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 decorator)

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

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

static Surface	setup_particle (IMP::ParticleAdaptor decorator, 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 decorator)

static XYZ	setup_particle (Model *m, ParticleIndex pi)

static XYZ	setup_particle (IMP::ParticleAdaptor decorator, 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.

Here is the call graph for this function:

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.

Here is the call graph for this function:

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.

Here is the call graph for this function:

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.

Here is the call graph for this function:

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

static

Setup the particle so it can be used with this decorator.

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.

Setup the particle so that it can be used with this decorator

Definition at line 47 of file Surface.h.

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

static

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

Setup the particle so that it can be used with this decorator

Definition at line 48 of file Surface.h.

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

static

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

Setup the particle so it can be used with this decorator.

Definition at line 49 of file Surface.h.

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

Surface.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation