BALL::FragmentDB Class Reference
[Miscellaneous]

#include <BALL/STRUCTURE/fragmentDB.h>

List of all members.

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) throw (Exception::FileNotFound)
	FragmentDB (const FragmentDB &db, bool deep=true)
FragmentDB &	operator= (const FragmentDB &db)
	Assignment operator.
virtual	~FragmentDB ()
void	destroy ()
Database Setup
void	init () throw (Exception::FileNotFound, NoFragmentNode)
Inspectors and mutators
void	setFilename (const String &filename) throw (Exception::FileNotFound)
const String &	getFilename () const
bool	has (const String &fragment_name) const
const std::vector< Residue * > &	getFragments ()
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 throw (StringHashMap<String>::IllegalKey)
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) throw (Exception::FileNotFound)
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.

---

Member Typedef Documentation

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

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

typedef short BALL::FragmentDB::Type

Type definition for the fragment type

---

Member Enumeration Documentation

enum BALL::FragmentDB::FragmentTypes

Fragment types

Enumerator:

TYPE__UNKNOWN
TYPE__FRAGMENT
TYPE__RESIDUE
TYPE__MOLECULE

---

Constructor & Destructor Documentation

BALL::FragmentDB::FragmentDB

(

)

Creates a default but invalid FragmentDB instance.

BALL::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

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

)

throw (Exception::FileNotFound) [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

(

)

[inline]

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 throw (StringHashMap<String>::IllegalKey)

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

(

)

throw (Exception::FileNotFound, NoFragmentNode)

Initialization of the database.

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

)

throw (Exception::FileNotFound)

Assigns a filename.

---

Friends And Related Function Documentation

friend class FragmentDB::AddHydrogensProcessor [friend]

---

Member Data Documentation

ReconstructFragmentProcessor BALL::FragmentDB::add_hydrogens

The standard hydrogen adder

BuildBondsProcessor BALL::FragmentDB::build_bonds

The standard bond builder

String BALL::FragmentDB::default_standard_ [private]

String BALL::FragmentDB::filename_ [private]

std::vector<Residue*> BALL::FragmentDB::fragments_ [private]

StringHashMap<Position> BALL::FragmentDB::name_to_frag_index_ [private]

NameMap BALL::FragmentDB::name_to_path_ [private]

StringHashMap<list<Position> > BALL::FragmentDB::name_to_variants_ [private]

NormalizeNamesProcessor BALL::FragmentDB::normalize_names

The standard name normalization processor

StringHashMap<NameMap> BALL::FragmentDB::standards_ [private]

ResourceEntry* BALL::FragmentDB::tree

The resource tree read from the database file

bool BALL::FragmentDB::valid_ [private]