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IMP Reference Guide  develop.660a833c7e,2021/01/16
The Integrative Modeling Platform
IMP::npc::CompositeRestraint Class Reference

Score a set of particles that form a composite. More...

#include <IMP/npc/CompositeRestraint.h>

+ Inheritance diagram for IMP::npc::CompositeRestraint:

Detailed Description

Score a set of particles that form a composite.

Similarly to IMP::core::ConnectivityRestraint, this ensures that a set of Particles remains connected, but allows how they are connected to change (for example, A-B-C would score as well as B-A-C). However, unlike that restraint, it acts on Particle type (in the case where there are several distinct Particles of the same type) and allows the stoichiometry to change (For example, A1-B1-C1 would score similarly to A1-B2-C2 or A1-B1-B2-C1).

To use, first create the restraint and then call add_type() for each distinct protein type, e.g. to enforce the composite ABC where there are two copies of protein A and B and a single copy of protein C use: {code} add_type([A1, A2]) add_type([B1, B2]) add_type([C1]) {code}

The restraint scores by computing the complete graph connecting all the particles (where the particles are the vertices and the edges are the value of the PairScore), then calculating the minimum spanning tree, and then using the lowest scoring subgraph that includes at least one of each protein type. This is made much more efficient if the restraint's maximum score is set (set_maximum_score()).

See Also
IMP::core::ConnectivityRestraint
IMP::core::MSConnectivityRestraint

Definition at line 46 of file npc/CompositeRestraint.h.

Public Member Functions

 CompositeRestraint (Model *m, PairScore *ps)
 Create with the given PairScore. More...
 
void add_type (ParticleIndexes ps)
 Add all Particles of a single type. More...
 
ModelObjectsTemp do_get_inputs () const
 
ParticleIndexPairs get_connected_pairs () const
 Return the set of pairs which are connected by the restraint. 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...
 
double unprotected_evaluate (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::npc::CompositeRestraint::CompositeRestraint ( Model m,
PairScore ps 
)

Create with the given PairScore.

Definition at line 54 of file npc/CompositeRestraint.h.

Member Function Documentation

void IMP::npc::CompositeRestraint::add_type ( ParticleIndexes  ps)

Add all Particles of a single type.

The restraint will ensure that at least one Particle of each type is present in the composite.

Definition at line 61 of file npc/CompositeRestraint.h.

ModelObjectsTemp IMP::npc::CompositeRestraint::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.

ParticleIndexPairs IMP::npc::CompositeRestraint::get_connected_pairs ( ) const

Return the set of pairs which are connected by the restraint.

This set of pairs reflects the current configuration at the time of the get_connected_pairs() call, not the set at the time of the last evaluate() call.

virtual ::IMP::VersionInfo IMP::npc::CompositeRestraint::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 78 of file npc/CompositeRestraint.h.


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