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IMP Reference Guide  2.20.0
The Integrative Modeling Platform
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:

Detailed Description

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

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.

Public Member Functions

 LennardJones (::IMP::Model *m,::IMP::ParticleIndex id)
 
 LennardJones (const IMP::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::Model *m,::IMP::ParticleIndex id)
 
 XYZR (const IMP::ParticleAdaptor &d)
 
void add_to_radius_derivative (double v, DerivativeAccumulator &d)
 add v to the derivative of the radius attribute More...
 
double get_radius () const
 
const algebra::Sphere3Dget_sphere () const
 Return a sphere object. More...
 
void set_radius (double r) const
 
void set_sphere (const algebra::Sphere3D &s)
 Set the attributes from a sphere. 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::Vector3Dget_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...
 
Modelget_model () const
 Returns the Model containing the particle. More...
 
Particleget_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
 
Particleoperator-> () const
 

Static Public Member Functions

static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 Return true if the particle is an instance of a LennardJones. More...
 
static FloatKey get_well_depth_key ()
 
static LennardJones setup_particle (Model *m, ParticleIndex pi)
 
static LennardJones setup_particle (IMP::ParticleAdaptor pa)
 
static LennardJones setup_particle (Model *m, ParticleIndex pi, Float well_depth)
 
static LennardJones setup_particle (IMP::ParticleAdaptor pa, Float well_depth)
 
- Static Public Member Functions inherited from IMP::core::XYZR
static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 Check if the particle has the required attributes. More...
 
static FloatKey get_radius_key ()
 Get the key for the radius. More...
 
static XYZR setup_particle (Model *m, ParticleIndex pi)
 
static XYZR setup_particle (IMP::ParticleAdaptor pa)
 
static XYZR setup_particle (IMP::ParticleAdaptor pa, Float radius)
 
static XYZR setup_particle (Model *m, ParticleIndex pi, Float radius)
 
static XYZR setup_particle (Model *m, ParticleIndex pi, algebra::Sphere3D ball)
 
static XYZR setup_particle (IMP::ParticleAdaptor pa, algebra::Sphere3D ball)
 
- 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 FloatKeysget_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 bool IMP::atom::LennardJones::get_is_setup ( Model m,
ParticleIndex  pi 
)
static

Return true if the particle is an instance of a LennardJones.

Definition at line 49 of file LennardJones.h.

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static LennardJones IMP::atom::LennardJones::setup_particle ( Model m,
ParticleIndex  pi 
)
static
Returns
a LennardJones object that decorates particle pi

Definition at line 36 of file LennardJones.h.

static LennardJones IMP::atom::LennardJones::setup_particle ( IMP::ParticleAdaptor  pa)
static
Returns
a LennardJones object that decorates the particle specified by pa
See Also
setup_particle(m, p)

Definition at line 36 of file LennardJones.h.

static LennardJones IMP::atom::LennardJones::setup_particle ( IMP::ParticleAdaptor  pa,
Float  well_depth 
)
static
Returns
a LennardJones object that decorates the particle specified by pa
See Also
setup_particle(m, pi, well_depth )

Definition at line 37 of file LennardJones.h.

static LennardJones IMP::atom::LennardJones::setup_particle ( Model m,
ParticleIndex  pi,
Float  well_depth 
)
static
Returns
a LennardJones object that decorates particle pi

Definition at line 37 of file LennardJones.h.


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