BALL::MOLFile Class Reference
[Molecular structure file formats]

#include <BALL/FORMAT/MOLFile.h>

Inheritance diagram for BALL::MOLFile:

List of all members.

Classes
class	AtomStruct
class	BondStruct
class	CountsStruct
struct	Property
Public Member Functions
Constructors and Destructors
	MOLFile ()
	MOLFile (const String &filename, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound)
	MOLFile (const MOLFile &file) throw (Exception::FileNotFound)
virtual	~MOLFile ()
	Destructor.
Reading and Writing of Kernel Datastructures
virtual bool	write (const Molecule &molecule) throw (File::CannotWrite)
virtual bool	write (const System &system) throw (File::CannotWrite)
virtual bool	read (System &system) throw (Exception::ParseError)
virtual Molecule *	read () throw (Exception::ParseError)
const MOLFile &	operator= (const MOLFile &file)
Protected Member Functions
Molecule *	readCTAB_ (std::vector< Atom * > &atom_map) throw (Exception::ParseError)
	Read the CTAB of a MOL file and construct a Molecule from its data.
bool	readCountsLine_ (CountsStruct &counts)
	Read the Counts line of a MOL file.
bool	readAtomLine_ (AtomStruct &atom)
	Read a line from the atom block.
bool	readBondLine_ (BondStruct &bond)
	Read a line from the bond block.
void	writeCountsLine_ (const CountsStruct &counts)
	Write the Counts line.
void	writeAtomLine_ (const AtomStruct &atom)
	Write a line of the atom block.
void	writeBondLine_ (const BondStruct &bond)
	Write a line of the bond block.
Static Protected Attributes
Format definitions
static const String	counts_format_
	The format of the counts line.
static const String	atom_format_
	The format of an entry of the atom block.
static const String	bond_format_
	The format of an entry of the bond block.

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Detailed Description

MDL MOL file class. This class enables BALL to read and write MDL MOL files.

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Constructor & Destructor Documentation

BALL::MOLFile::MOLFile

(

)

Default constructor

BALL::MOLFile::MOLFile	(	const String &	filename,
		File::OpenMode	open_mode = std::ios::in
	)			throw (Exception::FileNotFound)

Detailed constructor.

BALL::MOLFile::MOLFile

(

const MOLFile &

file

)

throw (Exception::FileNotFound)

Copy constructor

virtual BALL::MOLFile::~MOLFile

(

)

[virtual]

Destructor.

---

Member Function Documentation

const MOLFile& BALL::MOLFile::operator=

(

const MOLFile &

file

)

virtual Molecule* BALL::MOLFile::read

(

)

throw (Exception::ParseError) [virtual]

Read a single molecule from the file

Reimplemented from BALL::GenericMolFile.

Reimplemented in BALL::SDFile.

virtual bool BALL::MOLFile::read

(

System &

system

)

throw (Exception::ParseError) [virtual]

Read a system from the MOL file

Reimplemented from BALL::GenericMolFile.

Reimplemented in BALL::SDFile.

bool BALL::MOLFile::readAtomLine_

(

AtomStruct &

atom

)

[protected]

Read a line from the atom block.

bool BALL::MOLFile::readBondLine_

(

BondStruct &

bond

)

[protected]

Read a line from the bond block.

bool BALL::MOLFile::readCountsLine_

(

CountsStruct &

counts

)

[protected]

Read the Counts line of a MOL file.

Molecule* BALL::MOLFile::readCTAB_

(

std::vector< Atom * > &

atom_map

)

throw (Exception::ParseError) [protected]

Read the CTAB of a MOL file and construct a Molecule from its data.

virtual bool BALL::MOLFile::write

(

const System &

system

)

throw (File::CannotWrite) [virtual]

Write a system to the MOL file. Note that this changes the properties of atoms in the system.

Reimplemented from BALL::GenericMolFile.

Reimplemented in BALL::SDFile.

virtual bool BALL::MOLFile::write

(

const Molecule &

molecule

)

throw (File::CannotWrite) [virtual]

Write a molecule to the file

Reimplemented from BALL::GenericMolFile.

Reimplemented in BALL::SDFile.

void BALL::MOLFile::writeAtomLine_

(

const AtomStruct &

atom

)

[protected]

Write a line of the atom block.

void BALL::MOLFile::writeBondLine_

(

const BondStruct &

bond

)

[protected]

Write a line of the bond block.

void BALL::MOLFile::writeCountsLine_

(

const CountsStruct &

counts

)

[protected]

Write the Counts line.

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Member Data Documentation

const String BALL::MOLFile::atom_format_ [static, protected]

The format of an entry of the atom block.

const String BALL::MOLFile::bond_format_ [static, protected]

The format of an entry of the bond block.

const String BALL::MOLFile::counts_format_ [static, protected]

The format of the counts line.