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. More...
void	setFragmentDB (const FragmentDB &fragment_db)
	Set the fragment database. More...
Bond building methods
Size	buildFragmentBonds (Fragment &fragment) const
Size	buildFragmentBonds (Fragment &fragment, const Fragment &tplate) const
Size	buildInterFragmentBonds (Fragment &first, Fragment &second) const
Public Member Functions inherited from BALL::UnaryProcessor< Fragment >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()

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

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::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::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.

Member Data Documentation

Size BALL::FragmentDB::BuildBondsProcessor::bonds_built_

protected

Definition at line 462 of file fragmentDB.h.

ConnectionList BALL::FragmentDB::BuildBondsProcessor::connections_

protected

Definition at line 466 of file fragmentDB.h.

FragmentDB* BALL::FragmentDB::BuildBondsProcessor::fragment_db_

protected

A pointer to the fragment database

Definition at line 449 of file fragmentDB.h.

std::list<Fragment*> BALL::FragmentDB::BuildBondsProcessor::fragment_list_

protected

A list of all fragments. This list is constructed incrementally by the operator () and is used by finish() to create the inter-fragment bonds

Definition at line 455 of file fragmentDB.h.