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IMP Reference Guide  develop.cb6747d2d1,2024/03/28
The Integrative Modeling Platform
IMP::npctransport::LinearInteractionPairScore Class Reference

#include <IMP/npctransport/linear_distance_pair_scores.h>

+ Inheritance diagram for IMP::npctransport::LinearInteractionPairScore:

Detailed Description

A soft linear attractive / repulsive score between two spheres. The score is 0 if the spheres are beyond the attractive range. Within the attractive range, the score decreases linearly (= attraction) with slope k_attr_ until the spheres touch. Once the spheres begin to penetrate each other, the score rises linearly with slope k_rep_ (= repulsion), though it may be negative for small penetration.

Definition at line 206 of file linear_distance_pair_scores.h.

Classes

struct  EvaluationCache
 

Public Member Functions

 LinearInteractionPairScore (double k_rep, double range_attr, double k_attr, std::string name="LinearIDPairScore%1%")
 
ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const override
 Overload this method to specify the inputs. More...
 
double evaluate_if_good_index (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual double evaluate_indexes (Model *m, const ParticleIndexPairs &pips, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const override
 
EvaluationCache const & get_evaluation_cache () const
 
double get_k_attraction () const
 returns the k for sphere-sphere attraction in kcal/mol/A units More...
 
double get_k_repulsion () const
 returns the k for sphere-sphere repulsion in kcal/mol/A units More...
 
double get_range_attraction () const
 returns the range for sphere-sphere attraction in A 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...
 
void set_k_attraction (double k_attr)
 set k for sphere-sphere attraction in kcal/mol/A units More...
 
void set_k_repulsion (double k_rep)
 set k for sphere-sphere repulsion in kcal/mol/A units More...
 
- Public Member Functions inherited from IMP::PairScore
 PairScore (std::string name="PairScore %1%")
 
Restraints create_current_decomposition (Model *m, const ParticleIndexPair &vt) const
 
virtual double evaluate_if_good_index (Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
 Compute the score and the derivative if needed, only if "good". More...
 
virtual double evaluate_if_good_indexes (Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual double evaluate_index (Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da) const =0
 Compute the score and the derivative if needed. More...
 
virtual double evaluate_indexes_delta (Model *m, const ParticleIndexPairs &o, 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...
 
virtual double evaluate_indexes_scores (Model *m, const ParticleIndexPairs &o, 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...
 
- 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)
 

Protected Member Functions

double evaluate_index (algebra::Sphere3D const &s0, algebra::Sphere3D const &s1, algebra::Sphere3D &ds0, algebra::Sphere3D &ds1, DerivativeAccumulator *da) const
 
- Protected Member Functions inherited from IMP::PairScore
virtual Restraints do_create_current_decomposition (Model *m, const ParticleIndexPair &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 ()
 

Additional Inherited Members

- Public Types inherited from IMP::PairScore
typedef ParticlePair Argument
 
typedef ParticleIndexPair IndexArgument
 
typedef PairModifier Modifier
 
typedef const ParticlePairPassArgument
 
typedef const ParticleIndexPairPassIndexArgument
 

Constructor & Destructor Documentation

IMP::npctransport::LinearInteractionPairScore::LinearInteractionPairScore ( double  k_rep,
double  range_attr,
double  k_attr,
std::string  name = "LinearIDPairScore%1%" 
)

The score is 0 if the spheres are beyond the attractive range. Within the attractive range, the score decreases linearly (= attraction) with slope k_attr_ until the spheres touch. Once the spheres begin to penetrate each other, the score rises linearly with slope k_rep_ (= repulsion), though it may be negative for small penetration.

The energy potential difference between the unbound state and when the beads touch is: DELTA-U=0.5*k_attr*range_attr [kcal/mol]

Parameters
k_reprepulsion force constant in kcal/mol/A units
range_attrattraction range between sphere surfaces
k_attrattraction force constant in kcal/mol/A unit
namescore object names

Member Function Documentation

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

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

Reimplemented in IMP::npctransport::SitesPairScore.

double IMP::npctransport::LinearInteractionPairScore::evaluate_index ( algebra::Sphere3D const &  s0,
algebra::Sphere3D const &  s1,
algebra::Sphere3D ds0,
algebra::Sphere3D ds1,
DerivativeAccumulator da 
) const
protected

evaluates the linear interaction score, for spheres s0 and s1, outputting derivatives to ds0 and ds1 scaled by da, if da is not null

virtual double IMP::npctransport::LinearInteractionPairScore::evaluate_indexes ( Model m,
const ParticleIndexPairs pips,
DerivativeAccumulator da,
unsigned int  lower_bound,
unsigned int  upper_bound 
) const
overridevirtual

evaluate all index pairs between pips[lower_bound] and pis[upper_bound] and update their coordinate derivatives scaled by da, if da is not null

Reimplemented from IMP::PairScore.

Reimplemented in IMP::npctransport::SitesPairScore.

double IMP::npctransport::LinearInteractionPairScore::get_k_attraction ( ) const

returns the k for sphere-sphere attraction in kcal/mol/A units

Definition at line 303 of file linear_distance_pair_scores.h.

double IMP::npctransport::LinearInteractionPairScore::get_k_repulsion ( ) const

returns the k for sphere-sphere repulsion in kcal/mol/A units

Definition at line 311 of file linear_distance_pair_scores.h.

double IMP::npctransport::LinearInteractionPairScore::get_range_attraction ( ) const

returns the range for sphere-sphere attraction in A

Definition at line 300 of file linear_distance_pair_scores.h.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Reimplemented in IMP::npctransport::SitesPairScore.

Definition at line 318 of file linear_distance_pair_scores.h.

void IMP::npctransport::LinearInteractionPairScore::set_k_attraction ( double  k_attr)

set k for sphere-sphere attraction in kcal/mol/A units

Definition at line 306 of file linear_distance_pair_scores.h.

void IMP::npctransport::LinearInteractionPairScore::set_k_repulsion ( double  k_rep)

set k for sphere-sphere repulsion in kcal/mol/A units

Definition at line 314 of file linear_distance_pair_scores.h.


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