MTK++ Latest version: 0.2.0

Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes
MTKpp::atomTyper Class Reference

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

Collaboration diagram for MTKpp::atomTyper:
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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
collectionpCollection
 collection pointer
moleculepMolecule
 molecule pointer
submoleculepSubMolecule
 submolecule pointer
atompAtom
 atom pointer
stdLibrarypStdLibrary
 standard library pointer
stdGrouppStdGroup
 standard group pointer
stdFragpStdFrag
 standard fragment pointer
stdAtompStdAtom
 standard atom pointer
parameterspParameters
 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 ( )
MTKpp::atomTyper::atomTyper ( int  b)
MTKpp::atomTyper::~atomTyper ( ) [virtual]

atomTyper destructor


Member Function Documentation

void MTKpp::atomTyper::atomTypeByLib ( collection c)
void MTKpp::atomTyper::atomTypeByLib ( molecule m)
void MTKpp::atomTyper::atomTypeByCon ( collection c)

Atom type by connectivity.

Parameters:
ccollection pointer

References MTKpp::collection::getName().

void MTKpp::atomTyper::assignStdProperties ( molecule m)
void MTKpp::atomTyper::perceiveHistidines ( ) [protected]
void MTKpp::atomTyper::perceiveCysteines ( ) [protected]
void MTKpp::atomTyper::assignStdRings ( molecule pMolecule) [protected]
void MTKpp::atomTyper::assignStdFunctionalGroups ( molecule pMolecule) [protected]
void MTKpp::atomTyper::assignStdHydrophobicGroups ( molecule pMolecule) [protected]

Member Data Documentation

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

molecule vector

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

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

atom vector

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

molecule pointer

Referenced by atomTypeByLib(), and atomTyper().

standard library pointer

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

standard group pointer

Referenced by atomTyper().

parameters pointer

Referenced by assignStdProperties(), and atomTypeByLib().

Perceive Histidines boolean.

Referenced by atomTypeByLib(), and atomTyper().

Perceive Cysteines boolean.

Referenced by atomTypeByLib(), and atomTyper().


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

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