#include <BALL/STRUCTURE/buildBondsProcessor.h>
|
Size | buildBondsHashGrid3_ (AtomContainer &ac) |
| builds bonds, based on atom distances read from parameter file using a 3D hash grid More...
|
|
void | estimateBondOrders_ (AtomContainer &ac) |
| after the bonds are built, the orders are estimated More...
|
|
void | reestimateBondOrdersRings_ (AtomContainer &ac) |
| reestimate the bond orders of rings, as aromatic rings are often detected wrong More...
|
|
void | deleteOverestimatedBonds_ (AtomContainer &ac) |
| deletes bonds, like from multiple bonded hydrogens or halogens More...
|
|
void | readBondLengthsFromFile_ (const String &file_name="") throw (Exception::FileNotFound) |
| method to read the paramter file More...
|
|
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) |
|
Bond creation processor
Definition at line 34 of file buildBondsProcessor.h.
§ BuildBondsProcessor() [1/3]
BALL::BuildBondsProcessor::BuildBondsProcessor |
( |
| ) |
|
§ BuildBondsProcessor() [2/3]
§ BuildBondsProcessor() [3/3]
constructor with parameter filename
§ ~BuildBondsProcessor()
virtual BALL::BuildBondsProcessor::~BuildBondsProcessor |
( |
| ) |
|
|
virtual |
§ BALL_CREATE()
§ buildBondsHashGrid3_()
builds bonds, based on atom distances read from parameter file using a 3D hash grid
§ deleteOverestimatedBonds_()
void BALL::BuildBondsProcessor::deleteOverestimatedBonds_ |
( |
AtomContainer & |
ac | ) |
|
|
protected |
deletes bonds, like from multiple bonded hydrogens or halogens
§ estimateBondOrders_()
void BALL::BuildBondsProcessor::estimateBondOrders_ |
( |
AtomContainer & |
ac | ) |
|
|
protected |
after the bonds are built, the orders are estimated
§ getBondMap()
§ getMaxBondLength_()
bool BALL::BuildBondsProcessor::getMaxBondLength_ |
( |
float & |
length, |
|
|
Size |
an1, |
|
|
Size |
an2 |
|
) |
| |
|
protected |
§ getMinBondLength_()
bool BALL::BuildBondsProcessor::getMinBondLength_ |
( |
float & |
length, |
|
|
Size |
an1, |
|
|
Size |
an2 |
|
) |
| |
|
protected |
§ getNearestBondOrder_()
§ getNumberOfBondsBuilt()
Size BALL::BuildBondsProcessor::getNumberOfBondsBuilt |
( |
| ) |
|
Return the number of bonds built during the last application.
§ operator()()
§ operator=()
§ readBondLengthsFromFile_()
method to read the paramter file
§ reestimateBondOrdersRings_()
void BALL::BuildBondsProcessor::reestimateBondOrdersRings_ |
( |
AtomContainer & |
ac | ) |
|
|
protected |
reestimate the bond orders of rings, as aromatic rings are often detected wrong
§ setBondLengths()
§ setDefaultOptions()
void BALL::BuildBondsProcessor::setDefaultOptions |
( |
| ) |
|
reset the options to default values
§ start()
virtual bool BALL::BuildBondsProcessor::start |
( |
| ) |
|
|
virtual |
§ bond_lengths_
§ max_bond_lengths_
§ max_length_
float BALL::BuildBondsProcessor::max_length_ |
|
protected |
§ min_bond_lengths_
§ num_bonds_
Size BALL::BuildBondsProcessor::num_bonds_ |
|
protected |
§ options
Options BALL::BuildBondsProcessor::options |