#include <BALL/STRUCTURE/buildBondsProcessor.h>

Inheritance diagram for BALL::BuildBondsProcessor:

Classes
struct	Default
	Default values for options. More...

struct	Option
	Option names. More...

Public Member Functions
Constructors and Destructors
	BALL_CREATE (BuildBondsProcessor)

	BuildBondsProcessor ()
	default constructor More...

	BuildBondsProcessor (const BuildBondsProcessor &bbp)
	copy construcor More...

	BuildBondsProcessor (const String &file_name) throw (Exception::FileNotFound)
	constructor with parameter filename More...

virtual	~BuildBondsProcessor ()
	destructor More...

Processor-related methods
virtual bool	start ()
	processor method which is called before the operator () call More...

virtual Processor::Result	operator() (AtomContainer &ac)
	operator () for the processor More...

Accessors
Size	getNumberOfBondsBuilt ()
	Return the number of bonds built during the last application. More...

void	setBondLengths (const String &file_name) throw (Exception::FileNotFound)
	sets the parameters file More...

HashMap< Size, HashMap< Size, HashMap< int, float > > >	getBondMap ()
	Return the bond length Hashmap. More...

Assignment
BuildBondsProcessor &	operator= (const BuildBondsProcessor &bbp)
	assignment operator More...

Public Member Functions inherited from BALL::UnaryProcessor< AtomContainer >
	UnaryProcessor ()

	UnaryProcessor (const UnaryProcessor &)

virtual	~UnaryProcessor ()

virtual bool	finish ()

Protected Member Functions
Size	buildBondsHashGrid3_ (AtomContainer &ac)
	builds bonds, based on atom distances read from parameter file using a 3D hash grid More...

void	estimateBondOrders_ (AtomContainer &ac)
	after the bonds are built, the orders are estimated More...

void	reestimateBondOrdersRings_ (AtomContainer &ac)
	reestimate the bond orders of rings, as aromatic rings are often detected wrong More...

void	deleteOverestimatedBonds_ (AtomContainer &ac)
	deletes bonds, like from multiple bonded hydrogens or halogens More...

void	readBondLengthsFromFile_ (const String &file_name="") throw (Exception::FileNotFound)
	method to read the paramter file More...

Bond::BondOrder	getNearestBondOrder_ (float length, Size e1, Size e2)

bool	getMaxBondLength_ (float &length, Size an1, Size an2)

bool	getMinBondLength_ (float &length, Size an1, Size an2)

Protected Attributes
Size	num_bonds_
	number of bonds, which are created during the processor call More...

HashMap< Size, HashMap< Size, HashMap< int, float > > >	bond_lengths_
	structure where bond order distances are stored in More...

HashMap< Size, HashMap< Size, float > >	max_bond_lengths_
	structure were the bond maxima stored in (used in buildBonds_) More...

HashMap< Size, HashMap< Size, float > >	min_bond_lengths_
	structure were the bond minima stored in (used in buildBonds_) More...

float	max_length_
	parameter which holds the longest possible bond More...

Public Attributes
Options	options
	options More...

void	setDefaultOptions ()

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< AtomContainer, Processor::Result >
typedef Processor::Result	result_type

typedef AtomContainer	argument_type

typedef AtomContainer &	argument_reference

typedef const AtomContainer &	const_argument_reference

typedef AtomContainer *	argument_pointer

typedef const AtomContainer *	const_argument_pointer

Detailed Description

Bond creation processor

Definition at line 47 of file buildBondsProcessor.h.

Constructor & Destructor Documentation

BALL::BuildBondsProcessor::BuildBondsProcessor ( )

default constructor

BALL::BuildBondsProcessor::BuildBondsProcessor ( const BuildBondsProcessor & bbp )

copy construcor

BALL::BuildBondsProcessor::BuildBondsProcessor ( const String & file_name ) throw (Exception::FileNotFound)

constructor with parameter filename

virtual BALL::BuildBondsProcessor::~BuildBondsProcessor ( )

virtual

destructor

Member Function Documentation

BALL::BuildBondsProcessor::BALL_CREATE ( BuildBondsProcessor )

Size BALL::BuildBondsProcessor::buildBondsHashGrid3_ ( AtomContainer & ac )

protected

builds bonds, based on atom distances read from parameter file using a 3D hash grid

void BALL::BuildBondsProcessor::deleteOverestimatedBonds_ ( AtomContainer & ac )

protected

deletes bonds, like from multiple bonded hydrogens or halogens

void BALL::BuildBondsProcessor::estimateBondOrders_ ( AtomContainer & ac )

protected

after the bonds are built, the orders are estimated

HashMap<Size, HashMap<Size, HashMap<int, float> > > BALL::BuildBondsProcessor::getBondMap ( )

inline

Return the bond length Hashmap.

Definition at line 145 of file buildBondsProcessor.h.

bool BALL::BuildBondsProcessor::getMaxBondLength_	(	float &	length,
		Size	an1,
		Size	an2
	)

protected

bool BALL::BuildBondsProcessor::getMinBondLength_	(	float &	length,
		Size	an1,
		Size	an2
	)

protected

Bond::BondOrder BALL::BuildBondsProcessor::getNearestBondOrder_	(	float	length,
		Size	e1,
		Size	e2
	)

protected

Size BALL::BuildBondsProcessor::getNumberOfBondsBuilt ( )

Return the number of bonds built during the last application.

virtual Processor::Result BALL::BuildBondsProcessor::operator() ( AtomContainer & ac )

virtual

operator () for the processor

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

BuildBondsProcessor& BALL::BuildBondsProcessor::operator= ( const BuildBondsProcessor & bbp )

assignment operator

void BALL::BuildBondsProcessor::readBondLengthsFromFile_ ( const String & file_name = "" ) throw (Exception::FileNotFound)

protected

method to read the paramter file

void BALL::BuildBondsProcessor::reestimateBondOrdersRings_ ( AtomContainer & ac )

protected

reestimate the bond orders of rings, as aromatic rings are often detected wrong

void BALL::BuildBondsProcessor::setBondLengths ( const String & file_name ) throw (Exception::FileNotFound)

sets the parameters file

void BALL::BuildBondsProcessor::setDefaultOptions ( )

reset the options to default values

virtual bool BALL::BuildBondsProcessor::start ( )

virtual

processor method which is called before the operator () call

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

Member Data Documentation

HashMap<Size, HashMap<Size, HashMap<int, float> > > BALL::BuildBondsProcessor::bond_lengths_

protected

structure where bond order distances are stored in

Definition at line 188 of file buildBondsProcessor.h.

HashMap<Size, HashMap<Size, float> > BALL::BuildBondsProcessor::max_bond_lengths_

protected

structure were the bond maxima stored in (used in buildBonds_)

Definition at line 191 of file buildBondsProcessor.h.

float BALL::BuildBondsProcessor::max_length_

protected

parameter which holds the longest possible bond

Definition at line 214 of file buildBondsProcessor.h.

HashMap<Size, HashMap<Size, float> > BALL::BuildBondsProcessor::min_bond_lengths_

protected

structure were the bond minima stored in (used in buildBonds_)

Definition at line 194 of file buildBondsProcessor.h.

Size BALL::BuildBondsProcessor::num_bonds_

protected

number of bonds, which are created during the processor call

Definition at line 185 of file buildBondsProcessor.h.

Options BALL::BuildBondsProcessor::options

options

Definition at line 160 of file buildBondsProcessor.h.

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation