Detailed Description

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

Such particles must be XYZ particles (they must have a position) but need not be true atoms. Note that if the particle is an XYZR particle, the radius used for Lennard-Jones is the LennardJonesTyped radius, not the XYZR radius.

See Also: LennardJonesType; LennardJonesTypedPairScore

Definition at line 103 of file LennardJonesType.h.

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

	LennardJonesTyped (const IMP::ParticleAdaptor &d)

int	get_index () const

double	get_radius () const

LennardJonesType *	get_type () const

double	get_well_depth () const

void	set_type (LennardJonesType *type)

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 bool	get_is_setup (const IMP::ParticleAdaptor &p)

static bool	get_is_setup (Model *m, ParticleIndex pi)

static const int *	get_type_array (Model *m)
	Access the raw attribute data for the type. More...

static IntKey	get_type_key ()
	Get the key used to store the type. More...

static LennardJonesTyped	setup_particle (Model m, ParticleIndex pi, LennardJonesType type)

static LennardJonesTyped	setup_particle (IMP::ParticleAdaptor pa, LennardJonesType *type)

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

static const int* IMP::atom::LennardJonesTyped::get_type_array ( Model * m )

static

Access the raw attribute data for the type.

This array may become invalid if particles or attributes are added or removed.

Definition at line 145 of file LennardJonesType.h.

static IntKey IMP::atom::LennardJonesTyped::get_type_key ( )

static

Get the key used to store the type.

static LennardJonesTyped IMP::atom::LennardJonesTyped::setup_particle	(	Model *	m,
		ParticleIndex	pi,
		LennardJonesType *	type
	)

static

Returns: a LennardJonesTyped object that decorates particle pi

Definition at line 112 of file LennardJonesType.h.

static LennardJonesTyped IMP::atom::LennardJonesTyped::setup_particle	(	IMP::ParticleAdaptor	pa,
		LennardJonesType *	type
	)

static

Returns: a LennardJonesTyped object that decorates the particle specified by pa

See Also: setup_particle(m, pi, type )

Definition at line 112 of file LennardJonesType.h.

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

LennardJonesType.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation