IMP  2.0.0
The Integrative Modeling Platform
IMP::saxs::Restraint Class Reference

Calculate score based on fit to SAXS profile. More...

#include <IMP/saxs/Restraint.h>

+ Inheritance diagram for IMP::saxs::Restraint:

Public Member Functions

 Restraint (const Particles &particles, const Profile &exp_profile, FormFactorType ff_type=HEAVY_ATOMS)
 Constructor. More...
 
virtual void do_show (std::ostream &out) const
 
- Public Member Functions inherited from IMP::kernel::Restraint
 Restraint (Model *m, std::string name)
 
void add_score_and_derivatives (ScoreAccumulator sa) const
 
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
 
ContainersTemp get_input_containers () const
 
ParticlesTemp get_input_particles () const
 
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 (Model *m, std::string name)
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
virtual IMP::base::VersionInfo get_version_info () const =0
 Get information about the module and version of the object.
 
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

void compute_profile (Profile &model_profile)
 
- 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
 
virtual void do_update_dependencies ()
 
- Protected Member Functions inherited from IMP::kernel::ModelObject
virtual ModelObjectsTemp do_get_inputs () const =0
 
virtual ModelObjectsTemps do_get_interactions () const
 
virtual void update_dependencies ()
 
- Protected Member Functions inherited from IMP::base::Object
 Object (std::string name)
 Construct an object with the given name. More...
 

Protected Attributes

Pointer< DerivativeCalculator > derivative_calculator_
 
Profile exp_profile_
 
FormFactorType ff_type_
 
Particles particles_
 
Pointer< ProfileFitter
< ChiScore > > 
profile_fitter_
 
std::vector< Particles > rigid_bodies_
 
std::vector< core::RigidBodyrigid_bodies_decorators_
 
Profile rigid_bodies_profile_
 

Additional Inherited Members

Detailed Description

The restraint takes rigid bodies into account, in order to speed up the calculations. Rigid body should be gived as single RigidBody Particle. Other, non-rigid body Particles can also be given.

The shape of a rigid body is assumed to be defined by the set of atom::Hierarchy leaves of the atom::Hierarchy rooted at the rigid body particle.

Algorithmic details:
The distances between the atoms of rigid body do not change, therefore their contribution to the profile is pre-computed and stored.

Definition at line 42 of file saxs/Restraint.h.

Constructor & Destructor Documentation

IMP::saxs::Restraint::Restraint ( const Particles &  particles,
const Profile exp_profile,
FormFactorType  ff_type = HEAVY_ATOMS 
)
Parameters
[in]particlesThe particles participating in the fitting score
[in]exp_profileThe experimental profile used in the fitting score
[in]ff_typeType of the form factors for profile calculations: ALL_ATOMS - all atoms including hydrogens HEAVY_ATOMS - no hydrogens, all other atoms included CA_ATOMS - residue level, residue represented by CA

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