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

#include <BALL/FORMAT/SDFile.h>

Inheritance diagram for BALL::SDFile:

[legend]

List of all members.

Public Member Functions
Constructors and Destructors
	SDFile ()
	SDFile (const String &filename, File::OpenMode open_mode=std::ios::in)
virtual	~SDFile ()
	Destructor.
Reading and Writing of Kernel Datastructures
virtual bool	write (const System &system)
virtual bool	write (const Molecule &molecule)
virtual bool	read (System &system)
virtual Molecule *	read ()
void	disableAtoms ()
void	enableAtoms ()
const SDFile &	operator= (const SDFile &file)
Protected Member Functions
void	readPropertyBlock_ (Molecule &molecule)
void	writePropertyBlock_ (const Molecule &molecule)
Protected Attributes
bool	read_atoms_

---

Detailed Description

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

A description of this file format (and the related MOLFile format) can be obtained from the MDL webpage http://www.mdli.com

Definition at line 22 of file SDFile.h.

---

Constructor & Destructor Documentation

BALL::SDFile::SDFile

(

)

Default constructor

BALL::SDFile::SDFile	(	const String &	filename,
		File::OpenMode	open_mode = std::ios::in
	)

Detailed constructor.

Exceptions:

Exception::FileNotFound

if the file could not be opened

virtual BALL::SDFile::~SDFile

(

)

[virtual]

Destructor.

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Member Function Documentation

void BALL::SDFile::disableAtoms

(

)

Do not read atoms and bonds. This (seemingly strange) option allows the user to read the properties of the molecules only. Since SD files can contain all kinds of information besides the molecular structure and reading the structure can be rather time and space consuming, you can disable it with this option. The read and write methods will still create molecules, but they will be empty. However, the NamedProperties of the molecules contain the optional information contained in the SD file.

void BALL::SDFile::enableAtoms

(

)

Read atoms and bonds.

See also:

disableAtoms

const SDFile& BALL::SDFile::operator=

(

const SDFile &

file

)

virtual Molecule* BALL::SDFile::read

(

)

[virtual]

Read a single molecule from an SD file.

Exceptions:

Exception::ParseError

if a syntax error was encountered

Reimplemented from BALL::MOLFile.

virtual bool BALL::SDFile::read

(

System &

system

)

[virtual]

Read a system from the SD file

Exceptions:

Exception::ParseError

if a syntax error was encountered

Reimplemented from BALL::MOLFile.

void BALL::SDFile::readPropertyBlock_

(

Molecule &

molecule

)

[protected]

Read the property block of an SD file. The values are stored as named properties in the molecule read.

virtual bool BALL::SDFile::write

(

const Molecule &

molecule

)

[virtual]

Append a single molecule to the SD file.

Exceptions:

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::MOLFile.

virtual bool BALL::SDFile::write

(

const System &

system

)

[virtual]

Write a system to the SD file. Write all molecules contained in the system to the SD file. All named properties are included in the property section.

Exceptions:

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::MOLFile.

void BALL::SDFile::writePropertyBlock_

(

const Molecule &

molecule

)

[protected]

Read the propertyblock of an SD file. The values are stored as named properties in the molecule read.

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Member Data Documentation

bool BALL::SDFile::read_atoms_ [protected]

Whether atoms and bonds should be read

Definition at line 110 of file SDFile.h.