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.
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| LennardJones (::IMP::Model *m,::IMP::ParticleIndex id) |
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| LennardJones (const IMP::ParticleAdaptor &d) |
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Float | get_well_depth () const |
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void | set_well_depth (Float well_depth) |
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void | show (std::ostream &out=std::cout) const |
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| XYZR (::IMP::Model *m,::IMP::ParticleIndex id) |
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| XYZR (const IMP::ParticleAdaptor &d) |
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| void | add_to_radius_derivative (double v, DerivativeAccumulator &d) |
| | add v to the derivative of the radius attribute More...
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double | get_radius () const |
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| const algebra::Sphere3D & | get_sphere () const |
| | Return a sphere object. More...
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void | set_radius (double r) const |
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| void | set_sphere (const algebra::Sphere3D &s) |
| | Set the attributes from a sphere. More...
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void | show (std::ostream &out=std::cout) const |
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| XYZ (::IMP::Model *m,::IMP::ParticleIndex id) |
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| XYZ (const IMP::ParticleAdaptor &d) |
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| void | add_to_derivative (int i, Float v, DerivativeAccumulator &d) |
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| 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...
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| Float | get_coordinate (int i) const |
| | Get the ith coordinate. More...
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| const algebra::Vector3D & | get_coordinates () const |
| | Convert it to a vector. More...
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| bool | get_coordinates_are_optimized () const |
| | Get whether the coordinates are optimized. More...
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| Float | get_derivative (int i) const |
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| algebra::Vector3D | get_derivatives () const |
| | Get the vector of derivatives accumulated by add_to_derivatives(). More...
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| algebra::Vector3D | get_vector_to (const XYZ &b) const |
| | Get the vector from this particle to another. More...
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| Float | get_x () const |
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| Float | get_y () const |
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| Float | get_z () const |
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| void | set_coordinate (unsigned int i, Float v) |
| | set the ith coordinate More...
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| void | set_coordinates (const algebra::Vector3D &v) |
| | set all coordinates from a vector More...
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| void | set_coordinates_are_optimized (bool tf) const |
| | Set whether the coordinates are optimized. More...
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| void | set_x (Float t) |
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| void | set_y (Float t) |
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| void | set_z (Float t) |
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void | show (std::ostream &out=std::cout) const |
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| bool | get_is_valid () const |
| | Returns true if constructed with a non-default constructor. More...
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| Model * | get_model () const |
| | Returns the Model containing the particle. More...
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| Particle * | get_particle () const |
| | Returns the particle decorated by this decorator. More...
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| ParticleIndex | get_particle_index () const |
| | Returns the particle index decorated by this decorator. More...
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| operator Particle * () const |
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| operator ParticleIndex () const |
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Particle * | operator-> () const |
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static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
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| static bool | get_is_setup (Model *m, ParticleIndex pi) |
| | Return true if the particle is an instance of a LennardJones. More...
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static FloatKey | get_well_depth_key () |
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| static LennardJones | setup_particle (Model *m, ParticleIndex pi) |
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| static LennardJones | setup_particle (IMP::ParticleAdaptor pa) |
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| static LennardJones | setup_particle (Model *m, ParticleIndex pi, Float well_depth) |
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| static LennardJones | setup_particle (IMP::ParticleAdaptor pa, Float well_depth) |
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static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
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| static bool | get_is_setup (Model *m, ParticleIndex pi) |
| | Check if the particle has the required attributes. More...
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| static FloatKey | get_radius_key () |
| | Get the key for the radius. More...
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| static XYZR | setup_particle (Model *m, ParticleIndex pi) |
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| static XYZR | setup_particle (IMP::ParticleAdaptor pa) |
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| static XYZR | setup_particle (IMP::ParticleAdaptor pa, Float radius) |
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| static XYZR | setup_particle (Model *m, ParticleIndex pi, Float radius) |
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| static XYZR | setup_particle (Model *m, ParticleIndex pi, algebra::Sphere3D ball) |
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| static XYZR | setup_particle (IMP::ParticleAdaptor pa, algebra::Sphere3D ball) |
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static FloatKey | get_coordinate_key (unsigned int i) |
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static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
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static bool | get_is_setup (Model *m, ParticleIndex pi) |
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| static const FloatKeys & | get_xyz_keys () |
| | Get a vector containing the keys for x,y,z. More...
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| static XYZ | setup_particle (IMP::ParticleAdaptor pa) |
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| static XYZ | setup_particle (Model *m, ParticleIndex pi) |
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| static XYZ | setup_particle (IMP::ParticleAdaptor pa, algebra::Vector3D v) |
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| static XYZ | setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D v) |
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Inheritance diagram for IMP::atom::LennardJones: