% +------------------------------------------------------------------------+
% | Reference manual page: Model.tex
% +------------------------------------------------------------------------+
% | 10.04.2009   Author
% | Package: PDB
% |
\RCSdef{\RCSModelRev}{$Id: header.tex 40270 2007-09-07 15:29:10Z lsaboret $}
\RCSdefDate{\RCSModelDate}{$Date: 2007-09-07 08:29:10 -0700 (Fri, 07 Sep 2007) $}
% |
\ccRefPageBegin
%%RefPage: end of header, begin of main body
% +------------------------------------------------------------------------+


\begin{ccRefClass}[PDB::]{Model}  %% add template arg's if necessary

%% \ccHtmlCrossLink{}     %% add further rules for cross referencing links
%% \ccHtmlIndexC[class]{} %% add further index entries

\ccDefinition

% The section below is automatically generated. Do not edit!
%START-AUTO(\ccDefinition)

A class representing a single model from a PDB file.

You can iterator through the chains and soon the heterogens.

%END-AUTO(\ccDefinition)
  
% The section below is automatically generated. Do not edit!
%START-AUTO(\ccInclude)

\ccInclude{CGAL/PDB/Model.h}

%END-AUTO(\ccInclude)

\ccIsModel

\ccTypes

% The section below is automatically generated. Do not edit!
%START-AUTO(\ccTypes)

\ccNestedType{Heterogen_key}
{
}
\ccGlue
\ccNestedType{Chain_key}
{
}
\ccGlue
\ccNestedType{Chains}
{
Iterator through the chains.
}
\ccGlue
\ccNestedType{Chain_consts}
{
}
\ccGlue
\ccNestedType{Heterogens}
{
An iterator through the heterogen objects.
}
\ccGlue
\ccNestedType{Heterogen_consts}
{
}
\ccGlue
\ccNestedType{Bond}
{
A chemical bond within the protein.
}
\ccGlue
\ccNestedType{Atoms}
{
An iterator to iterate through all the atoms of the protein
}
\ccGlue
\ccNestedType{Atom_consts}
{
}
\ccGlue
\ccNestedType{Bonds}
{
}
\ccGlue

%END-AUTO(\ccTypes)

\ccCreation
\ccCreationVariable{a}  %% choose variable name

% The section below is automatically generated. Do not edit!
%START-AUTO(\ccCreation)

\ccConstructor{Model();}
{
Construct an empty model.
}
\ccGlue

%END-AUTO(\ccCreation)

\ccOperations

% The section below is automatically generated. Do not edit!
%START-AUTO(\ccOperations)

\ccMethod{void swap_with(Model& o);}
{
}
\ccGlue
\ccMethod{void write(int model_index, std::ostream& out) const;}
{
write to a pdb
}
\ccGlue
\ccMethod{std::ostream& write(std::ostream& out) const;}
{
write screen
}
\ccGlue
\ccMethod{Chains chains();}
{
}
\ccGlue
\ccMethod{Chain_consts chains() const;}
{
}
\ccGlue
\ccMethod{bool contains(Chain_key k) const;}
{
get the chain identified by k
}
\ccGlue
\ccMethod{Chains::iterator::reference get(Chain_key k);}
{
}
\ccGlue
\ccMethod{Chains::iterator find(Chain_key k);}
{
}
\ccGlue
\ccMethod{Chain_consts::const_iterator::value_type get(Chain_key k) const;}
{
}
\ccGlue
\ccMethod{Chain_consts::const_iterator find(Chain_key k) const;}
{
}
\ccGlue
\ccMethod{void insert(Chain_key k, const Chain& m);}
{
}
\ccGlue
\ccMethod{Heterogens heterogens();}
{
}
\ccGlue
\ccMethod{Heterogen_consts heterogens() const;}
{
}
\ccGlue
\ccMethod{bool contains(Heterogen_key k) const;}
{
get the chain identified by k
}
\ccGlue
\ccMethod{Heterogens::iterator::reference get(Heterogen_key k);}
{
}
\ccGlue
\ccMethod{Heterogens::iterator find(Heterogen_key k);}
{
}
\ccGlue
\ccMethod{Heterogen_consts::const_iterator::value_type get(Heterogen_key k) const;}
{
}
\ccGlue
\ccMethod{Heterogen_consts::const_iterator find(Heterogen_key k) const;}
{
}
\ccGlue
\ccMethod{void insert(Heterogen_key k, const Heterogen& m);}
{
}
\ccGlue
\ccMethod{Atoms atoms();}
{
}
\ccGlue
\ccMethod{Atom_consts atoms() const;}
{
}
\ccGlue
\ccMethod{Bonds bonds() const;}
{
}
\ccGlue

%END-AUTO(\ccOperations)

\ccSeeAlso

\ccExample

A short example program.
Instead of a short program fragment, a full running program can be
included using the 
\verb|\ccIncludeExampleCode{PDB/Model.C}| 
macro. The program example would be part of the source code distribution and
also part of the automatic test suite.

\begin{ccExampleCode}
void your_example_code() {
}
\end{ccExampleCode}

%% \ccIncludeExampleCode{PDB/Model.C}

\end{ccRefClass}

% +------------------------------------------------------------------------+
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\ccRefPageEnd
% EOF
% +------------------------------------------------------------------------+

