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IMP Reference Guide  develop.8b7eb21230,2024/06/24
The Integrative Modeling Platform
IMP::core::GenericBoundingBox3DSingletonScore< UF > Class Template Reference

#include <IMP/core/BoundingBox3DSingletonScore.h>

+ Inheritance diagram for IMP::core::GenericBoundingBox3DSingletonScore< UF >:

Detailed Description

template<class UF>
class IMP::core::GenericBoundingBox3DSingletonScore< UF >

A generic C++ template for scoring particles based on how far outside a box they are using unary function UF. The bounding box score is evaluated by applying a function f of class UF to a particle based on the distance of its center from the bounding box walls. The radius of the particle is ignored. If the particle is within the bounding box, the score is always 0. Logically, it is exepcted that f(0) = 0 and f(x) > 0 if x>0.

In Python, use the templated BoundingBox3DSingletonScore class as in the following example. In the example, 10 particles of radius 1.0 are generated in a 10 A x 10 A x 10 A bounding box. The particles are restrained in the bounding box by applying an upper-bounded harmonic potential. It is upper bounded because it is active only outside the bounding box.

1 k_bb = 10.0 # bounding box force coefficient in kcal/mol/A^2
2 bb_side = 10.0 # in A
3 radius = 1.0 # in A
4 number
5 m = IMP.Model()
7  IMP.algebra.Vector3D(bb_side, bb_side, bb_side))
8 particles = []
9 for i in range(0,10):
10  p = IMP.Particle(m)
14  d.set_coordinates_are_optimized(True)
15  particles.append(p)
18 bbr = IMP.container.SingletonsRestraint(bbss, particles)
See Also
BoundingBox3DSingletonScore
create_bounding_box_3d_singleton_score

Definition at line 64 of file BoundingBox3DSingletonScore.h.

Public Member Functions

 GenericBoundingBox3DSingletonScore (UF *f, const algebra::BoundingBoxD< 3 > &bb)
 
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const override
 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 override
 
virtual double evaluate_index (Model *m, ParticleIndex p, DerivativeAccumulator *da) const override
 
double evaluate_indexes (Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const overridefinal
 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 overridefinal
 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 overridefinal
 Compute the score and the derivative if needed over a set. More...
 
virtual std::string get_type_name () const override
 
virtual ::IMP::VersionInfo get_version_info () const override
 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)
 

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 ()
 

Constructor & Destructor Documentation

Parameters
fan unary function applied to particles that are outside the box. f is passed the distance of the particle center from the bounding box walls, ignoring the particle radius. Logically, it is exepcted to satisfy f(0) = 0 and f(x) > 0 if x>0.
bbthe bounding box to which f is applied

Member Function Documentation

template<class UF >
virtual ModelObjectsTemp IMP::core::GenericBoundingBox3DSingletonScore< UF >::do_get_inputs ( Model m,
const ParticleIndexes pis 
) const
overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

Definition at line 87 of file BoundingBox3DSingletonScore.h.

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template<class UF >
double IMP::core::GenericBoundingBox3DSingletonScore< UF >::evaluate_if_good_indexes ( Model m,
const ParticleIndexes o,
DerivativeAccumulator da,
double  max,
unsigned int  lower_bound,
unsigned int  upper_bound 
) const
overridevirtual

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
An implementation for this is provided by the IMP_SINGLETON_SCORE_METHODS() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 91 of file BoundingBox3DSingletonScore.h.

template<class UF >
virtual double IMP::core::GenericBoundingBox3DSingletonScore< UF >::evaluate_index ( Model m,
ParticleIndex  p,
DerivativeAccumulator da 
) const
overridevirtual

return 0 if the p is within the bounding box or f(d) if it is outside the bounding box, where f is the unary function provided during construction and d is the distance of the center of p from the bounding box walls. Update derivatives as needed, weighted using da.

Implements IMP::SingletonScore.

template<class UF >
double IMP::core::GenericBoundingBox3DSingletonScore< UF >::evaluate_indexes ( Model m,
const ParticleIndexes o,
DerivativeAccumulator da,
unsigned int  lower_bound,
unsigned int  upper_bound 
) const
finaloverridevirtual

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 one past last item in o to evaluate
Note
An implementation for this is provided by the IMP_SINGLETON_SCORE_METHODS() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 91 of file BoundingBox3DSingletonScore.h.

template<class UF >
double IMP::core::GenericBoundingBox3DSingletonScore< UF >::evaluate_indexes_delta ( Model m,
const ParticleIndexes o,
DerivativeAccumulator da,
const std::vector< unsigned > &  indexes,
std::vector< double > &  score 
) const
finaloverridevirtual

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.

Note
An implementation for this is provided by the IMP_SINGLETON_SCORE_METHODS() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 91 of file BoundingBox3DSingletonScore.h.

template<class UF >
double IMP::core::GenericBoundingBox3DSingletonScore< UF >::evaluate_indexes_scores ( Model m,
const ParticleIndexes o,
DerivativeAccumulator da,
unsigned int  lower_bound,
unsigned int  upper_bound,
std::vector< double > &  score 
) const
finaloverridevirtual

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].

Note
An implementation for this is provided by the IMP_SINGLETON_SCORE_METHODS() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 91 of file BoundingBox3DSingletonScore.h.

template<class UF >
virtual ::IMP::VersionInfo IMP::core::GenericBoundingBox3DSingletonScore< UF >::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 92 of file BoundingBox3DSingletonScore.h.


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