IMP logo
IMP Reference Guide  develop.374319d7bb,2024/06/17
The Integrative Modeling Platform
IMP::container::SingletonsRestraint Class Reference

Applies a SingletonScore to each Singleton in a list. More...

#include <IMP/container/SingletonsRestraint.h>

+ Inheritance diagram for IMP::container::SingletonsRestraint:

Detailed Description

Applies a SingletonScore to each Singleton in a list.

This restraint stores the used particle indexes in a ParticleIndexes. The container used can be set so that the list can be shared with other containers (or a nonbonded list can be used).

Examples using various multiplicity containers:

1 ## \example core/
2 # This fragment shows how to restrain a set of points stored in a
3 # SingletonContainer in a sphere of radius 'radius' centered around
4 # 'center'.
6 import IMP
7 import IMP.core
8 import sys
10 IMP.setup_from_argv(sys.argv, "restrain in sphere")
12 radius = 10
13 stiffness = 2
14 center = IMP.algebra.Vector3D(1, 2, 3)
15 m = IMP.Model()
16 p = m.add_particle("particle")
18  m, p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(100, 0, 0), 1))
20 ub = IMP.core.HarmonicUpperBound(radius, stiffness)
22 # Restrain based on the distance to a single point (hence a ball
23 ss = IMP.core.DistanceToSingletonScore(ub, center)
25 r = IMP.core.SingletonRestraint(m, ss, p)
26 r.evaluate(False)
1 ## \example container/
2 # This example shows how to set up an excluded volume restraint for a set
3 # of XYZRDecorator-style particles.
5 import IMP
6 import IMP.core
7 import IMP.atom
8 import IMP.container
9 import sys
11 IMP.setup_from_argv(sys.argv, "nonbonded interactions")
13 # This example adds a restraint on nonbonded interactions
14 # after excluding a set of bonded interactions.
16 m = IMP.Model()
17 # The set of particles
19  m, IMP.core.create_xyzr_particles(m, 20, 1.0))
21 # create a bond between two particles
22 bd0 = IMP.atom.Bonded.setup_particle(m, ps.get_indexes()[0])
23 bd1 = IMP.atom.Bonded.setup_particle(m, ps.get_indexes()[1])
24 IMP.atom.create_custom_bond(bd0, bd1, 2.0)
26 # Set up the nonbonded list for all pairs that are touching
27 # and let things move 3 before updating the list
28 nbl = IMP.container.ClosePairContainer(ps, 0.0, 3.0)
29 nbl.add_pair_filter(IMP.atom.BondedPairFilter())
31 # Set up excluded volume
33 evr = IMP.container.PairsRestraint(sdps, nbl)
35 # Set up optimizer
37 o.set_scoring_function([evr])
39 o.optimize(1000)
See Also

Definition at line 36 of file SingletonsRestraint.h.

Public Member Functions

 SingletonsRestraint (SingletonScore *ss, SingletonContainerAdaptor pc, std::string name="SingletonsRestraint %1%")
 Create the restraint with a shared container. More...
IMP::ModelObjectsTemp do_get_inputs () const
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
 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)

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_current_decomposition () 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::container::SingletonsRestraint::SingletonsRestraint ( SingletonScore ss,
SingletonContainerAdaptor  pc,
std::string  name = "SingletonsRestraint %1%" 

Create the restraint with a shared container.

[in]ssThe function to apply to each particle.
[in]pcThe container containing the stored particles. This container is not copied.
[in]nameThe object name

Definition at line 60 of file SingletonsRestraint.h.

Member Function Documentation

IMP::ModelObjectsTemp IMP::container::SingletonsRestraint::do_get_inputs ( ) const

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.

virtual ::IMP::VersionInfo IMP::container::SingletonsRestraint::get_version_info ( ) const

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 69 of file SingletonsRestraint.h.

double IMP::container::SingletonsRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator da) const

Return the unweighted score for the restraint.

Reimplemented from IMP::Restraint.

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