Import('env')

env.IMPModuleDoc(env.IMPModuleGetDocs(),
                 authors= ['Daniel Russel', 'Keren Lasker', 'Ben Webb',
                           'Javier Angel Velazquez-Muriel'],
                 brief='MODULENAME contains general purpose algebraic and geometric methods.',
                 overview="""MODULENAME contains general purpose algebraic and geometric methods that are expected to be used by a wide variety of \\imp modules.

\\par Geometric primitives\\anchor geometricprimitives
\\imp has a number of geometry primitives. They support the following namespace
functions as appropriate
  - IMP::algebra::get_bounding_box()
  - IMP::algebra::get_surface_area()
  - IMP::algebra::get_volume()\\n\\n
In addition, they cannot be compared against one another.

\\par Geometry and dimensions
Many of the geometric primitives and operations in \imp are written to work in any dimension.
In C++, this is implemented via templates (such as IMP::algebra::VectorD).
In the python side, the different dimensions are named explicitly instead. That
means, a 2-D point is IMP::algebra::VectorD<2> in C++, and IMP::algbra::Vector2D in python
and the function IMP::algebra::get_basis_vector_d<3>() in C++ becomes \c IMP.algebra.get_basis_vector_3d() in Python.
Similarly, a collection of 2D points is
std::vector<IMP::algebra::VectorD<2> > in C++ and IMP.algebra.Vector2Ds in python, which
as with all collections, look like python lists.
For convenience, we provide typedefs in C++ to the IMP::algbra::Vector2D and
IMP::algebra::Vector2Ds style names.

\\anchor genericgeometry
\\par Generic geometry
 Geometry in IMP can be stored in a variety of ways. For %example, a
 point in 3D can be stored using an IMP::algebra::VectorD<3> or using an
 IMP::core::XYZ particle. It is often useful to be able to write
 algorithms that work on sets of points without worring how they are
 stored, the Generic Geometry layer provides that. It works using a
 set of functions IMP::core::get_geometry() and
 IMP::core::set_geometry() which manipulate the geometetry in terms of the IMP::algebra
 representation of the geometry in question. That is, IMP::core::get_geometry()
 returns a IMP::algebra::VectorD<3> for both an IMP::algebra::Vector3D and
 a IMP::core::XYZ. Algorithms take their arguments as C++
 templates and use the generic geometry methods to manipulate the
 geometry. And versions of the function for both types of storage are
 exported to python, so one could also write generic functions in python.\\n\\n
 For %example, IMP::atom::rmsd() takes any combination of IMP::algebra::Vector3Ds
 or IMP::core::XYZs or IMP::core::XYZsTemp as arguments. Versions for all combinations
 of those are exported to python.

\\par Uninitialized default values\\anchor uninitialized
Some geometric primitives are not put into a defined state by their
constructor. Such classes mimic POD types (int, float etc) in C++ and
are optimized for efficiency.  All operations on a default initialized
instance other than assigning to it from a non-default initialized
instance should be assumed to be invalid.
\\code
IMP::algebra::VectorD<3> v0, v1;
v0 != v1;
// only legal operations initialize v0, eg
v0= IMP::algebra::VectorD<3>(1,2,3);
\\endcode


\\par CGAL\\anchor cgal
Certain functionality provided in \\imp requires or benefits from using CGAL.
\\external{www.cgal.org,CGAL} is a library of geometry-related
algorithms and data structures written in C++. The relevant parts of
CGAL are licensed under LGPL and QPL and commercial licenses are
available if needed. More information can be found on the
\\external{www.cgal.org/license.html, CGAL license page}.
""",
                 publications=env.StandardPublications(),
                 license=env.StandardLicense())