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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 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).
#-- 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.
Examples: ms connectivity restraint
Inheritance diagram for IMP::core::MSConnectivityRestraint:Public Member Functions | |
| MSConnectivityRestraint (PairScore *ps, double eps=0.1) | |
| Use the given PairScore. | |
| Restraints | do_create_current_decomposition () const |
| ParticlePairs | get_connected_pairs () const |
| Return the set of pairs which are connected by the restraint. | |
| PairScore * | get_pair_score () const |
| Return the pair score used for scoring. | |
| Public Member Functions inherited from IMP::Restraint | |
| Restraint (Model *m, std::string name) | |
| Restraint * | create_current_decomposition () const |
| Decompose this restraint into constituent terms for the current conf. | |
| Restraint * | create_decomposition () const |
| Decompose this restraint into constituent terms. | |
| double | evaluate (bool calc_derivs) const |
| Return the score for this restraint for the current state of the model. | |
| double | evaluate_if_below (bool calc_derivatives, double max) const |
| See Model::evaluate_with_maximum() | |
| double | evaluate_if_good (bool calc_derivatives) const |
| See Model::evaluate_if_good() | |
| double | get_last_score () const |
| bool | get_was_good () const |
| virtual double | unprotected_evaluate (DerivativeAccumulator *) const =0 |
| virtual double | unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const |
| virtual double | unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const |
| virtual ContainersTemp | get_input_containers () const =0 |
| virtual ParticlesTemp | get_input_particles () const =0 |
| 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) | |
| ModelObjectsTemp | get_inputs () const |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| Public Member Functions inherited from IMP::base::Object | |
| std::size_t | __hash__ () const |
| virtual std::string | get_type_name () const =0 |
| Return a string identifying the type of the object. | |
| 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. | |
| 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) |
Static Public Member Functions | |
| static MSConnectivityRestraint * | get_from (IMP::base::Object *o) |
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 Restraints | do_create_decomposition () const |
| Protected Member Functions inherited from IMP::ModelObject | |
| virtual ModelObjectsTemp | do_get_inputs () const =0 |
| virtual ModelObjectsTemp | do_get_outputs () const =0 |
| virtual void | do_update_dependencies (const DependencyGraph &, const DependencyGraphVertexIndex &) |
| void | update_dependencies (const DependencyGraph &dg, const DependencyGraphVertexIndex &index) |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| IMP::core::MSConnectivityRestraint::MSConnectivityRestraint | ( | 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.
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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::Restraint.
| ParticlePairs 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.
