IMP::bff::AV Class Reference

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

#include <IMP/bff/AV.h>

Inheritance diagram for IMP::bff::AV:

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

Definition at line 94 of file AV.h.

Public Member Functions
	AV (::IMP::Model *m,::IMP::ParticleIndex id)
	AV (const IMP::ParticleAdaptor &d)
IMP::bff::PathMapHeader	create_path_map_header ()
	Creates a path map header. More...
Float	get_allowed_sphere_radius () const
Float	get_contact_volume_thickness () const
Float	get_contact_volume_trapped_fraction () const
algebra::Vector3D	get_derivatives () const
	Get the vector of derivatives accumulated by add_to_derivatives(). More...
Float	get_linker_length () const
Float	get_linker_width () const
IMP::bff::PathMap *	get_map () const
	Get the PathMap associated with the AV object. More...
IMP::algebra::Vector3D	get_mean_position (bool include_source=true) const
	Get the mean position of the AV object. More...
bool	get_parameters_are_optimized () const
	Get whether the coordinates are optimized. More...
Particle *	get_particle () const
	Get the particle pointer of the AV object. More...
Particle *	get_particle (unsigned int i) const
	Get the particle pointer of the AV object at the specified index. More...
ParticleIndex	get_particle_index () const
	Get the particle index of the AV object. More...
ParticleIndex	get_particle_index (unsigned int i) const
	Get the particle index of the AV object at the specified index. More...
IMP::algebra::Vector3D	get_radii ()
	Returns the radii of an object. More...
Float	get_radius1 () const
Float	get_radius2 () const
Float	get_radius3 () const
Float	get_simulation_grid_resolution () const
Particle *	get_source () const
	Get the source particle of the AV object. More...
IMP::algebra::Vector3D	get_source_coordinates () const
	Get the source coordinates of the AV object. More...
void	init_path_map ()
	Initializes the path map. More...
void	resample (bool shift_xyz=true)
	Resample the AV object. More...
void	set_allowed_sphere_radius (Float t)
void	set_av_parameter (const nlohmann::json &j)
	Sets the AV parameter using a JSON object. More...
void	set_av_parameters_are_optimized (bool tf) const
	Set whether the coordinates are optimized. More...
void	set_contact_volume_thickness (Float t)
void	set_contact_volume_trapped_fraction (Float t)
void	set_linker_length (Float t)
void	set_linker_width (Float t)
void	set_radius1 (Float t)
void	set_radius2 (Float t)
void	set_radius3 (Float t)
void	set_simulation_grid_resolution (Float t)
void	show (std::ostream &out=std::cout) const
Public Member Functions inherited from IMP::core::Gaussian
	Gaussian (::IMP::Model *m,::IMP::ParticleIndex id)
	Gaussian (const IMP::ParticleAdaptor &d)
algebra::Gaussian3D	get_gaussian () const
	create Gaussian3D from these attributes More...
Eigen::Matrix3d	get_global_covariance ()
	retrieve global covariance More...
Eigen::Matrix3d	get_local_covariance () const
	retrieve local covariance (as diagonal matrix) More...
algebra::Vector3D	get_variances () const
	retrieve local variances as Vector3D More...
void	set_gaussian (const algebra::Gaussian3D &g)
	Get the covariance attributes from a Gaussian3D object. More...
void	set_global_covariance (Eigen::Matrix3d covar)
	set the global-frame covariance. does NOT update local frame! More...
void	set_local_covariance (const Eigen::Vector3d covar)
	set the local-frame covariance. More...
void	set_variances (const algebra::Vector3D v)
	equivalent to set_local_covariance, used for backwards compatibility More...
void	show (std::ostream &out=std::cout) const
void	update_global_covariance ()
	update the global covariance More...
Public Member Functions inherited from IMP::core::RigidBody
	RigidBody (::IMP::Model *m,::IMP::ParticleIndex id)
	RigidBody (const IMP::ParticleAdaptor &d)
	RigidBody (const RigidBody &)=default
void	add_member (ParticleIndexAdaptor p)
void	add_non_rigid_member (ParticleIndexAdaptor p)
void	add_to_derivatives (const algebra::Vector3D &local_derivative, const algebra::Vector3D &local_location, DerivativeAccumulator &da)
void	add_to_derivatives (const algebra::Vector3D &local_derivative, const algebra::Vector3D &global_derivative, const algebra::Vector3D &local_location, const algebra::Rotation3D &rot_local_to_global, DerivativeAccumulator &da)
void	add_to_rotational_derivatives (const algebra::Vector4D &other_qderiv, const algebra::Rotation3D &rot_other_to_local, const algebra::Rotation3D &rot_local_to_global, DerivativeAccumulator &da)
void	add_to_rotational_derivatives (const algebra::Vector4D &qderiv, DerivativeAccumulator &da)
void	add_to_torque (const algebra::Vector3D &torque_local, DerivativeAccumulator &da)
const ParticleIndexes &	get_body_member_particle_indexes () const
algebra::Vector3D	get_coordinates () const
bool	get_coordinates_are_optimized () const
ParticleIndexes	get_member_indexes () const
const ParticleIndexes &	get_member_particle_indexes () const
IMP::algebra::ReferenceFrame3D	get_reference_frame () const
RigidMembers	get_rigid_members () const
IMP::algebra::Rotation3D	get_rotation () const
algebra::VectorD< 4 >	get_rotational_derivatives () const
	Get the derivatives of the quaternion. More...
algebra::Vector3D	get_torque () const
void	normalize_rotation ()
	Normalize the quaternion. More...
RigidBody &	operator= (const RigidBody &)=default
void	pull_back_body_member_adjoints (ParticleIndex pi, DerivativeAccumulator &da)
	Pull back global adjoints from member that is also a rigid body. More...
void	pull_back_body_member_adjoints (ParticleIndex pi, const algebra::Transformation3D &TA, algebra::Transformation3D &TB, algebra::Transformation3DAdjoint &DTC, algebra::Transformation3DAdjoint &DTA, algebra::Transformation3DAdjoint &DTB, algebra::Vector3D &betatorque, DerivativeAccumulator &da)
void	pull_back_member_adjoints (ParticleIndex pi, DerivativeAccumulator &da)
	Pull back global adjoints from member that is a point. More...
void	pull_back_member_adjoints (ParticleIndex pi, const algebra::Transformation3D &T, algebra::Vector3D &x, algebra::Vector3D &Dy, algebra::Vector3D &Dx, algebra::Transformation3DAdjoint &DT, algebra::Vector3D &xtorque, DerivativeAccumulator &da)
void	pull_back_members_adjoints (DerivativeAccumulator &da)
	Pull back global adjoints from members. More...
void	remove_member (ParticleIndexAdaptor p)
	Remove the member from this rigid body. More...
void	set_coordinates_are_optimized (bool tf)
void	set_is_rigid_member (ParticleIndex pi, bool tf)
void	set_reference_frame (const IMP::algebra::ReferenceFrame3D &tr)
	Set the current reference frame. More...
void	set_reference_frame_from_members (const ParticleIndexes &members)
void	set_reference_frame_lazy (const IMP::algebra::ReferenceFrame3D &tr)
	Change the reference, delay updating the members until evaluate. More...
void	show (std::ostream &out=std::cout) const
void	update_members ()
Public Member Functions inherited from IMP::core::XYZ
	XYZ (::IMP::Model *m,::IMP::ParticleIndex id)
	XYZ (const IMP::ParticleAdaptor &d)
void	add_to_derivative (int i, Float v, DerivativeAccumulator &d)
void	add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
	Add the vector v to the derivative vector of the x,y,z coordinates. More...
Float	get_coordinate (int i) const
	Get the ith coordinate. More...
const algebra::Vector3D &	get_coordinates () const
	Convert it to a vector. More...
bool	get_coordinates_are_optimized () const
	Get whether the coordinates are optimized. More...
Float	get_derivative (int i) const
algebra::Vector3D	get_derivatives () const
	Get the vector of derivatives accumulated by add_to_derivatives(). More...
algebra::Vector3D	get_vector_to (const XYZ &b) const
	Get the vector from this particle to another. More...
Float	get_x () const
Float	get_y () const
Float	get_z () const
void	set_coordinate (unsigned int i, Float v)
	set the ith coordinate More...
void	set_coordinates (const algebra::Vector3D &v)
	set all coordinates from a vector More...
void	set_coordinates_are_optimized (bool tf) const
	Set whether the coordinates are optimized. More...
void	set_x (Float t)
void	set_y (Float t)
void	set_z (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...
Model *	get_model () const
	Returns the Model containing the particle. More...
Particle *	get_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
Particle *	operator-> () const

Static Public Member Functions
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. More...
static FloatKey	get_av_key (unsigned int i)
	Get the FloatKey object for a specific AV feature. More...
static bool	get_is_setup (const IMP::ParticleAdaptor &p)
static bool	get_is_setup (Model *m, ParticleIndex pi)
static ParticleIndexKey	get_particle_key (unsigned int i)
	Get the particle key for the specified index. More...
static AV	setup_particle (Model *m, ParticleIndex pi, IMP::ParticleIndex pi_source)
static AV	setup_particle (IMP::ParticleAdaptor pa, IMP::ParticleIndex pi_source)
Static Public Member Functions inherited from IMP::core::Gaussian
static ObjectKey	get_global_covariance_key ()
static bool	get_is_setup (const IMP::ParticleAdaptor &p)
static bool	get_is_setup (Model *m, ParticleIndex pi)
static ObjectKey	get_local_covariance_key ()
static Gaussian	setup_particle (Model *m, ParticleIndex pi)
static Gaussian	setup_particle (IMP::ParticleAdaptor pa)
static Gaussian	setup_particle (Model *m, ParticleIndex pi, algebra::Gaussian3D g)
static Gaussian	setup_particle (IMP::ParticleAdaptor pa, algebra::Gaussian3D g)
Static Public Member Functions inherited from IMP::core::RigidBody
static bool	get_is_setup (const IMP::ParticleAdaptor &p)
static bool	get_is_setup (Model *m, ParticleIndex pi)
	Return true if the particle is a rigid body. More...
static FloatKeys	get_rotation_keys ()
	Get keys for rotation quaternion. More...
static RigidBody	setup_particle (IMP::ParticleAdaptor pa, ParticleIndexesAdaptor ps)
static RigidBody	setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps)
static RigidBody	setup_particle (IMP::ParticleAdaptor pa, algebra::ReferenceFrame3D rf)
static RigidBody	setup_particle (Model *m, ParticleIndex pi, algebra::ReferenceFrame3D rf)
static void	teardown_particle (RigidBody rb)
	Make the rigid body no longer rigid. More...
Static Public Member Functions inherited from IMP::core::XYZ
static FloatKey	get_coordinate_key (unsigned int i)
static bool	get_is_setup (const IMP::ParticleAdaptor &p)
static bool	get_is_setup (Model *m, ParticleIndex pi)
static const FloatKeys &	get_xyz_keys ()
	Get a vector containing the keys for x,y,z. More...
static XYZ	setup_particle (IMP::ParticleAdaptor pa)
static XYZ	setup_particle (Model *m, ParticleIndex pi)
static XYZ	setup_particle (IMP::ParticleAdaptor pa, algebra::Vector3D v)
static XYZ	setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D v)

