IMP Reference Guide  develop.1a04b19ae7,2021/11/27 The Integrative Modeling Platform
IMP::spb::TiltSingletonScore Class Reference

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

#include <IMP/spb/TiltSingletonScore.h>

Inheritance diagram for IMP::spb::TiltSingletonScore:

## Detailed Description

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: ## \example core/restrain_in_sphere.py # This fragment shows how to restrain a set of points stored in a # SingletonContainer in a sphere of radius 'radius' centered around # 'center'. import IMP import IMP.core import sys IMP.setup_from_argv(sys.argv, "restrain in sphere") radius = 10 stiffness = 2 center = IMP.algebra.Vector3D(1, 2, 3) m = IMP.Model() p = m.add_particle("particle") IMP.core.XYZR.setup_particle( m, p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(100, 0, 0), 1)) ub = IMP.core.HarmonicUpperBound(radius, stiffness) # Restrain based on the distance to a single point (hence a ball ss = IMP.core.DistanceToSingletonScore(ub, center) r = IMP.core.SingletonRestraint(m, ss, p) r.evaluate(False)

Definition at line 29 of file TiltSingletonScore.h.

## Public Member Functions

TiltSingletonScore (UnaryFunction *f, const algebra::VectorD< 3 > &v1, const algebra::VectorD< 3 > &v2)

virtual IMP::ModelObjectsTemp do_get_inputs (IMP::Model *m, const IMP::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 (IMP::Model *m, const IMP::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...

double evaluate_indexes_delta (Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set. More...

double evaluate_indexes_scores (Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) 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...

void show (std::ostream &out=std::cout) const

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

 virtual IMP::ModelObjectsTemp IMP::spb::TiltSingletonScore::do_get_inputs ( IMP::Model * m, const IMP::ParticleIndexes & pis ) const
virtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

 double IMP::spb::TiltSingletonScore::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 44 of file TiltSingletonScore.h.

 virtual double IMP::spb::TiltSingletonScore::evaluate_index ( IMP::Model * m, const IMP::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.

 double IMP::spb::TiltSingletonScore::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 one past 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 44 of file TiltSingletonScore.h.

 double IMP::spb::TiltSingletonScore::evaluate_indexes_delta ( Model * m, const ParticleIndexes & o, DerivativeAccumulator * da, const std::vector< unsigned > & indexes, std::vector< double > & score ) const
virtual

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

The score for each o[indexes[x]] is updated in score[indexes[x]] and the total difference between the old and new score values (over the set) is returned.

Reimplemented from IMP::SingletonScore.

Definition at line 44 of file TiltSingletonScore.h.

 double IMP::spb::TiltSingletonScore::evaluate_indexes_scores ( Model * m, const ParticleIndexes & o, DerivativeAccumulator * da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > & score ) const
virtual

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

Like regular evaluate_indexes(), but the score for each o[x] is also returned as score[x].

Reimplemented from IMP::SingletonScore.

Definition at line 44 of file TiltSingletonScore.h.

 virtual ::IMP::VersionInfo IMP::spb::TiltSingletonScore::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 45 of file TiltSingletonScore.h.

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