BALL::BuildBondsProcessor Class Reference

#include <BALL/STRUCTURE/buildBondsProcessor.h>

Inheritance diagram for BALL::BuildBondsProcessor:
BALL::UnaryProcessor< AtomContainer > BALL::UnaryFunctor< AtomContainer, Processor::Result >

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
BuildBondsProcessoroperator= (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

structure where bond order distances are stored in

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

parameter which holds the longest possible bond

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

number of bonds, which are created during the processor call