Protected Member Functions
IMP::algebra::VectorD< 9 >	get_parameter () const
Protected Member Functions inherited from IMP::Decorator
	Decorator (Model *m, ParticleIndex pi)
	Decorator (ParticleAdaptor p)

Member Function Documentation

IMP::bff::PathMapHeader IMP::bff::AV::create_path_map_header

(

)

Creates a path map header.

Returns

The created path map header.

static void IMP::bff::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  )

static

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.

Definition at line 181 of file AV.h.

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Float IMP::bff::AV::get_allowed_sphere_radius

(

)

const

returns the value of the allowed_sphere_radius attribute

Definition at line 259 of file AV.h.

static FloatKey IMP::bff::AV::get_av_key ( unsigned int  i )

static

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.

Definition at line 146 of file AV.h.

Float IMP::bff::AV::get_contact_volume_thickness

(

)

const

returns the value of the contact_volume_thickness attribute

Definition at line 260 of file AV.h.

Float IMP::bff::AV::get_contact_volume_trapped_fraction

(

)

const

returns the value of the contact_volume_trapped_fraction attribute

Definition at line 261 of file AV.h.

algebra::Vector3D IMP::bff::AV::get_derivatives

(

)

const

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

Definition at line 312 of file AV.h.

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Float IMP::bff::AV::get_linker_length

(

)

const

returns the value of the linker_length attribute

Definition at line 254 of file AV.h.

Float IMP::bff::AV::get_linker_width

(

)

const

returns the value of the linker_width attribute

Definition at line 258 of file AV.h.

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

(

)

const

Get the PathMap associated with the AV object.

Returns

A pointer to the PathMap object.

IMP::algebra::Vector3D IMP::bff::AV::get_mean_position

(

bool

include_source = true

)

const

Get the mean position of the AV object.

Returns

The mean position as a Vector3D.

bool IMP::bff::AV::get_parameters_are_optimized

(

)

const

Get whether the coordinates are optimized.

