Ensure that a set of particles remains connected with one another. More...
#include <IMP/core/MSConnectivityRestraint.h>
Inheritance diagram for IMP::core::MSConnectivityRestraint:Public Member Functions | |
| MSConnectivityRestraint (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... | |
| PairScore * | get_pair_score () const |
| Return the pair score used for scoring. | |
| double | unprotected_evaluate (IMP::kernel::DerivativeAccumulator *accum) const |
| Public Member Functions inherited from IMP::kernel::Restraint | |
| Restraint (Model *m, std::string name) | |
| void | add_score_and_derivatives (ScoreAccumulator sa) const |
| Restraint * | create_current_decomposition () const |
| Decompose this restraint into constituent terms for the current conf. More... | |
| Restraint * | create_decomposition () const |
| Decompose this restraint into constituent terms. More... | |
| virtual ScoringFunction * | create_scoring_function (double weight=1.0, double max=NO_MAX) const |
| ContainersTemp | get_input_containers () const |
| ParticlesTemp | get_input_particles () const |
| 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 (Model *m, std::string name) | |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| Public Member Functions inherited from IMP::base::Object | |
| virtual void | clear_caches () |
| 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. 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::kernel::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const |
| virtual void | do_update_dependencies () |
| Related Functions inherited from IMP::kernel::Restraint | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > > | RestraintsTemp |
Detailed Description
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).
## \example core/ms_connectivity_restraint.py ## 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. ## #-- 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.
Definition at line 59 of file MSConnectivityRestraint.h.
Constructor & Destructor Documentation
| IMP::core::MSConnectivityRestraint::MSConnectivityRestraint | ( | PairScore * | ps, |
| double | eps = 0.1 |
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| ) |
If sc is nullptr, a ListSingletonContainer is created internally. eps is set to 0.1 by default.
Member Function Documentation
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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::kernel::Restraint.
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virtual |
Override if this reads other objects during evaluate.
Implements IMP::kernel::ModelObject.
| ParticlePairsTemp IMP::core::MSConnectivityRestraint::get_connected_pairs | ( | ) | const |
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.
The documentation for this class was generated from the following file: