BALL::FragmentDB::BuildBondsProcessor Class Reference

#include <BALL/STRUCTURE/fragmentDB.h>

Inheritance diagram for BALL::FragmentDB::BuildBondsProcessor:

Classes
struct	Connection
Public Types
Type definitions

typedef std::list< Connection >	ConnectionList
Public Member Functions
Constructors and Destructors

	BuildBondsProcessor ()
	BuildBondsProcessor (const FragmentDB &db)
virtual	~BuildBondsProcessor ()
Processor-related methods

virtual bool	finish ()
virtual bool	start ()
virtual Processor::Result	operator() (Fragment &fragment)
Accessors

Size	getNumberOfBondsBuilt ()
	Return the number of bonds built during the last application.
void	setFragmentDB (const FragmentDB &fragment_db)
	Set the fragment database.
Bond building methods

Size	buildFragmentBonds (Fragment &fragment) const
Size	buildFragmentBonds (Fragment &fragment, const Fragment &tplate) const
Size	buildInterFragmentBonds (Fragment &first, Fragment &second) const
Protected Member Functions
void	storeConnections_ (Fragment &fragment)
bool	buildConnection_ (Connection &con1, Connection &con2)
Protected Attributes
FragmentDB *	fragment_db_
std::list< Fragment * >	fragment_list_
Size	bonds_built_
ConnectionList	connections_

Detailed Description

Bond creation processor

Definition at line 338 of file fragmentDB.h.

Member Typedef Documentation

typedef std::list<Connection> BALL::FragmentDB::BuildBondsProcessor::ConnectionList

Definition at line 359 of file fragmentDB.h.

Constructor & Destructor Documentation

BALL::FragmentDB::BuildBondsProcessor::BuildBondsProcessor ( )

BALL::FragmentDB::BuildBondsProcessor::BuildBondsProcessor ( const FragmentDB & db )

virtual BALL::FragmentDB::BuildBondsProcessor::~BuildBondsProcessor ( ) [virtual]

Member Function Documentation

bool BALL::FragmentDB::BuildBondsProcessor::buildConnection_	(	Connection &	con1,
		Connection &	con2
	)			`[protected]`

Build a connection between two atoms, if possible

Exceptions:

Exception::TooManyBonds

if an atom would be assigned too many bonds

Size BALL::FragmentDB::BuildBondsProcessor::buildFragmentBonds	(	Fragment &	fragment,
		const Fragment &	tplate
	)			const

Build all bonds in a fragment according to a manually supplied template. This method builds all bonds that are contained in manually provided template.

Returns:: the number of bonds built

Exceptions:

Exception::TooManyBonds

if an atom would be assigned too many bonds

Size BALL::FragmentDB::BuildBondsProcessor::buildFragmentBonds ( Fragment & fragment ) const

Build all bonds in a fragment. This method builds all bonds that are contained in the template.

Returns:: the number of bonds built

Size BALL::FragmentDB::BuildBondsProcessor::buildInterFragmentBonds	(	Fragment &	first,
		Fragment &	second
	)			const

Build all possible bonds between two fragments. This method builds all bonds that are allowed by the Connections entries in a resource database.

Returns:: the number of bonds built

Exceptions:

Exception::TooManyBonds

if an atom would be assigned too many bonds

virtual bool BALL::FragmentDB::BuildBondsProcessor::finish ( ) [virtual]

finish method

Reimplemented from BALL::UnaryProcessor< Fragment >.

Size BALL::FragmentDB::BuildBondsProcessor::getNumberOfBondsBuilt ( )

Return the number of bonds built during the last application.

virtual Processor::Result BALL::FragmentDB::BuildBondsProcessor::operator() ( Fragment & ) [virtual]

operator ()

Reimplemented from BALL::UnaryProcessor< Fragment >.

void BALL::FragmentDB::BuildBondsProcessor::setFragmentDB ( const FragmentDB & fragment_db )

Set the fragment database.

virtual bool BALL::FragmentDB::BuildBondsProcessor::start ( ) [virtual]

start method

Reimplemented from BALL::UnaryProcessor< Fragment >.

void BALL::FragmentDB::BuildBondsProcessor::storeConnections_ ( Fragment & fragment ) [protected]

Store connections for a fragment. This method extracts all possible connections for a given fragment and stores them in a list of possible connections. finish will then check that list for possible inter-residue bonds.