BALL::BuildBondsProcessor Class Reference
[Miscellaneous]
#include <BALL/STRUCTURE/buildBondsProcessor.h>
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
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.
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.
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
Definition at line 160 of file buildBondsProcessor.h.
