MTK++ Latest version: 0.2.0

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

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

Collaboration diagram for MTKpp::parameters:
Collaboration graph
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List of all members.

Public Member Functions

void printAtomTypes ()
 print atom types
atomTypeaddAtomType ()
 Add atom type.
atomTypeaddAtomType (atomType *a, std::string n, std::string g)
 Add atom type.
bondParamaddBondParam ()
 Add bond parameter.
angleParamaddAngleParam ()
 Add angle parameter.
torsionParamaddTorsionParam ()
 Add torsion parameter.
improperParamaddImproperParam ()
 Add improper parameter.
hBondParamaddHBondParam ()
 Add H-Bond parameter.
equivalentAtomsParamaddEquivalentAtomsParam ()
 Add equivalent atoms parameter.
void calculateSigmaEpsilon ()
 Calculate sigma and epsilon values for each pair of atom types.
void setAtomNumber (atomType *a)
 Set atomic number of atomType.
int getAtomicNum (const std::string &at)
 Get atomic number using atom name.
bool hasAtomType (const std::string &a, const std::string &g)
 Has atom type using atom name.
atomTypegetAtomType (const std::string &a)
 Get atom type using atom name.
std::vector< atomType * > getAtomTypes ()
 Get atom types.
std::vector< bondParam * > getBondParams ()
 Get bond parameters.
std::vector< angleParam * > getAngleParams ()
 Get angle parameters.
std::vector< torsionParam * > getTorsionParams ()
 Get torsion parameters.
std::vector< improperParam * > getImproperParams ()
 Get improper parameters.
std::string getAtomTypeSymbol (const std::string &a)
 Get element symbol using atom type.
std::string getAtomTypeHybridization (const std::string &a)
 Get atom hybridization using atom type.
bondParamgetBondParam (const std::string &at1, const std::string &at2)
 Get bond parameter.
bool hasBondParam (const std::string &at1, const std::string &at2, const std::string &g)
 Get bond parameter.
angleParamgetAngleParam (const std::string &at1, const std::string &at2, const std::string &at3)
 Get angle parameter.
bool hasAngleParam (const std::string &at1, const std::string &at2, const std::string &at3, const std::string &g)
 Get angle parameter.
std::vector< torsionParam * > getTorsionParamList (const std::string &at1, const std::string &at2, const std::string &at3, const std::string &at4)
 Get torsion parameter vector.
void removeProlineTorsion (std::vector< torsionParam * > &t)
 Remove Proline torsion.
std::vector< improperParam * > getImproperParamList (const std::string &at1, const std::string &at2, const std::string &at3, const std::string &at4, std::vector< std::vector< int > > &l)
 Get improper parameter vector.
std::vector
< equivalentAtomsParam * > 
getEquivalentAtomList ()
LJ612SEgetLJ612SE (const std::string &, const std::string &)

Static Public Member Functions

static parametersgetInstance (elements *p)
 Returns the singleton for the parameter. It will be used by all collections.

Protected Types

typedef std::vector< atomType * >
::iterator 
atomTypeIterator
 atom type iterator
typedef std::vector< bondParam * >
::iterator 
bondParamIterator
 bond parameter iterator
typedef std::vector
< angleParam * >::iterator 
angleParamIterator
 angle parameter iterator
typedef std::vector
< torsionParam * >::iterator 
torsionParamIterator
 torsion parameter iterator
typedef std::vector
< improperParam * >::iterator 
improperParamIterator
 improper parameter iterator
typedef std::vector
< hBondParam * >::iterator 
hBondParamIterator
 H-Bond parameter iterator.
typedef std::vector< LJ612SE * >
::iterator 
LJ612SEIterator
 L-J 6-12 parameter iterator.

Protected Member Functions

 parameters (elements *p)
 parameters Constructor
virtual ~parameters ()
 parameters Destructor

Protected Attributes

elementspElements
 elements pointer
std::vector< atomType * > itsTypeList
 atom type vector
std::vector< bondParam * > itsBondList
 bond parameter vector
std::vector< angleParam * > itsAngleList
 angle parameter vector
std::vector< torsionParam * > itsTorsionList
 torsion parameter vector
std::vector< improperParam * > itsImproperList
 improper parameter vector
std::vector< hBondParam * > itsHBondList
 H-Bond parameter vector.
std::vector
< equivalentAtomsParam * > 
itsEquivalentAtomsList
 equivalent atom parameter vector
std::vector< LJ612SE * > itsLJ612SEList
 L-J 6-12 parameter vector.
atomTypepAtomType
 atom type pointer
bondParampBondParam
 bond parameter pointer
angleParampAngleParam
 angle parameter pointer
torsionParampTorsionParam
 torsion parameter pointer
improperParampImproperParam
 improper parameter pointer
hBondParampHBondParam
 H-Bond parameter pointer.
equivalentAtomsParampEquivalentAtomsParam
 equivalent atom pointer
LJ612SEpLJ612SE
 L-J 6-12 parameter pointer.
bool bLJ612SE
 L-J 6-12 parameter boolean.

