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IMP Reference Guide  develop.cb6747d2d1,2024/03/28
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:

Detailed Description

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

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).

1 ## \example core/ms_connectivity_restraint.py
2 # This example shows how to use the MSConnectivityRestraint to ensure that
3 # all the particles that are part of complexes end up in a connected
4 # conformation following the optimization. It allows multiple copies of
5 # particles and takes an experimental tree as an input.
6 #
7 
8 # -- File: ms_connectivity_restraint.py --#
9 
10 import IMP
11 import IMP.core
12 import IMP.algebra
13 import sys
14 
15 IMP.setup_from_argv(sys.argv, "ms connectivity restraint")
16 
17 # Setup model
18 
19 m = IMP.Model()
20 ps = [IMP.Particle(m) for x in range(6)]
21 ds = []
23  ps[0], IMP.algebra.Vector3D(0.0, 0.0, 0.0)))
25  ps[1], IMP.algebra.Vector3D(1.0, 1.0, 0.0)))
27  ps[2], IMP.algebra.Vector3D(2.0, 0.0, 0.0)))
29  ps[3], IMP.algebra.Vector3D(3.0, 0.0, 0.0)))
31  ps[4], IMP.algebra.Vector3D(4.0, -1.0, 0.0)))
33  ps[5], IMP.algebra.Vector3D(1000, 1000, 1000)))
34 
35 # Create MS connectivity restraint
36 
37 ub = IMP.core.HarmonicUpperBound(1.0, 0.1)
40 
41 # Add particle types to the restraint
42 # add_type() returns a unique type handle that can be used as an argument
43 # to add_composite() later on.
44 
45 pa = r.add_type([ds[0], ds[1]])
46 pb = r.add_type([ds[2], ds[3]])
47 pc = r.add_type([ds[4]])
48 pd = r.add_type([ds[5]])
49 
50 # Enter experimental tree data into restraint
51 # In add_composite(), the first argument is node label and the second
52 # argument is the parent.
53 
54 i1 = r.add_composite([pa, pa, pb, pb, pc])
55 i2 = r.add_composite([pa, pb, pb, pc], i1)
56 i3 = r.add_composite([pa, pa, pb, pb], i1)
57 i4 = r.add_composite([pa, pb], i1)
58 i5 = r.add_composite([pa, pb, pb], i2)
59 i6 = r.add_composite([pb, pc], i2)
60 i7 = r.add_composite([pa, pa, pb], i3)
61 i8 = r.add_composite([pa, pb], i5)
62 
63 # Evaluate the restraint score
64 r.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 54 of file MSConnectivityRestraint.h.

Public Member Functions

 MSConnectivityRestraint (Model *m, PairScore *ps, double eps=0.1)
 Use the given PairScore. More...
 
Restraints do_create_current_decomposition () const override
 
ModelObjectsTemp do_get_inputs () const override
 
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 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)
 

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::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::MSConnectivityRestraint::MSConnectivityRestraint ( Model m,
PairScore ps,
double  eps = 0.1 
)

Use the given PairScore.

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
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.

ModelObjectsTemp IMP::core::MSConnectivityRestraint::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.

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

Return the pair score used for scoring.

Definition at line 91 of file MSConnectivityRestraint.h.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 100 of file MSConnectivityRestraint.h.

double IMP::core::MSConnectivityRestraint::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: