BALL::FragmentDB::FragmentDB::BuildBondsProcessor Class Reference
Bond creation processor. More...#include <fragmentDB.h>
Inheritance diagram for
BALL::FragmentDB::FragmentDB::BuildBondsProcessor:
[legend]
Public Types |
|
|
Type definitions
|
|
| typedef std::list< Connection > | ConnectionList |
Public Member Functions |
|
|
Constructors and Destructors
|
|
| BuildBondsProcessor () | |
| BuildBondsProcessor (const FragmentDB &db) | |
| virtual | ~BuildBondsProcessor () |
|
Processor-related methods
|
|
| virtual bool | finish () |
| finish method |
|
| virtual bool | start () |
| start method |
|
| virtual Processor::Result | operator() (Fragment &fragment) |
| operator () |
|
|
Accessors
|
|
| Size | getNumberOfBondsBuilt () |
| Return the number of bonds built
during the last application. |
|
| void | setFragmentDB (const FragmentDB &fragment_db) |
| Set the fragment
database. |
|
|
Bond building methods
|
|
| Size | buildFragmentBonds (Fragment &fragment) const |
| Build all bonds in a fragment.
|
|
| Size | buildFragmentBonds (Fragment &fragment, const Fragment &tplate) const throw (Exception::TooManyBonds) |
| Build all bonds in a fragment
according to a manually supplied template. |
|
| Size | buildInterFragmentBonds (Fragment &first, Fragment &second) const throw (Exception::TooManyBonds) |
| Build all possible bonds between two
fragments. |
|
Protected Member Functions |
|
| void | storeConnections_ (Fragment &fragment) |
| Store connections for a fragment.
|
|
| bool | buildConnection_ (Connection &con1, Connection &con2) throw (Exception::TooManyBonds) |
| Build a connection between two
atoms, if possible. |
|
Protected Attributes |
|
| FragmentDB * | fragment_db_ |
| A pointer to the fragment
database. |
|
| std::list< Fragment * > | fragment_list_ |
| A list of all fragments. |
|
| Size | bonds_built_ |
| ConnectionList | connections_ |
Detailed Description
Bond creation processor.Member Function Documentation
| Size BALL::FragmentDB::FragmentDB::BuildBondsProcessor::buildFragmentBonds | ( | Fragment & | fragment, | |
| const Fragment & | tplate | |||
| ) | const throw (Exception::TooManyBonds) |
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
| Size BALL::FragmentDB::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
| Size BALL::FragmentDB::FragmentDB::BuildBondsProcessor::buildInterFragmentBonds | ( | Fragment & | first, | |
| Fragment & | second | |||
| ) | const throw (Exception::TooManyBonds) |
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
| void BALL::FragmentDB::FragmentDB::BuildBondsProcessor::storeConnections_ | ( | Fragment & | fragment | ) | [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.
