp IMP::core::SphereDistanceToSingletonScore::do_get_inputs ( kernel::Model *  m,
const kernel::ParticleIndexes &  pis 
) const
virtual

Overload this method to specify the inputs.

Reimplemented from IMP::kernel::ParticleInputs.

Definition at line 110 of file DistanceToSingletonScore.h.

+ Here is the call graph for this function:

double IMP::core::SphereDistanceToSingletonScore::evaluate_if_good_indexes ( kernel::Model *  m,
const ParticleIndexes &  o,
DerivativeAccumulator *  da,
double  max,
unsigned int  lower_bound,
unsigned int  upper_bound 
) const
virtual

Implementations for these are provided by the IMP_SINGLETON_SCORE() macro.

Reimplemented from IMP::kernel::SingletonScore.

Definition at line 114 of file DistanceToSingletonScore.h.

double IMP::core::SphereDistanceToSingletonScore::evaluate_indexes ( kernel::Model *  m,
const ParticleIndexes &  o,
DerivativeAccumulator *  da,
unsigned int  lower_bound,
unsigned int  upper_bound 
) const
virtual

Implementations for these are provided by the IMP_SINGLETON_SCORE() macro.

Reimplemented from IMP::kernel::SingletonScore.

Definition at line 114 of file DistanceToSingletonScore.h.

The documentation for this class was generated from the following file: