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IMP Reference Guide  2.20.2
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 pa, 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 length
Returns
a RelaxingSpring object that decorates particle pi

Definition at line 67 of file RelaxingSpring.h.

static RelaxingSpring IMP::npctransport::RelaxingSpring::setup_particle ( IMP::ParticleAdaptor  pa,
ParticleIndex  bonded_pi0,
ParticleIndex  bonded_pi1,
double  equilibrium_rest_length_factor,
double  rest_length_diffusion_coefficient 
)
static
Returns
a RelaxingSpring object that decorates the particle specified by pa
See Also
setup_particle(m, pi, bonded_pi0 , bonded_pi1 , equilibrium_rest_length_factor , rest_length_diffusion_coefficient )

Definition at line 67 of file RelaxingSpring.h.


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