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IMP Reference Guide  2.12.0
The Integrative Modeling Platform
IMP::npctransport::RelaxingSpring Class Reference

A decorator for a spring particle connecting two diffusing particles. More...

#include <IMP/npctransport/RelaxingSpring.h>

+ Inheritance diagram for IMP::npctransport::RelaxingSpring:

Detailed Description

A decorator for a spring particle connecting two diffusing particles.

Definition at line 25 of file RelaxingSpring.h.

Public Member Functions

 RelaxingSpring (::IMP::Model *m,::IMP::ParticleIndex id)
 
 RelaxingSpring (const IMP::ParticleAdaptor &d)
 
void add_to_rest_length_derivative (double d, DerivativeAccumulator &da)
 
Particleget_bonded_particle_0 () const
 
Particleget_bonded_particle_1 () const
 
ParticleIndex get_bonded_particle_index_0 () const
 
ParticleIndex get_bonded_particle_index_1 () const
 
Float get_equilibrium_rest_length_factor () const
 
Float get_rest_length () const
 
double get_rest_length_derivative ()
 
Float get_rest_length_diffusion_coefficient () const
 
void set_equilibrium_rest_length_factor (Float t)
 
void set_rest_length (Float t)
 
void set_rest_length_diffusion_coefficient (Float t)
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::Decorator
bool get_is_valid () const
 Returns true if constructed with a non-default constructor. More...
 
Modelget_model () const
 Returns the Model containing the particle. More...
 
Particleget_particle () const
 Returns the particle decorated by this decorator. More...
 
ParticleIndex get_particle_index () const
 Returns the particle index decorated by this decorator. More...
 
 operator Particle * () const
 
 operator ParticleIndex () const
 
Particleoperator-> () const
 

Static Public Member Functions

static ParticleIndexKey get_bonded_particle_0_key ()
 
static ParticleIndexKey get_bonded_particle_1_key ()
 
static FloatKey get_equilibrium_rest_length_factor_key ()
 get decorator key for spring equilibrium rest length factor More...
 
static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 Return true if the particle is an instance of an Transporting. More...
 
static FloatKey get_rest_length_diffusion_coefficient_key ()
 get decorator key for diffusion coefficient of rest length More...
 
static FloatKey get_rest_length_key ()
 get decorator key for spring rest length More...
 
static RelaxingSpring setup_particle (IMP::ParticleAdaptor decorator, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient)
 
static RelaxingSpring setup_particle (Model *m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient)
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::Decorator
 Decorator (Model *m, ParticleIndex pi)
 
 Decorator (ParticleAdaptor p)
 

Member Function Documentation

Float IMP::npctransport::RelaxingSpring::get_equilibrium_rest_length_factor ( ) const

returns the value of the equilibrium_rest_length_factor attribute

Definition at line 110 of file RelaxingSpring.h.

static FloatKey IMP::npctransport::RelaxingSpring::get_equilibrium_rest_length_factor_key ( )
static

get decorator key for spring equilibrium rest length factor

static bool IMP::npctransport::RelaxingSpring::get_is_setup ( Model m,
ParticleIndex  pi 
)
static

Return true if the particle is an instance of an Transporting.

Definition at line 70 of file RelaxingSpring.h.

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Float IMP::npctransport::RelaxingSpring::get_rest_length ( ) const

returns the value of the rest_length attribute

Definition at line 114 of file RelaxingSpring.h.

Float IMP::npctransport::RelaxingSpring::get_rest_length_diffusion_coefficient ( ) const

returns the value of the rest_length_diffusion_coefficient attribute

Definition at line 118 of file RelaxingSpring.h.

static FloatKey IMP::npctransport::RelaxingSpring::get_rest_length_diffusion_coefficient_key ( )
static

get decorator key for diffusion coefficient of rest length

static FloatKey IMP::npctransport::RelaxingSpring::get_rest_length_key ( )
static

get decorator key for spring rest length

void IMP::npctransport::RelaxingSpring::set_equilibrium_rest_length_factor ( Float  t)

sets the value of the equilibrium_rest_length_factor attribute to t

Definition at line 110 of file RelaxingSpring.h.

void IMP::npctransport::RelaxingSpring::set_rest_length ( Float  t)

sets the value of the rest_length attribute to t

Definition at line 114 of file RelaxingSpring.h.

void IMP::npctransport::RelaxingSpring::set_rest_length_diffusion_coefficient ( Float  t)

sets the value of the rest_length_diffusion_coefficient attribute to t

Definition at line 118 of file RelaxingSpring.h.

static RelaxingSpring IMP::npctransport::RelaxingSpring::setup_particle ( Model m,
ParticleIndex  pi,
ParticleIndex  bonded_pi0,
ParticleIndex  bonded_pi1,
double  equilibrium_rest_length_factor,
double  rest_length_diffusion_coefficient 
)
static

Decorate a spring particle that connects two particles in no particular order, with a dynamic rest length that may relax towards some equilibrium value

Parameters
mthe model
pithe particle index
bonded_pi0particle on first side of spring
bonded_pi1particle on second side of spring
equilibrium_rest_length_factorthe rest length factor of the spring at equilibrium (relative to sum of the radii of the bonded particles)
rest_length_diffusion_coefficientthe diffusion coefficient for the rest lengthSetup the particle so it can be used with this decorator.

Definition at line 67 of file RelaxingSpring.h.


The documentation for this class was generated from the following file: