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IMP Reference Guide
2.17.0
The Integrative Modeling Platform
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A decorator for a particle that has a Lennard-Jones potential well. More...
#include <IMP/atom/LennardJones.h>
Inheritance diagram for IMP::atom::LennardJones: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.
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::Sphere3D & | get_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::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) |
| 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 decorator) |
| static LennardJones | setup_particle (Model *m, ParticleIndex pi, Float well_depth) |
| static LennardJones | setup_particle (IMP::ParticleAdaptor decorator, 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 decorator) |
| static XYZR | setup_particle (IMP::ParticleAdaptor decorator, 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 decorator, 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 FloatKeys & | get_xyz_keys () |
| Get a vector containing the keys for x,y,z. More... | |
| static XYZ | setup_particle (IMP::ParticleAdaptor decorator) |
| static XYZ | setup_particle (Model *m, ParticleIndex pi) |
| static XYZ | setup_particle (IMP::ParticleAdaptor decorator, 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) | |
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Return true if the particle is an instance of a LennardJones.
Definition at line 49 of file LennardJones.h.
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Setup the particle so it can be used with this decorator.
Definition at line 36 of file LennardJones.h.
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Definition at line 37 of file LennardJones.h.
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Setup the particle so that it can be used with this decorator
Definition at line 37 of file LennardJones.h.