home
about
news
download
doc
source
systems
tests
bugs
contact
IMP Reference Guide
2.20.2
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
Examples
include
IMP
isd
version 2.20.2
TALOSRestraint.h
Go to the documentation of this file.
1
/**
2
* \file IMP/isd/TALOSRestraint.h
3
* \brief TALOS dihedral restraint between four particles.
4
*
5
* Copyright 2007-2022 IMP Inventors. All rights reserved.
6
*
7
*/
8
9
#ifndef IMPISD_TALOS_RESTRAINT_H
10
#define IMPISD_TALOS_RESTRAINT_H
11
12
#include <IMP/isd/isd_config.h>
13
#include "
Scale.h
"
14
#include "
vonMisesSufficient.h
"
15
16
#include <
IMP/Restraint.h
>
17
#include <
IMP/Particle.h
>
18
19
IMPISD_BEGIN_NAMESPACE
20
21
//! phi/psi dihedral restraint between four particles, using data from TALOS.
22
/** The likelihood is
23
\f[
24
f(\chi_{exp}^1,\cdots,\chi_{exp}^N|\chi(X),\kappa,I)
25
= \frac{1}{2\pi I_0(\kappa)^N}
26
\exp \left(R_0 \kappa \cos (\chi_{exp}-\chi(X)) \right)
27
\f]
28
where the sufficient statistics are \f$N\f$ the number of observations,
29
\f$R\f$ and \f$\chi_{exp}\f$.
30
\see vonMisesSufficient.h for further detail.
31
*/
32
class
IMPISDEXPORT
TALOSRestraint
:
public
Restraint
{
33
public
:
34
//! Create restraint from a list of particles and the data.
35
/** \param[in] m the Model
36
\param[in] p list of 4 particles that make the dihedral angle.
37
\param[in] data list of observations for that angle.
38
\param[in] kappa Pointer to the \f$\kappa\f$ concentration particle.
39
*/
40
TALOSRestraint
(
Model
*m,
Particles
p,
Floats
data,
41
Particle
*kappa);
42
43
//! Create restraint from 4 particles and the data.
44
/** \param[in] m the Model
45
\param[in] p1 Pointer to first particle in dihedral restraint.
46
\param[in] p2 Pointer to second particle in dihedral restraint.
47
\param[in] p3 Pointer to third particle in dihedral restraint.
48
\param[in] p4 Pointer to fourth particle in dihedral restraint.
49
\param[in] data list of observations for that angle.
50
\param[in] kappa Pointer to the \f$\kappa\f$ concentration particle.
51
*/
52
TALOSRestraint
(
Model
*m,
Particle
*p1,
Particle
*p2,
53
Particle
*p3,
Particle
*p4,
Floats
data,
54
Particle
*kappa);
55
56
//! Create restraint from a list of particles and the sufficient statistics.
57
/** \param[in] m the Model
58
\param[in] p list of 4 particles that make the dihedral angle.
59
\param[in] N Number of observations
60
\param[in] R0 component on the x axis
61
\param[in] chiexp average observed angle.
62
\param[in] kappa Pointer to the \f$\kappa\f$ concentration particle.
63
*/
64
TALOSRestraint
(
Model
*m,
Particles
p,
unsigned
N,
double
R0,
65
double
chiexp,
Particle
*kappa);
66
67
//! Create restraint from 4 particles and the sufficient statistics.
68
/** \param[in] m the Model
69
\param[in] p1 Pointer to first particle in dihedral restraint.
70
\param[in] p2 Pointer to second particle in dihedral restraint.
71
\param[in] p3 Pointer to third particle in dihedral restraint.
72
\param[in] p4 Pointer to fourth particle in dihedral restraint.
73
\param[in] N Number of observations
74
\param[in] R0 component on the x axis
75
\param[in] chiexp average observed angle.
76
\param[in] kappa Pointer to the \f$\kappa\f$ concentration particle.
77
*/
78
TALOSRestraint
(
Model
*m,
Particle
*p1,
Particle
*p2,
79
Particle
*p3,
Particle
*p4,
unsigned
N,
80
double
R0,
double
chiexp,
Particle
*kappa);
81
82
//! Call for probability
83
double
get_probability
()
const
{
return
exp(-
unprotected_evaluate
(
nullptr
)); }
84
85
double
get_R0()
const
{
return
mises_->get_R0(); }
86
87
double
get_chiexp()
const
{
return
mises_->get_chiexp(); }
88
89
virtual
double
unprotected_evaluate
(
IMP::DerivativeAccumulator
*accum)
90
const override
;
91
virtual
IMP::ModelObjectsTemp
do_get_inputs
()
const override
;
92
IMP_OBJECT_METHODS
(
TALOSRestraint
);
93
94
private
:
95
Pointer<Particle>
p_[4];
96
Pointer<Particle>
kappa_;
97
Pointer<vonMisesSufficient>
mises_;
98
};
99
100
IMPISD_END_NAMESPACE
101
102
#endif
/* IMPISD_TALOS_RESTRAINT_H */
vonMisesSufficient.h
Normal distribution of Function.
IMP_OBJECT_METHODS
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition:
object_macros.h:25
IMP::Restraint::unprotected_evaluate
virtual double unprotected_evaluate(DerivativeAccumulator *da) const
Return the unweighted score for the restraint.
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::Vector< Pointer< Particle > >
IMP::Pointer
A smart pointer to a reference counted object.
Definition:
Pointer.h:87
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition:
Model.h:86
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 is in int...
IMP::Particle
Class to handle individual particles of a Model object.
Definition:
Particle.h:43
Restraint.h
Abstract base class for all restraints.
IMP::ModelObject::do_get_inputs
virtual ModelObjectsTemp do_get_inputs() const =0
IMP::DerivativeAccumulator
Class for adding derivatives from restraints to the model.
Definition:
DerivativeAccumulator.h:24
IMP::Restraint
A restraint is a term in an IMP ScoringFunction.
Definition:
Restraint.h:56