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 (Model *m, ParticleIndex id) | |
| LennardJones (::IMP::kernel::Particle *p) | |
| 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 (Model *m, ParticleIndex id) | |
| XYZR (::IMP::kernel::Particle *p) | |
| 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 (Model *m, ParticleIndex id) | |
| XYZ (::IMP::kernel::Particle *p) | |
| 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 FloatKey | get_well_depth_key () |
| static bool | particle_is_instance (Particle *p) |
| Return true if the particle is an instance of a LennardJones. | |
| static LennardJones | setup_particle (Particle *p, Float well_depth=0) |
| Static Public Member Functions inherited from IMP::core::XYZR | |
| static XYZR | decorate_particle (::IMP::kernel::Particle *p) |
| static FloatKey | get_radius_key () |
| Get the default radius key. | |
| static bool | particle_is_instance (Particle *p) |
| Check if the particle has the required attributes. | |
| static XYZR | setup_particle (Particle *p) |
| static XYZR | setup_particle (Particle *p, Float radius) |
| static XYZR | setup_particle (Particle *p, const algebra::Sphere3D s) |
| static XYZR | setup_particle (Model *m, ParticleIndex pi, const algebra::Sphere3D s) |
| 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 const FloatKeys & | get_xyz_keys () |
| Get a vector containing the keys for x,y,z. More... | |
| static bool | particle_is_instance (Particle *p) |
| static bool | particle_is_instance (Model *m, ParticleIndex pi) |
| static XYZ | setup_particle (Model *m, ParticleIndex pi, const algebra::Vector3D v=algebra::Vector3D(0, 0, 0)) |
| static XYZ | setup_particle (Particle *p, const algebra::Vector3D v=algebra::Vector3D(0, 0, 0)) |
| Static Public Member Functions inherited from IMP::kernel::Decorator | |
| static bool | particle_is_instance (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 (Model *m, ParticleIndex pi) | |
| Decorator (Particle *p) | |
| Related Functions inherited from IMP::core::XYZR | |
| XYZRs | create_xyzr_particles (Model *m, unsigned int num, Float radius, Float box_side=10) |
| Create a set of particles with random coordinates. More... | |
| double | get_distance (XYZR a, XYZR b) |
| Compute the distance between a pair of particles. | |
| algebra::Sphere3D | get_enclosing_sphere (const XYZs &v) |
| Get a sphere enclosing the set of XYZRs. More... | |
| void | set_enclosing_radius (XYZR b, const XYZs &v) |
| Set the radius of the first to enclose the list. More... | |
| void | set_enclosing_sphere (XYZR b, const XYZs &v, double slack=0) |
| Set the coordinates and radius of the first to enclose the list. More... | |
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
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static |
Create a decorator with the passed well depth. The particle is assumed to already have x,y,z,r attributes.
Definition at line 34 of file LennardJones.h.
The documentation for this class was generated from the following file: