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IMP Reference Guide  develop.d247202c1c,2019/10/23
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...
 
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)
 

Additional Inherited Members

- 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
mthe model of vt
vtthe index in m of an object of type Particle
daa 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
mthe model of o
oobjects of type Particle, specified by index
daa derivative accumulator that weights computed derivatives. If nullptr, derivatives will not be computed.
lower_boundindex of first item in o to evaluate
upper_boundindex 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 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: