MTKpp::atomTyper Class Reference

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

Collaboration diagram for MTKpp::atomTyper:

List of all members.

Public Member Functions
	atomTyper ()
	atomTyper constructor
	atomTyper (int b)
	atomTyper constructor
virtual	~atomTyper ()
	atomTyper destructor
void	atomTypeByLib (collection *c)
	Atom type by library.
void	atomTypeByLib (molecule *m)
	Atom type by library.
void	atomTypeByCon (collection *c)
	Atom type by connectivity.
void	assignStdProperties (molecule *m)
	Assign Standard Properties.
Protected Types
typedef std::vector< molecule * > ::iterator	moleculeIterator
	molecule iterator
typedef std::vector < submolecule * >::iterator	subMoleculeIterator
	submolecule iterator
typedef std::vector< atom * > ::iterator	atomIterator
	atom iterator
Protected Member Functions
void	perceiveHistidines ()
	Perceive Histidine residues.
void	perceiveCysteines ()
	Perceive Cysteine residues.
void	assignStdRings (molecule *pMolecule)
	Assigns all rings in a Molecule.
void	assignStdFunctionalGroups (molecule *pMolecule)
	Assigns all functional groups in a Molecule.
void	assignStdHydrophobicGroups (molecule *pMolecule)
	Assigns all hydrophobic groups in a Molecule.
Protected Attributes
std::vector< molecule * >	moleculeList
	molecule vector
std::vector< submolecule * >	subMoleculeList
	submolecule vector
std::vector< atom * >	atomList
	atom vector
collection *	pCollection
	collection pointer
molecule *	pMolecule
	molecule pointer
submolecule *	pSubMolecule
	submolecule pointer
atom *	pAtom
	atom pointer
stdLibrary *	pStdLibrary
	standard library pointer
stdGroup *	pStdGroup
	standard group pointer
stdFrag *	pStdFrag
	standard fragment pointer
stdAtom *	pStdAtom
	standard atom pointer
parameters *	pParameters
	parameters pointer
int	bPerceiveHistidines
	Perceive Histidines boolean.
int	bPerceiveCysteines
	Perceive Cysteines boolean.

---

Member Typedef Documentation

typedef std::vector<molecule*>::iterator MTKpp::atomTyper::moleculeIterator [protected]

molecule iterator

typedef std::vector<submolecule*>::iterator MTKpp::atomTyper::subMoleculeIterator [protected]

submolecule iterator

typedef std::vector<atom*>::iterator MTKpp::atomTyper::atomIterator [protected]

atom iterator

---

Constructor & Destructor Documentation

MTKpp::atomTyper::atomTyper

(

)

atomTyper constructor

References bPerceiveCysteines, bPerceiveHistidines, pAtom, pCollection, pMolecule, pStdAtom, pStdFrag, pStdGroup, pStdLibrary, and pSubMolecule.

MTKpp::atomTyper::atomTyper

(

int

b

)

atomTyper constructor

References bPerceiveCysteines, bPerceiveHistidines, pAtom, pCollection, pMolecule, pStdAtom, pStdFrag, pStdGroup, pStdLibrary, and pSubMolecule.

MTKpp::atomTyper::~atomTyper

(

)

[virtual]

atomTyper destructor

---

Member Function Documentation

void MTKpp::atomTyper::atomTypeByLib

(

collection *

c

)

Atom type by library.

Parameters:

c	collection pointer

References bPerceiveCysteines, bPerceiveHistidines, MTKpp::collection::getMoleculeList(), MTKpp::collection::getParameters(), MTKpp::collection::getStdLibrary(), moleculeList, pCollection, perceiveCysteines(), perceiveHistidines(), pMolecule, pParameters, and pStdLibrary.

Referenced by main().

void MTKpp::atomTyper::atomTypeByLib

(

molecule *

m

)

Atom type by library.

