FragmentDB Class Reference
[Miscellaneous]

FragmentDB - fragment database class. More...

#include <fragmentDB.h>

List of all members.

Public Types
Type Definitions
typedef short	Type
	Type definition for the fragment type.
typedef StringHashMap< String >	NameMap
	A hash map used to convert one atom naming convention to another.
Enums
enum	FragmentTypes { TYPE__UNKNOWN = -1, TYPE__FRAGMENT, TYPE__RESIDUE, TYPE__MOLECULE }
	Fragment types.
Public Member Functions
Constructors and destructors
	FragmentDB ()
	Creates a default but invalid FragmentDB instance.
	FragmentDB (const String &filename) throw (Exception::FileNotFound)
	Creates a FragmentDB object and reads the contents of filename.
	FragmentDB (const FragmentDB &db, bool deep=true)
	Copy constructor.
FragmentDB &	operator= (const FragmentDB &db) throw ()
	Assignment operator.
virtual	~FragmentDB ()
	Destructor.
void	destroy ()
Database Setup
void	init () throw (Exception::FileNotFound, NoFragmentNode)
	Initialization of the database.
Inspectors and mutators
void	setFilename (const String &filename) throw (Exception::FileNotFound)
	Assigns a filename.
const String &	getFilename () const
	Get the filename.
bool	has (const String &fragment_name) const
	Checks whether a specified fragment is known to the fragment database.
const std::vector< Residue * > &	getFragments ()
FragmentDB::Type	getFragmentType (const String &fragment_name) const
	Return a fragment.
list< String >	getVariantNames (const String &name) const
	Return a list containing all variant names.
const Fragment *	getFragment (const String &fragment_name) const
	Return a fragment.
const Fragment *	getReferenceFragment (const Fragment &fragment) const
	Return a reference fragment.
const Residue *	getResidue (const String &fragment_name) const
	Return a residue.
Fragment *	getFragmentCopy (const String &fragment_name) const
	Return a copy of a fragment.
Molecule *	getMoleculeCopy (const String &fragment_name) const
	Return a copy of a fragment as a molecule.
Residue *	getResidueCopy (const String &fragment_name) const
	Return a copy of a residue.
const String &	getDefaultNamingStandard () const
	Return the default naming standard.
StringHashMap< NameMap > &	getNamingStandards ()
	Return a hash map containing all naming maps.
Debugging and diagnostics
bool	isValid () const
Public Attributes
Public Variables
NormalizeNamesProcessor	normalize_names
	The standard name normalization processor.
ReconstructFragmentProcessor	add_hydrogens
	The standard hydrogen adder.
BuildBondsProcessor	build_bonds
	The standard bond builder.
ResourceEntry *	tree
	The resource tree read from the database file.
Friends
class	FragmentDB::AddHydrogensProcessor

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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.

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Constructor & Destructor Documentation

FragmentDB::FragmentDB (   )

Creates a default but invalid FragmentDB instance.

FragmentDB::FragmentDB (  const String &  filename  )  throw (Exception::FileNotFound)

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

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

Copy constructor.

virtual FragmentDB::~FragmentDB (   )  [virtual]

Destructor.

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Member Function Documentation

const String& FragmentDB::getFilename (   )  const

Get the filename.

const Fragment* FragmentDB::getFragment (  const String &  fragment_name  )  const

Return a fragment.

Fragment* 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

FragmentDB::Type FragmentDB::getFragmentType (  const String &  fragment_name  )  const

Return a fragment.

Molecule* 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

StringHashMap<NameMap>& FragmentDB::getNamingStandards (   )

Return a hash map containing all naming maps.

const Fragment* 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* FragmentDB::getResidue (  const String &  fragment_name  )  const

Return a residue.

Residue* 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> FragmentDB::getVariantNames (  const String &  name  )  const

Return a list containing all variant names.

bool FragmentDB::has (  const String &  fragment_name  )  const

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

void FragmentDB::init (   )  throw (Exception::FileNotFound, NoFragmentNode)

Initialization of the database.

void FragmentDB::setFilename (  const String &  filename  )  throw (Exception::FileNotFound)

Assigns a filename.