IMP  2.4.0 The Integrative Modeling Platform
IMP::core::ConnectivityRestraint Class Reference

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

#include <IMP/core/ConnectivityRestraint.h>

Inheritance diagram for IMP::core::ConnectivityRestraint:

## Detailed Description

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

The restraint implements ambiguous connectivity. That is, it takes several particles and ensures that they remain connected, but allows how they are connected to change. If you wish to restraint 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).

1 ## \example core/connectivity_restraint.py
2 # This example shows how to use the ConnectivityRestraint to ensure that
3 # all the particles end up in a connected conformation following the
4 # optimization. One should also check out the
5 # IMP::atom::create_connectivity_restraint() helper functions.
6
7 import IMP
8 import IMP.core
9 import IMP.algebra
10 import IMP.atom
11
12 m = IMP.kernel.Model()
13
14 # Put the parent particles for each molecule
15 hs = []
16
17 # create the molecules, with 5 particles for each of 10 molecules
18 for i in range(0, 10):
19  pr = IMP.kernel.Particle(m)
20  pr.set_name("root " + str(i))
22  for j in range(0, 5):
23  p = IMP.kernel.Particle(m)
24  p.set_name("fragment " + str(i) + " " + str(j))
28  p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(3 * i, j, 0), 1))
29  hs.append(pr)
30
31
34
35 # score based on the one closest particle from each set of balls
36 lrps = IMP.core.KClosePairsPairScore(ps, cps, 1)
37 # connect all 10 molecules together
39 cr.set_particles(hs)
41
42 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 38 of file ConnectivityRestraint.h.

## Public Member Functions

Use the given PairScore. More...

ConnectivityRestraint (Model *m, PairScore *ps)

kernel::Restraints do_create_current_decomposition () const

IMP::kernel::ModelObjectsTemp do_get_inputs () const

kernel::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. More...

virtual std::string get_type_name () const

virtual ::IMP::base::VersionInfo get_version_info () const
Get information about the module and version of the object. More...

double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const

Public Member Functions inherited from IMP::kernel::Restraint
Restraint (kernel::Model *m, std::string name)

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 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 (kernel::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::base::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 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

Protected Member Functions inherited from IMP::kernel::ModelObject
virtual ModelObjectsTemps do_get_interactions () const

virtual void handle_set_has_required_score_states (bool)

Protected Member Functions inherited from IMP::base::Object
Object (std::string name)
Construct an object with the given name. More...

virtual void do_destroy ()

## Constructor & Destructor Documentation

 IMP::core::ConnectivityRestraint::ConnectivityRestraint ( PairScore * ps, SingletonContainerAdaptor sc )

Use the given PairScore.

## Member Function Documentation

 kernel::Restraints IMP::core::ConnectivityRestraint::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.

 IMP::kernel::ModelObjectsTemp IMP::core::ConnectivityRestraint::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::kernel::ModelObject.

 kernel::ParticlePairsTemp IMP::core::ConnectivityRestraint::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.

 PairScore* IMP::core::ConnectivityRestraint::get_pair_score ( ) const

Return the pair score used for scoring.

Definition at line 72 of file ConnectivityRestraint.h.

 virtual ::IMP::base::VersionInfo IMP::core::ConnectivityRestraint::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 80 of file ConnectivityRestraint.h.

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