IMP  2.4.0
The Integrative Modeling Platform
Public Member Functions | List of all members
IMP::isd::FretRestraint Class Reference

#include <IMP/isd/FretRestraint.h>

+ Inheritance diagram for IMP::isd::FretRestraint:

Detailed Description

A restraint for using in-vivo ensemble FRET data. See Muller et al. Mol Biol Cell 16, 3341, 2005 for more info.

Definition at line 23 of file FretRestraint.h.

Public Member Functions

 FretRestraint (kernel::Particles pd, kernel::Particles pa, kernel::Particle *kda, kernel::Particle *Ida, kernel::Particle *R0, kernel::Particle *sigma0, kernel::Particle *Pbl, double fexp, double m_d=1.0, double m_a=1.0)
 Create the restraint. More...
 FretRestraint (kernel::Particle *kda, kernel::Particle *Ida, kernel::Particle *sumFi, kernel::Particle *sigma0, kernel::Particle *Pbl, double fexp)
 FretRestraint (kernel::Particle *prd, algebra::Vector3D GMMterd, algebra::Vector3Ds GMMctrd, Floats GMMwd, Floats GMMsigd, kernel::Particle *pra, algebra::Vector3D GMMtera, algebra::Vector3Ds GMMctra, Floats GMMwa, Floats GMMsiga, kernel::Particle *kda, kernel::Particle *Ida, kernel::Particle *sigma0, kernel::Particle *Pbl, FretData *data, double fexp)
do_get_inputs () const
double get_average_sigma (double fmod) const
double get_experimental_value () const
double get_model_fretr () const
double get_probability () const
double get_standard_error () const
double get_sumFi () const
virtual std::string get_type_name () const
virtual ::IMP::base::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
void set_experimental_value (double fexp)
virtual double unprotected_evaluate (IMP::kernel::DerivativeAccumulator *accum) const
- Public Member Functions inherited from IMP::kernel::Restraint
 Restraint (kernel::Model *m, std::string name)
void add_score_and_derivatives (ScoreAccumulator sa) const
 Perform the actual restraint scoring. 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 double get_last_score () const
double get_score () const
bool get_was_good () 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::kernel::ModelObject
 ModelObject (kernel::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::base::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

- Protected Member Functions inherited from IMP::kernel::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) const
virtual Restraints do_create_current_decomposition () const
virtual Restraints do_create_decomposition () const
ModelObjectsTemp do_get_outputs () const
- Protected Member Functions inherited from IMP::kernel::ModelObject
virtual ModelObjectsTemps do_get_interactions () const
virtual void handle_set_has_required_score_states (bool)
- Protected Member Functions inherited from IMP::base::Object
 Object (std::string name)
 Construct an object with the given name. More...
virtual void do_destroy ()

Constructor & Destructor Documentation

IMP::isd::FretRestraint::FretRestraint ( kernel::Particles  pd,
kernel::Particles  pa,
kernel::Particle kda,
kernel::Particle Ida,
kernel::Particle R0,
kernel::Particle sigma0,
kernel::Particle Pbl,
double  fexp,
double  m_d = 1.0,
double  m_a = 1.0 

Create the restraint.

kernel::Restraints should store the particles they are to act on, preferably in a Singleton or PairContainer as appropriate.

Member Function Documentation

virtual IMP::kernel::ModelObjectsTemp IMP::isd::FretRestraint::do_get_inputs ( ) const

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::kernel::ModelObject.

virtual ::IMP::base::VersionInfo IMP::isd::FretRestraint::get_version_info ( ) const

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 103 of file FretRestraint.h.

virtual double IMP::isd::FretRestraint::unprotected_evaluate ( IMP::kernel::DerivativeAccumulator accum) const

This macro declares the basic needed methods: evaluate and show

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