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IMP Reference Guide  develop.d247202c1c,2019/10/23
The Integrative Modeling Platform
IMP::npctransport::HarmonicSpringSingletonScore Class Reference

#include <IMP/npctransport/HarmonicSpringSingletonScore.h>

+ Inheritance diagram for IMP::npctransport::HarmonicSpringSingletonScore:

Detailed Description

A harmonic score between two bonded spheres connected by a spring whose resting length is dynamic

Definition at line 28 of file HarmonicSpringSingletonScore.h.

Public Member Functions

 HarmonicSpringSingletonScore (double k1, double k2, std::string name="HarmonicSpringSingletonScore%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 ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual double evaluate_index (Model *m, ParticleIndex pi, 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...
 
double get_k1 () const
 
double get_k2 () const
 
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 set_k1 (double k1)
 
void set_k2 (double k2)
 
- 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::HarmonicSpringSingletonScore::HarmonicSpringSingletonScore ( double  k1,
double  k2,
std::string  name = "HarmonicSpringSingletonScore%1%" 
)

a harmonic well pair potential that keeps two particles connected by a spring particle whose resting length itself is dynamic

Parameters
k1the force constant applied by the string on tethered particles in units of kcal/mol/A^2 - attractive if spring is longer than rest length, repulsive if shorter than rest length. The spring applies a force of k1*dX on each particle, and a counter force of 2*k1*dX acts on the spring, where dX=|distance(p1,p2)-(rest_length)|
k2the force constant for relaxation of the spring rest length to its equilibrium value in kcal/mol/A^2. The force equals k2*dX where dX=|(rest_length)-(equilibrium length)|
namethe name of the score

Member Function Documentation

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

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

double IMP::npctransport::HarmonicSpringSingletonScore::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 85 of file HarmonicSpringSingletonScore.h.

virtual double IMP::npctransport::HarmonicSpringSingletonScore::evaluate_index ( Model m,
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::npctransport::HarmonicSpringSingletonScore::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 85 of file HarmonicSpringSingletonScore.h.

double IMP::npctransport::HarmonicSpringSingletonScore::get_k1 ( ) const

returns the force constant to bring particles to the current rest length in kcal/mol/A^2

Definition at line 63 of file HarmonicSpringSingletonScore.h.

double IMP::npctransport::HarmonicSpringSingletonScore::get_k2 ( ) const

returns the force constant to bring the current rest length to equilibrium in kcal/mol/A^2

Definition at line 73 of file HarmonicSpringSingletonScore.h.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 87 of file HarmonicSpringSingletonScore.h.

void IMP::npctransport::HarmonicSpringSingletonScore::set_k1 ( double  k1)

sets the force constant to bring particles to the current rest length in kcal/mol/A^2

Definition at line 58 of file HarmonicSpringSingletonScore.h.

void IMP::npctransport::HarmonicSpringSingletonScore::set_k2 ( double  k2)

sets the force constant to bring the current rest length to equilibrium in kcal/mol/A^2

Definition at line 68 of file HarmonicSpringSingletonScore.h.


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