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FretRestraint.h
Go to the documentation of this file.
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/**
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* \file IMP/isd/FretRestraint.h
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* \brief FRET_R restraint
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* to use in vivo FRET data [Muller et al. Mol Biol Cell 16, 3341, 2005]
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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 IMPISD_FRET_RESTRAINT_H
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#define IMPISD_FRET_RESTRAINT_H
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#include <
IMP/isd/Scale.h
>
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#include "isd_config.h"
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#include <
IMP/kernel/Restraint.h
>
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#include <
IMP/isd/FretData.h
>
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IMPISD_BEGIN_NAMESPACE
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/** A restraint for using in-vivo ensemble FRET data,
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see Muller et al. Mol Biol Cell 16, 3341, 2005 for more info.
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*/
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class
IMPISDEXPORT
FretRestraint
:
public
kernel::Restraint
{
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kernel::Particles
pd_;
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kernel::Particles
pa_;
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base::Pointer<kernel::Particle>
prd_;
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algebra::Vector3D
GMMterd_;
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algebra::Vector3Ds
GMMctrd_;
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base::Pointer<kernel::Particle>
pra_;
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algebra::Vector3D
GMMtera_;
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algebra::Vector3Ds
GMMctra_;
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base::Pointer<kernel::Particle>
kda_;
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base::Pointer<kernel::Particle>
Ida_;
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base::Pointer<kernel::Particle>
R0_;
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base::Pointer<kernel::Particle>
sumFi_;
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base::Pointer<kernel::Particle>
sigma0_;
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base::Pointer<kernel::Particle>
Pbl_;
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base::PointerMember<FretData>
data_;
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double
fexp_;
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double
multi_d_;
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int
constr_type_;
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Floats
GMMsig_;
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Floats
GMMw_;
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unsigned
Na_;
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mutable
Floats
power6_;
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std::vector<std::vector<unsigned> > states_;
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double
get_sumFi(
double
Pbleach)
const
;
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std::vector<unsigned> get_indices(
unsigned
index,
int
dimension)
const
;
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public
:
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//! Create the restraint.
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/** kernel::Restraints should store the particles they are to act on,
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preferably in a Singleton or PairContainer as appropriate.
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*/
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FretRestraint
(
kernel::Particles
pd,
kernel::Particles
pa,
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kernel::Particle
*kda,
kernel::Particle
*Ida,
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kernel::Particle
*R0,
kernel::Particle
*sigma0,
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kernel::Particle
*Pbl,
double
fexp,
double
m_d = 1.0,
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double
m_a = 1.0);
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FretRestraint
(
kernel::Particle
*kda,
kernel::Particle
*Ida,
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kernel::Particle
*sumFi,
kernel::Particle
*sigma0,
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kernel::Particle
*Pbl,
double
fexp);
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FretRestraint
(
kernel::Particle
*prd,
algebra::Vector3D
GMMterd,
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algebra::Vector3Ds
GMMctrd,
Floats
GMMwd,
Floats
GMMsigd,
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kernel::Particle
*pra,
algebra::Vector3D
GMMtera,
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algebra::Vector3Ds
GMMctra,
Floats
GMMwa,
Floats
GMMsiga,
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kernel::Particle
*kda,
kernel::Particle
*Ida,
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kernel::Particle
*sigma0,
kernel::Particle
*Pbl,
FretData
*data,
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double
fexp);
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// get sumFi
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double
get_sumFi()
const
;
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// get average sigma
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double
get_average_sigma(
double
fmod)
const
;
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// lognormal standard error (according to Wikipedia)
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double
get_standard_error()
const
;
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// get model fret_r (for the two constructors, i.e. type 0 and 1)
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double
get_model_fretr()
const
;
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// get probability
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double
get_probability()
const
;
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// get experimental value
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double
get_experimental_value()
const
{
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return
fexp_;
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};
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// set experimental value
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void
set_experimental_value(
double
fexp);
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/** This macro declares the basic needed methods: evaluate and show
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*/
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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
(
FretRestraint
);
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private
:
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double
get_model_fretr_type_0()
const
;
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double
get_model_fretr_type_1()
const
;
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algebra::Vector3Ds
get_current_centers(
kernel::Particle
*p,
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const
algebra::Vector3Ds
&ctrs)
const
;
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algebra::Vector3D
get_current_center(
kernel::Particle
*p,
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const
algebra::Vector3D
&ctr)
const
;
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};
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IMPISD_END_NAMESPACE
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#endif
/* IMPISD_FRET_RESTRAINT_H */
IMP::kernel::DerivativeAccumulator
Class for adding derivatives from restraints to the model.
Definition:
kernel/DerivativeAccumulator.h:25
IMP::base::PointerMember
A smart pointer to a ref-counted Object that is a class member.
Definition:
Pointer.h:147
IMP_OBJECT_METHODS
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition:
object_macros.h:25
Scale.h
A decorator for scale parameters particles.
IMP::base::Pointer
A smart pointer to a reference counted object.
Definition:
Pointer.h:87
IMP::base::Vector< base::Pointer< Particle > >
Restraint.h
Abstract base class for all restraints.
IMP::isd::FretRestraint
Definition:
FretRestraint.h:22
IMP::kernel::Restraint
A restraint is a term in an IMP ScoringFunction.
Definition:
kernel/Restraint.h:52
IMP::kernel::Particle
Class to handle individual model particles.
Definition:
kernel/Particle.h:37
IMP::algebra::Vector3D
VectorD< 3 > Vector3D
Definition:
VectorD.h:395
IMP::kernel::ModelObject::do_get_inputs
virtual ModelObjectsTemp do_get_inputs() const =0
IMP::isd::FretData
Auxiliary class for FRET_R restraint.
Definition:
FretData.h:22
FretData.h
Auxiliary class useful for FRET_R restraint.
IMP_OVERRIDE
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Definition:
compiler_macros.h:75