AV Class Reference

A decorator for a particle with accessible volume (AV). More...

#include <AV.h>

Inheritance diagram for AV:

Collaboration diagram for AV:

Public Member Functions
IMP::bff::PathMapHeader	create_path_map_header ()
	Creates a path map header.
void	init_path_map ()
	Initializes the path map.
ParticleIndex	get_particle_index () const
	Get the particle index of the AV object.
ParticleIndex	get_particle_index (unsigned int i) const
	Get the particle index of the AV object at the specified index.
Particle *	get_particle () const
	Get the particle pointer of the AV object.
Particle *	get_particle (unsigned int i) const
	Get the particle pointer of the AV object at the specified index.
	IMP_DECORATOR_METHODS (AV, IMP::core::Gaussian)
	IMP_DECORATOR_SETUP_1 (AV, IMP::ParticleIndex, pi_source)
	IMP_DECORATOR_GET_SET (linker_length, get_av_key(0), Float, Float)
	IMP_DECORATOR_GET_SET (radius1, get_av_key(1), Float, Float)
	IMP_DECORATOR_GET_SET (radius2, get_av_key(2), Float, Float)
	IMP_DECORATOR_GET_SET (radius3, get_av_key(3), Float, Float)
	IMP_DECORATOR_GET_SET (linker_width, get_av_key(4), Float, Float)
	IMP_DECORATOR_GET_SET (allowed_sphere_radius, get_av_key(5), Float, Float)
	IMP_DECORATOR_GET_SET (contact_volume_thickness, get_av_key(6), Float, Float)
	IMP_DECORATOR_GET_SET (contact_volume_trapped_fraction, get_av_key(7), Float, Float)
	IMP_DECORATOR_GET_SET (simulation_grid_resolution, get_av_key(8), Float, Float)
IMP::algebra::Vector3D	get_radii ()
	Returns the radii of an object.
bool	get_parameters_are_optimized () const
	Get whether the coordinates are optimized.
void	set_av_parameters_are_optimized (bool tf) const
	Set whether the coordinates are optimized.
void	set_av_parameter (const nlohmann::json &j)
	Sets the AV parameter using a JSON object.
algebra::Vector3D	get_derivatives () const
	Get the vector of derivatives accumulated by add_to_derivatives().
IMP::bff::PathMap *	get_map () const
	Get the PathMap associated with the AV object.
void	resample (bool shift_xyz=true)
	Resample the AV object.
IMP::algebra::Vector3D	get_mean_position (bool include_source=true) const
	Get the mean position of the AV object.
IMP::algebra::Vector3D	get_source_coordinates () const
	Get the source coordinates of the AV object.
Particle *	get_source () const
	Get the source particle of the AV object.

Static Public Member Functions
static FloatKey	get_av_key (unsigned int i)
	Get the FloatKey object for a specific AV feature.
static void	do_setup_particle (Model *m, ParticleIndex pi, ParticleIndex pi_source, double linker_length=20.0, const algebra::Vector3D radii=algebra::Vector3D(3.5, 0, 0), double linker_width=0.5, double allowed_sphere_radius=1.5, double contact_volume_thickness=0.0, double contact_volume_trapped_fraction=-1, double simulation_grid_resolution=1.5)
	Sets up the attributes for a particle in a model for AV (Anisotropic Volume) calculations.
static ParticleIndexKey	get_particle_key (unsigned int i)
	Get the particle key for the specified index.
static bool	get_is_setup (Model *m, ParticleIndex pi)

Protected Member Functions
IMP::algebra::VectorD< 9 >	get_parameter () const

Detailed Description

A decorator for a particle with accessible volume (AV).

Using the decorator one can get and set AV parameters and modify derivatives.

AV must have IMP.Hierarchy parent with XYZ -> is labeling site AV coordinates = AV mean position

Member Function Documentation

create_path_map_header()

IMP::bff::PathMapHeader AV::create_path_map_header

(

)

Creates a path map header.

Returns

The created path map header.

do_setup_particle()

static void AV::do_setup_particle ( Model *  m, ParticleIndex  pi, ParticleIndex  pi_source, double  linker_length = 20.0, const algebra::Vector3D  radii = algebra::Vector3D(3.5, 0, 0), double  linker_width = 0.5, double  allowed_sphere_radius = 1.5, double  contact_volume_thickness = 0.0, double  contact_volume_trapped_fraction = -1, double  simulation_grid_resolution = 1.5  )

inlinestatic

Sets up the attributes for a particle in a model for AV (Anisotropic Volume) calculations.

This function sets up the attributes for a particle in a model for AV calculations. The attributes include linker length, radii, linker width, allowed sphere radius, contact volume thickness, contact volume trapped fraction, and simulation grid resolution. It also sets up a particle attribute to store the source particle index.

Parameters

m	The model in which the particle resides.
pi	The index of the particle to set up.
pi_source	The index of the source particle.
linker_length	The length of the linker.
radii	The radii of the particle in the x, y, and z directions.
linker_width	The width of the linker.
allowed_sphere_radius	The radius of the allowed sphere.
contact_volume_thickness	The thickness of the contact volume.
contact_volume_trapped_fraction	The fraction of the contact volume that is trapped.
simulation_grid_resolution	The resolution of the simulation grid.

get_av_key()

static FloatKey AV::get_av_key ( unsigned int  i )

inlinestatic

Get the FloatKey object for a specific AV feature.

This function returns a FloatKey object representing a specific AV feature based on the given index.

Parameters

i	The index of the AV feature.

Returns

The FloatKey object for the AV feature at the given index.

Note

The valid range for the index is 0 to 8.

