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

#include <IMP/npc/SlabWithToroidalPore.h>

+ Inheritance diagram for IMP::npc::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::npc::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
 
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 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 pa, 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 pa, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio)
 
- Static Public Member Functions inherited from IMP::npc::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 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

static bool IMP::npc::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::npc::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::npc::SlabWithToroidalPore::get_toroidal_pore_key ( )
static

Get the decorator key indicating a toroidal pore.

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

Definition at line 70 of file SlabWithToroidalPore.h.

static SlabWithToroidalPore IMP::npc::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 radius
Returns
a SlabWithToroidalPore object that decorates particle pi

Definition at line 70 of file SlabWithToroidalPore.h.

static SlabWithToroidalPore IMP::npc::SlabWithToroidalPore::setup_particle ( IMP::ParticleAdaptor  pa,
double  thickness,
double  major_radius,
double  minor_radius_h2v_aspect_ratio 
)
static
Returns
a SlabWithToroidalPore object that decorates the particle specified by pa
See Also
setup_particle(m, pi, thickness , major_radius , minor_radius_h2v_aspect_ratio )

Definition at line 93 of file SlabWithToroidalPore.h.

static SlabWithToroidalPore IMP::npc::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 radius
Returns
a SlabWithToroidalPore object that decorates particle pi

Definition at line 93 of file SlabWithToroidalPore.h.


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