BALL::FragmentDB Class Reference

#include <BALL/STRUCTURE/fragmentDB.h>

Classes
class	BuildBondsProcessor
class	NoFragmentNode
class	NormalizeNamesProcessor

Public Types
Enums
enum	FragmentTypes { TYPE__UNKNOWN = -1, TYPE__FRAGMENT, TYPE__RESIDUE, TYPE__MOLECULE }
Type Definitions
typedef short	Type
typedef StringHashMap< String >	NameMap

Public Member Functions
Constructors and destructors
	FragmentDB ()
	FragmentDB (const String &filename)
	FragmentDB (const FragmentDB &db, bool deep=true)
FragmentDB &	operator= (const FragmentDB &db)
	Assignment operator. More...
virtual	~FragmentDB ()
void	destroy ()
Database Setup
void	init ()
Inspectors and mutators
void	setFilename (const String &filename)
const String &	getFilename () const
bool	has (const String &fragment_name) const
const std::vector< Residue * > &	getFragments () const
FragmentDB::Type	getFragmentType (const String &fragment_name) const
list< String >	getVariantNames (const String &name) const
const Fragment *	getFragment (const String &fragment_name) const
const Fragment *	getReferenceFragment (const Fragment &fragment) const
const Residue *	getResidue (const String &fragment_name) const
Fragment *	getFragmentCopy (const String &fragment_name) const
Molecule *	getMoleculeCopy (const String &fragment_name) const
Residue *	getResidueCopy (const String &fragment_name) const
const String &	getDefaultNamingStandard () const
StringHashMap< NameMap > &	getNamingStandards ()
const StringHashMap< String > &	getNamingStandard (const String &std) const
std::vector< String >	getAvailableNamingStandards () const
Debugging and diagnostics
bool	isValid () const

Public Attributes
Public Variables
NormalizeNamesProcessor	normalize_names
ReconstructFragmentProcessor	add_hydrogens
BuildBondsProcessor	build_bonds
ResourceEntry *	tree

Private Member Functions
void	parseAtoms_ (ResourceEntry &entry, Fragment &fragment)
void	parseBonds_ (ResourceEntry &entry, Fragment &fragment)
void	parseProperties_ (ResourceEntry &entry, PropertyManager &property_man)
void	parseDelete_ (ResourceEntry &entry, Fragment &fragment)
void	parseRename_ (ResourceEntry &entry, Fragment &fragment)
Position	addNewFragment_ (Residue *fragment)
void	expandTree_ (ResourceEntry &root_entry)
bool	expandFirst_ (ResourceEntry &root_entry)

Private Attributes
bool	valid_
String	filename_
String	default_standard_
std::vector< Residue * >	fragments_
NameMap	name_to_path_
StringHashMap< Position >	name_to_frag_index_
StringHashMap< list< Position > >	name_to_variants_
StringHashMap< NameMap >	standards_

Friends
class	FragmentDB::AddHydrogensProcessor

Detailed Description

FragmentDB - fragment database class. The fragment database is used to store commonly used subunits as amino acids, sugars and the like. They are entered in a special format described below. The main resource file resides under data/fragments/Fragments.db.

Definition at line 44 of file fragmentDB.h.

Member Typedef Documentation

typedef StringHashMap<String> BALL::FragmentDB::NameMap

A hash map used to convert one atom naming convention to another

Definition at line 76 of file fragmentDB.h.

typedef short BALL::FragmentDB::Type

Type definition for the fragment type

Definition at line 74 of file fragmentDB.h.

Member Enumeration Documentation

enum BALL::FragmentDB::FragmentTypes

Fragment types

Enumerator
TYPE__UNKNOWN
TYPE__FRAGMENT
TYPE__RESIDUE
TYPE__MOLECULE

Definition at line 59 of file fragmentDB.h.

Constructor & Destructor Documentation

BALL::FragmentDB::FragmentDB

(

)

Creates a default but invalid FragmentDB instance.

BALL::FragmentDB::FragmentDB

(

const String &

filename

)

Creates a FragmentDB object and reads the contents of filename. If filename is an empty string, the default value "fragments/Fragments.db" is used.

Exceptions

Exception::FileNotFound

if the file is not found in the BALL_DATA_PATH

BALL::FragmentDB::FragmentDB	(	const FragmentDB &	db,
		bool	deep = true
	)

Copy constructor.

virtual BALL::FragmentDB::~FragmentDB ( )

virtual

Destructor.

Member Function Documentation

Position BALL::FragmentDB::addNewFragment_ ( Residue *  fragment )

private

Add a new fragment pointer to the database (while parsing)

void BALL::FragmentDB::destroy

(

)

bool BALL::FragmentDB::expandFirst_ ( ResourceEntry &  root_entry )

private

void BALL::FragmentDB::expandTree_ ( ResourceEntry &  root_entry )

private

std::vector<String> BALL::FragmentDB::getAvailableNamingStandards

(

)

const

Return a vector of available naming standards

const String& BALL::FragmentDB::getDefaultNamingStandard

(

)

const

Return the default naming standard

const String& BALL::FragmentDB::getFilename

(

)

const

Get the filename.

const Fragment* BALL::FragmentDB::getFragment

(

const String &

fragment_name

)

const

Return a fragment.

