#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

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

void BALL::FragmentDB::destroy ( )

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::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.

NormalizeNamesProcessor BALL::FragmentDB::normalize_names

The standard name normalization processor

Definition at line 476 of file fragmentDB.h.

ResourceEntry* BALL::FragmentDB::tree

The resource tree read from the database file

Definition at line 488 of file fragmentDB.h.

Classes

Public Types

Public Member Functions

Public Attributes

Friends

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation