BALL::BuildBondsProcessor Class Reference
[Miscellaneous]

#include <BALL/STRUCTURE/buildBondsProcessor.h>

Inheritance diagram for BALL::BuildBondsProcessor:

List of all members.

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
	BuildBondsProcessor (const BuildBondsProcessor &bbp)
	copy construcor
	BuildBondsProcessor (const String &file_name) throw (Exception::FileNotFound)
	constructor with parameter filename
virtual	~BuildBondsProcessor ()
	destructor
Processor-related methods
virtual bool	start ()
	processor method which is called before the operator () call
virtual Processor::Result	operator() (AtomContainer &ac)
	operator () for the processor
Accessors
Size	getNumberOfBondsBuilt ()
	Return the number of bonds built during the last application.
void	setBondLengths (const String &file_name) throw (Exception::FileNotFound)
	sets the parameters file
HashMap< Size, HashMap< Size, HashMap< int, float > > >	getBondMap ()
	Return the bond length Hashmap.
Assignment
BuildBondsProcessor &	operator= (const BuildBondsProcessor &bbp)
	assignment operator
Protected Member Functions
Size	buildBondsHashGrid3_ (AtomContainer &ac)
	builds bonds, based on atom distances read from parameter file using a 3D hash grid
void	estimateBondOrders_ (AtomContainer &ac)
	after the bonds are built, the orders are estimated
void	reestimateBondOrdersRings_ (AtomContainer &ac)
	reestimate the bond orders of rings, as aromatic rings are often detected wrong
void	deleteOverestimatedBonds_ (AtomContainer &ac)
	deletes bonds, like from multiple bonded hydrogens or halogens
void	readBondLengthsFromFile_ (const String &file_name="") throw (Exception::FileNotFound)
	method to read the paramter file
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
HashMap< Size, HashMap< Size, HashMap< int, float > > >	bond_lengths_
	structure where bond order distances are stored in
HashMap< Size, HashMap< Size, float > >	max_bond_lengths_
	structure were the bond maxima stored in (used in buildBonds_)
HashMap< Size, HashMap< Size, float > >	min_bond_lengths_
	structure were the bond minima stored in (used in buildBonds_)
float	max_length_
	parameter which holds the longest possible bond
Public Attributes
Options	options
	options
void	setDefaultOptions ()

---

Detailed Description

Bond creation processor

---

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.

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

HashMap<Size, HashMap<Size, float> > BALL::BuildBondsProcessor::max_bond_lengths_ [protected]

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

float BALL::BuildBondsProcessor::max_length_ [protected]

parameter which holds the longest possible bond

HashMap<Size, HashMap<Size, float> > BALL::BuildBondsProcessor::min_bond_lengths_ [protected]

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

Size BALL::BuildBondsProcessor::num_bonds_ [protected]

number of bonds, which are created during the processor call

Options BALL::BuildBondsProcessor::options

options