A decorator for a particle that has a Lennard-Jones potential well. More...

#include <IMP/atom/LennardJones.h>

Inheritance diagram for IMP::atom::LennardJones:

Public Member Functions
	LennardJones (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)

	LennardJones (const IMP::kernel::ParticleAdaptor &d)

Float	get_well_depth () const

void	set_well_depth (Float well_depth)

void	show (std::ostream &out=std::cout) const

Public Member Functions inherited from IMP::core::XYZR
	XYZR (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)

	XYZR (const IMP::kernel::ParticleAdaptor &d)

void	add_to_radius_derivative (double v, DerivativeAccumulator &d)

double	get_radius () const

const algebra::Sphere3D &	get_sphere () const
	Return a sphere object.

void	set_radius (double r) const

void	set_sphere (const algebra::Sphere3D &s)
	Set the attributes from a sphere.

void	show (std::ostream &out=std::cout) const

Public Member Functions inherited from IMP::core::XYZ
	XYZ (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)

	XYZ (const IMP::kernel::ParticleAdaptor &d)

void	add_to_derivative (int i, Float v, DerivativeAccumulator &d)
	Add something to the derivative of the ith coordinate.

void	add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
	Add something to the derivative of the coordinates.

Float	get_coordinate (int i) const
	Get the ith coordinate.

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
	Get the ith coordinate derivative.

algebra::Vector3D	get_derivatives () const
	Get the vector of derivatives. More...

algebra::Vector3D	get_vector_to (const XYZ &b) const
	Get the vector from this particle to another.

Float	get_x () const

Float	get_y () const

Float	get_z () const

void	set_coordinate (unsigned int i, Float v)
	set the ith coordinate

void	set_coordinates (const algebra::Vector3D &v)
	set all coordinates from a vector

void	set_coordinates_are_optimized (bool tf) const
	Set whether the coordinates are optimized.

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::kernel::Decorator
ParticleIndex	get_particle_index () const

Particle *	get_particle () const

Model *	get_model () const
	Returns the Model containing the particle.

	Decorator (Particle *p)

	Decorator ()

Static Public Member Functions
static LennardJones	decorate_particle (::IMP::kernel::Particle *p)

static bool	get_is_setup (const IMP::kernel::ParticleAdaptor &p)

static bool	get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
	Return true if the particle is an instance of a LennardJones.

static FloatKey	get_well_depth_key ()

static bool	particle_is_instance (::IMP::kernel::Particle *p)

static bool	particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)

static LennardJones	setup_particle (kernel::Model *m, ParticleIndex pi)

static LennardJones	setup_particle (IMP::kernel::ParticleAdaptor decorator)

static LennardJones	setup_particle (IMP::kernel::ParticleAdaptor decorator, Float well_depth)

static LennardJones	setup_particle (kernel::Model *m, ParticleIndex pi, Float well_depth)

Static Public Member Functions inherited from IMP::core::XYZR
static XYZR	decorate_particle (::IMP::kernel::Particle *p)

static bool	get_is_setup (const IMP::kernel::ParticleAdaptor &p)

static bool	get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
	Check if the particle has the required attributes. More...

static FloatKey	get_radius_key ()

static bool	particle_is_instance (::IMP::kernel::Particle *p)

static bool	particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)

static XYZR	setup_particle (kernel::Model *m, ParticleIndex pi)

static XYZR	setup_particle (IMP::kernel::ParticleAdaptor decorator)

static XYZR	setup_particle (IMP::kernel::ParticleAdaptor decorator, Float radius)

static XYZR	setup_particle (kernel::Model *m, ParticleIndex pi, Float radius)

static XYZR	setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Sphere3D ball)

static XYZR	setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Sphere3D ball)

Static Public Member Functions inherited from IMP::core::XYZ
static XYZ	decorate_particle (::IMP::kernel::Particle *p)

static FloatKey	get_coordinate_key (unsigned int i)

static bool	get_is_setup (const IMP::kernel::ParticleAdaptor &p)

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

static const FloatKeys &	get_xyz_keys ()
	Get a vector containing the keys for x,y,z. More...

static bool	particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)

static bool	particle_is_instance (::IMP::kernel::Particle *p)

static XYZ	setup_particle (IMP::kernel::ParticleAdaptor decorator)

static XYZ	setup_particle (kernel::Model *m, ParticleIndex pi)

static XYZ	setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Vector3D v)

static XYZ	setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Vector3D v)

Static Public Member Functions inherited from IMP::kernel::Decorator
static bool	get_is_setup (Particle *p)
	Return true if the particle can be cast to the decorator. More...

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

	Decorator (ParticleAdaptor p)

Detailed Description

Such particles must be XYZR particles (they must have a position and a radius) but need not be true atoms.

The well depth should be a non-negative value.

See Also: LennardJonesPairScore

Definition at line 26 of file LennardJones.h.

Member Function Documentation

static LennardJones IMP::atom::LennardJones::decorate_particle ( ::IMP::kernel::Particle * p )

static

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.

Definition at line 35 of file LennardJones.h.

static bool IMP::atom::LennardJones::particle_is_instance ( ::IMP::kernel::Particle * p )

static

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 35 of file LennardJones.h.

static bool IMP::atom::LennardJones::particle_is_instance	(	IMP::kernel::Model *	m,
		IMP::kernel::ParticleIndex	pi
	)

static

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 35 of file LennardJones.h.

static LennardJones IMP::atom::LennardJones::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi
	)

static

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

Definition at line 36 of file LennardJones.h.

static LennardJones IMP::atom::LennardJones::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi,
		Float	well_depth
	)

static

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

Definition at line 37 of file LennardJones.h.

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

LennardJones.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation