MTK++ Latest version: 0.2.0
#include <mtkpp/src/Molecule/atomTyper.h>
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. |
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
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
void MTKpp::atomTyper::atomTypeByLib | ( | collection * | c | ) |
Atom type by library.
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.
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 | ) |
void MTKpp::atomTyper::assignStdProperties | ( | molecule * | m | ) |
Assign Standard Properties.
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.
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.
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.
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().
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().
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