Member Typedef Documentation

typedef std::vector<atomType*>::iterator MTKpp::parameters::atomTypeIterator [protected]

atom type iterator

typedef std::vector<bondParam*>::iterator MTKpp::parameters::bondParamIterator [protected]

bond parameter iterator

typedef std::vector<angleParam*>::iterator MTKpp::parameters::angleParamIterator [protected]

angle parameter iterator

typedef std::vector<torsionParam*>::iterator MTKpp::parameters::torsionParamIterator [protected]

torsion parameter iterator

typedef std::vector<improperParam*>::iterator MTKpp::parameters::improperParamIterator [protected]

improper parameter iterator

typedef std::vector<hBondParam*>::iterator MTKpp::parameters::hBondParamIterator [protected]

H-Bond parameter iterator.

typedef std::vector<LJ612SE*>::iterator MTKpp::parameters::LJ612SEIterator [protected]

L-J 6-12 parameter iterator.


Constructor & Destructor Documentation

MTKpp::parameters::parameters ( elements p) [protected]

parameters Constructor

Parameters:
pelements pointer

References bLJ612SE, and pElements.

Referenced by getInstance().

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

Member Function Documentation

parameters * MTKpp::parameters::getInstance ( elements p) [static]

Returns the singleton for the parameter. It will be used by all collections.

Parameters:
pelements pointer

References MTKpp::Parameters, and parameters().

Referenced by MTKpp::collection::addParameters().

void MTKpp::parameters::printAtomTypes ( )
atomType * MTKpp::parameters::addAtomType ( )
atomType * MTKpp::parameters::addAtomType ( atomType a,
std::string  n,
std::string  g 
)
bondParam * MTKpp::parameters::addBondParam ( )
angleParam * MTKpp::parameters::addAngleParam ( )
torsionParam * MTKpp::parameters::addTorsionParam ( )
improperParam * MTKpp::parameters::addImproperParam ( )
hBondParam * MTKpp::parameters::addHBondParam ( )
equivalentAtomsParam * MTKpp::parameters::addEquivalentAtomsParam ( )

Add equivalent atoms parameter.

Returns:
equivalent atoms parameter pointer

References MTKpp::equivalentAtomsParam::groupName, itsEquivalentAtomsList, MTKpp::equivalentAtomsParam::original, and pEquivalentAtomsParam.

void MTKpp::parameters::calculateSigmaEpsilon ( )
void MTKpp::parameters::setAtomNumber ( atomType a)

Set atomic number of atomType.

Parameters:
aatomType pointer

References MTKpp::atomType::atNum, MTKpp::atomType::element, and pElements.

int MTKpp::parameters::getAtomicNum ( const std::string &  at)

Get atomic number using atom name.

Parameters:
atatom name
Returns:
atomic number

References MTKpp::atomType::atNum, itsTypeList, MTKpp::atomType::name, and pAtomType.

bool MTKpp::parameters::hasAtomType ( const std::string &  a,
const std::string &  g 
)

Has atom type using atom name.

Parameters:
aatom name
ggroup name
Returns:
boolean

References MTKpp::atomType::groupName, itsTypeList, MTKpp::atomType::name, and pAtomType.

Referenced by addAtomType().

atomType * MTKpp::parameters::getAtomType ( const std::string &  a)
std::vector< atomType * > MTKpp::parameters::getAtomTypes ( )

Get atom types.

Returns:
atomType vector

References itsTypeList.

Referenced by MTKpp::frcmodParser::Write().

std::vector< bondParam * > MTKpp::parameters::getBondParams ( )

Get bond parameters.

Returns:
bondParam vector

References itsBondList.

Referenced by MTKpp::frcmodParser::Write().

std::vector< angleParam * > MTKpp::parameters::getAngleParams ( )

Get angle parameters.

Returns:
angleParams vector

References itsAngleList.

Referenced by MTKpp::frcmodParser::Write().

std::vector< torsionParam * > MTKpp::parameters::getTorsionParams ( )

Get torsion parameters.

Returns:
torsionParams vector

References itsTorsionList.

