BALL::FragmentDB::NormalizeNamesProcessor Class Reference

#include <BALL/STRUCTURE/fragmentDB.h>

Inheritance diagram for BALL::FragmentDB::NormalizeNamesProcessor:

List of all members.

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)
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_

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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).

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Member Enumeration Documentation

enum BALL::FragmentDB::NormalizeNamesProcessor::CountingMode [private]

Enumerator:

ADD
OVERWRITE

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Constructor & Destructor Documentation

BALL::FragmentDB::NormalizeNamesProcessor::NormalizeNamesProcessor

(

)

Default constructor

BALL::FragmentDB::NormalizeNamesProcessor::NormalizeNamesProcessor

(

FragmentDB &

db

)

Constructor

virtual BALL::FragmentDB::NormalizeNamesProcessor::~NormalizeNamesProcessor

(

)

[virtual]

Destructor

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Member Function Documentation

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

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

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Member Data Documentation

FragmentDB* BALL::FragmentDB::NormalizeNamesProcessor::fragment_db_ [private]

std::list<Fragment*> BALL::FragmentDB::NormalizeNamesProcessor::fragments_ [private]

String BALL::FragmentDB::NormalizeNamesProcessor::naming_standard_ [private]