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

#include <BALL/FORMAT/MOL2File.h>

Inheritance diagram for BALL::MOL2File:

[legend]

List of all members.

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)
virtual	~MOL2File ()
	Destructor.
Reading and Writing of Kernel Datastructures
virtual bool	write (const System &system)
virtual bool	read (System &system)
virtual Molecule *	read ()
virtual bool	write (const Molecule &molecule)
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
	)

Detailed constructor

Exceptions:

Exception::FileNotFound

if the file could not be opened

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

(

)

[virtual]

Read a molecule from the MOL2 file

Exceptions:

Exception::ParseError

if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::MOL2File::read

(

System &

system

)

[virtual]

Read a system from the MOL2 file

Exceptions:

Exception::ParseError

if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

void BALL::MOL2File::readAtomSection_

(

)

[protected]

void BALL::MOL2File::readBondSection_

(

)

[protected]

void BALL::MOL2File::readCommentSection_

(

)

[protected]

void BALL::MOL2File::readMoleculeSection_

(

)

[protected]

void BALL::MOL2File::readSetSection_

(

)

[protected]

void BALL::MOL2File::readSubstructureSection_

(

)

[protected]

virtual bool BALL::MOL2File::write

(

const Molecule &

molecule

)

[virtual]

Write a molecule to a HIN file.

Exceptions:

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::MOL2File::write

(

const System &

system

)

[virtual]

Write a system to the MOL2 file

Exceptions:

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::GenericMolFile.

---

Member Data Documentation

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

Definition at line 188 of file MOL2File.h.

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

Definition at line 189 of file MOL2File.h.

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

Definition at line 197 of file MOL2File.h.

vector<CommentStruct> BALL::MOL2File::comments_ [protected]

Definition at line 192 of file MOL2File.h.

bool BALL::MOL2File::found_next_header_ [protected]

Definition at line 199 of file MOL2File.h.

String BALL::MOL2File::line_ [protected]

buffer for the line in use

Reimplemented from BALL::LineBasedFile.

Definition at line 198 of file MOL2File.h.

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

Definition at line 196 of file MOL2File.h.

MoleculeStruct BALL::MOL2File::molecule_ [protected]

Definition at line 193 of file MOL2File.h.

Size BALL::MOL2File::number_of_lines_ [protected]

Definition at line 195 of file MOL2File.h.

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

Definition at line 190 of file MOL2File.h.

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

Definition at line 191 of file MOL2File.h.

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

Tripos Record Type Identifier (RTI)

Definition at line 56 of file MOL2File.h.