Parameters:

m	molecule pointer

References atomList, MTKpp::molecule::bAtomHybridizationsAssigned, MTKpp::molecule::bMMAtomTypesAssigned, MTKpp::errorLogger, MTKpp::submolecule::getAtomList(), MTKpp::parameters::getAtomType(), MTKpp::submolecule::getName(), MTKpp::atom::getName(), MTKpp::molecule::getNumAtoms(), MTKpp::collection::getParameters(), MTKpp::molecule::getParent(), MTKpp::stdFrag::getStdAtom(), MTKpp::stdFrag::getStdAtomList(), MTKpp::stdLibrary::getStdFrag(), MTKpp::submolecule::getStdFrag(), MTKpp::collection::getStdLibrary(), MTKpp::molecule::getSubMoleculeList(), MTKpp::submolecule::getSubMolId(), MTKpp::stdFrag::getType(), MTKpp::atomType::hybridization, MTKpp::i2s(), MTKpp::stdAtom::identity, MTKpp::INFO, MTKpp::stdAtom::kind, pAtom, pCollection, pParameters, pStdAtom, pStdFrag, pStdLibrary, pSubMolecule, MTKpp::atom::setHybridization(), MTKpp::atom::setName(), MTKpp::atom::setStdAtom(), MTKpp::submolecule::setStdFrag(), MTKpp::atom::setType(), subMoleculeList, MTKpp::errorHandler::throwError(), MTKpp::stdAtom::type, and MTKpp::WARNING.

void MTKpp::atomTyper::atomTypeByCon

(

collection *

c

)

Atom type by connectivity.

Parameters:

c	collection pointer

References MTKpp::collection::getName().

void MTKpp::atomTyper::assignStdProperties

(

molecule *

m

)

Assign Standard Properties.

Parameters:

m	molecule pointer

References assignStdFunctionalGroups(), assignStdHydrophobicGroups(), assignStdRings(), MTKpp::molecule::bAtomHybridizationsAssigned, MTKpp::molecule::bMMAtomTypesAssigned, MTKpp::molecule::getNumSubMolecules(), MTKpp::collection::getParameters(), MTKpp::molecule::getParent(), MTKpp::collection::getStdLibrary(), pCollection, pParameters, and pStdLibrary.

Referenced by main().

void MTKpp::atomTyper::perceiveHistidines

(

)

[protected]

Perceive Histidine residues.

References atomList, MTKpp::errorLogger, MTKpp::collection::getNumHeavyNeighbors(), MTKpp::INFO, moleculeList, pCollection, and MTKpp::errorHandler::throwError().

Referenced by atomTypeByLib().

void MTKpp::atomTyper::perceiveCysteines

(

)

[protected]

Perceive Cysteine residues.

References atomList, MTKpp::errorLogger, MTKpp::collection::getNumHeavyNeighbors(), MTKpp::INFO, moleculeList, pCollection, and MTKpp::errorHandler::throwError().

Referenced by atomTypeByLib().

void MTKpp::atomTyper::assignStdRings

(

molecule *

pMolecule

)

[protected]

Assigns all rings in a Molecule.

Parameters:

pMolecule

Molecule pointer

References MTKpp::molecule::addRing(), MTKpp::ring::aromatic, MTKpp::errorLogger, MTKpp::molecule::getAtom(), MTKpp::molecule::getLastAddedRing(), MTKpp::molecule::getName(), MTKpp::rings::getPlaneNormal(), MTKpp::stdFrag::getStdAtom(), MTKpp::submolecule::getStdFrag(), MTKpp::stdFrag::getStdRingList(), MTKpp::molecule::getSubMoleculeList(), MTKpp::ring::hetero, MTKpp::INFO, MTKpp::MTK_ERROR, MTKpp::ring::nHetero, MTKpp::ring::nNitrogen, MTKpp::ring::nOxygen, MTKpp::ring::nSulfur, pAtom, MTKpp::ring::planar, pStdAtom, pStdFrag, pSubMolecule, MTKpp::ring::size, subMoleculeList, and MTKpp::errorHandler::throwError().

Referenced by assignStdProperties().

void MTKpp::atomTyper::assignStdFunctionalGroups

(

molecule *

pMolecule

)

[protected]

Assigns all functional groups in a Molecule.

