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A a decorator for a particle with x,y,z coordinates.
Using the decorator one can get and set coordinates and modify derivatives.
import IMP import IMP.core import IMP.algebra m= IMP.Model() p0= IMP.Particle(m) # add x,y,z coordinates to the particle d0= IMP.core.XYZ.setup_particle(p0, IMP.algebra.Vector3D(0,1,2)) p1= IMP.Particle(m) # add slots for the coordinates, but leave them uninitialized d1= IMP.core.XYZ.setup_particle(p1) # set the coordinate values d1.set_coordinates(IMP.algebra.Vector3D(3,4,5)) # return the distance between the two points described by the decorated # particles print IMP.core.get_distance(d0, d1)
Examples: XYZR Decorator, symmetry, XYZ Decorator, custom filter, displaying ensembles, tasks, score protein with ligand, adding data, simplex, six particles optimization, pdb, interactive with containers, ms connectivity restraint, multiscale, setup, interactive, nup84 cg, restrain diameter, nup84 rb, domino approach
Inheritance diagram for IMP::core::XYZ:Public Member Functions | |
| XYZ (Model *m, ParticleIndex id) | |
| XYZ (::IMP::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. | |
| bool | get_coordinates_are_optimized () const |
| Get whether the coordinates are optimized. | |
| Float | get_derivative (int i) const |
| Get the ith coordinate derivative. | |
| algebra::Vector3D | get_derivatives () const |
| Get the vector of derivatives. | |
| 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) |
Static Public Member Functions | |
| static XYZ | decorate_particle (::IMP::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. | |
| static bool | particle_is_instance (Particle *p) |
| Return true if the particle can be cast to the decorator. | |
| static bool | particle_is_instance (Model *m, ParticleIndex pi) |
| static XYZ | setup_particle (Particle *p, const algebra::Vector3D &v=algebra::Vector3D(0, 0, 0)) |
Related Functions | |
(Note that these are not member functions.) | |
| double | get_dihedral (XYZ a, XYZ b, XYZ c, XYZ d) |
| Compute the dihedral angle (in radians) between the four particles. | |
| double | get_distance (XYZ a, XYZ b) |
| Compute the distance between a pair of particles. | |
| void IMP::core::XYZ::add_to_derivative | ( | int | i, |
| Float | v, | ||
| DerivativeAccumulator & | d | ||
| ) |
Add something to the derivative of the ith coordinate.
| void IMP::core::XYZ::add_to_derivatives | ( | const algebra::Vector3D & | v, |
| DerivativeAccumulator & | d | ||
| ) |
Add something to the derivative of the coordinates.
| Float IMP::core::XYZ::get_coordinate | ( | int | i | ) | const |
Get the ith coordinate.
| const algebra::Vector3D& IMP::core::XYZ::get_coordinates | ( | ) | const |
Convert it to a vector.
Somewhat suspect based on wanting a Point/Vector differentiation but we don't have points
Reimplemented in IMP::core::RigidBody.
| bool IMP::core::XYZ::get_coordinates_are_optimized | ( | ) | const |
Get whether the coordinates are optimized.
Reimplemented in IMP::core::RigidBody.
| Float IMP::core::XYZ::get_derivative | ( | int | i | ) | const |
Get the ith coordinate derivative.
| algebra::Vector3D IMP::core::XYZ::get_derivatives | ( | ) | const |
Get the vector of derivatives.
Somewhat suspect based on wanting a Point/Vector differentiation but we don't have points
| algebra::Vector3D IMP::core::XYZ::get_vector_to | ( | const XYZ & | b | ) | const |
Get the vector from this particle to another.
| static const FloatKeys& IMP::core::XYZ::get_xyz_keys | ( | ) | [static] |
Get a vector containing the keys for x,y,z.
This is quite handy for initializing movers and things.
| static bool IMP::core::XYZ::particle_is_instance | ( | Particle * | p | ) | [static] |
Return true if the particle can be cast to the decorator.
That is, if particle_is_instance() returns true, then it is legal to construct an instance of the decorator with that particle. If not, setup_particle() must be called first.
IMP::Particle *p = new IMP::Particle(m); // it is false std::cout << IMP::core::XYZ::particle_is_instance(p) << std::endl; // As a result this is an error IMP::core::XYZ d(p); // now set it up IMP::core::XYZ(p); // now it is true std::cout << IMP::core::XYZ::particle_is_instance(p) << std::endl; // and now this code is OK IMP::core::XYZ d(p);
Reimplemented from IMP::Decorator.
Reimplemented in IMP::core::RigidMember, IMP::core::RigidBody, IMP::atom::RigidBodyDiffusion, IMP::core::XYZR, IMP::core::Cover, IMP::atom::Diffusion, IMP::atom::Charged, IMP::atom::LennardJones, and IMP::core::Centroid.
| void IMP::core::XYZ::set_coordinate | ( | unsigned int | i, |
| Float | v | ||
| ) |
set the ith coordinate
| void IMP::core::XYZ::set_coordinates | ( | const algebra::Vector3D & | v | ) |
set all coordinates from a vector
Reimplemented in IMP::core::RigidMember.
| void IMP::core::XYZ::set_coordinates_are_optimized | ( | bool | tf | ) | const |
Set whether the coordinates are optimized.
| static XYZ IMP::core::XYZ::setup_particle | ( | Particle * | p, |
| const algebra::Vector3D & | v = algebra::Vector3D(0,0,0) |
||
| ) | [static] |
Create a decorator with the passed coordinates.
Compute the dihedral angle (in radians) between the four particles.
