BALL::FragmentDB::NormalizeNamesProcessor Class Reference

#include <BALL/STRUCTURE/fragmentDB.h>

Inheritance diagram for BALL::FragmentDB::NormalizeNamesProcessor:

Public Member Functions
Constructors and Destructors
	NormalizeNamesProcessor ()
	NormalizeNamesProcessor (FragmentDB &db)
virtual	~NormalizeNamesProcessor ()
Inspectors and Mutators
void	setFragmentDB (FragmentDB &db)
void	setNamingStandard (const String &naming_standard)
const String &	getNamingStandard ()
bool	matchName (String &res_name, String &atom_name, const NameMap &map) const
Processor specific methods
virtual bool	start ()
virtual bool	finish ()
virtual Processor::Result	operator() (Fragment &fragment)
Public Member Functions inherited from BALL::UnaryProcessor< Fragment >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()

Private Types
enum	CountingMode { ADD, OVERWRITE }

Private Member Functions
String	getSuffix_ (const Fragment *frag) const
bool	doMatch_ (String &res_name, const String &res_name_suffix, String &atom_name, const NameMap &map) const
void	countHits_ (HashMap< NameMap *, Index > &maps, const std::list< Fragment * > &frags)
void	countHits_ (HashMap< NameMap *, Index > &maps, const Fragment *frag, CountingMode mode=OVERWRITE)
const NameMap *	getBestMap_ (const HashMap< NameMap *, Index > &maps) const
void	normalizeFragments_ (const NameMap *map, const std::list< Fragment * > &frags)
void	normalizeFragment_ (const NameMap *map, Fragment *frag)

Private Attributes
String	naming_standard_
FragmentDB *	fragment_db_
std::list< Fragment * >	fragments_

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< Fragment, Processor::Result >
typedef Processor::Result	result_type
typedef Fragment	argument_type
typedef Fragment &	argument_reference
typedef const Fragment &	const_argument_reference
typedef Fragment *	argument_pointer
typedef const Fragment *	const_argument_pointer

Detailed Description

Name normalization processor. This class is used to adopt all names in a molecular system to a given naming standard (usually the PDB standard).

Definition at line 254 of file fragmentDB.h.

Member Enumeration Documentation

enum BALL::FragmentDB::NormalizeNamesProcessor::CountingMode

private

Enumerator
ADD
OVERWRITE

Definition at line 318 of file fragmentDB.h.

Constructor & Destructor Documentation

BALL::FragmentDB::NormalizeNamesProcessor::NormalizeNamesProcessor

(

)

Default constructor

BALL::FragmentDB::NormalizeNamesProcessor::NormalizeNamesProcessor

(

FragmentDB &

db

)

Constructor

virtual BALL::FragmentDB::NormalizeNamesProcessor::~NormalizeNamesProcessor ( )

virtual

Destructor

Member Function Documentation

void BALL::FragmentDB::NormalizeNamesProcessor::countHits_ ( HashMap< NameMap *, Index > &  maps, const std::list< Fragment * > &  frags  )

private

void BALL::FragmentDB::NormalizeNamesProcessor::countHits_ ( HashMap< NameMap *, Index > &  maps, const Fragment *  frag, CountingMode  mode = OVERWRITE  )

private

bool BALL::FragmentDB::NormalizeNamesProcessor::doMatch_ ( String &  res_name, const String &  res_name_suffix, String &  atom_name, const NameMap &  map  ) const

private

virtual bool BALL::FragmentDB::NormalizeNamesProcessor::finish ( )

virtual

Finish method

Reimplemented from BALL::UnaryProcessor< Fragment >.

const NameMap* BALL::FragmentDB::NormalizeNamesProcessor::getBestMap_ ( const HashMap< NameMap *, Index > &  maps ) const

private

const String& BALL::FragmentDB::NormalizeNamesProcessor::getNamingStandard

(

)

Retrieve the current naming standard

String BALL::FragmentDB::NormalizeNamesProcessor::getSuffix_ ( const Fragment *  frag ) const

private

bool BALL::FragmentDB::NormalizeNamesProcessor::matchName	(	String &	res_name,
		String &	atom_name,
		const NameMap &	map
	)		const

Try to match a name in one of the maps

void BALL::FragmentDB::NormalizeNamesProcessor::normalizeFragment_ ( const NameMap *  map, Fragment *  frag  )

private

void BALL::FragmentDB::NormalizeNamesProcessor::normalizeFragments_ ( const NameMap *  map, const std::list< Fragment * > &  frags  )

private

virtual Processor::Result BALL::FragmentDB::NormalizeNamesProcessor::operator() ( Fragment &  fragment )

virtual

Application method

Reimplemented from BALL::UnaryProcessor< Fragment >.

void BALL::FragmentDB::NormalizeNamesProcessor::setFragmentDB

(

FragmentDB &

db

)

Bind the processor to a fragment database.

void BALL::FragmentDB::NormalizeNamesProcessor::setNamingStandard

(

const String &

naming_standard

)

virtual bool BALL::FragmentDB::NormalizeNamesProcessor::start ( )

virtual

Start method

Reimplemented from BALL::UnaryProcessor< Fragment >.

Member Data Documentation

FragmentDB* BALL::FragmentDB::NormalizeNamesProcessor::fragment_db_

private

Definition at line 329 of file fragmentDB.h.

std::list<Fragment*> BALL::FragmentDB::NormalizeNamesProcessor::fragments_

private

Definition at line 331 of file fragmentDB.h.

String BALL::FragmentDB::NormalizeNamesProcessor::naming_standard_

private

Definition at line 327 of file fragmentDB.h.