IMP::atom::LennardJones Class Reference

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
Model *	get_model () const
	Returns the Model containing the particle.
Particle *	get_particle () const
ParticleIndex	get_particle_index () const
	operator Particle * () const
	operator ParticleIndex () const
Particle *	operator-> () const

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 LennardJones	setup_particle (IMP::kernel::ParticleAdaptor decorator)
static LennardJones	setup_particle (kernel::Model *m, ParticleIndex pi)
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 XYZR	setup_particle (IMP::kernel::ParticleAdaptor decorator)
static XYZR	setup_particle (kernel::Model *m, ParticleIndex pi)
static XYZR	setup_particle (kernel::Model *m, ParticleIndex pi, Float radius)
static XYZR	setup_particle (IMP::kernel::ParticleAdaptor decorator, 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 XYZ	setup_particle (IMP::kernel::ParticleAdaptor decorator)
static XYZ	setup_particle (kernel::Model *m, ParticleIndex pi)
static XYZ	setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Vector3D v)
static XYZ	setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Vector3D v)

Additional Inherited Members
Protected Member Functions inherited from IMP::kernel::Decorator
	Decorator (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 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 ( IMP::kernel::ParticleAdaptor  decorator, Float  well_depth  )

static

See Also

setup_particle(m, pi, well_depth )

Definition at line 37 of file LennardJones.h.

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

static

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

Definition at line 37 of file LennardJones.h.

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

• LennardJones.h