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IMP Reference Guide  2.20.1
The Integrative Modeling Platform
IMP::multifit::RadiusOfGyrationRestraint Class Reference

Ensure the radius of gyration of particles fits the predicted one. More...

#include <IMP/multifit/RadiusOfGyrationRestraint.h>

+ Inheritance diagram for IMP::multifit::RadiusOfGyrationRestraint:

Detailed Description

Ensure the radius of gyration of particles fits the predicted one.

Note
a harmonic upper bound is applied between the predicted radius and the actual radius

Definition at line 27 of file multifit/RadiusOfGyrationRestraint.h.

Public Member Functions

 RadiusOfGyrationRestraint (Particles ps, int num_residues, Float scale=1.)
 Constructor. More...
 
unsigned int add_particle (Particle *obj)
 
void add_particles (const Particles &objs)
 
void clear_particles ()
 
virtual IMP::ModelObjectsTemp do_get_inputs () const override
 
void erase_particle (unsigned int i)
 
bool get_has_particles ()
 
unsigned int get_number_of_particles () const
 
Particleget_particle (unsigned int i) const
 
Particles get_particles () const
 
Float get_radius_of_gyration ()
 Get the predicted radius of gyration used in the restraint. 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 remove_particle (Particle *d)
 
void remove_particles (const Particles &d)
 
void reserve_particles (unsigned int sz)
 
void set_particles (const Particles &ps)
 
void set_particles_order (const Particles &objs)
 
void set_radius_of_gyration (Float r)
 Set the predicted radius of gyration used in the restraint. More...
 
virtual double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const override
 Return the unweighted score for the restraint. More...
 
- Public Member Functions inherited from IMP::Restraint
 Restraint (Model *m, std::string name)
 Create a restraint and register it with the model. More...
 
 Restraint ()
 Default constructor. More...
 
Restraintcreate_current_decomposition () const
 Decompose this restraint into constituent terms for the current conf. More...
 
Restraintcreate_decomposition () const
 Decompose this restraint into constituent terms. More...
 
virtual ScoringFunctioncreate_scoring_function (double weight=1.0, double max=NO_MAX) const
 Create a scoring function with only this restraint. More...
 
virtual RestraintInfoget_dynamic_info () const
 
bool get_is_aggregate () const
 Return whether this restraint wraps a number of other restraints. More...
 
double get_last_last_score () const
 Get the unweighted score from the last-but-one time it was evaluated. More...
 
virtual double get_last_score () const
 
double get_score () const
 
virtual RestraintInfoget_static_info () const
 
bool get_was_good () const
 
double evaluate (bool calc_derivs) const
 
double evaluate_moved (bool calc_derivs, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
 
double evaluate_moved_if_below (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const
 
double evaluate_moved_if_good (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
 
double evaluate_if_good (bool calc_derivatives) const
 
double evaluate_if_below (bool calc_derivatives, double max) const
 
virtual double unprotected_evaluate_moved (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
 Return the unweighted score, taking moving particles into account. More...
 
virtual double unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const
 
virtual double unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const
 The function calling this will treat any score >= max as bad. More...
 
virtual double unprotected_evaluate_moved_if_below (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const
 
virtual double unprotected_evaluate_moved_if_good (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const
 
void set_weight (Float weight)
 
Float get_weight () const
 
double get_maximum_score () const
 
void set_maximum_score (double s)
 
- Public Member Functions inherited from IMP::ModelObject
 ModelObject (Model *m, std::string name)
 
bool get_has_dependencies () const
 Return whether this object has dependencies computed. More...
 
bool get_has_required_score_states () const
 Return whether score states are computed. More...
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 Get the interacting sets induced by this ModelObject. More...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_required_score_states () const
 Get the score states that are ancestors of this in the dependency graph. More...
 
void set_has_dependencies (bool tf)
 Either invalidate the dependencies or ensure they are correct. More...
 
void set_has_required_score_states (bool tf)
 Compute the required score states. 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)
 

Public Attributes

list particles
 A Python list of Particles More...
 

Protected Attributes

Pointer< core::HarmonicUpperBoundhub_
 
Modelmdl_
 
Float predicted_rog_
 
Float scale_
 
- Protected Attributes inherited from IMP::Restraint
bool is_aggregate_
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) const
 
virtual void do_add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
 
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const override
 
- Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemps do_get_interactions () const
 
virtual void handle_set_has_required_score_states (bool)
 
- 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::multifit::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint ( Particles  ps,
int  num_residues,
Float  scale = 1. 
)

Constructor.

Parameters
[in]psthe particles to work on
[in]num_residuesthe number of residues the particles represent
[in]scaleallow the radius of gyration of the particles to be at most scale times the predicted one

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::multifit::RadiusOfGyrationRestraint::do_get_inputs ( ) const
overridevirtual

Get any Particle, Container or other ModelObjects read by this during evaluation. If you read everything in a container, you can just return that container.

Implements IMP::ModelObject.

Float IMP::multifit::RadiusOfGyrationRestraint::get_radius_of_gyration ( )

Get the predicted radius of gyration used in the restraint.

Definition at line 48 of file multifit/RadiusOfGyrationRestraint.h.

virtual ::IMP::VersionInfo IMP::multifit::RadiusOfGyrationRestraint::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 41 of file multifit/RadiusOfGyrationRestraint.h.

void IMP::multifit::RadiusOfGyrationRestraint::set_radius_of_gyration ( Float  r)

Set the predicted radius of gyration used in the restraint.

Definition at line 43 of file multifit/RadiusOfGyrationRestraint.h.

virtual double IMP::multifit::RadiusOfGyrationRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator da) const
overridevirtual

Return the unweighted score for the restraint.

Reimplemented from IMP::Restraint.

Member Data Documentation

list IMP::multifit::RadiusOfGyrationRestraint::particles

A Python list of Particles

Note
This class member is only available in Python.

Definition at line 51 of file multifit/RadiusOfGyrationRestraint.h.


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