IMP logo
IMP Reference Guide  develop.731656d855,2020/02/17
The Integrative Modeling Platform
IMP::isd::CrossLinkMSRestraint Class Reference

A restraint for ambiguous cross-linking MS data and multiple state approach. More...

#include <IMP/isd/CrossLinkMSRestraint.h>

+ Inheritance diagram for IMP::isd::CrossLinkMSRestraint:

Detailed Description

A restraint for ambiguous cross-linking MS data and multiple state approach.

It marginalizes the false positive rate and depends on the expected fpr and an uncertainty parameter beta.

Definition at line 22 of file CrossLinkMSRestraint.h.

Public Member Functions

 CrossLinkMSRestraint (IMP::Model *m, double length, bool get_log_prob=false, std::string name="CrossLinkMSRestraint%1%")
 Create the restraint. More...
 
 CrossLinkMSRestraint (IMP::Model *m, IMP::ParticleIndexAdaptor lengthi, bool get_log_prob=false, std::string name="CrossLinkMSRestraint%1%")
 
 CrossLinkMSRestraint (IMP::Model *m, double length, double slope, bool get_log_prob=false, std::string name="CrossLinkMSRestraint%1%")
 
void add_contribution (const IMP::ParticleIndexPair &pps, const IMP::ParticleIndexPair &sigmas, IMP::ParticleIndex psi)
 
virtual IMP::ModelObjectsTemp do_get_inputs () const
 
ParticleIndexPair get_contribution_particle_indexes (int i) const
 Get the particle indexes from a contribution. More...
 
unsigned int get_number_of_contributions () const
 
double get_probability () 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
 
virtual RestraintInfoget_static_info () 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)
 

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::isd::CrossLinkMSRestraint::CrossLinkMSRestraint ( IMP::Model m,
double  length,
bool  get_log_prob = false,
std::string  name = "CrossLinkMSRestraint%1%" 
)

Create the restraint.

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::isd::CrossLinkMSRestraint::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.

ParticleIndexPair IMP::isd::CrossLinkMSRestraint::get_contribution_particle_indexes ( int  i) const

Get the particle indexes from a contribution.

Definition at line 61 of file CrossLinkMSRestraint.h.

virtual ::IMP::VersionInfo IMP::isd::CrossLinkMSRestraint::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 68 of file CrossLinkMSRestraint.h.


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