IMP  2.0.0
The Integrative Modeling Platform
IMP::core::MSConnectivityRestraint Class Reference

Ensure that a set of particles remains connected with one another. More...

#include <IMP/core/MSConnectivityRestraint.h>

+ Inheritance diagram for IMP::core::MSConnectivityRestraint:

Public Member Functions

 MSConnectivityRestraint (PairScore *ps, double eps=0.1)
 Use the given PairScore. More...
 
Restraints do_create_current_decomposition () const
 
ModelObjectsTemp do_get_inputs () const
 
ParticlePairsTemp get_connected_pairs () const
 Return the set of pairs which are connected by the restraint. More...
 
PairScoreget_pair_score () const
 Return the pair score used for scoring.
 
double unprotected_evaluate (IMP::kernel::DerivativeAccumulator *accum) 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)
 

Particles to be connected

The following methods are used to manipulate the list of particles that are to be connected. Each particle should have all the attributes expected by the PairScore used.

Ideally, one should pass a singleton container instead. These can only be used if none is passed.

unsigned int add_type (const ParticlesTemp &ps)
 
unsigned int add_composite (const Ints &components)
 
unsigned int add_composite (const Ints &components, unsigned int parent)
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::kernel::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
virtual void do_update_dependencies ()
 

Detailed Description

The restraint implements ambiguous connectivity. That is, it takes several particles including multiple copies and ensures that they remain connected, but allows how they are connected to change. If you wish to restrain the connectivity of sets of particles (i.e. each protein is represented using a set of balls) use an appropriate PairScore which calls a Refiner (such as ClosePairsPairScore).

## \example core/ms_connectivity_restraint.py
## This example shows how to use the MSConnectivityRestraint to ensure that all the particles that are part of complexes end up in a connected conformation following the optimization. It allows multiple copies of particles and takes an experimental tree as an input.
##

#-- File: ms_connectivity_restraint.py --#

import IMP
import IMP.core
import IMP.algebra

# Setup model

m = IMP.Model()
ps= [IMP.Particle(m) for x in xrange(6)]
ds= []
ds.append(IMP.core.XYZ.setup_particle(ps[0], IMP.algebra.Vector3D(0.0, 0.0, 0.0)))
ds.append(IMP.core.XYZ.setup_particle(ps[1], IMP.algebra.Vector3D(1.0, 1.0, 0.0)))
ds.append(IMP.core.XYZ.setup_particle(ps[2], IMP.algebra.Vector3D(2.0, 0.0, 0.0)))
ds.append(IMP.core.XYZ.setup_particle(ps[3], IMP.algebra.Vector3D(3.0, 0.0, 0.0)))
ds.append(IMP.core.XYZ.setup_particle(ps[4], IMP.algebra.Vector3D(4.0, -1.0, 0.0)))
ds.append(IMP.core.XYZ.setup_particle(ps[5], IMP.algebra.Vector3D(1000, 1000, 1000)))

# Create MS connectivity restraint

ub = IMP.core.HarmonicUpperBound(1.0, 0.1)
ss= IMP.core.DistancePairScore(ub)
r= IMP.core.MSConnectivityRestraint(ss)

# Add particle types to the restraint
# add_type() returns a unique type handle that can be used as an argument to add_composite() later on.

pa = r.add_type([ds[0], ds[1]])
pb = r.add_type([ds[2], ds[3]])
pc = r.add_type([ds[4]])
pd = r.add_type([ds[5]])

# Enter experimental tree data into restraint
# In add_composite(), the first argument is node label and the second argument is the parent.

i1 = r.add_composite([pa, pa, pb, pb, pc])
i2 = r.add_composite([pa, pb, pb, pc], i1)
i3 = r.add_composite([pa, pa, pb, pb], i1)
i4 = r.add_composite([pa, pb], i1)
i5 = r.add_composite([pa, pb, pb], i2)
i6 = r.add_composite([pb, pc], i2)
i7 = r.add_composite([pa, pa, pb], i3)
i8 = r.add_composite([pa, pb], i5)

# Add restraint to the model and evaluate the model score

m.add_restraint(r)
m.evaluate(False)

More precisely, the restraint scores by computing the MST on the complete graph connecting all the particles. The edge weights are given by the value of the PairScore for the two endpoints of the edge.

Definition at line 59 of file MSConnectivityRestraint.h.

Constructor & Destructor Documentation

IMP::core::MSConnectivityRestraint::MSConnectivityRestraint ( PairScore ps,
double  eps = 0.1 
)

If sc is nullptr, a ListSingletonContainer is created internally. eps is set to 0.1 by default.

Member Function Documentation

Restraints IMP::core::MSConnectivityRestraint::do_create_current_decomposition ( ) const
virtual

A Restraint should override this if they want to decompose themselves for display and other purposes. The returned restraints will be made in to a RestraintSet, if needed and the weight and maximum score set for the restraint set.

The returned restraints should be only the non-zero terms and should have their last scores set appropriately;

Reimplemented from IMP::kernel::Restraint.

ModelObjectsTemp IMP::core::MSConnectivityRestraint::do_get_inputs ( ) const
virtual

Override if this reads other objects during evaluate.

Implements IMP::kernel::ModelObject.

ParticlePairsTemp IMP::core::MSConnectivityRestraint::get_connected_pairs ( ) const

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.


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