IMP::core::Surface Class Reference

A decorator for a particle that represents a surface, its coordinates, and orientation. More...

#include <IMP/core/Surface.h>

Inheritance diagram for IMP::core::Surface:

Detailed Description

A decorator for a particle that represents a surface, its coordinates, and orientation.

See Also

XYZ

Direction

Definition at line 35 of file Surface.h.

Public Member Functions
	Surface (::IMP::Model *m,::IMP::ParticleIndex id)
	Surface (const IMP::ParticleAdaptor &d)
void	add_to_normal_derivative (int i, Float v, DerivativeAccumulator &d)
	Add v to the derivative of the ith coordinate of the normal. More...
void	add_to_normal_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
	Add v to the derivatives of the x,y,z coordinates of the normal. More...
double	get_depth (const algebra::Vector3D &v) const
	Get depth of point below surface. More...
double	get_distance_to (const algebra::Vector3D &v) const
	Get distance from point to surface. More...
double	get_distance_to_center (const algebra::Vector3D &v) const
	Get distance from point to center of surface. More...
double	get_height (const algebra::Vector3D &v) const
	Get height of point above surface. More...
algebra::Vector3D	get_normal () const
	Get unit vector normal to surface. More...
Float	get_normal_derivative (int i) const
	Get the vector of derivatives added to the surface normal. More...
algebra::Vector3D	get_normal_derivatives () const
	Get the vector of derivatives added to the surface normal. More...
bool	get_normal_is_optimized () const
	Get whether surface normal is optimized. More...
Float	get_normal_x () const
Float	get_normal_y () const
Float	get_normal_z () const
algebra::Plane3D	get_plane () const
	Get a plane that lies along the surface. More...
algebra::ReferenceFrame3D	get_reference_frame () const
	Get surface orientation as a reference frame. More...
void	reflect ()
	Flip surface so normal is reversed. More...
void	set_normal (const algebra::Vector3D &normal)
	Set surface normal. More...
void	set_normal_is_optimized (bool tf) const
	Set whether surface normal is optimized. More...
void	set_normal_x (Float t)
void	set_normal_y (Float t)
void	set_normal_z (Float t)
void	set_reference_frame (const algebra::ReferenceFrame3D &rf)
	Set coordinates and normal from a reference frame. More...
void	show (std::ostream &out=std::cout) const
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, const algebra::Vector3D &center=algebra::Vector3D(0, 0, 0), const algebra::Vector3D &normal=algebra::Vector3D(0, 0, 1))
static void	do_setup_particle (Model *m, ParticleIndex pi, const algebra::ReferenceFrame3D &rf)
static bool	get_is_setup (const IMP::ParticleAdaptor &p)
static bool	get_is_setup (Model *m, ParticleIndex pi)
	Check if particle is setup as a surface. More...
static FloatKey	get_normal_key (unsigned int i)
static Surface	setup_particle (Model *m, ParticleIndex pi)
static Surface	setup_particle (IMP::ParticleAdaptor pa)
static Surface	setup_particle (IMP::ParticleAdaptor pa, algebra::ReferenceFrame3D rf)
static Surface	setup_particle (Model *m, ParticleIndex pi, algebra::ReferenceFrame3D rf)
	Set up the surface to align with the reference frame. More...
static Surface	setup_particle (IMP::ParticleAdaptor pa, algebra::Vector3D center)
static Surface	setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D center)
static Surface	setup_particle (IMP::ParticleAdaptor pa, algebra::Vector3D center, algebra::Vector3D normal)
static Surface	setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D center, algebra::Vector3D normal)
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)

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

Member Function Documentation

void IMP::core::Surface::add_to_normal_derivative	(	int	i,
		Float	v,
		DerivativeAccumulator &	d
	)

Add v to the derivative of the ith coordinate of the normal.

Definition at line 68 of file Surface.h.

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void IMP::core::Surface::add_to_normal_derivatives	(	const algebra::Vector3D &	v,
		DerivativeAccumulator &	d
	)

Add v to the derivatives of the x,y,z coordinates of the normal.

double IMP::core::Surface::get_depth

(

const algebra::Vector3D &

v

)

const

Get depth of point below surface.

Note

If point is above surface, value is negative.

double IMP::core::Surface::get_distance_to

(

const algebra::Vector3D &

v

)

const

Get distance from point to surface.

double IMP::core::Surface::get_distance_to_center

(

const algebra::Vector3D &

v

)

const

Get distance from point to center of surface.

double IMP::core::Surface::get_height

(

const algebra::Vector3D &

v

)

const

Get height of point above surface.

