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IMP Reference Guide  develop.3e83b1f578,2019/10/15
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 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.
3 #
4 
5 # -- File: ms_connectivity_restraint.py --#
6 
7 import IMP
8 import IMP.core
9 import IMP.algebra
10 import sys
11 
12 IMP.setup_from_argv(sys.argv, "ms connectivity restraint")
13 
14 # Setup model
15 
16 m = IMP.Model()
17 ps = [IMP.Particle(m) for x in range(6)]
18 ds = []
20  ps[0], IMP.algebra.Vector3D(0.0, 0.0, 0.0)))
22  ps[1], IMP.algebra.Vector3D(1.0, 1.0, 0.0)))
24  ps[2], IMP.algebra.Vector3D(2.0, 0.0, 0.0)))
26  ps[3], IMP.algebra.Vector3D(3.0, 0.0, 0.0)))
28  ps[4], IMP.algebra.Vector3D(4.0, -1.0, 0.0)))
30  ps[5], IMP.algebra.Vector3D(1000, 1000, 1000)))
31 
32 # Create MS connectivity restraint
33 
34 ub = IMP.core.HarmonicUpperBound(1.0, 0.1)
37 
38 # Add particle types to the restraint
39 # add_type() returns a unique type handle that can be used as an argument
40 # to add_composite() later on.
41 
42 pa = r.add_type([ds[0], ds[1]])
43 pb = r.add_type([ds[2], ds[3]])
44 pc = r.add_type([ds[4]])
45 pd = r.add_type([ds[5]])
46 
47 # Enter experimental tree data into restraint
48 # In add_composite(), the first argument is node label and the second
49 # argument is the parent.
50 
51 i1 = r.add_composite([pa, pa, pb, pb, pc])
52 i2 = r.add_composite([pa, pb, pb, pc], i1)
53 i3 = r.add_composite([pa, pa, pb, pb], i1)
54 i4 = r.add_composite([pa, pb], i1)
55 i5 = r.add_composite([pa, pb, pb], i2)
56 i6 = r.add_composite([pb, pc], i2)
57 i7 = r.add_composite([pa, pa, pb], i3)
58 i8 = r.add_composite([pa, pb], i5)
59 
60 # Evaluate the restraint score
61 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
 
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. 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 (IMP::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)
 

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
 A restraint should override this to compute the score and derivatives. More...
 
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::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
virtual

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
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.

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
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 99 of file MSConnectivityRestraint.h.


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