#include <BALL/STRUCTURE/fragmentDB.h>
Bond creation processor
Definition at line 338 of file fragmentDB.h.
§ ConnectionList
§ BuildBondsProcessor() [1/2]
BALL::FragmentDB::BuildBondsProcessor::BuildBondsProcessor |
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| ) |
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§ BuildBondsProcessor() [2/2]
BALL::FragmentDB::BuildBondsProcessor::BuildBondsProcessor |
( |
const FragmentDB & |
db | ) |
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§ ~BuildBondsProcessor()
virtual BALL::FragmentDB::BuildBondsProcessor::~BuildBondsProcessor |
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virtual |
§ buildConnection_()
Build a connection between two atoms, if possible
- Exceptions
-
§ buildFragmentBonds() [1/2]
Size BALL::FragmentDB::BuildBondsProcessor::buildFragmentBonds |
( |
Fragment & |
fragment | ) |
const |
Build all bonds in a fragment. This method builds all bonds that are contained in the template.
- Returns
- the number of bonds built
§ buildFragmentBonds() [2/2]
Size BALL::FragmentDB::BuildBondsProcessor::buildFragmentBonds |
( |
Fragment & |
fragment, |
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const Fragment & |
tplate |
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) |
| const |
Build all bonds in a fragment according to a manually supplied template. This method builds all bonds that are contained in manually provided template.
- Returns
- the number of bonds built
- Exceptions
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§ buildInterFragmentBonds()
Size BALL::FragmentDB::BuildBondsProcessor::buildInterFragmentBonds |
( |
Fragment & |
first, |
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Fragment & |
second |
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) |
| const |
Build all possible bonds between two fragments. This method builds all bonds that are allowed by the Connections entries in a resource database.
- Returns
- the number of bonds built
- Exceptions
-
§ finish()
virtual bool BALL::FragmentDB::BuildBondsProcessor::finish |
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virtual |
§ getNumberOfBondsBuilt()
Size BALL::FragmentDB::BuildBondsProcessor::getNumberOfBondsBuilt |
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| ) |
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Return the number of bonds built during the last application.
§ operator()()
§ setFragmentDB()
void BALL::FragmentDB::BuildBondsProcessor::setFragmentDB |
( |
const FragmentDB & |
fragment_db | ) |
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Set the fragment database.
§ start()
virtual bool BALL::FragmentDB::BuildBondsProcessor::start |
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| ) |
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virtual |
§ storeConnections_()
void BALL::FragmentDB::BuildBondsProcessor::storeConnections_ |
( |
Fragment & |
fragment | ) |
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protected |
Store connections for a fragment. This method extracts all possible connections for a given fragment and stores them in a list of possible connections. finish will then check that list for possible inter-residue bonds.
§ bonds_built_
Size BALL::FragmentDB::BuildBondsProcessor::bonds_built_ |
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protected |
§ connections_
§ fragment_db_
FragmentDB* BALL::FragmentDB::BuildBondsProcessor::fragment_db_ |
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protected |
A pointer to the fragment database
Definition at line 449 of file fragmentDB.h.
§ fragment_list_
std::list<Fragment*> BALL::FragmentDB::BuildBondsProcessor::fragment_list_ |
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protected |
A list of all fragments. This list is constructed incrementally by the operator () and is used by finish() to create the inter-fragment bonds
Definition at line 455 of file fragmentDB.h.