Note

If point is below surface, value is negative.

static bool IMP::core::Surface::get_is_setup ( Model *  m, ParticleIndex  pi  )

static

Check if particle is setup as a surface.

algebra::Vector3D IMP::core::Surface::get_normal

(

)

const

Get unit vector normal to surface.

Float IMP::core::Surface::get_normal_derivative

(

int

i

)

const

Get the vector of derivatives added to the surface normal.

Definition at line 60 of file Surface.h.

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algebra::Vector3D IMP::core::Surface::get_normal_derivatives

(

)

const

Get the vector of derivatives added to the surface normal.

bool IMP::core::Surface::get_normal_is_optimized

(

)

const

Get whether surface normal is optimized.

Float IMP::core::Surface::get_normal_x

(

)

const

returns the value of the normal_x attribute

Definition at line 50 of file Surface.h.

Float IMP::core::Surface::get_normal_y

(

)

const

returns the value of the normal_y attribute

Definition at line 51 of file Surface.h.

Float IMP::core::Surface::get_normal_z

(

)

const

returns the value of the normal_z attribute

Definition at line 52 of file Surface.h.

algebra::Plane3D IMP::core::Surface::get_plane

(

)

const

Get a plane that lies along the surface.

Definition at line 117 of file Surface.h.

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algebra::ReferenceFrame3D IMP::core::Surface::get_reference_frame

(

)

const

Get surface orientation as a reference frame.

void IMP::core::Surface::reflect

(

)

Flip surface so normal is reversed.

Definition at line 89 of file Surface.h.

void IMP::core::Surface::set_normal

(

const algebra::Vector3D &

normal

)

Set surface normal.

void IMP::core::Surface::set_normal_is_optimized

(

bool

tf

)

const

Set whether surface normal is optimized.

void IMP::core::Surface::set_normal_x

(

Float

t

)

sets the value of the normal_x attribute to t

Definition at line 50 of file Surface.h.

void IMP::core::Surface::set_normal_y

(

Float

t

)

sets the value of the normal_y attribute to t

Definition at line 51 of file Surface.h.

void IMP::core::Surface::set_normal_z

(

Float

t

)

sets the value of the normal_z attribute to t

Definition at line 52 of file Surface.h.

void IMP::core::Surface::set_reference_frame

(

const algebra::ReferenceFrame3D &

rf

)

Set coordinates and normal from a reference frame.

Definition at line 106 of file Surface.h.

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static Surface IMP::core::Surface::setup_particle ( IMP::ParticleAdaptor  pa )

static

Returns

a Surface object that decorates the particle specified by pa

See Also

setup_particle(m, p)

Definition at line 45 of file Surface.h.

static Surface IMP::core::Surface::setup_particle ( Model *  m, ParticleIndex  pi  )

static

Returns

a Surface object that decorates particle pi

Definition at line 45 of file Surface.h.

static Surface IMP::core::Surface::setup_particle ( Model *  m, ParticleIndex  pi, algebra::ReferenceFrame3D  rf  )

static

Set up the surface to align with the reference frame.

Returns

a Surface object that decorates particle pi

Definition at line 47 of file Surface.h.

static Surface IMP::core::Surface::setup_particle ( IMP::ParticleAdaptor  pa, algebra::ReferenceFrame3D  rf  )

static

Returns

a Surface object that decorates the particle specified by pa

See Also

setup_particle(m, pi, rf )

Definition at line 47 of file Surface.h.

static Surface IMP::core::Surface::setup_particle ( Model *  m, ParticleIndex  pi, algebra::Vector3D  center  )

static

Returns

a Surface object that decorates particle pi

Definition at line 48 of file Surface.h.

static Surface IMP::core::Surface::setup_particle ( IMP::ParticleAdaptor  pa, algebra::Vector3D  center  )

static

Returns

a Surface object that decorates the particle specified by pa

See Also

setup_particle(m, pi, center )

Definition at line 48 of file Surface.h.

static Surface IMP::core::Surface::setup_particle ( Model *  m, ParticleIndex  pi, algebra::Vector3D  center, algebra::Vector3D  normal  )

static

Returns

a Surface object that decorates particle pi

Definition at line 49 of file Surface.h.

static Surface IMP::core::Surface::setup_particle ( IMP::ParticleAdaptor  pa, algebra::Vector3D  center, algebra::Vector3D  normal  )

static

Returns

a Surface object that decorates the particle specified by pa

See Also

setup_particle(m, p, center , normal )

Definition at line 49 of file Surface.h.

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

• Surface.h