Referenced by MTKpp::frcmodParser::Write().

std::vector< improperParam * > MTKpp::parameters::getImproperParams ( )

Get improper parameters.

Returns:
torsionParams vector

References itsImproperList.

Referenced by MTKpp::frcmodParser::Write().

std::string MTKpp::parameters::getAtomTypeSymbol ( const std::string &  a)

Get element symbol using atom type.

Parameters:
aatom type
Returns:
atom symbol

References MTKpp::atomType::element, itsTypeList, MTKpp::atomType::name, and pAtomType.

Referenced by MTKpp::molecule::addFunctionalGroup(), MTKpp::proProtonate::addHydrogens(), and MTKpp::proProtonate::buildMissingAtoms().

std::string MTKpp::parameters::getAtomTypeHybridization ( const std::string &  a)

Get atom hybridization using atom type.

Parameters:
aatom type
Returns:
atom hybridization

References MTKpp::atomType::hybridization, itsTypeList, MTKpp::atomType::name, and pAtomType.

bondParam * MTKpp::parameters::getBondParam ( const std::string &  at1,
const std::string &  at2 
)
bool MTKpp::parameters::hasBondParam ( const std::string &  at1,
const std::string &  at2,
const std::string &  g 
)

Get bond parameter.

Parameters:
at1atom type 1
at2atom type 2
groupname

References MTKpp::bondParam::atomType1, MTKpp::bondParam::atomType2, MTKpp::bondParam::groupName, itsBondList, and pBondParam.

Referenced by addAtomType().

angleParam * MTKpp::parameters::getAngleParam ( const std::string &  at1,
const std::string &  at2,
const std::string &  at3 
)
bool MTKpp::parameters::hasAngleParam ( const std::string &  at1,
const std::string &  at2,
const std::string &  at3,
const std::string &  g 
)

Get angle parameter.

Parameters:
at1atom type 1
at2atom type 2
at3atom type 3
groupname

References MTKpp::angleParam::atomType1, MTKpp::angleParam::atomType2, MTKpp::angleParam::atomType3, MTKpp::angleParam::groupName, itsAngleList, and pAngleParam.

Referenced by addAtomType().

std::vector< torsionParam * > MTKpp::parameters::getTorsionParamList ( const std::string &  at1,
const std::string &  at2,
const std::string &  at3,
const std::string &  at4 
)
void MTKpp::parameters::removeProlineTorsion ( std::vector< torsionParam * > &  t)
std::vector< improperParam * > MTKpp::parameters::getImproperParamList ( const std::string &  at1,
const std::string &  at2,
const std::string &  at3,
const std::string &  at4,
std::vector< std::vector< int > > &  l 
)
std::vector< equivalentAtomsParam * > MTKpp::parameters::getEquivalentAtomList ( )
LJ612SE * MTKpp::parameters::getLJ612SE ( const std::string &  at1,
const std::string &  at2 
)

Member Data Documentation

elements pointer

Referenced by parameters(), and setAtomNumber().

std::vector<atomType*> MTKpp::parameters::itsTypeList [protected]
std::vector<bondParam*> MTKpp::parameters::itsBondList [protected]
std::vector<angleParam*> MTKpp::parameters::itsAngleList [protected]
std::vector<hBondParam*> MTKpp::parameters::itsHBondList [protected]

H-Bond parameter vector.

Referenced by addHBondParam(), and ~parameters().

equivalent atom parameter vector

Referenced by addEquivalentAtomsParam(), and getEquivalentAtomList().

std::vector<LJ612SE*> MTKpp::parameters::itsLJ612SEList [protected]

L-J 6-12 parameter vector.

Referenced by calculateSigmaEpsilon(), and getLJ612SE().

bond parameter pointer

Referenced by addBondParam(), getBondParam(), hasBondParam(), and ~parameters().

angle parameter pointer

Referenced by addAngleParam(), getAngleParam(), hasAngleParam(), and ~parameters().

torsion parameter pointer

Referenced by addTorsionParam(), getTorsionParamList(), removeProlineTorsion(), and ~parameters().

improper parameter pointer

Referenced by addImproperParam(), getImproperParamList(), and ~parameters().

H-Bond parameter pointer.

Referenced by addHBondParam(), and ~parameters().

equivalent atom pointer

Referenced by addEquivalentAtomsParam().

L-J 6-12 parameter pointer.

Referenced by calculateSigmaEpsilon(), and getLJ612SE().

bool MTKpp::parameters::bLJ612SE [protected]

L-J 6-12 parameter boolean.

Referenced by addAtomType(), calculateSigmaEpsilon(), getLJ612SE(), and parameters().


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

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