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TALOSRestraint.h
Go to the documentation of this file.
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/**
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* \file IMP/isd/TALOSRestraint.h
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* \brief TALOS dihedral restraint between four particles.
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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_TALOS_RESTRAINT_H
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#define IMPISD_TALOS_RESTRAINT_H
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#include <IMP/isd/isd_config.h>
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#include "
Scale.h
"
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#include "
vonMisesSufficient.h
"
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#include <
IMP/kernel/Restraint.h
>
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#include <
IMP/kernel/Particle.h
>
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IMPISD_BEGIN_NAMESPACE
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//! phi/psi dihedral restraint between four particles, using data from TALOS.
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/** The likelihood is
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\f[
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f(\chi_{exp}^1,\cdots,\chi_{exp}^N|\chi(X),\kappa,I)
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= \frac{1}{2\pi I_0(\kappa)^N}
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\exp \left(R_0 \kappa \cos (\chi_{exp}-\chi(X)) \right)
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\f]
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where the sufficient statistics are \f$N\f$ the number of observations,
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\f$R\f$ and \f$\chi_{exp}\f$.
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\see vonMisesSufficient.h for further detail.
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*/
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class
IMPISDEXPORT
TALOSRestraint
:
public
kernel::Restraint
{
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public
:
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//! Create restraint from a list of particles and the data.
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/** \param[in] m the Model
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\param[in] p list of 4 particles that make the dihedral angle.
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\param[in] data list of observations for that angle.
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\param[in] kappa Pointer to the \f$\kappa\f$ concentration particle.
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*/
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TALOSRestraint
(
kernel::Model
*m,
kernel::Particles
p,
Floats
data,
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kernel::Particle
*kappa);
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//! Create restraint from 4 particles and the data.
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/** \param[in] m the Model
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\param[in] p1 Pointer to first particle in dihedral restraint.
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\param[in] p2 Pointer to second particle in dihedral restraint.
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\param[in] p3 Pointer to third particle in dihedral restraint.
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\param[in] p4 Pointer to fourth particle in dihedral restraint.
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\param[in] data list of observations for that angle.
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\param[in] kappa Pointer to the \f$\kappa\f$ concentration particle.
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*/
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TALOSRestraint
(
kernel::Model
*m,
kernel::Particle
*p1,
kernel::Particle
*p2,
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kernel::Particle
*p3,
kernel::Particle
*p4,
Floats
data,
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kernel::Particle
*kappa);
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//! Create restraint from a list of particles and the sufficient statistics.
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/** \param[in] m the Model
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\param[in] p list of 4 particles that make the dihedral angle.
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\param[in] N Number of observations
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\param[in] R0 component on the x axis
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\param[in] chiexp average observed angle.
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\param[in] kappa Pointer to the \f$\kappa\f$ concentration particle.
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*/
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TALOSRestraint
(
kernel::Model
*m,
kernel::Particles
p,
unsigned
N,
double
R0,
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double
chiexp,
kernel::Particle
*kappa);
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//! Create restraint from 4 particles and the sufficient statistics.
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/** \param[in] m the Model
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\param[in] p1 Pointer to first particle in dihedral restraint.
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\param[in] p2 Pointer to second particle in dihedral restraint.
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\param[in] p3 Pointer to third particle in dihedral restraint.
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\param[in] p4 Pointer to fourth particle in dihedral restraint.
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\param[in] N Number of observations
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\param[in] R0 component on the x axis
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\param[in] chiexp average observed angle.
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\param[in] kappa Pointer to the \f$\kappa\f$ concentration particle.
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*/
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TALOSRestraint
(
kernel::Model
*m,
kernel::Particle
*p1,
kernel::Particle
*p2,
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kernel::Particle
*p3,
kernel::Particle
*p4,
unsigned
N,
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double
R0,
double
chiexp,
kernel::Particle
*kappa);
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//! Call for probability
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double
get_probability
()
const
{
return
exp(-unprotected_evaluate(
nullptr
)); }
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double
get_R0()
const
{
return
mises_->get_R0(); }
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double
get_chiexp()
const
{
return
mises_->get_chiexp(); }
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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
(
TALOSRestraint
);
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private:
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base::Pointer<kernel::
Particle
> p_[4];
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base::Pointer<kernel::
Particle
> kappa_;
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base::Pointer<
vonMisesSufficient
> mises_;
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};
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IMPISD_END_NAMESPACE
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#endif
/* IMPISD_TALOS_RESTRAINT_H */
vonMisesSufficient.h
Normal distribution of Function.
IMP::kernel::DerivativeAccumulator
Class for adding derivatives from restraints to the model.
Definition:
kernel/DerivativeAccumulator.h:25
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::isd::TALOSRestraint::get_probability
double get_probability() const
Call for probability.
Definition:
TALOSRestraint.h:83
IMP::base::Vector< base::Pointer< Particle > >
IMP::isd::vonMisesSufficient
vonMisesSufficient
Definition:
vonMisesSufficient.h:36
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::kernel::Particle
Class to handle individual model particles.
Definition:
kernel/Particle.h:37
IMP::isd::TALOSRestraint
phi/psi dihedral restraint between four particles, using data from TALOS.
Definition:
TALOSRestraint.h:32
Particle.h
Classes to handle individual model particles. (Note that implementation of inline functions in in int...
IMP::kernel::ModelObject::do_get_inputs
virtual ModelObjectsTemp do_get_inputs() const =0
IMP_OVERRIDE
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Definition:
compiler_macros.h:75
IMP::kernel::Model
Class for storing model, its restraints, constraints, and particles.
Definition:
kernel/Model.h:73