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IMP Reference Guide
2.14.0
The Integrative Modeling Platform
IMP Manual
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include
IMP
npctransport
version 2.14.0
ChainStatisticsOptimizerState.h
Go to the documentation of this file.
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/**
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* \file npctransport/ChainStatisticsOptimizerState.h
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* \brief description
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*
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* Copyright 2007-2020 IMP Inventors. All rights reserved.
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*/
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#ifndef IMPNPCTRANSPORT_CHAIN_STATISTICS_OPTIMIZER_STATE_H
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#define IMPNPCTRANSPORT_CHAIN_STATISTICS_OPTIMIZER_STATE_H
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#include "npctransport_config.h"
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#include <
IMP/Particle.h
>
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#include <
IMP/OptimizerState.h
>
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//#include <IMP/optimizer_state_macros.h>
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#include <
IMP/core/PeriodicOptimizerState.h
>
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#include <
IMP/npctransport/typedefs.h
>
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#include <deque>
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IMPNPCTRANSPORT_BEGIN_NAMESPACE
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/** Compute various statistics of a chain.*/
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class
IMPNPCTRANSPORTEXPORT
ChainStatisticsOptimizerState
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:
public
core::PeriodicOptimizerState
{
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private
:
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typedef
core::PeriodicOptimizerState
P
;
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// particles in the chain:
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ParticlesTemp
ps_;
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// time series of the positions of particles in the chain:
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std::deque<algebra::Vector3Ds> positions_;
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std::deque<double> times_fs_;
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// mean radius-of-gyration and its square since last reset
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double
mean_rgyr_;
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double
mean_rgyr2_;
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// mean end-to-end length and its square since last reset
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double
mean_end_to_end_;
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double
mean_end_to_end2_;
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// mean bond distance and its square since last reset
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double
mean_bond_distance_;
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double
mean_bond_distance2_;
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// number of samples over which means are computed
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int
n_;
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double
get_dt()
const
;
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public
:
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/**
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@param ps the particles being wrapped
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@param periodicity frame interval for statistics, equiv. to set_period(1)
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*/
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ChainStatisticsOptimizerState
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(
const
ParticlesTemp
&ps,
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unsigned
int
periodicity = 1);
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double
get_correlation_time()
const
;
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//! returns a vector of diffusion coefficients
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//! for each particle in the chain, computed in the local
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//! reference frame of the chain (by locally aligning
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//! the chain)
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Floats
get_local_diffusion_coefficients()
const
;
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//! get an estimate of the diffusion coefficient
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//! of the entire chain in A^2/fs units
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double
get_diffusion_coefficient
()
const
;
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//! returns the mean Rgyr of this chain
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double
get_mean_radius_of_gyration
()
const
{
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return
mean_rgyr_;
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}
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//! returns the mean Rgyr^2, which can be used to compute
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//! std-dev (but recorded separately so it could be averaged with
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//! other chains)
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double
get_mean_square_radius_of_gyration
()
const
{
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return
mean_rgyr2_;
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}
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//! returns the mean end-to-end distance of this chain
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double
get_mean_end_to_end_distance
()
const
{
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return
mean_end_to_end_;
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}
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//! returns the mean square end-to-end distance, which can be used to compute
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//! std-dev (but recorded separately so it could be averaged with
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//! other chains)
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double
get_mean_square_end_to_end_distance
()
const
{
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return
mean_end_to_end2_;
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}
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//! returns the mean bond distance of this chain
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double
get_mean_bond_distance
()
const
{
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return
mean_bond_distance_;
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}
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//! returns the mean square bond distance, which can be used to compute
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//! std-dev (but recorded separately so it could be averaged with
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//! other chains)
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double
get_mean_square_bond_distance
()
const
{
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return
mean_bond_distance2_;
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}
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/**
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Resets all the statistics about that chain
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*/
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void
reset
();
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virtual
void
do_update
(
unsigned
int
call_num)
IMP_OVERRIDE
;
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IMP_OBJECT_METHODS
(
ChainStatisticsOptimizerState
);
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};
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IMP_OBJECTS
(
ChainStatisticsOptimizerState
,
ChainStatisticsOptimizerStates
);
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IMPNPCTRANSPORT_END_NAMESPACE
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#endif
/* IMPNPCTRANSPORT_CHAIN_STATISTICS_OPTIMIZER_STATE_H */
IMP_OBJECT_METHODS
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition:
object_macros.h:25
IMP::npctransport::ChainStatisticsOptimizerState
Definition:
ChainStatisticsOptimizerState.h:22
PeriodicOptimizerState.h
Angle restraint between three particles.
IMP::OptimizerState::do_update
virtual void do_update(unsigned int)
Definition:
OptimizerState.h:120
IMP::Vector< WeakPointer< Particle > >
IMP::npctransport::ChainStatisticsOptimizerState::get_mean_square_end_to_end_distance
double get_mean_square_end_to_end_distance() const
Definition:
ChainStatisticsOptimizerState.h:92
IMP::npctransport::ChainStatisticsOptimizerState::get_mean_end_to_end_distance
double get_mean_end_to_end_distance() const
returns the mean end-to-end distance of this chain
Definition:
ChainStatisticsOptimizerState.h:85
IMP::npctransport::ChainStatisticsOptimizerState::get_mean_radius_of_gyration
double get_mean_radius_of_gyration() const
returns the mean Rgyr of this chain
Definition:
ChainStatisticsOptimizerState.h:73
IMP::npctransport::ChainStatisticsOptimizerState::get_mean_bond_distance
double get_mean_bond_distance() const
returns the mean bond distance of this chain
Definition:
ChainStatisticsOptimizerState.h:97
IMP::OptimizerState::reset
virtual void reset()
Reset counters, as if at the start of an optimize run.
IMP::npctransport::ChainStatisticsOptimizerState::get_mean_square_radius_of_gyration
double get_mean_square_radius_of_gyration() const
Definition:
ChainStatisticsOptimizerState.h:80
Particle.h
Classes to handle individual model particles. (Note that implementation of inline functions is in int...
IMP_OBJECTS
#define IMP_OBJECTS(Name, PluralName)
Define the types for storing lists of object pointers.
Definition:
object_macros.h:44
IMP::npctransport::ChainStatisticsOptimizerState::get_mean_square_bond_distance
double get_mean_square_bond_distance() const
Definition:
ChainStatisticsOptimizerState.h:104
IMP::OptimizerState
Shared optimizer state that is invoked upon commitment of new coordinates.
Definition:
OptimizerState.h:43
typedefs.h
description
OptimizerState.h
Shared optimizer state.
IMP::atom::get_diffusion_coefficient
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
IMP_OVERRIDE
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Definition:
compiler_macros.h:78