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IMP Reference Guide  develop.182d9373c4,2021/04/12
The Integrative Modeling Platform
IMP::npctransport::LinearSoftSpherePairScore Class Reference

#include <IMP/npctransport/linear_distance_pair_scores.h>

+ Inheritance diagram for IMP::npctransport::LinearSoftSpherePairScore:

Detailed Description

A soft linear repulsive score between two spheres. If the spheres penetrate each other, the score is ( k_ * [penetration-magnitude] kcal/mol), otherwise the score is 0.

Definition at line 69 of file linear_distance_pair_scores.h.

Public Member Functions

 LinearSoftSpherePairScore (double k, std::string name="LinearSSPairScore%1%")
 
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const
 Overload this method to specify the inputs. More...
 
double evaluate_if_good_indexes (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual double evaluate_index (Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed. More...
 
virtual double evaluate_indexes (Model *m, const ParticleIndexPairs &pips, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
 Compute the score and the derivative if needed over a set. More...
 
double get_k () const
 returns the k for sphere-sphere repulsion 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...
 
- 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...
 
- 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
 

Member Function Documentation

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

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

double IMP::npctransport::LinearSoftSpherePairScore::evaluate_if_good_indexes ( Model m,
const ParticleIndexPairs 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_PAIR_SCORE() macro.

Reimplemented from IMP::PairScore.

Definition at line 99 of file linear_distance_pair_scores.h.

+ Here is the call graph for this function:

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

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

virtual double IMP::npctransport::LinearSoftSpherePairScore::evaluate_index ( Model m,
const ParticleIndexPair 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 ParticlePair
daa DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed.

Implements IMP::PairScore.

virtual double IMP::npctransport::LinearSoftSpherePairScore::evaluate_indexes ( Model m,
const ParticleIndexPairs 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 ParticlePair, 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_PAIR_SCORE() macro.

Reimplemented from IMP::PairScore.

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

returns the k for sphere-sphere repulsion

Definition at line 117 of file linear_distance_pair_scores.h.

virtual ::IMP::VersionInfo IMP::npctransport::LinearSoftSpherePairScore::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 119 of file linear_distance_pair_scores.h.


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