A decorator for a particle that represents a surface, its coordinates, and orientation.
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A decorator for a particle that represents a surface, its coordinates, and orientation.
- See Also
- XYZ
-
Direction
Definition at line 35 of file Surface.h.
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| Surface (::IMP::Model *m,::IMP::ParticleIndex id) |
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| Surface (const IMP::ParticleAdaptor &d) |
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void | add_to_normal_derivative (int i, Float v, DerivativeAccumulator &d) |
| Add v to the derivative of the ith coordinate of the normal. More...
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void | add_to_normal_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d) |
| Add v to the derivatives of the x,y,z coordinates of the normal. More...
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double | get_depth (const algebra::Vector3D &v) const |
| Get depth of point below surface. More...
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double | get_distance_to (const algebra::Vector3D &v) const |
| Get distance from point to surface. More...
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double | get_distance_to_center (const algebra::Vector3D &v) const |
| Get distance from point to center of surface. More...
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double | get_height (const algebra::Vector3D &v) const |
| Get height of point above surface. More...
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algebra::Vector3D | get_normal () const |
| Get unit vector normal to surface. More...
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Float | get_normal_derivative (int i) const |
| Get the vector of derivatives added to the surface normal. More...
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algebra::Vector3D | get_normal_derivatives () const |
| Get the vector of derivatives added to the surface normal. More...
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bool | get_normal_is_optimized () const |
| Get whether surface normal is optimized. More...
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Float | get_normal_x () const |
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Float | get_normal_y () const |
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Float | get_normal_z () const |
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algebra::Plane3D | get_plane () const |
| Get a plane that lies along the surface. More...
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algebra::ReferenceFrame3D | get_reference_frame () const |
| Get surface orientation as a reference frame. More...
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void | reflect () |
| Flip surface so normal is reversed. More...
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void | set_normal (const algebra::Vector3D &normal) |
| Set surface normal. More...
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void | set_normal_is_optimized (bool tf) const |
| Set whether surface normal is optimized. More...
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void | set_normal_x (Float t) |
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void | set_normal_y (Float t) |
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void | set_normal_z (Float t) |
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void | set_reference_frame (const algebra::ReferenceFrame3D &rf) |
| Set coordinates and normal from a reference frame. 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 void | do_setup_particle (Model *m, ParticleIndex pi, const algebra::Vector3D ¢er=algebra::Vector3D(0, 0, 0), const algebra::Vector3D &normal=algebra::Vector3D(0, 0, 1)) |
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static void | do_setup_particle (Model *m, ParticleIndex pi, const algebra::ReferenceFrame3D &rf) |
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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 particle is setup as a surface. More...
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static FloatKey | get_normal_key (unsigned int i) |
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static Surface | setup_particle (Model *m, ParticleIndex pi) |
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static Surface | setup_particle (IMP::ParticleAdaptor decorator) |
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static Surface | setup_particle (IMP::ParticleAdaptor decorator, algebra::ReferenceFrame3D rf) |
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static Surface | setup_particle (Model *m, ParticleIndex pi, algebra::ReferenceFrame3D rf) |
| Set up the surface to align with the reference frame. More...
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static Surface | setup_particle (IMP::ParticleAdaptor decorator, algebra::Vector3D center) |
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static Surface | setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D center) |
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static Surface | setup_particle (IMP::ParticleAdaptor decorator, algebra::Vector3D center, algebra::Vector3D normal) |
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static Surface | setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D center, algebra::Vector3D normal) |
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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 decorator) |
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static XYZ | setup_particle (Model *m, ParticleIndex pi) |
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static XYZ | setup_particle (IMP::ParticleAdaptor decorator, algebra::Vector3D v) |
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static XYZ | setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D v) |
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