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MTKpp::proProtonate Class Reference

Class to add hydrogens to proteins. More...

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

Collaboration diagram for MTKpp::proProtonate:
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List of all members.

Public Member Functions

 proProtonate ()
 protonate Constructor
virtual ~proProtonate ()
 proProtonate Destructor
void addHydrogens (submolecule *s1, stdFrag *f1)
 add hydrogens by library

Protected Member Functions

void buildMissingAtoms (submolecule *pSubMolecule, std::vector< stdAtom * > missingChainAtoms, std::vector< atom * > first3Atoms)
 Builds the missing atoms in the first residue.
void buildDummyAtoms (std::vector< atom * > first3Atoms)
 Builds the 3 dummy atom for protonating the first standard residue.
std::vector< double > getBestTorsions (stdFrag *pStdFrag, stdAtom *stdAt1, atom *at2, atom *at3, atom *at4)
 Determine the best torsion.
void optimizePolarHs ()
 Optimize polar hydrogens.

Protected Attributes

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
atompAtom1
 atom pointer
atompAtom2
 atom pointer
atompAtom3
 atom pointer
atompAtom4
 atom pointer
BondpBond
 Bond pointer.
vector3dcoord1
 vector3d pointer
vector3dcoord2
 vector3d pointer
stdLibrarypStdLibrary
 stdLibrary pointer
stdGrouppStdGroup
 stdGroup pointer
stdFragpStdFrag
 stdFrag pointer
stdFragpStdFragMinus1
 stdFrag pointer
stdAtompStdAtom
 stdAtom pointer
stdAtompStdAtom1
 stdAtom pointer
stdAtompStdAtom2
 stdAtom pointer
stdAtompStdAtom3
 stdAtom pointer
stdAtompStdAtom4
 stdAtom pointer
atomdummyAtom1
 dummy atom 1
atomdummyAtom2
 dummy atom 2
atomdummyAtom3
 dummy atom 3
parameterspParam
 parameters
std::vector< atom * > prev3Atoms

Friends

class protonate

Detailed Description

Class to add hydrogens to proteins.

Author:
Martin Peters
Version:
0.1
Date:
2006

Constructor & Destructor Documentation

MTKpp::proProtonate::proProtonate ( )

protonate Constructor

References dummyAtom1, dummyAtom2, and dummyAtom3.

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

proProtonate Destructor

References dummyAtom1, dummyAtom2, and dummyAtom3.


Member Function Documentation

void MTKpp::proProtonate::addHydrogens ( submolecule s1,
stdFrag f1 
)
void MTKpp::proProtonate::buildMissingAtoms ( submolecule pSubMolecule,
std::vector< stdAtom * >  missingChainAtoms,
std::vector< atom * >  first3Atoms 
) [protected]
void MTKpp::proProtonate::buildDummyAtoms ( std::vector< atom * >  first3Atoms) [protected]
std::vector< double > MTKpp::proProtonate::getBestTorsions ( stdFrag pStdFrag,
stdAtom stdAt1,
atom at2,
atom at3,
atom at4 
) [protected]
void MTKpp::proProtonate::optimizePolarHs ( ) [protected]

Friends And Related Function Documentation

friend class protonate [friend]

Member Data Documentation

collection pointer

Referenced by addHydrogens(), buildMissingAtoms(), and optimizePolarHs().

bool MTKpp::proProtonate::bCol [protected]

collection boolean

molecule pointer

Referenced by buildMissingAtoms(), and optimizePolarHs().

bool MTKpp::proProtonate::bMol [protected]

molecule boolean

submolecule list

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

atom list

Referenced by addHydrogens(), and optimizePolarHs().

submolecule pointer

submolecule pointer

atom pointer

Referenced by addHydrogens(), and buildMissingAtoms().

atom pointer

Referenced by addHydrogens().

atom pointer

Referenced by addHydrogens().

atom pointer

Referenced by addHydrogens().

vector3d pointer

vector3d pointer

stdLibrary pointer

stdGroup pointer

stdFrag pointer

Referenced by optimizePolarHs().

stdFrag pointer

stdAtom pointer

stdAtom pointer

Referenced by addHydrogens().

stdAtom pointer

Referenced by addHydrogens(), and getBestTorsions().

stdAtom pointer

Referenced by addHydrogens().

stdAtom pointer

Referenced by addHydrogens().

dummy atom 1

Referenced by buildDummyAtoms(), proProtonate(), and ~proProtonate().

dummy atom 2

Referenced by buildDummyAtoms(), proProtonate(), and ~proProtonate().

dummy atom 3

Referenced by buildDummyAtoms(), proProtonate(), and ~proProtonate().

parameters

Referenced by addHydrogens(), and buildMissingAtoms().

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

Referenced by addHydrogens(), and buildDummyAtoms().


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

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