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IMP Reference Guide
2.14.0
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
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include
IMP
npctransport
version 2.14.0
BodyStatisticsOptimizerState.h
Go to the documentation of this file.
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/**
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* \file npctransport/BodyStatisticsOptimizerState.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_BODY_STATISTICS_OPTIMIZER_STATE_H
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#define IMPNPCTRANSPORT_BODY_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/algebra/Transformation3D.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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class
Statistics;
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/** Track the rotational correlation time of a rigid body particle*/
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/** The correlation with at most the last 100 updates is tracked*/
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class
IMPNPCTRANSPORTEXPORT
BodyStatisticsOptimizerState
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:
public
core::PeriodicOptimizerState
{
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private
:
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typedef
core::PeriodicOptimizerState
P
;
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Particle
*p_;
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WeakPointer<IMP::npctransport::Statistics>
statistics_manager_;
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// time series of the positions of particles in the chain:
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std::deque<algebra::Transformation3D> positions_;
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std::deque<double> times_fs_;
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Particle
*get_particle()
const
{
return
p_; }
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void
add_orientation(
algebra::Rotation3D
rot) { positions_.push_back(rot); }
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double
get_dt()
const
;
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public
:
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/**
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@param p the particle being wrapped
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@param statistics_manager an optional statistical manager to which statistical updates are sent
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(of e.g. zr-distribution that are collectively gathered)
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@param periodicity frame interval for statistics, equiv. to set_period(1)
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*/
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BodyStatisticsOptimizerState
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(
Particle
*p,
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IMP::npctransport::Statistics
* statistics_manager =
nullptr
,
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unsigned
int
periodicity=1);
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double
get_correlation_time()
const
;
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double
get_diffusion_coefficient
()
const
;
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void
reset
();
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/** updates the z-r distriubution table in owner's statistics
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for this particle type (distribution of z coordinates and r coordinates)
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*/
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void
update_particle_type_zr_distribution_map();
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virtual
void
do_update
(
unsigned
int
call_num)
IMP_OVERRIDE
;
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IMP_OBJECT_METHODS
(
BodyStatisticsOptimizerState
);
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};
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IMP_OBJECTS
(
BodyStatisticsOptimizerState
,
BodyStatisticsOptimizerStates
);
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IMPNPCTRANSPORT_END_NAMESPACE
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#endif
/* IMPNPCTRANSPORT_BODY_STATISTICS_OPTIMIZER_STATE_H */
IMP::WeakPointer
Smart pointer to Object-derived classes that does not refcount.
Definition:
WeakPointer.h:76
IMP_OBJECT_METHODS
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition:
object_macros.h:25
PeriodicOptimizerState.h
Angle restraint between three particles.
IMP::OptimizerState::do_update
virtual void do_update(unsigned int)
Definition:
OptimizerState.h:120
IMP::npctransport::Statistics
Statistics and order parameters about the simulations.
Definition:
npctransport/Statistics.h:61
IMP::Vector
A more IMP-like version of the std::vector.
Definition:
Vector.h:39
IMP::OptimizerState::reset
virtual void reset()
Reset counters, as if at the start of an optimize run.
Transformation3D.h
Simple 3D transformation class.
IMP::algebra::Rotation3D
3D rotation class.
Definition:
Rotation3D.h:51
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::OptimizerState
Shared optimizer state that is invoked upon commitment of new coordinates.
Definition:
OptimizerState.h:43
typedefs.h
description
IMP::Particle
Class to handle individual particles of a Model object.
Definition:
Particle.h:41
OptimizerState.h
Shared optimizer state.
IMP::atom::get_diffusion_coefficient
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
IMP::npctransport::BodyStatisticsOptimizerState
Definition:
BodyStatisticsOptimizerState.h:26
IMP_OVERRIDE
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Definition:
compiler_macros.h:78