BALL  1.4.1
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Classes | Protected Member Functions | Protected Attributes
BALL::FragmentDB::BuildBondsProcessor Class Reference

#include <BALL/STRUCTURE/fragmentDB.h>

Inheritance diagram for BALL::FragmentDB::BuildBondsProcessor:
BALL::UnaryProcessor< Fragment > BALL::UnaryFunctor< Fragment, Processor::Result >

List of all members.

Classes

struct  Connection

Public Types

Type definitions
typedef std::list< ConnectionConnectionList

Public Member Functions

Constructors and Destructors
 BuildBondsProcessor ()
 BuildBondsProcessor (const FragmentDB &db)
virtual ~BuildBondsProcessor ()
Processor-related methods
virtual bool finish ()
virtual bool start ()
virtual Processor::Result operator() (Fragment &fragment)
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
Size buildFragmentBonds (Fragment &fragment, const Fragment &tplate) const
Size buildInterFragmentBonds (Fragment &first, Fragment &second) const

Protected Member Functions

void storeConnections_ (Fragment &fragment)
bool buildConnection_ (Connection &con1, Connection &con2)

Protected Attributes

FragmentDBfragment_db_
std::list< Fragment * > fragment_list_
Size bonds_built_
ConnectionList connections_

Detailed Description

Bond creation processor

Definition at line 338 of file fragmentDB.h.


Member Typedef Documentation

Definition at line 359 of file fragmentDB.h.


Constructor & Destructor Documentation


Member Function Documentation

Build a connection between two atoms, if possible

Exceptions:
Exception::TooManyBondsif an atom would be assigned too many bonds

Build all bonds in a fragment. This method builds all bonds that are contained in the template.

Returns:
the number of bonds built

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:
Exception::TooManyBondsif an atom would be assigned too many bonds

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:
Exception::TooManyBondsif an atom would be assigned too many bonds

finish method

Reimplemented from BALL::UnaryProcessor< Fragment >.

Return the number of bonds built during the last application.

virtual Processor::Result BALL::FragmentDB::BuildBondsProcessor::operator() ( Fragment ) [virtual]

operator ()

Reimplemented from BALL::UnaryProcessor< Fragment >.

Set the fragment database.

start method

Reimplemented from BALL::UnaryProcessor< Fragment >.

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.


Member Data Documentation

Definition at line 462 of file fragmentDB.h.

Definition at line 466 of file fragmentDB.h.

A pointer to the fragment database

Definition at line 449 of file fragmentDB.h.

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.

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