IMP  2.1.0
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:

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::Sphere3Dget_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::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
 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
 
Particleget_particle () const
 
Modelget_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 FloatKeysget_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: