KCFFile Class Reference
[Molecular structure file formats]

KEGG KCF file class. More...

#include <KCFFile.h>

Inheritance diagram for KCFFile:

List of all members.

Public Types
Type definitions
typedef HashMap< const Atom *, Position >	AtomIndexMap
typedef HashMap< Position, Atom * >	IndexAtomMap
Public Member Functions
Constructors and Destructors
	KCFFile (const String &filename, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound)
	KCFFile (const KCFFile &file) throw (Exception::FileNotFound)
Reading and Writing of Kernel Datastructures
virtual bool	write (const Molecule &molecule) throw (File::CannotWrite)
	Write a molecule to the file.
virtual bool	write (const System &system) throw (File::CannotWrite)
	Write a system to the KCF file.
virtual bool	read (System &system) throw (Exception::ParseError)
	Read a system from a KCF File.
virtual Molecule *	read () throw (Exception::ParseError)
	Read a single molecule from the file If unscuccesful, a NULL pointer is returned.
const KCFFile &	operator= (const KCFFile &file) throw ()
Static Public Attributes
Constants
const char *	ENTRY_TAG
const char *	NODE_TAG
const char *	EDGE_TAG
const char *	DELIMITER_TAG
const char *	CONTINUED_LINE
Protected Member Functions
bool	readENTRY_ (Molecule &mol)
bool	readNODE_ (Molecule &mol, IndexAtomMap &index_to_atom)
bool	readEDGE_ (IndexAtomMap &index_to_atom)
bool	readDELIMITER_ ()

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Detailed Description

KEGG KCF file class.

This class reads and writes KEGG (Kyoto Encyclopedia of Genes and Genomes) KCF (KEGG Chemical Function) files.

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Member Function Documentation

virtual Molecule* KCFFile::read (   )  throw (Exception::ParseError) [virtual]

Read a single molecule from the file If unscuccesful, a NULL pointer is returned. Reimplemented from GenericMolFile.

virtual bool KCFFile::read (  System &  system  )  throw (Exception::ParseError) [virtual]

Read a system from a KCF File. Each molecule in the file is stored as an individual instance of Molecule within the system. Previous contents of the system are erased. Reimplemented from GenericMolFile.

virtual bool KCFFile::write (  const System &  system  )  throw (File::CannotWrite) [virtual]

Write a system to the KCF file. Each Molecule in the system is written as distinct molecule in the KCF file. Reimplemented from GenericMolFile.