Returns

true only if all of them are optimized.

Definition at line 279 of file AV.h.

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Particle* IMP::bff::AV::get_particle

(

)

const

Get the particle pointer of the AV object.

Returns

The particle pointer of the AV object.

Definition at line 238 of file AV.h.

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Particle* IMP::bff::AV::get_particle

(

unsigned int

i

)

const

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.

Definition at line 247 of file AV.h.

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ParticleIndex IMP::bff::AV::get_particle_index

(

)

const

Get the particle index of the AV object.

Returns

The particle index of the AV object.

Definition at line 221 of file AV.h.

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ParticleIndex IMP::bff::AV::get_particle_index

(

unsigned int

i

)

const

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.

Definition at line 230 of file AV.h.

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static ParticleIndexKey IMP::bff::AV::get_particle_key ( unsigned int  i )

static

Get the particle key for the specified index.

Parameters

i	The index of the particle key.

Returns

The particle key at the specified index.

Definition at line 210 of file AV.h.

IMP::algebra::Vector3D IMP::bff::AV::get_radii

(

)

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.

Definition at line 272 of file AV.h.

Float IMP::bff::AV::get_radius1

(

)

const

returns the value of the radius1 attribute

Definition at line 255 of file AV.h.

Float IMP::bff::AV::get_radius2

(

)

const

returns the value of the radius2 attribute

Definition at line 256 of file AV.h.

Float IMP::bff::AV::get_radius3

(

)

const

returns the value of the radius3 attribute

Definition at line 257 of file AV.h.

Float IMP::bff::AV::get_simulation_grid_resolution

(

)

const

returns the value of the simulation_grid_resolution attribute

Definition at line 262 of file AV.h.

Particle* IMP::bff::AV::get_source

(

)

const

Get the source particle of the AV object.

Returns

A pointer to the source Particle object.

IMP::algebra::Vector3D IMP::bff::AV::get_source_coordinates

(

)

const

Get the source coordinates of the AV object.

Returns

The source coordinates as a Vector3D.

void IMP::bff::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

void IMP::bff::AV::resample

(

bool

shift_xyz = true

)

Resample the AV object.

Parameters

shift_xyz

Flag indicating whether to shift the XYZ coordinates.

void IMP::bff::AV::set_allowed_sphere_radius

(

Float

t

)

sets the value of the allowed_sphere_radius attribute to t

Definition at line 259 of file AV.h.

void IMP::bff::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.

void IMP::bff::AV::set_av_parameters_are_optimized

(

bool

tf

)

const

Set whether the coordinates are optimized.

Definition at line 290 of file AV.h.

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void IMP::bff::AV::set_contact_volume_thickness

(

Float

t

)

sets the value of the contact_volume_thickness attribute to t

Definition at line 260 of file AV.h.

void IMP::bff::AV::set_contact_volume_trapped_fraction

(

Float

t

)

sets the value of the contact_volume_trapped_fraction attribute to t

Definition at line 261 of file AV.h.

void IMP::bff::AV::set_linker_length

(

Float

t

)

sets the value of the linker_length attribute to t

Definition at line 254 of file AV.h.

void IMP::bff::AV::set_linker_width

(

Float

t

)

sets the value of the linker_width attribute to t

Definition at line 258 of file AV.h.

void IMP::bff::AV::set_radius1

(

Float

t

)

sets the value of the radius1 attribute to t

Definition at line 255 of file AV.h.

void IMP::bff::AV::set_radius2

(

Float

t

)

sets the value of the radius2 attribute to t

Definition at line 256 of file AV.h.

void IMP::bff::AV::set_radius3

(

Float

t

)

sets the value of the radius3 attribute to t

Definition at line 257 of file AV.h.

void IMP::bff::AV::set_simulation_grid_resolution

(

Float

t

)

sets the value of the simulation_grid_resolution attribute to t

Definition at line 262 of file AV.h.

static AV IMP::bff::AV::setup_particle ( IMP::ParticleAdaptor  pa, IMP::ParticleIndex  pi_source  )

static

Returns

a AV object that decorates the particle specified by pa

See Also

setup_particle(m, pi, pi_source )

Definition at line 253 of file AV.h.

static AV IMP::bff::AV::setup_particle ( Model *  m, ParticleIndex  pi, IMP::ParticleIndex  pi_source  )

static

Setup the particle with unspecified AV - uses default values.

Returns

a AV object that decorates particle pi

Definition at line 253 of file AV.h.

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

• AV.h