IMP Reference Guide  2.7.0 The Integrative Modeling Platform
IMP::core::GenericDistanceToSingletonScore< UF > Class Template Reference

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

#include <IMP/core/DistanceToSingletonScore.h>

Inheritance diagram for IMP::core::GenericDistanceToSingletonScore< UF >:

## Detailed Description

### template<class UF> class IMP::core::GenericDistanceToSingletonScore< UF >

Apply a function to the distance to a fixed point.

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
4 # 'center'.
5
6 import IMP
7 import IMP.core
8 import sys
9
10 IMP.setup_from_argv(sys.argv, "restrain in sphere")
11
13 stiffness = 2
14 center = IMP.algebra.Vector3D(1, 2, 3)
15 m = IMP.Model()
18  m, p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(100, 0, 0), 1))
19
21
22 # Restrain based on the distance to a single point (hence a ball
23 ss = IMP.core.DistanceToSingletonScore(ub, center)
24
25 r = IMP.core.SingletonRestraint(m, ss, p)
26 r.evaluate(False)

Definition at line 34 of file DistanceToSingletonScore.h.

## Public Member Functions

GenericDistanceToSingletonScore (UF *f, const algebra::Vector3D &pt)

virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs. More...

double evaluate_if_good_indexes (Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const

virtual double evaluate_index (Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed. More...

double evaluate_indexes (Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set. More...

virtual std::string get_type_name () const

virtual ::IMP::VersionInfo get_version_info () const
Get information about the module and version of the object. More...

Public Member Functions inherited from IMP::SingletonScore
SingletonScore (std::string name="SingletonScore %1%")

Restraints create_current_decomposition (Model *m, ParticleIndex vt) const

virtual double evaluate_if_good_index (Model *m, ParticleIndex vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed, only if "good". More...

Public Member Functions inherited from IMP::ParticleInputs
ModelObjectsTemp get_inputs (Model *m, const ParticleIndexes &pis) const
Get the ModelObjects read when the given list of particles is used. More...

Public Member Functions inherited from IMP::Object
virtual void clear_caches ()

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)

Public Types inherited from IMP::SingletonScore
typedef ParticleArgument

typedef ParticleIndex IndexArgument

typedef SingletonModifier Modifier

typedef ParticlePassArgument

typedef ParticleIndex PassIndexArgument

Protected Member Functions inherited from IMP::SingletonScore
virtual Restraints do_create_current_decomposition (Model *m, ParticleIndex vt) const
Override this to return your own decomposition. More...

Protected Member Functions inherited from IMP::Object
Object (std::string name)
Construct an object with the given name. More...

virtual void do_destroy ()

## Member Function Documentation

template<class UF >
 virtual ModelObjectsTemp IMP::core::GenericDistanceToSingletonScore< UF >::do_get_inputs ( Model * m, const ParticleIndexes & pis ) const
virtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

Definition at line 51 of file DistanceToSingletonScore.h.

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template<class UF >
 double IMP::core::GenericDistanceToSingletonScore< UF >::evaluate_if_good_indexes ( Model * m, const ParticleIndexes & o, DerivativeAccumulator * da, double max, unsigned int lower_bound, unsigned int upper_bound ) const
virtual

Compute the score and the derivative if needed over a set, only if "good". This functions similarly to evaluate_indexes(), but may terminate the computation early if the total score is higher than max.

Returns
the score if score<= max or some arbitrary value > max otherwise.
Note
Implementations for these are provided by the IMP_SINGLETON_SCORE() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 55 of file DistanceToSingletonScore.h.

template<class UF >
 virtual double IMP::core::GenericDistanceToSingletonScore< UF >::evaluate_index ( Model * m, ParticleIndex vt, DerivativeAccumulator * da ) const
virtual

Compute the score and the derivative if needed.

Parameters
 m the model of vt vt the index in m of an object of type Particle da a DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed.

Implements IMP::SingletonScore.

template<class UF >
 double IMP::core::GenericDistanceToSingletonScore< UF >::evaluate_indexes ( Model * m, const ParticleIndexes & o, DerivativeAccumulator * da, unsigned int lower_bound, unsigned int upper_bound ) const
virtual

Compute the score and the derivative if needed over a set.

Parameters
 m the model of o o objects of type Particle, specified by index da a derivative accumulator that weights computed derivatives. If nullptr, derivatives will not be computed. lower_bound index of first item in o to evaluate upper_bound index of last item in o to evaluate
Note
Implementations for these are provided by the IMP_SINGLETON_SCORE() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 55 of file DistanceToSingletonScore.h.

template<class UF >
 virtual ::IMP::VersionInfo IMP::core::GenericDistanceToSingletonScore< UF >::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 56 of file DistanceToSingletonScore.h.

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