BALL::MOL2File Class Reference
[Molecular structure file formats]

#include <BALL/FORMAT/MOL2File.h>

Inheritance diagram for BALL::MOL2File:

Classes
struct	AtomStruct
struct	BondStruct
struct	CommentStruct
struct	MoleculeStruct
struct	SetStruct
	A class used for storing TRIPOS sets. More...
struct	SubstructureStruct
Public Member Functions
Constructors and Destructors

	MOL2File ()
	MOL2File (const String &filename, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound)
virtual	~MOL2File ()
	Destructor.
Reading and Writing of Kernel Datastructures

virtual bool	write (const System &system) throw (File::CannotWrite)
virtual bool	read (System &system) throw (Exception::ParseError)
virtual Molecule *	read () throw (Exception::ParseError)
virtual bool	write (const Molecule &molecule) throw (File::CannotWrite)
const MOL2File &	operator= (const MOL2File &file)
Size	getNumberOfSets () const
	Return the number of TRIPOS-Sets defined in this instance.
SetStruct &	getSet (Position i)
	Return the i-th TRIPOS set. NOTE: no range checking is performed.
const SetStruct &	getSet (Position i) const
	Return the i-th TRIPOS set, const version. NOTE: no range checking is performed.
Static Public Attributes
Constants

static const String	TRIPOS
Protected Member Functions
void	readAtomSection_ ()
void	readBondSection_ ()
void	readMoleculeSection_ ()
void	readSetSection_ ()
void	readSubstructureSection_ ()
void	readCommentSection_ ()
String	getSybylType_ (const Atom &atom) const
bool	nextLine_ ()
void	clear_ ()
bool	buildAll_ (Molecule &molecule)
bool	containsAtomChilds_ (AtomContainerConstIterator &frag_it)
Protected Attributes
vector< AtomStruct >	atoms_
vector< BondStruct >	bonds_
vector< SetStruct >	sets_
vector< SubstructureStruct >	substructures_
vector< CommentStruct >	comments_
MoleculeStruct	molecule_
Size	number_of_lines_
char	buffer_ [4096]
String	line_
	buffer for the line in use
bool	found_next_header_
Static Protected Attributes
static const Size	MAX_LENGTH_

Detailed Description

SYBYL MOL2 file class. This class is used to read and write SYBYL MOL2 files (Tripos).

Definition at line 30 of file MOL2File.h.

Constructor & Destructor Documentation

BALL::MOL2File::MOL2File ( )

Default constructor

BALL::MOL2File::MOL2File	(	const String &	filename,
		File::OpenMode	open_mode = `std::ios::in`
	)			throw (Exception::FileNotFound)

Detailed constructor

virtual BALL::MOL2File::~MOL2File ( ) [virtual]

Destructor.

Member Function Documentation

bool BALL::MOL2File::buildAll_ ( Molecule & molecule ) [protected]

void BALL::MOL2File::clear_ ( ) [protected]

bool BALL::MOL2File::containsAtomChilds_ ( AtomContainerConstIterator & frag_it ) [protected]

Size BALL::MOL2File::getNumberOfSets ( ) const [inline]

Return the number of TRIPOS-Sets defined in this instance.

Definition at line 105 of file MOL2File.h.

const SetStruct& BALL::MOL2File::getSet ( Position i ) const [inline]

Return the i-th TRIPOS set, const version. NOTE: no range checking is performed.

Definition at line 111 of file MOL2File.h.

SetStruct& BALL::MOL2File::getSet ( Position i ) [inline]

Return the i-th TRIPOS set. NOTE: no range checking is performed.

Definition at line 108 of file MOL2File.h.

String BALL::MOL2File::getSybylType_ ( const Atom & atom ) const [protected]

bool BALL::MOL2File::nextLine_ ( ) [protected]

const MOL2File& BALL::MOL2File::operator= ( const MOL2File & file )

virtual Molecule* BALL::MOL2File::read ( ) throw (Exception::ParseError) [virtual]

Read a molecule. This method will load the first (or the next, on subsequent invocation) molecule from the file. If the file format does not support multiple molecules, only the first call to read will be successful. This method will create an instance of molecule and its the user's responsibility to destroy that molecule.