BALL::BuildBondsProcessor Class Reference
[Miscellaneous]

Bond creation processor. More...

#include <buildBondsProcessor.h>

Inheritance diagram for BALL::BuildBondsProcessor:

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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 ()
	reset the options to default values

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Detailed Description

Bond creation processor.