If the index is out of range, an error message will be generated.

get_derivatives()

algebra::Vector3D AV::get_derivatives ( ) const

inline

Get the vector of derivatives accumulated by add_to_derivatives().

Somewhat suspect based on wanting a Point/Vector differentiation but we don't have points

get_is_setup()

static bool AV::get_is_setup ( Model *  m, ParticleIndex  pi  )

inlinestatic

get_map()

IMP::bff::PathMap * AV::get_map

(

)

const

Get the PathMap associated with the AV object.

Returns

A pointer to the PathMap object.

get_mean_position()

IMP::algebra::Vector3D AV::get_mean_position

(

bool

include_source = true

)

const

Get the mean position of the AV object.

Returns

The mean position as a Vector3D.

get_parameter()

IMP::algebra::VectorD< 9 > AV::get_parameter ( ) const

inlineprotected

get_parameters_are_optimized()

bool AV::get_parameters_are_optimized ( ) const

inline

Get whether the coordinates are optimized.

Returns

true only if all of them are optimized.

get_particle() [1/2]

Particle * AV::get_particle ( ) const

inline

Get the particle pointer of the AV object.

Returns

The particle pointer of the AV object.

get_particle() [2/2]

Particle * AV::get_particle ( unsigned int  i ) const

inline

Get the particle pointer of the AV object at the specified index.

Parameters

i	The index of the AV object.

Returns

The particle pointer of the AV object at the specified index.

get_particle_index() [1/2]

ParticleIndex AV::get_particle_index ( ) const

inline

Get the particle index of the AV object.

Returns

The particle index of the AV object.

get_particle_index() [2/2]

ParticleIndex AV::get_particle_index ( unsigned int  i ) const

inline

Get the particle index of the AV object at the specified index.

Parameters

i	The index of the AV object.

Returns

The particle index of the AV object at the specified index.

get_particle_key()

static ParticleIndexKey AV::get_particle_key ( unsigned int  i )

inlinestatic

Get the particle key for the specified index.

Parameters

i	The index of the particle key.

Returns

The particle key at the specified index.

get_radii()

IMP::algebra::Vector3D AV::get_radii ( )

inline

Returns the radii of an object.

This function returns the radii of an object as a 3D vector. The radii are obtained by calling the functions get_radius1(), get_radius2(), and get_radius3() and storing the values in a Vector3D object.

Returns

A Vector3D object representing the radii of the object.

get_source()

Particle * AV::get_source

(

)

const

Get the source particle of the AV object.

Returns

A pointer to the source Particle object.

get_source_coordinates()

IMP::algebra::Vector3D AV::get_source_coordinates

(

)

const

Get the source coordinates of the AV object.

Returns

The source coordinates as a Vector3D.

IMP_DECORATOR_GET_SET() [1/9]

AV::IMP_DECORATOR_GET_SET	(	allowed_sphere_radius	,
		get_av_key(5)	,
		Float	,
		Float
	)

IMP_DECORATOR_GET_SET() [2/9]

AV::IMP_DECORATOR_GET_SET	(	contact_volume_thickness	,
		get_av_key(6)	,
		Float	,
		Float
	)

IMP_DECORATOR_GET_SET() [3/9]

AV::IMP_DECORATOR_GET_SET	(	contact_volume_trapped_fraction	,
		get_av_key(7)	,
		Float	,
		Float
	)

IMP_DECORATOR_GET_SET() [4/9]

AV::IMP_DECORATOR_GET_SET	(	linker_length	,
		get_av_key(0)	,
		Float	,
		Float
	)

IMP_DECORATOR_GET_SET() [5/9]

AV::IMP_DECORATOR_GET_SET	(	linker_width	,
		get_av_key(4)	,
		Float	,
		Float
	)

IMP_DECORATOR_GET_SET() [6/9]

AV::IMP_DECORATOR_GET_SET	(	radius1	,
		get_av_key(1)	,
		Float	,
		Float
	)

IMP_DECORATOR_GET_SET() [7/9]

AV::IMP_DECORATOR_GET_SET	(	radius2	,
		get_av_key(2)	,
		Float	,
		Float
	)

IMP_DECORATOR_GET_SET() [8/9]

AV::IMP_DECORATOR_GET_SET	(	radius3	,
		get_av_key(3)	,
		Float	,
		Float
	)

IMP_DECORATOR_GET_SET() [9/9]

AV::IMP_DECORATOR_GET_SET	(	simulation_grid_resolution	,
		get_av_key(8)	,
		Float	,
		Float
	)

IMP_DECORATOR_METHODS()

AV::IMP_DECORATOR_METHODS	(	AV	,
		IMP::core::Gaussian
	)

IMP_DECORATOR_SETUP_1()

AV::IMP_DECORATOR_SETUP_1	(	AV	,
		IMP::ParticleIndex	,
		pi_source
	)

Setup the particle with unspecified AV - uses default values.

init_path_map()

void AV::init_path_map

(

)

Initializes the path map.

This function initializes the path map used by the AV system. The path map is a data structure that stores information about the available paths or routes in the system.

Returns

void

resample()

void AV::resample

(

bool

shift_xyz = true

)

Resample the AV object.

Parameters

shift_xyz

Flag indicating whether to shift the XYZ coordinates.

set_av_parameter()

void AV::set_av_parameter

(

const nlohmann::json &

j

)

Sets the AV parameter using a JSON object.

This function takes a JSON object as input and sets the AV parameter accordingly.

Parameters

j	The JSON object containing the AV parameter.

set_av_parameters_are_optimized()

void AV::set_av_parameters_are_optimized ( bool  tf ) const

inline

Set whether the coordinates are optimized.

---

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

• /Users/tpeulen/dev/imp.bff/include/AV.h