 |
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) d0= IMP.core.XYZ.setup_particle(p0, IMP.algebra.Vector3D(0,1,2)) p1= IMP.Particle(m) d1= IMP.core.XYZ.setup_particle(p1) d1.set_coordinates(IMP.algebra.Vector3D(3,4,5)) print IMP.core.get_distance(d0, d1)
Examples: nup84 cg, custom filter, restrain diameter, six particles optimization, XYZR Decorator, symmetry, score protein with ligand, sample 0, nup84 rb, domino approach, six particles loopy optimization, XYZ Decorator, analyze 0, simplex, setup, displaying ensembles
Inheritance diagram for IMP::core::XYZ:Public Member Functions | |
| 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::VectorD< 3 > &v, DerivativeAccumulator &d) |
| Add something to the derivative of the coordinates. | |
| Float | get_coordinate (int i) const |
| Get the ith coordinate. | |
| const algebra::VectorD< 3 > & | 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::VectorD< 3 > | get_derivatives () const |
| Get the vector of derivatives. | |
| algebra::VectorD< 3 > | 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::VectorD< 3 > &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) |
| static XYZ | setup_particle (Particle *p, const algebra::VectorD< 3 > &v=algebra::VectorD< 3 >(0, 0, 0)) |
Related Functions | |
| (Note that these are not member functions.) | |
| double | get_distance (XYZ a, XYZ b) |
| Compute the distance between a pair of particles. | |
| const algebra::VectorD<3>& 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.
| algebra::VectorD<3> 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
| 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 XYZ IMP::core::XYZ::setup_particle | ( | Particle * | p, |
| const algebra::VectorD< 3 > & | v = algebra::VectorD<3>(0,0,0) |
||
| ) | [static] |
Create a decorator with the passed coordinates.