Parameters:

pMolecule

Molecule pointer

References MTKpp::molecule::addFunctionalGroup(), MTKpp::funcGroup::atomMap, MTKpp::errorLogger, MTKpp::molecule::getAtom(), MTKpp::molecule::getName(), MTKpp::stdFrag::getStdAtom(), MTKpp::stdGroup::getStdFrag(), MTKpp::submolecule::getStdFrag(), MTKpp::stdFrag::getStdFuncGroupList(), MTKpp::stdLibrary::getStdGroup(), MTKpp::molecule::getSubMoleculeList(), MTKpp::stdAtom::identity, MTKpp::INFO, MTKpp::MTK_ERROR, pAtom, pStdAtom, MTKpp::funcGroup::pStdFrag, pStdFrag, pStdLibrary, pSubMolecule, subMoleculeList, and MTKpp::errorHandler::throwError().

Referenced by assignStdProperties().

void MTKpp::atomTyper::assignStdHydrophobicGroups

(

molecule *

pMolecule

)

[protected]

Assigns all hydrophobic groups in a Molecule.

Parameters:

pMolecule

Molecule pointer

References MTKpp::molecule::addHydrophobicGroup(), MTKpp::errorLogger, MTKpp::molecule::getAtom(), MTKpp::molecule::getName(), MTKpp::stdFrag::getStdAtom(), MTKpp::stdFrag::getStdFeatureList(), MTKpp::submolecule::getStdFrag(), MTKpp::molecule::getSubMoleculeList(), MTKpp::stdAtom::identity, MTKpp::INFO, MTKpp::MTK_ERROR, pAtom, pStdAtom, pStdFrag, pSubMolecule, subMoleculeList, and MTKpp::errorHandler::throwError().

Referenced by assignStdProperties().

---

Member Data Documentation

std::vector<molecule*> MTKpp::atomTyper::moleculeList [protected]

molecule vector

Referenced by atomTypeByLib(), perceiveCysteines(), and perceiveHistidines().

std::vector<submolecule*> MTKpp::atomTyper::subMoleculeList [protected]

submolecule vector

Referenced by assignStdFunctionalGroups(), assignStdHydrophobicGroups(), assignStdRings(), and atomTypeByLib().

std::vector<atom*> MTKpp::atomTyper::atomList [protected]

atom vector

Referenced by atomTypeByLib(), perceiveCysteines(), and perceiveHistidines().

collection* MTKpp::atomTyper::pCollection [protected]

collection pointer

Referenced by assignStdProperties(), atomTypeByLib(), atomTyper(), perceiveCysteines(), and perceiveHistidines().

molecule* MTKpp::atomTyper::pMolecule [protected]

molecule pointer

Referenced by atomTypeByLib(), and atomTyper().

submolecule* MTKpp::atomTyper::pSubMolecule [protected]

submolecule pointer

Referenced by assignStdFunctionalGroups(), assignStdHydrophobicGroups(), assignStdRings(), atomTypeByLib(), and atomTyper().

atom* MTKpp::atomTyper::pAtom [protected]

atom pointer

Referenced by assignStdFunctionalGroups(), assignStdHydrophobicGroups(), assignStdRings(), atomTypeByLib(), and atomTyper().

stdLibrary* MTKpp::atomTyper::pStdLibrary [protected]

standard library pointer

Referenced by assignStdFunctionalGroups(), assignStdProperties(), atomTypeByLib(), and atomTyper().

stdGroup* MTKpp::atomTyper::pStdGroup [protected]

standard group pointer

Referenced by atomTyper().

stdFrag* MTKpp::atomTyper::pStdFrag [protected]

standard fragment pointer

Referenced by assignStdFunctionalGroups(), assignStdHydrophobicGroups(), assignStdRings(), atomTypeByLib(), and atomTyper().

stdAtom* MTKpp::atomTyper::pStdAtom [protected]

standard atom pointer

Referenced by assignStdFunctionalGroups(), assignStdHydrophobicGroups(), assignStdRings(), atomTypeByLib(), and atomTyper().

parameters* MTKpp::atomTyper::pParameters [protected]

parameters pointer

Referenced by assignStdProperties(), and atomTypeByLib().

int MTKpp::atomTyper::bPerceiveHistidines [protected]

Perceive Histidines boolean.

Referenced by atomTypeByLib(), and atomTyper().

int MTKpp::atomTyper::bPerceiveCysteines [protected]

Perceive Cysteines boolean.

Referenced by atomTypeByLib(), and atomTyper().

---

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

• atomTyper.h
• atomTyper.cpp