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multifit/RadiusOfGyrationRestraint.h
Go to the documentation of this file.
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/**
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* \file IMP/multifit/RadiusOfGyrationRestraint.h
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* \brief radius of gyration restraint.
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*
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* Restrict max distance between every pair of particle
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*
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* Copyright 2007-2014 IMP Inventors. All rights reserved.
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*
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*/
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#ifndef IMPMULTIFIT_RADIUS_OF_GYRATION_RESTRAINT_H
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#define IMPMULTIFIT_RADIUS_OF_GYRATION_RESTRAINT_H
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#include <IMP/multifit/multifit_config.h>
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#include <
IMP/kernel/Restraint.h
>
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#include <
IMP/core/HarmonicUpperBound.h
>
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#include <
IMP/kernel/Particle.h
>
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#include <
IMP/kernel/container_macros.h
>
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IMPMULTIFIT_BEGIN_NAMESPACE
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//! Ensure the radius of gyration of particles fits the predicted one
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/**
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/note a harmonic upper bound is applied between
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the predicted radius and the actual radius
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*/
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class
IMPMULTIFITEXPORT
RadiusOfGyrationRestraint
:
public
kernel::Restraint
{
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public
:
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//! Constructor
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/**
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\param[in] ps the particles to work on
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\param[in] num_residues the number of residues the particles represent
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\param[in] scale allow the radius of gyration of the particles
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to be at most scale times the predicted one
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*/
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RadiusOfGyrationRestraint
(
kernel::Particles
ps,
int
num_residues,
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Float
scale = 1.);
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virtual
double
unprotected_evaluate(
IMP::kernel::DerivativeAccumulator
*accum)
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const
IMP_OVERRIDE;
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virtual
IMP::kernel::ModelObjectsTemp
do_get_inputs
()
const
IMP_OVERRIDE;
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IMP_OBJECT_METHODS
(
RadiusOfGyrationRestraint
);
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//! Set the predicted radius of gyration used in the restraint
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void
set_radius_of_gyration
(
Float
r) {
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predicted_rog_ = r;
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hub_ =
new
core::HarmonicUpperBound
(predicted_rog_ * scale_, 1);
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}
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//! Get the predicted radius of gyration used in the restraint
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inline
Float
get_radius_of_gyration
() {
return
predicted_rog_; }
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#ifndef SWIG
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IMP_LIST
(
private
,
Particle
, particle,
kernel::Particle
*,
kernel::Particles
);
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#endif
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protected
:
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kernel::Model
*mdl_;
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Float
predicted_rog_;
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Float
scale_;
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base::Pointer<core::HarmonicUpperBound>
hub_;
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};
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IMPMULTIFITEXPORT
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float
get_approximated_radius_of_gyration(
int
len);
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IMPMULTIFITEXPORT
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float
get_actual_radius_of_gyration(
kernel::ParticlesTemp
ps);
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IMPMULTIFITEXPORT
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float
get_approximated_radius(
int
len);
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IMPMULTIFIT_END_NAMESPACE
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#endif
/* IMPMULTIFIT_RADIUS_OF_GYRATION_RESTRAINT_H */
IMP::multifit::RadiusOfGyrationRestraint::set_radius_of_gyration
void set_radius_of_gyration(Float r)
Set the predicted radius of gyration used in the restraint.
Definition:
multifit/RadiusOfGyrationRestraint.h:43
IMP::kernel::DerivativeAccumulator
Class for adding derivatives from restraints to the model.
Definition:
kernel/DerivativeAccumulator.h:25
IMP::core::HarmonicUpperBound
Upper bound harmonic function (non-zero when feature > mean)
Definition:
core/HarmonicUpperBound.h:20
IMP::multifit::RadiusOfGyrationRestraint::get_radius_of_gyration
Float get_radius_of_gyration()
Get the predicted radius of gyration used in the restraint.
Definition:
multifit/RadiusOfGyrationRestraint.h:48
IMP::base::Pointer< core::HarmonicUpperBound >
IMP::base::Vector< base::Pointer< Particle > >
Restraint.h
Abstract base class for all restraints.
IMP::kernel::Restraint
A restraint is a term in an IMP ScoringFunction.
Definition:
kernel/Restraint.h:52
IMP_OBJECT_METHODS
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition:
base/object_macros.h:25
IMP::kernel::Particle
Class to handle individual model particles.
Definition:
kernel/Particle.h:34
Particle.h
Classes to handle individual model particles.
IMP::multifit::RadiusOfGyrationRestraint
Ensure the radius of gyration of particles fits the predicted one.
Definition:
multifit/RadiusOfGyrationRestraint.h:27
IMP::kernel::ModelObject::do_get_inputs
virtual ModelObjectsTemp do_get_inputs() const =0
IMP::Float
double Float
Basic floating-point value (could be float, double...)
Definition:
base/types.h:20
IMP_LIST
#define IMP_LIST(protection, Ucname, lcname, Data, PluralData)
A macro to provide a uniform interface for storing lists of objects.
Definition:
kernel/container_macros.h:90
container_macros.h
Macros to define containers of objects.
HarmonicUpperBound.h
Harmonic upper bound function.
IMP::kernel::Model
Class for storing model, its restraints, constraints, and particles.
Definition:
kernel/Model.h:72