MTK++ Latest version: 0.2.0

Public Member Functions | Protected Member Functions | Protected Attributes
MTKpp::protonate Class Reference

Class to add hydrogens. More...

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

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

List of all members.

Public Member Functions

 protonate (collection *col=0)
 protonate Constructor
 protonate (molecule *mol=0)
 protonate Constructor
virtual ~protonate ()
 protonate Destructor
void run ()
 Adds hydrogens.
void optimizePolarHs ()
 Optimize polar hydrogen in a collection.

Protected Member Functions

void initialize ()
 Initialize.
void runCol ()
 Adds hydrogens.
void runMol (molecule *pMolecule)
 Adds hydrogens.
int buildMissingHeavyAtoms (submolecule *pSubMolecule)

Protected Attributes

proProtonatepPro
 proProtonate
ligProtonatepLig
 ligProtonate
watProtonatepWat
 watProtonate
collectionpCol
 collection pointer
bool bCol
 collection boolean
moleculepMol
 molecule pointer
bool bMol
 molecule boolean
std::vector< submolecule * > subMoleculeList
 submolecule list
std::vector< atom * > atomList
 atom list
submoleculepSubMolecule
 submolecule pointer
submoleculepSubMoleculeMinus1
 submolecule pointer
stdLibrarypStdLibrary
 stdLibrary pointer
stdGrouppStdGroup
 stdGroup pointer
stdFragpStdFrag
 stdFrag pointer
stdFragpStdFragMinus1
 stdFrag pointer
parameterspParam
 parameters
std::vector< atom * > prev3Atoms

Detailed Description

Class to add hydrogens.


Constructor & Destructor Documentation

MTKpp::protonate::protonate ( collection col = 0)

protonate Constructor

Parameters:
colcollection pointer

References bCol, bMol, initialize(), pLig, pParam, pPro, and pWat.

MTKpp::protonate::protonate ( molecule mol = 0)

protonate Constructor

Parameters:
molmolecule pointer

References bCol, bMol, MTKpp::molecule::getParent(), initialize(), pCol, pLig, pParam, pPro, and pWat.

MTKpp::protonate::~protonate ( ) [virtual]

protonate Destructor

References pLig, pPro, and pWat.


Member Function Documentation

void MTKpp::protonate::run ( )

Adds hydrogens.

References bCol, bMol, pMol, runCol(), and runMol().

Referenced by MTKpp::molecule::addHydrogens(), and main().

void MTKpp::protonate::optimizePolarHs ( )
void MTKpp::protonate::initialize ( ) [protected]
void MTKpp::protonate::runCol ( ) [protected]
void MTKpp::protonate::runMol ( molecule pMolecule) [protected]
int MTKpp::protonate::buildMissingHeavyAtoms ( submolecule pSubMolecule) [protected]

Member Data Documentation

bool MTKpp::protonate::bCol [protected]

collection boolean

Referenced by protonate(), and run().

molecule pointer

Referenced by optimizePolarHs(), run(), and runCol().

bool MTKpp::protonate::bMol [protected]

molecule boolean

Referenced by protonate(), and run().

submolecule list

Referenced by runMol().

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

atom list

Referenced by optimizePolarHs(), and runMol().

submolecule pointer

Referenced by buildMissingHeavyAtoms(), and runMol().

submolecule pointer

Referenced by runMol().

stdLibrary pointer

stdGroup pointer

stdFrag pointer

Referenced by runMol().

parameters

Referenced by buildMissingHeavyAtoms(), and protonate().

std::vector<atom*> MTKpp::protonate::prev3Atoms [protected]

Referenced by runMol().


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