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

#include <BALL/FORMAT/MOL2File.h>

Inheritance diagram for BALL::MOL2File:

List of all members.

Classes
struct	AtomStruct
struct	BondStruct
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)
	MOL2File (const MOL2File &file) 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_ ()
String	getSybylType_ (const Atom &atom) const
bool	nextLine_ ()
void	clear_ ()
bool	buildAll_ (System &system)
bool	containsAtomChilds_ (AtomContainerConstIterator &frag_it)
Protected Attributes
vector< AtomStruct >	atoms_
vector< BondStruct >	bonds_
vector< SetStruct >	sets_
vector< SubstructureStruct >	substructures_
MoleculeStruct	molecule_
Size	number_of_lines_
char	buffer_ [4096]
String	line_
	buffer for the line in use
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).

---

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

BALL::MOL2File::MOL2File

(

const MOL2File &

file

)

throw (Exception::FileNotFound)

Copy constructor

virtual BALL::MOL2File::~MOL2File

(

)

[virtual]

Destructor.

---

Member Function Documentation

bool BALL::MOL2File::buildAll_

(

System &

system

)

[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.

const SetStruct& BALL::MOL2File::getSet

(

Position

i

)

const [inline]

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

SetStruct& BALL::MOL2File::getSet

(

Position

i

)

[inline]

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

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.

Returns:

a pointer to a molecule, 0 if the file was not open, empty, or at its end

Exceptions:

Exception::ParseError

if the contents of the file could not be parsed

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::MOL2File::read

(

System &

system

)

throw (Exception::ParseError) [virtual]

Read a system from the MOL2 file

Reimplemented from BALL::GenericMolFile.

void BALL::MOL2File::readAtomSection_

(

)

[protected]

void BALL::MOL2File::readBondSection_

(

)

[protected]

void BALL::MOL2File::readMoleculeSection_

(

)

[protected]

void BALL::MOL2File::readSetSection_

(

)

[protected]

void BALL::MOL2File::readSubstructureSection_

(

)

[protected]

virtual bool BALL::MOL2File::write

(

const Molecule &

molecule

)

throw (File::CannotWrite) [virtual]

Write a molecule. Repeated invocations of this method append molecules to the same file.

The default implementation does nothing.

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::MOL2File::write

(

const System &

system

)

throw (File::CannotWrite) [virtual]

Write a system to the MOL2 file

Reimplemented from BALL::GenericMolFile.

---

Member Data Documentation

vector<AtomStruct> BALL::MOL2File::atoms_ [protected]

vector<BondStruct> BALL::MOL2File::bonds_ [protected]

char BALL::MOL2File::buffer_[4096] [protected]

String BALL::MOL2File::line_ [protected]

buffer for the line in use

Reimplemented from BALL::LineBasedFile.

const Size BALL::MOL2File::MAX_LENGTH_ [static, protected]

MoleculeStruct BALL::MOL2File::molecule_ [protected]

Size BALL::MOL2File::number_of_lines_ [protected]

vector<SetStruct> BALL::MOL2File::sets_ [protected]

vector<SubstructureStruct> BALL::MOL2File::substructures_ [protected]

const String BALL::MOL2File::TRIPOS [static]

Tripos Record Type Identifier (RTI)