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/*! \page p_develop_model Developing using Atomic Models
\section s_model_basic Core model handling facilities
Requirements for the manipulation of atomic models in crystallographic
calculations are very varied, and often the objects required must be
tailored to the specific calculation. Therefore, Clipper provides only
the minimum tools required for atomic models to interact with
structure factors and maps. More advanced facilities are provided
through optional packages.
The most common interaction between atomic models and structure factors
or maps is through electron density or mask calculation. For this
purpose, only a subset of atomic properties are required: element,
coordinate, occupancy and temperature factor (U-value). Clipper
therefore provides a simple class, clipper::Atom, which contains this
information. It has a template constructor which allows it to be
initialised from any Atom-like object.
Electron density and mask calculations require a list of atoms,
therefore a simple class for holding a list of atoms,
clipper::Atom_list is provided. This is a trivial extension of
std::vector<clipper::Atom>, and provides a template constructor to
build an atom list from any vector-like object of atom-like objects.
Atom lists can also be constructed using the standard vector methods,
e.g. push_back(), insert().
Clipper methods requiring an atom list, e.g. a <a
href=contrib/classclipper_1_1SFcalc__aniso__fft.html>structure factor
calculation</a> may be given a Clipper::Atom_list, any class derived
from that class, or a std::vector<clipper::Atom> as an argument.
<hr>
\section s_model_opt Optional model handling packages
Two optional packages are provided for model manipulation. Both
require the the 'MMDB' coordinate library by E. Krissinel to be
installed (see http://msd.ebi.ac.uk/~keb/cldoc/).
\subsection ss_model_mmdb MMDB interface.
The <a href=mmdb>MMDB interface</a> is a lightweight interface to
allow MMDB to be used with Clipper. It consists of one main class:
clipper::MMDBAtom_list. This is a trivial extension of
clipper::Atom_list which may be used anywhere an Atom_list would be
used. It provides an additional constructor which will build an atom
list from an MMDB atom selection (i.e. PPCAtom + count).
Other classes are provided which may optionally be used to access
information in the MMDB hierarchy in the form of Clipper
objects. These are trivial extensions of MMDB objects. The MMDB
objects may therefore be cast to the Clipper types to access the
additional conversion methods.
\subsection ss_model_mini MiniMol package.
The <a href=minimol>MiniMol package</a> is a lightweight, STL based
implementation of a small subset of the MMDB functionality. It
provides simpler tools for manipulating single models and their
constituents. The use of STL-style code means that no memory
management is required, and all common operations such as assignment
and passing variables have the most obvious effect.
The minimum necessary information is stored for each object in the
hierarchy, however additional information of any type may be added to
any object through use of the clipper::PropertyManager.
Basic searching and selection tools are provided, and logical 'and'
and 'or' operators may be used to combine models, polymers, and
monomers.
MiniMol provides an MMDBfile class which may be used to extract models
from and store models back into an MMDB, or a file.
<hr>
\section s_model_which Choosing a model package.
If you have very specific model requirements, you may be better off
writing your own objects tailored to those requirements, and then
deriving an Atom_list class to allow your objects to be communicated
to Clipper. Otherwise, consider the following points:
- MMDB is a very powerful package, with an enormous range of
facilities. However, it requires a good knowledge of C++, and the API
can be quite complex.
- MiniMol is a very simple package with a concise and intuitive
interface. It has a simple API accessible to non-C++ programmers.
MiniMol will do simple tasks much more easily than MMDB, but it won't
do hard tasks at all. If MiniMol does everything you will need (or can
easily be extended to do so), then it is probably a good choice,
otherwise use MMDB.
*/
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