Fragment* BALL::FragmentDB::getFragmentCopy

(

const String &

fragment_name

)

const

Return a copy of a fragment. If a fragment with name fragment_name exists in the fragment database, a copy is created and returned. Otherwise, a null pointer is returned. Take care to destruct the copy again to avoid memory leaks.

Returns

a pointer to the copied fragment or 0

Parameters

fragent_name

the name of the fragment in the database

const std::vector<Residue*>& BALL::FragmentDB::getFragments ( ) const

inline

Definition at line 158 of file fragmentDB.h.

FragmentDB::Type BALL::FragmentDB::getFragmentType

(

const String &

fragment_name

)

const

Return a fragment.

Molecule* BALL::FragmentDB::getMoleculeCopy

(

const String &

fragment_name

)

const

Return a copy of a fragment as a molecule. If a fragment with name fragment_name exists in the fragment database, a copy is created, inserted into a new molecule, and returned. Otherwise, a null pointer is returned. Take care to destruct the copy again to avoid memory leaks.

Returns

a pointer to the copied fragment or 0

Parameters

fragent_name

the name of the fragment in the database

const StringHashMap<String>& BALL::FragmentDB::getNamingStandard

(

const String &

std

)

const

Return the naming standard given by std

Returns

A StringHashMap that maps atom names to atom names

Exceptions

StringHashMap<String>::IllegalKey

if std is not a valid naming standard

StringHashMap<NameMap>& BALL::FragmentDB::getNamingStandards

(

)

Return a hash map containing all naming maps.

const Fragment* BALL::FragmentDB::getReferenceFragment

(

const Fragment &

fragment

)

const

Return a reference fragment. This method returns a standard template of a given fragment or a NULL pointer if the fragment is not known. The first criterion is the fragment name. If there exist multiple variants of the fragment, the correct variant is chosen according to the properties set in fragment.

const Residue* BALL::FragmentDB::getResidue

(

const String &

fragment_name

)

const

Return a residue.

Residue* BALL::FragmentDB::getResidueCopy

(

const String &

fragment_name

)

const

Return a copy of a residue. If a fragment with name fragment_name exists in the fragment database, a copy is created and returned as a residue. Otherwise, a null pointer is returned. Take care to destruct the copy again to avoid memory leaks.

Returns

a pointer to the copied fragment or 0

Parameters

fragent_name

the name of the fragment in the database

list<String> BALL::FragmentDB::getVariantNames

(

const String &

name

)

const

Return a list containing all variant names.

bool BALL::FragmentDB::has

(

const String &

fragment_name

)

const

Checks whether a specified fragment is known to the fragment database.

void BALL::FragmentDB::init

(

)

Initialization of the database.

Exceptions

Exception::FileNotFound	if the file is not found in the BALL_DATA_PATH
Exception::NoFragmentNode	if the FragmentDB file did not contain any node entries

bool BALL::FragmentDB::isValid

(

)

const

FragmentDB& BALL::FragmentDB::operator=

(

const FragmentDB &

db

)

Assignment operator.

void BALL::FragmentDB::parseAtoms_ ( ResourceEntry &  entry, Fragment &  fragment  )

private

void BALL::FragmentDB::parseBonds_ ( ResourceEntry &  entry, Fragment &  fragment  )

private

void BALL::FragmentDB::parseDelete_ ( ResourceEntry &  entry, Fragment &  fragment  )

private

void BALL::FragmentDB::parseProperties_ ( ResourceEntry &  entry, PropertyManager &  property_man  )

private

void BALL::FragmentDB::parseRename_ ( ResourceEntry &  entry, Fragment &  fragment  )

private

void BALL::FragmentDB::setFilename

(

const String &

filename

)

Assigns a filename.

Exceptions

Exception::FileNotFound

if the file is not found in the BALL_DATA_PATH

Friends And Related Function Documentation

friend class FragmentDB::AddHydrogensProcessor

friend

Definition at line 48 of file fragmentDB.h.

Member Data Documentation

ReconstructFragmentProcessor BALL::FragmentDB::add_hydrogens

The standard hydrogen adder

Definition at line 480 of file fragmentDB.h.

BuildBondsProcessor BALL::FragmentDB::build_bonds

The standard bond builder

Definition at line 484 of file fragmentDB.h.

String BALL::FragmentDB::default_standard_

private

Definition at line 550 of file fragmentDB.h.

String BALL::FragmentDB::filename_

private

Definition at line 547 of file fragmentDB.h.

std::vector<Residue*> BALL::FragmentDB::fragments_

private

Definition at line 553 of file fragmentDB.h.

StringHashMap<Position> BALL::FragmentDB::name_to_frag_index_

private

Definition at line 559 of file fragmentDB.h.

NameMap BALL::FragmentDB::name_to_path_

private

Definition at line 556 of file fragmentDB.h.

StringHashMap<list<Position> > BALL::FragmentDB::name_to_variants_

private

Definition at line 562 of file fragmentDB.h.

NormalizeNamesProcessor BALL::FragmentDB::normalize_names

The standard name normalization processor

Definition at line 476 of file fragmentDB.h.

StringHashMap<NameMap> BALL::FragmentDB::standards_

private

Definition at line 565 of file fragmentDB.h.

ResourceEntry* BALL::FragmentDB::tree

The resource tree read from the database file

Definition at line 488 of file fragmentDB.h.

bool BALL::FragmentDB::valid_

private

Definition at line 544 of file fragmentDB.h.