MTK++ Latest version: 0.2.0

Public Member Functions | Static Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes
MTKpp::stdLibrary Class Reference

#include <mtkpp/src/Molecule/stdLibrary.h>

Collaboration diagram for MTKpp::stdLibrary:
Collaboration graph
[legend]

List of all members.

Public Member Functions

void setName (const std::string &n)
 Set name of library.
std::string getName ()
 Get name of library.
virtual stdGroupaddStdGroup ()
 Add a stdGroup to the library.
virtual stdGroupgetStdGroup (const std::string &n)
 Get stdGroup from library by name.
std::vector< stdGroup * > getStdGroupList ()
 Get stdGroups from library.
stdFraggetStdFrag (const std::string &fragName)
 Get stdFrag from library by name.
stdFraggetStdFrag (const std::string &fragName, const std::string &grpName)
 Get stdFrag from library by fragment name and group name.
int getNumberStdFrag ()
 Get number of stdFrags in the library.
void setL (std::string lll, std::string l)
 Set one letter code of amino acid or base.
std::string getL (std::string lll)
 Get one letter code of amino acid or base.
void generateSimpleFP ()
 generate simple fingerprints
void generateAdjMatrices ()
 generate adjacency matrices
void generateAtomKinds ()
 generate atom kind matrices
bool hasSimpleFPGenerated ()
bool hasAdjMatricesGenerated ()
bool hasAtomKindsGenerated ()

Static Public Member Functions

static stdLibrarygetInstance ()

Protected Types

typedef std::vector< stdGroup * >
::iterator 
stdGroupIterator
 stdGroup iterator

Protected Member Functions

 stdLibrary ()
 stdLibrary Constructor
virtual ~stdLibrary ()
 Standard Library Destructor.

Protected Attributes

std::string itsName
 stdLibrary name
std::vector< stdGroup * > itsStdGroupList
 stdGroup list
stdGrouppStdGroup
 stdGroup pointer
stdFragpStdFrag
 stdFrag pointer
std::map< std::string,
std::string > 
LLL2L
 3L code to 1L code for proteins and dna
bool bSimpleFPGenerated
bool bAdjMatricesGenerated
bool bAtomKindsGenerated

Member Typedef Documentation

typedef std::vector<stdGroup*>::iterator MTKpp::stdLibrary::stdGroupIterator [protected]

stdGroup iterator


Constructor & Destructor Documentation

MTKpp::stdLibrary::stdLibrary ( ) [protected]
MTKpp::stdLibrary::~stdLibrary ( ) [protected, virtual]

Standard Library Destructor.

References itsStdGroupList, and pStdGroup.


Member Function Documentation

stdLibrary * MTKpp::stdLibrary::getInstance ( ) [static]
void MTKpp::stdLibrary::setName ( const std::string &  n)

Set name of library.

Parameters:
nname of library

References itsName.

std::string MTKpp::stdLibrary::getName ( )

Get name of library.

Returns:
name of library

References itsName.

stdGroup * MTKpp::stdLibrary::addStdGroup ( ) [virtual]

Add a stdGroup to the library.

Returns:
stdGroup pointer

References itsStdGroupList, and pStdGroup.

Referenced by main().

stdGroup * MTKpp::stdLibrary::getStdGroup ( const std::string &  n) [virtual]

Get stdGroup from library by name.

Parameters:
nstdGroup name
Returns:
stdGroup pointer

References MTKpp::stdGroup::getName(), itsStdGroupList, and pStdGroup.

Referenced by MTKpp::atomTyper::assignStdFunctionalGroups(), getStdFrag(), and main().

std::vector< stdGroup * > MTKpp::stdLibrary::getStdGroupList ( )
stdFrag * MTKpp::stdLibrary::getStdFrag ( const std::string &  fragName)

Get stdFrag from library by name.

Parameters:
fragNamestdFrag Name
Returns:
stdFrag pointer

References MTKpp::stdGroup::getStdFragList(), MTKpp::stdFrag::getSymbol(), itsStdGroupList, pStdFrag, and pStdGroup.

Referenced by MTKpp::atomTyper::atomTypeByLib(), and main().

stdFrag * MTKpp::stdLibrary::getStdFrag ( const std::string &  fragName,
const std::string &  grpName 
)

Get stdFrag from library by fragment name and group name.

Parameters:
fragNamestdFrag Name
grpNamestdGroup name or stdFrag type
Returns:
stdFrag pointer

References MTKpp::stdGroup::getStdFrag(), MTKpp::stdGroup::getStdFragList(), getStdGroup(), MTKpp::stdFrag::getSymbol(), MTKpp::stdFrag::getType(), itsStdGroupList, pStdFrag, and pStdGroup.

int MTKpp::stdLibrary::getNumberStdFrag ( )

Get number of stdFrags in the library.

Returns:
number of stdFrags

References MTKpp::stdGroup::getStdFragList(), itsStdGroupList, and pStdGroup.

void MTKpp::stdLibrary::setL ( std::string  lll,
std::string  l 
)

Set one letter code of amino acid or base.

Parameters:
lll3 letter code
l1 letter code

References LLL2L.

std::string MTKpp::stdLibrary::getL ( std::string  lll)

Get one letter code of amino acid or base.

Parameters:
lll3 leter code
Returns:
1 letter code

References MTKpp::errorLogger, LLL2L, MTKpp::errorHandler::throwError(), and MTKpp::WARNING.

Referenced by MTKpp::metalCenter::assignBondType().

void MTKpp::stdLibrary::generateSimpleFP ( )

generate simple fingerprints

References bSimpleFPGenerated, MTKpp::stdGroup::generateSimpleFP(), itsStdGroupList, and pStdGroup.

Referenced by main().

void MTKpp::stdLibrary::generateAdjMatrices ( )

generate adjacency matrices

References bAdjMatricesGenerated, MTKpp::stdGroup::generateAdjMatrices(), itsStdGroupList, and pStdGroup.

Referenced by main().

void MTKpp::stdLibrary::generateAtomKinds ( )
bool MTKpp::stdLibrary::hasSimpleFPGenerated ( ) [inline]
bool MTKpp::stdLibrary::hasAdjMatricesGenerated ( ) [inline]
bool MTKpp::stdLibrary::hasAtomKindsGenerated ( ) [inline]

Member Data Documentation

std::string MTKpp::stdLibrary::itsName [protected]

stdLibrary name

Referenced by getName(), setName(), and stdLibrary().

std::vector<stdGroup*> MTKpp::stdLibrary::itsStdGroupList [protected]

stdFrag pointer

Referenced by generateAtomKinds(), getStdFrag(), and stdLibrary().

std::map<std::string, std::string> MTKpp::stdLibrary::LLL2L [protected]

3L code to 1L code for proteins and dna

Referenced by getL(), setL(), and stdLibrary().


The documentation for this class was generated from the following files:

Generated on Fri Dec 23 2011 09:28:57 for MTK++ by Doxygen 1.7.5.1