Apply a PairFunction to a PairContainer to maintain an invariant. More...

#include <IMP/container/PairsConstraint.h>

Inheritance diagram for IMP::container::PairsConstraint:

Public Member Functions
	PairsConstraint (PairModifier before, PairDerivativeModifier after, PairContainerAdaptor c, std::string name="PairConstraint %1%")

Public Member Functions inherited from IMP::kernel::Constraint
	Constraint (Model *m, std::string name="Constraint %1%")

virtual void	do_after_evaluate (DerivativeAccumulator *da)

virtual void	do_before_evaluate ()

Public Member Functions inherited from IMP::kernel::ScoreState
	ScoreState (Model *m, std::string name="ScoreState %1%")

void	after_evaluate (DerivativeAccumulator *accpt)
	Do post evaluation work if needed.

void	before_evaluate ()
	Force update of the structure.

ContainersTemp	get_input_containers () const

ParticlesTemp	get_input_particles () const

ContainersTemp	get_output_containers () const

ParticlesTemp	get_output_particles () const

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)

Protected Member Functions
virtual ModelObjectsTemp	do_get_inputs () const

virtual ModelObjectsTemp	do_get_outputs () const

void	do_update_attributes ()

void	do_update_derivatives (DerivativeAccumulator *da)

Related Functions
(Note that these are not member functions.)
typedef IMP::base::Vector < IMP::base::WeakPointer < PairsConstraint > >	PairsConstraintsTemp

Related Functions inherited from IMP::kernel::Constraint
typedef IMP::base::Vector < IMP::base::WeakPointer < Constraint > >	ConstraintsTemp

Related Functions inherited from IMP::kernel::ScoreState
typedef IMP::base::Vector < IMP::base::WeakPointer < ScoreState > >	ScoreStatesTemp

Related Functions inherited from IMP::kernel::ModelObject
typedef IMP::base::Vector < IMP::base::WeakPointer < ModelObject > >	ModelObjectsTemp

Related Functions inherited from IMP::base::Object
typedef IMP::base::Vector < IMP::base::WeakPointer < Object > >	ObjectsTemp

Detailed Description

The score state is passed up to two PairModifiers, one to apply before evaluation and the other after. The one after should take a DerivativeAccumulator as its last argument for PairModifier::apply() and will only be called if the score was computed with derivatives.

An example showing a how to use such a score state to maintain a cover of the atoms of a protein by a sphere per residue.

## \example core/cover_particles.py
## Show how to maintain a sphere per residue which includes all atoms of the residue. The derivatives are propagated from the sphere cover to the atoms so that restraints can be used at multiple levels.

import IMP
import IMP.core
import IMP.atom
import IMP.atom

m= IMP.Model()
prot= IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m)
res= IMP.atom.get_by_type(prot, IMP.atom.RESIDUE_TYPE)
pr= IMP.core.ChildrenRefiner(IMP.atom.Hierarchy.get_traits())
for r in res:
    # add coordinates and a radius to the residue particle
    IMP.core.XYZR.setup_particle(r)
    # make sure that the coordinates and the radius define a sphere
    # which contains all of the leaves (atoms) of the residue
    IMP.core.Cover.setup_particle(r.get_particle(), pr)
# update the coordinates of the residue particles so that they cover the atoms
m.update()

See Also: core::PairConstraint

Definition at line 43 of file PairsConstraint.h.

Constructor & Destructor Documentation

IMP::container::PairsConstraint::PairsConstraint	(	PairModifier *	before,
		PairDerivativeModifier *	after,
		PairContainerAdaptor	c,
		std::string	name = `"PairConstraint %1%"`
	)

Parameters

[in]	c	The Container to hold the elements to process
[in]	before	The PairModifier to apply to all elements before evaluate.
[in]	after	The PairModifier to apply to all elements after evaluate.
[in]	name	The object name