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IMP Reference Guide  develop.8bf871cb5d,2024/11/14
The Integrative Modeling Platform
IMP::npctransport::ExcludeZRangeSingletonScore Class Reference

Exclude particles from the given range of z coordinates. More...

#include <IMP/npctransport/ExcludeZRangeSingletonScore.h>

+ Inheritance diagram for IMP::npctransport::ExcludeZRangeSingletonScore:

Detailed Description

Exclude particles from the given range of z coordinates.

Definition at line 18 of file ExcludeZRangeSingletonScore.h.

Public Member Functions

 ExcludeZRangeSingletonScore (double bottom, double top, double k)
 
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
 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 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...
 
double get_bottom_z () const
 
double get_k () const
 
double get_top_z () const
 
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

IMP::npctransport::ExcludeZRangeSingletonScore::ExcludeZRangeSingletonScore ( double  bottom,
double  top,
double  k 
)

Exclude particles from the range of z coordinates [bottom_..top_] with repulsive force constant k

Member Function Documentation

virtual ModelObjectsTemp IMP::npctransport::ExcludeZRangeSingletonScore::do_get_inputs ( Model m,
const ParticleIndexes pis 
) const
overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

double IMP::npctransport::ExcludeZRangeSingletonScore::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 45 of file ExcludeZRangeSingletonScore.h.

virtual double IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_index ( Model m,
ParticleIndex  vt,
DerivativeAccumulator da 
) const
overridevirtual

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::npctransport::ExcludeZRangeSingletonScore::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 45 of file ExcludeZRangeSingletonScore.h.

double IMP::npctransport::ExcludeZRangeSingletonScore::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 45 of file ExcludeZRangeSingletonScore.h.

double IMP::npctransport::ExcludeZRangeSingletonScore::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 45 of file ExcludeZRangeSingletonScore.h.

double IMP::npctransport::ExcludeZRangeSingletonScore::get_bottom_z ( ) const

returns the lowest slab z coordinate

Definition at line 32 of file ExcludeZRangeSingletonScore.h.

double IMP::npctransport::ExcludeZRangeSingletonScore::get_k ( ) const

returns the force constant for repulsion out of the z-range

Definition at line 38 of file ExcludeZRangeSingletonScore.h.

double IMP::npctransport::ExcludeZRangeSingletonScore::get_top_z ( ) const

returns the highest slab z coordinate

Definition at line 35 of file ExcludeZRangeSingletonScore.h.

virtual ::IMP::VersionInfo IMP::npctransport::ExcludeZRangeSingletonScore::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 46 of file ExcludeZRangeSingletonScore.h.


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