#include <BALL/STRUCTURE/fragmentDB.h>
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_ |
Name normalization processor. This class is used to adopt all names in a molecular system to a given naming standard (usually the PDB standard).
Definition at line 254 of file fragmentDB.h.
enum BALL::FragmentDB::NormalizeNamesProcessor::CountingMode [private] |
Definition at line 318 of file fragmentDB.h.
BALL::FragmentDB::NormalizeNamesProcessor::NormalizeNamesProcessor | ( | ) |
Default constructor
BALL::FragmentDB::NormalizeNamesProcessor::NormalizeNamesProcessor | ( | FragmentDB & | db | ) |
Constructor
virtual BALL::FragmentDB::NormalizeNamesProcessor::~NormalizeNamesProcessor | ( | ) | [virtual] |
Destructor
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 >.
Definition at line 329 of file fragmentDB.h.
std::list<Fragment*> BALL::FragmentDB::NormalizeNamesProcessor::fragments_ [private] |
Definition at line 331 of file fragmentDB.h.
Definition at line 327 of file fragmentDB.h.