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IMP Reference Guide  develop.c7bc4084d5,2021/01/22
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:

Detailed Description

Calculate score based on fit to SAXS profile.

The restraint takes rigid bodies into account, in order to speed up the calculations. Rigid body should be given 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.

Public Member Functions

 Restraint (const Particles &particles, const Profile *exp_profile, FormFactorType ff_type=HEAVY_ATOMS)
 Constructor. More...
 
virtual IMP::ModelObjectsTemp do_get_inputs () const
 
RestraintInfoget_static_info () 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...
 
virtual double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const
 
- Public Member Functions inherited from IMP::Restraint
 Restraint (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 RestraintInfoget_dynamic_info () 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::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)
 

Protected Attributes

Pointer< DerivativeCalculatorderivative_calculator_
 
FormFactorType ff_type_
 
Pointer
< RigidBodiesProfileHandler
handler_
 
Pointer< ProfileFitter
< ChiScore > > 
profile_fitter_
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) const
 A restraint should override this to compute the score and derivatives. More...
 
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
- 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::saxs::Restraint::Restraint ( const Particles particles,
const Profile exp_profile,
FormFactorType  ff_type = HEAVY_ATOMS 
)

Constructor.

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

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::saxs::Restraint::do_get_inputs ( ) const
virtual

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.

Reimplemented in IMP::saxs::RadiusOfGyrationRestraint.

RestraintInfo* IMP::saxs::Restraint::get_static_info ( ) const
virtual
Returns
Information for writing to RMF files

Reimplemented from IMP::Restraint.

virtual ::IMP::VersionInfo IMP::saxs::Restraint::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Reimplemented in IMP::saxs::RadiusOfGyrationRestraint.

Definition at line 64 of file saxs/Restraint.h.


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