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IMP Reference Guide  develop.671b0bd9ab,2020/09/24
The Integrative Modeling Platform
IMP::isd::AtomicCrossLinkMSRestraint Class Reference

Restrain atom pairs based on a set of crosslinks. More...

#include <IMP/isd/AtomicCrossLinkMSRestraint.h>

+ Inheritance diagram for IMP::isd::AtomicCrossLinkMSRestraint:

Detailed Description

Restrain atom pairs based on a set of crosslinks.

Definition at line 21 of file AtomicCrossLinkMSRestraint.h.

Public Member Functions

 AtomicCrossLinkMSRestraint (IMP::Model *m, double length, ParticleIndex psi, Float slope=0.0, bool part_of_log_score=false, std::string name="AtomicCrossLinkMSRestraint%1%")
 Constructor. More...
 
void add_contribution (const ParticleIndexPair &ppi, const ParticleIndexPair &sigmas)
 Add a contribution to this xlink. More...
 
virtual IMP::ModelObjectsTemp do_get_inputs () const
 
Float evaluate_for_contributions (Ints c, DerivativeAccumulator *accum) const
 Evaluate the restraint just for a subset of contribution indexes. More...
 
ParticleIndexPair get_contribution (int i) const
 Get the particles in a contribution. More...
 
ParticleIndexPair get_contribution_sigmas (int i) const
 Get the sigma nuisances in a contribution. More...
 
unsigned int get_number_of_contributions () const
 Get number of contributions added to the restraint. More...
 
ParticleIndex get_psi () const
 Get the psi nuisance in a contribution. More...
 
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...
 
void set_part_of_log_score (bool hey)
 
void set_slope (Float slope)
 
void show (std::ostream &out) const
 
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::AtomicCrossLinkMSRestraint::AtomicCrossLinkMSRestraint ( IMP::Model m,
double  length,
ParticleIndex  psi,
Float  slope = 0.0,
bool  part_of_log_score = false,
std::string  name = "AtomicCrossLinkMSRestraint%1%" 
)

Constructor.

Parameters
[in]mThe IMP model
[in]lengthThe maximum length of the crosslinker
[in]psiThe xlink uncertainty nuisance particle
[in]slopeExponential factor added to the score
[in]part_of_log_scoreIf true, will return probability instead of score (but the derivative will still be for a log)
[in]nameThe restraint name

Member Function Documentation

void IMP::isd::AtomicCrossLinkMSRestraint::add_contribution ( const ParticleIndexPair ppi,
const ParticleIndexPair sigmas 
)

Add a contribution to this xlink.

Parameters
[in]ppiThe particles to which you will apply the restraint
[in]sigmasNuisance parameters (one per residue involved in the XL)
virtual IMP::ModelObjectsTemp IMP::isd::AtomicCrossLinkMSRestraint::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.

Float IMP::isd::AtomicCrossLinkMSRestraint::evaluate_for_contributions ( Ints  c,
DerivativeAccumulator accum 
) const

Evaluate the restraint just for a subset of contribution indexes.

ParticleIndexPair IMP::isd::AtomicCrossLinkMSRestraint::get_contribution ( int  i) const

Get the particles in a contribution.

Definition at line 56 of file AtomicCrossLinkMSRestraint.h.

ParticleIndexPair IMP::isd::AtomicCrossLinkMSRestraint::get_contribution_sigmas ( int  i) const

Get the sigma nuisances in a contribution.

Definition at line 59 of file AtomicCrossLinkMSRestraint.h.

unsigned int IMP::isd::AtomicCrossLinkMSRestraint::get_number_of_contributions ( ) const

Get number of contributions added to the restraint.

Definition at line 53 of file AtomicCrossLinkMSRestraint.h.

ParticleIndex IMP::isd::AtomicCrossLinkMSRestraint::get_psi ( ) const

Get the psi nuisance in a contribution.

Definition at line 62 of file AtomicCrossLinkMSRestraint.h.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 73 of file AtomicCrossLinkMSRestraint.h.


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