BALL::AddHydrogenProcessor Class Reference

#include <BALL/STRUCTURE/addHydrogenProcessor.h>

Inheritance diagram for BALL::AddHydrogenProcessor:

Public Member Functions
	AddHydrogenProcessor ()
virtual	~AddHydrogenProcessor ()
	AddHydrogenProcessor (const AddHydrogenProcessor &hbp)
virtual bool	start ()
virtual Processor::Result	operator() (Composite &composite)
Size	getConnectivity (Atom &atom)
void	setRings (const vector< vector< Atom * > > &rings)
Size	getNumberOfAddedHydrogens ()
Public Member Functions inherited from BALL::UnaryProcessor< Composite >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()
virtual bool	finish ()

Protected Member Functions
Size	countBondOrders (Atom &atom)
void	addHydrogen_ (Atom &atom, Vector3 position)
bool	isRingAtom_ (Atom &atom)
vector< Atom * >	getPartners_ (Atom &atom)
Vector3	getNormal_ (const Vector3 &v)
bool	normalize_ (Vector3 &v)
bool	hasMultipleBond_ (Atom &atom)
float	getBondLength_ (Position element)

Protected Attributes
HashSet< Atom * >	ring_atoms_
Position	atom_nr_
Atom *	last_atom_
Size	nr_hydrogens_

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< Composite, Processor::Result >
typedef Processor::Result	result_type
typedef Composite	argument_type
typedef Composite &	argument_reference
typedef const Composite &	const_argument_reference
typedef Composite *	argument_pointer
typedef const Composite *	const_argument_pointer

Detailed Description

Saturate atoms with hydrogen atoms. Only works with main group elements. The formal charge of the atoms are taken into account. The placement of the hydrogen atoms only depends on the direct neighbour atoms. No additional optimization of the atom placement is done. The optimal bond lengths are calculized by a modified Schomaker-Stevenson rule (adapted from the MMFF94 force field).
Usage:

RingPerceptionProcessor rpp;
vector<vector<Atom*> > rings;
rpp.calculateSSSR(rings, system);
rings = rpp.getAllSmallRings();
AddHydrogenProcessor ap;
ap.setRings(rings);
system.apply(ap);

Definition at line 47 of file addHydrogenProcessor.h.

Constructor & Destructor Documentation

BALL::AddHydrogenProcessor::AddHydrogenProcessor

(

)

virtual BALL::AddHydrogenProcessor::~AddHydrogenProcessor ( )

virtual

BALL::AddHydrogenProcessor::AddHydrogenProcessor

(

const AddHydrogenProcessor &

hbp

)

Member Function Documentation

void BALL::AddHydrogenProcessor::addHydrogen_ ( Atom &  atom, Vector3  position  )

protected

Size BALL::AddHydrogenProcessor::countBondOrders ( Atom &  atom )

protected

float BALL::AddHydrogenProcessor::getBondLength_ ( Position  element )

protected

Size BALL::AddHydrogenProcessor::getConnectivity

(

Atom &

atom

)

Vector3 BALL::AddHydrogenProcessor::getNormal_ ( const Vector3 &  v )

protected

Size BALL::AddHydrogenProcessor::getNumberOfAddedHydrogens ( )

inline

Definition at line 74 of file addHydrogenProcessor.h.

vector<Atom*> BALL::AddHydrogenProcessor::getPartners_ ( Atom &  atom )

protected

bool BALL::AddHydrogenProcessor::hasMultipleBond_ ( Atom &  atom )

protected

bool BALL::AddHydrogenProcessor::isRingAtom_ ( Atom &  atom )

inlineprotected

bool BALL::AddHydrogenProcessor::normalize_ ( Vector3 &  v )

inlineprotected

virtual Processor::Result BALL::AddHydrogenProcessor::operator() ( Composite &  )

virtual

operator ()

Reimplemented from BALL::UnaryProcessor< Composite >.

void BALL::AddHydrogenProcessor::setRings

(

const vector< vector< Atom * > > &

rings

)

virtual bool BALL::AddHydrogenProcessor::start ( )

virtual

start method

Reimplemented from BALL::UnaryProcessor< Composite >.

Member Data Documentation

Position BALL::AddHydrogenProcessor::atom_nr_

protected

Definition at line 89 of file addHydrogenProcessor.h.

Atom* BALL::AddHydrogenProcessor::last_atom_

protected

Definition at line 90 of file addHydrogenProcessor.h.

Size BALL::AddHydrogenProcessor::nr_hydrogens_

protected

Definition at line 91 of file addHydrogenProcessor.h.

HashSet<Atom*> BALL::AddHydrogenProcessor::ring_atoms_

protected

Definition at line 88 of file addHydrogenProcessor.h.