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IMP Reference Guide  develop.8b7eb21230,2024/06/24
The Integrative Modeling Platform
IMP::npc::SlabWithPore Class Reference

#include <IMP/npc/SlabWithPore.h>

+ Inheritance diagram for IMP::npc::SlabWithPore:

Detailed Description

A decorator for a particle that represents a slab containing a cylindrical pore

Definition at line 23 of file SlabWithPore.h.

Public Member Functions

 SlabWithPore (::IMP::Model *m,::IMP::ParticleIndex id)
 
 SlabWithPore (const IMP::ParticleAdaptor &d)
 
void add_to_pore_radius_derivative (double v, DerivativeAccumulator &d)
 
Float get_pore_radius () const
 get cylindrical pore radius More...
 
bool get_pore_radius_is_optimized () const
 
Float get_thickness () const
 
void set_pore_radius (double r) const
 set cylindrical pore radius More...
 
void set_pore_radius_is_optimized (bool tf) const
 Set whether the pore radius is optimized. More...
 
void set_thickness (double thickness)
 sets slab thickness More...
 
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 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 SlabWithPore. More...
 
static FloatKey get_pore_radius_key ()
 Get the key for the pore radius. More...
 
static FloatKey get_thickness_key ()
 Get the key for the pore thickness. More...
 
static SlabWithPore setup_particle (IMP::ParticleAdaptor pa, double thickness, double pore_radius)
 
static SlabWithPore setup_particle (Model *m, ParticleIndex pi, double thickness, double pore_radius)
 

Additional Inherited Members

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

Member Function Documentation

void IMP::npc::SlabWithPore::add_to_pore_radius_derivative ( double  v,
DerivativeAccumulator d 
)

add v to the derivative of the cylindrical pore radius, using derivative accumulator d

Definition at line 102 of file SlabWithPore.h.

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static bool IMP::npc::SlabWithPore::get_is_setup ( Model m,
ParticleIndex  pi 
)
static

Return true if the particle is an instance of SlabWithPore.

Definition at line 73 of file SlabWithPore.h.

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Float IMP::npc::SlabWithPore::get_pore_radius ( ) const

get cylindrical pore radius

Definition at line 91 of file SlabWithPore.h.

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static FloatKey IMP::npc::SlabWithPore::get_pore_radius_key ( )
static

Get the key for the pore radius.

Float IMP::npc::SlabWithPore::get_thickness ( ) const

returns whether the particle last entered the transport moiety from its top

Definition at line 86 of file SlabWithPore.h.

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static FloatKey IMP::npc::SlabWithPore::get_thickness_key ( )
static

Get the key for the pore thickness.

void IMP::npc::SlabWithPore::set_pore_radius ( double  r) const

set cylindrical pore radius

Definition at line 96 of file SlabWithPore.h.

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void IMP::npc::SlabWithPore::set_pore_radius_is_optimized ( bool  tf) const

Set whether the pore radius is optimized.

Definition at line 110 of file SlabWithPore.h.

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void IMP::npc::SlabWithPore::set_thickness ( double  thickness)

sets slab thickness

Definition at line 79 of file SlabWithPore.h.

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static SlabWithPore IMP::npc::SlabWithPore::setup_particle ( IMP::ParticleAdaptor  pa,
double  thickness,
double  pore_radius 
)
static
Returns
a SlabWithPore object that decorates the particle specified by pa
See Also
setup_particle(m, p, thickness , pore_radius )

Definition at line 70 of file SlabWithPore.h.

static SlabWithPore IMP::npc::SlabWithPore::setup_particle ( Model m,
ParticleIndex  pi,
double  thickness,
double  pore_radius 
)
static

Decorate a particle that represents a slab (e.g. nuclear envelope) with specified thickness and a cylindrical pore of specified pore_radius.

The slab is parallel to the x,y plane from z=-0.5*thickness to z=0.5*thickness, and the central axis of the pore lies on the origin.

Parameters
mthe model
pithe particle index
thicknessslab thickness
pore_radiuspore radius
Note
the pore radius is initially not optimizable
Returns
a SlabWithPore object that decorates particle pi

Definition at line 70 of file SlabWithPore.h.


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