BALL  1.4.1
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Classes | Protected Member Functions | Protected Attributes
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

Definition at line 47 of file buildBondsProcessor.h.


Constructor & Destructor Documentation

default constructor

copy construcor

constructor with parameter filename

destructor


Member Function Documentation

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

deletes bonds, like from multiple bonded hydrogens or halogens

after the bonds are built, the orders are estimated

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]

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

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

sets the parameters file

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

Definition at line 188 of file buildBondsProcessor.h.

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

Definition at line 191 of file buildBondsProcessor.h.

parameter which holds the longest possible bond

Definition at line 214 of file buildBondsProcessor.h.

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

Definition at line 194 of file buildBondsProcessor.h.

number of bonds, which are created during the processor call

Definition at line 185 of file buildBondsProcessor.h.

options

Definition at line 160 of file buildBondsProcessor.h.

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