#include <BALL/STRUCTURE/buildBondsProcessor.h>
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Size | buildBondsHashGrid3_ (AtomContainer &ac) |
| builds bonds, based on atom distances read from parameter file using a 3D hash grid More...
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void | estimateBondOrders_ (AtomContainer &ac) |
| after the bonds are built, the orders are estimated More...
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void | reestimateBondOrdersRings_ (AtomContainer &ac) |
| reestimate the bond orders of rings, as aromatic rings are often detected wrong More...
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void | deleteOverestimatedBonds_ (AtomContainer &ac) |
| deletes bonds, like from multiple bonded hydrogens or halogens More...
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void | readBondLengthsFromFile_ (const String &file_name="") |
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Bond::BondOrder | getNearestBondOrder_ (float length, Size e1, Size e2) |
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bool | getMaxBondLength_ (float &length, Size an1, Size an2) |
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bool | getMinBondLength_ (float &length, Size an1, Size an2) |
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Bond creation processor
Definition at line 34 of file buildBondsProcessor.h.
◆ BuildBondsProcessor() [1/3]
BALL::BuildBondsProcessor::BuildBondsProcessor |
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◆ BuildBondsProcessor() [2/3]
◆ BuildBondsProcessor() [3/3]
BALL::BuildBondsProcessor::BuildBondsProcessor |
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const String & |
file_name | ) |
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constructor with parameter filename
- Exceptions
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◆ ~BuildBondsProcessor()
virtual BALL::BuildBondsProcessor::~BuildBondsProcessor |
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virtual |
◆ BALL_CREATE()
◆ buildBondsHashGrid3_()
builds bonds, based on atom distances read from parameter file using a 3D hash grid
◆ deleteOverestimatedBonds_()
void BALL::BuildBondsProcessor::deleteOverestimatedBonds_ |
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AtomContainer & |
ac | ) |
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protected |
deletes bonds, like from multiple bonded hydrogens or halogens
◆ estimateBondOrders_()
void BALL::BuildBondsProcessor::estimateBondOrders_ |
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AtomContainer & |
ac | ) |
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protected |
after the bonds are built, the orders are estimated
◆ getBondMap()
◆ getMaxBondLength_()
bool BALL::BuildBondsProcessor::getMaxBondLength_ |
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float & |
length, |
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Size |
an1, |
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Size |
an2 |
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) |
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protected |
◆ getMinBondLength_()
bool BALL::BuildBondsProcessor::getMinBondLength_ |
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float & |
length, |
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Size |
an1, |
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Size |
an2 |
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) |
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protected |
◆ getNearestBondOrder_()
◆ getNumberOfBondsBuilt()
Size BALL::BuildBondsProcessor::getNumberOfBondsBuilt |
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Return the number of bonds built during the last application.
◆ operator()()
◆ operator=()
◆ readBondLengthsFromFile_()
void BALL::BuildBondsProcessor::readBondLengthsFromFile_ |
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const String & |
file_name = "" | ) |
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protected |
method to read the paramter file
- Exceptions
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◆ reestimateBondOrdersRings_()
void BALL::BuildBondsProcessor::reestimateBondOrdersRings_ |
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AtomContainer & |
ac | ) |
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protected |
reestimate the bond orders of rings, as aromatic rings are often detected wrong
◆ setBondLengths()
void BALL::BuildBondsProcessor::setBondLengths |
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const String & |
file_name | ) |
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sets the parameters file
- Exceptions
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◆ setDefaultOptions()
void BALL::BuildBondsProcessor::setDefaultOptions |
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reset the options to default values
◆ start()
virtual bool BALL::BuildBondsProcessor::start |
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virtual |
◆ bond_lengths_
◆ max_bond_lengths_
◆ max_length_
float BALL::BuildBondsProcessor::max_length_ |
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protected |
◆ min_bond_lengths_
◆ num_bonds_
Size BALL::BuildBondsProcessor::num_bonds_ |
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protected |
◆ options
Options BALL::BuildBondsProcessor::options |