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IMP Reference Guide  2.13.0
The Integrative Modeling Platform
IMP::npctransport::SlabWithToroidalPore Class Reference

#include <IMP/npctransport/SlabWithToroidalPore.h>

+ Inheritance diagram for IMP::npctransport::SlabWithToroidalPore:

Detailed Description

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

Definition at line 24 of file SlabWithToroidalPore.h.

Public Member Functions

 SlabWithToroidalPore (::IMP::Model *m,::IMP::ParticleIndex id)
 
 SlabWithToroidalPore (const IMP::ParticleAdaptor &d)
 
double get_horizontal_minor_radius () const
 
double get_minor_radius_h2v_aspect_ratio () const
 
double get_vertical_minor_radius () const
 
void set_horizontal_minor_radius (double rh)
 
void set_minor_radius_h2v_aspect_ratio (double aspect_ratio)
 
void set_vertical_minor_radius (double rv)
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::npctransport::SlabWithPore
 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
 returns whether the particle last entered the transport moiety from its More...
 
void set_pore_radius (double r) const
 set cylindrical pore radius More...
 
void set_pore_radius_is_optimized (bool tf) const
 Set whether the coordinates are 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 SlabWithToroidalPore. More...
 
static FloatKey get_minor_radius_h2v_aspect_ratio_key ()
 Get the decorator key for the ratio between horizontal and vertical aspect ratio. More...
 
static IntKey get_toroidal_pore_key ()
 Get the decorator key indicating a toroidal pore. More...
 
static SlabWithToroidalPore setup_particle (Model *m, ParticleIndex pi, double thickness, double major_radius)
 
static SlabWithToroidalPore setup_particle (IMP::ParticleAdaptor decorator, double thickness, double major_radius)
 
static SlabWithToroidalPore setup_particle (Model *m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio)
 
static SlabWithToroidalPore setup_particle (IMP::ParticleAdaptor decorator, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio)
 
- Static Public Member Functions inherited from IMP::npctransport::SlabWithPore
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 decorator key for is_last_entry_from_top. More...
 
static SlabWithPore setup_particle (IMP::ParticleAdaptor decorator, 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

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

Return true if the particle is an instance of SlabWithToroidalPore.

Definition at line 96 of file SlabWithToroidalPore.h.

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static FloatKey IMP::npctransport::SlabWithToroidalPore::get_minor_radius_h2v_aspect_ratio_key ( )
static

Get the decorator key for the ratio between horizontal and vertical aspect ratio.

static IntKey IMP::npctransport::SlabWithToroidalPore::get_toroidal_pore_key ( )
static

Get the decorator key indicating a toroidal pore.

static SlabWithToroidalPore IMP::npctransport::SlabWithToroidalPore::setup_particle ( Model m,
ParticleIndex  pi,
double  thickness,
double  major_radius 
)
static

Decorate a particle that represents a slab (e.g. nuclear envelope) with specified thickness and a toroidal pore of specified major radius and minor radius of 0.5*thickness, with equal horizontal and vertical minor radii.

The slab is parallel to the x,y plain 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, also twice the minor radius
major_radiuspore major radiusSetup the particle so it can be used with this decorator.

Definition at line 70 of file SlabWithToroidalPore.h.

static SlabWithToroidalPore IMP::npctransport::SlabWithToroidalPore::setup_particle ( Model m,
ParticleIndex  pi,
double  thickness,
double  major_radius,
double  minor_radius_h2v_aspect_ratio 
)
static

Decorate a particle that represents a slab (e.g. nuclear envelope) with specified thickness and a toroidal pore of specified major radius and minor radius of 0.5*thickness, and specified ratio between horizontal and vertical minor radii.

The slab is parallel to the x,y plain 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, also twice the vertical minor radius
major_radiuspore major radius
minor_radius_h2v_aspect_ratioratio between horizontal and vertical minor radiusSetup the particle so it can be used with this decorator.

Definition at line 93 of file SlabWithToroidalPore.h.


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