IMP Reference Guide  develop.8b7eb21230,2024/06/24 The Integrative Modeling Platform

#include <IMP/container/QuadsRestraint.h>

## Detailed Description

This restraint stores the used particle indexes in a ParticleIndexQuads. 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/restrain_in_sphere.py
2 # This fragment shows how to restrain a set of points stored in a
4 # 'center'.
5
6 import IMP
7 import IMP.core
8 import sys
9
10 IMP.setup_from_argv(sys.argv, "restrain in sphere")
11
13 stiffness = 2
14 center = IMP.algebra.Vector3D(1, 2, 3)
15 m = IMP.Model()
18  m, p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(100, 0, 0), 1))
19
21
22 # Restrain based on the distance to a single point (hence a ball
23 ss = IMP.core.DistanceToSingletonScore(ub, center)
24
25 r = IMP.core.SingletonRestraint(m, ss, p)
26 r.evaluate(False)
1 ## \example container/nonbonded_interactions.py
2 # This example shows how to set up an excluded volume restraint for a set
3 # of XYZRDecorator-style particles.
4
5 import IMP
6 import IMP.core
7 import IMP.atom
8 import IMP.container
9 import sys
10
11 IMP.setup_from_argv(sys.argv, "nonbonded interactions")
12
13 # This example adds a restraint on nonbonded interactions
14 # after excluding a set of bonded interactions.
15
16 m = IMP.Model()
17 # The set of particles
19  m, IMP.core.create_xyzr_particles(m, 20, 1.0))
20
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)
25
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)
30
31 # Set up excluded volume
33 evr = IMP.container.PairsRestraint(sdps, nbl)
34
35 # Set up optimizer
37 o.set_scoring_function([evr])
38
39 o.optimize(1000)

Definition at line 36 of file QuadsRestraint.h.

## Public Member Functions

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)

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::QuadsRestraint::QuadsRestraint ( QuadScore * ss, QuadContainerAdaptor pc, std::string name = "QuadsRestraint %1%" )

Create the restraint with a shared container.

Parameters
 [in] ss The function to apply to each particle. [in] pc The container containing the stored particles. This container is not copied. [in] name The object name

Definition at line 60 of file QuadsRestraint.h.

## Member Function Documentation

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.

 virtual ::IMP::VersionInfo IMP::container::QuadsRestraint::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 69 of file QuadsRestraint.h.

 double IMP::container::QuadsRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator * da ) const
virtual

Return the unweighted score for the restraint.

Reimplemented from IMP::Restraint.

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