Representation of the structure in
IMP is via a collection of Particle objects. However, since particles are general purpose, they provide a basic set of tools for managing the data (e.g. IMP::Particle::add_attribute(), IMP::Particle::get_value() etc). Decorators wrap (or “decorate”) particles to provide a much richer interface. For example, most particles have Cartesian coordinates. The class IMP::core::XYZ decorates such a particle to provide functions to get and set the Cartesian coordinates as well as compute distances between particles.
d0= IMP.core.XYZ(p0) d1= IMP.core.XYZ(p1) print IMP.core.distance(d0,d1) print d0.get_coordinates()
Dealing with decorators and particles has two main parts
To set up a particle to be used with the IMP::core::XYZ decorator we do
d0= IMP.core.XYZ.setup_particle(p, IMP.algebra.Vector3D(0,2,3))
The method calls also decorates the particle and returns the decorator which can now be used to manipulate the particle. For example we can access the coordinates
(0,2,3) by doing
We now say the particle is an XYZ particle. If that particle is encountered later when we do not have the existing decorator available, we can decorate it again (since it is already set up) by doing
If you do not know if
p has been set up for the XYZ decorator, you can ask with
More abstractly, decorators can be used to
To see a list of all available decorators and to see what functions all decorators have, look at the list of classes which inherit from IMP::Decorator, below.
See the IMP::example::ExampleDecorator example for how to implement a simple decorator.
| The following methods are provided by the Decorator class. |
|Particle *||get_particle () const|
|Model *||get_model () const|
|Returns the Model containing the particle. |
| All decorators must have the following methods. Decorators which are parameterized (for example IMP::core::XYZR) take an (optional) extra parameter after the Particle in setup_particle(), and particle_is_instance().
|Decorator (Particle *p)|
|static Decorator||setup_particle (Particle *p, extra_arguments)|
|static bool||particle_is_instance (Particle *p)|
|Return true if the particle can be cast to the decorator. |
|Decorator (Particle *p)|
|int||compare (Particle *o) const|
Create an instance of the Decorator from the particle that has already been set up. The particle must have been set up already (eg particle_is_instance(p) must be true), but this is not necessarily checked.
The default constructor must be defined and create a NULL decorator, analogous to a
NULL pointer in C++ or a
None object in Python.
Returns the particle decorated by this decorator.
|static bool IMP::Decorator::particle_is_instance||(||Particle *||p||)||
Return true if the particle can be cast to the decorator.
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 in IMP::atom::Atom, IMP::atom::CHARMMAtom, IMP::atom::Charged, IMP::atom::Diffusion, IMP::atom::Hierarchy, IMP::atom::LennardJones, IMP::atom::Angle, IMP::atom::Dihedral, IMP::atom::Bond, IMP::atom::Bonded, IMP::core::XYZR, IMP::core::RigidBody, IMP::core::RigidMember, and IMP::example::ExampleDecorator.
Add the needed attributes to the particle and initialize them with values taken from initial_values.
It is an error to call this twice on the same particle for the same type of decorator.