IMP Reference Guide  develop.5de2a9ba5d,2024/02/25 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 restrain the connectivity of sets of particles (e.g. 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.container
10 import IMP.algebra
11 import IMP.atom
12 import sys
13
14 IMP.setup_from_argv(sys.argv, "Connectivity restraint")
15
16 m = IMP.Model()
17
18 # Put the parent particles for each molecule
19 hs = []
20
21 # create the molecules, with 5 particles for each of 10 molecules
22 for i in range(0, 10):
23  pr = IMP.Particle(m)
24  pr.set_name("root " + str(i))
26  for j in range(0, 5):
27  p = IMP.Particle(m)
28  p.set_name("fragment " + str(i) + " " + str(j))
32  p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(3 * i, j, 0), 1))
33  hs.append(pr)
34
35
38
39 # score based on the one closest particle from each set of balls
40 lrps = IMP.core.KClosePairsPairScore(ps, cps, 1)
41 # connect all 10 molecules together
43 cr = IMP.core.ConnectivityRestraint(lrps, lsc)
44
45 cr.evaluate(False)

More precisely, the restraint scores by computing the minimum spanning tree 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 39 of file ConnectivityRestraint.h.

## Public Member Functions

Use the given PairScore. More...

Restraints do_create_current_decomposition () const override

IMP::ModelObjectsTemp do_get_inputs () const override

ParticleIndexPairs get_connected_index_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 override

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

double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const override
Return the unweighted score for the restraint. More...

Public Member Functions inherited from IMP::Restraint
Restraint (Model *m, std::string name)
Create a restraint and register it with the model. More...

Restraint ()
Default constructor. 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

bool get_is_aggregate () const
Return whether this restraint wraps a number of other restraints. More...

double get_last_last_score () const
Get the unweighted score from the last-but-one time it was evaluated. More...

virtual double get_last_score () const

double get_score () const

virtual RestraintInfoget_static_info () const

bool get_was_good () const

double evaluate (bool calc_derivs) const

double evaluate_moved (bool calc_derivs, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double evaluate_moved_if_below (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

double evaluate_moved_if_good (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double evaluate_if_good (bool calc_derivatives) const

double evaluate_if_below (bool calc_derivatives, double max) const

virtual double unprotected_evaluate_moved (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Return the unweighted score, taking moving particles into account. More...

virtual double unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const

virtual double unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const
The function calling this will treat any score >= max as bad. More...

virtual double unprotected_evaluate_moved_if_below (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

virtual double unprotected_evaluate_moved_if_good (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) 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)

Protected Member Functions inherited from IMP::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) const

virtual void do_add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

virtual Restraints do_create_decomposition () const

ModelObjectsTemp do_get_outputs () const override

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 ()

Protected Attributes inherited from IMP::Restraint
bool is_aggregate_

## Constructor & Destructor Documentation

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

Use the given PairScore.

## Member Function Documentation

 Restraints IMP::core::ConnectivityRestraint::do_create_current_decomposition ( ) const
overridevirtual

A Restraint should override this if it wants to decompose itself for display and other purposes. The returned restraints will be made into a RestraintSet if needed, with suitable weight and maximum score.

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

Reimplemented from IMP::Restraint.

 IMP::ModelObjectsTemp IMP::core::ConnectivityRestraint::do_get_inputs ( ) const
overridevirtual

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::core::ConnectivityRestraint::get_connected_index_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 55 of file ConnectivityRestraint.h.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 63 of file ConnectivityRestraint.h.

 double IMP::core::ConnectivityRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator * da ) const
overridevirtual

Return the unweighted score for the restraint.

Reimplemented from IMP::Restraint.

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