BALL::SideChainPlacementProcessor Class Reference
[Miscellaneous]

#include <BALL/STRUCTURE/sideChainPlacementProcessor.h>

Inheritance diagram for BALL::SideChainPlacementProcessor:

Classes
struct	Default
	Default values for options. More...
struct	Method
struct	Option
	Option names. More...
Public Member Functions
	BALL_CREATE (SideChainPlacementProcessor)
Constructors and Destructors

	SideChainPlacementProcessor ()
	Default Constructor.
	SideChainPlacementProcessor (const SideChainPlacementProcessor &scpp)
	Copy Construcor.
virtual	~SideChainPlacementProcessor ()
	Destructor.
Processor-related methods

virtual bool	start ()
	Processor method which is called before the operator()-call.
void	clear ()
virtual Processor::Result	operator() (AtomContainer &ac)
virtual bool	finish ()
	Processor method which is called after the operator()-call.
Accessors

void	setDefaultOptions ()
void	setMutations (String mutated_seq)
const String &	getMutations () const
String	getMutations ()
Assignment

SideChainPlacementProcessor &	operator= (const SideChainPlacementProcessor &scpp)
	assignment operator
Public Attributes
Public Attributes

Options	options
	options
Protected Member Functions
bool	readOptions_ ()
Protected Attributes
String	mutated_sequence_
	Sequence in OneLetterCode with mutated residues.
bool	valid_

Detailed Description

Side Chain Placement Processor Placement of side chains.

Given the path to the SCWRL binary in the option Option::SCWRL_BINARY_PATH; the processor computes side chain conformations for the given side chains. If no selection is given all side chains are considered. The option Option::MUTATE_SELECTED_SIDE_CHAINS can be used to mutate selected amino acids as specified in the member mutated_sequence_.

Example code:

        SideChainPlacementProcessor scpp;
        scpp.options.set(SideChainPlacementProcessor::Option::MUTATE_SELECTED_SIDE_CHAINS, true);

        System sys; 
        PDBFile mol("myfile.pdb"); 
        mol >> sys;
        String mutated_seq = "arCdcCeg";
        scpp.setMutations(mutated_seq);
        sys.apply(scpp);

Definition at line 46 of file sideChainPlacementProcessor.h.

Constructor & Destructor Documentation

BALL::SideChainPlacementProcessor::SideChainPlacementProcessor ( )

Default Constructor.

BALL::SideChainPlacementProcessor::SideChainPlacementProcessor ( const SideChainPlacementProcessor & scpp )

Copy Construcor.

virtual BALL::SideChainPlacementProcessor::~SideChainPlacementProcessor ( ) [virtual]

Destructor.

Member Function Documentation

BALL::SideChainPlacementProcessor::BALL_CREATE ( SideChainPlacementProcessor )

void BALL::SideChainPlacementProcessor::clear ( )

Clears the datastructures. NOTE: The options remain! Use setDefaultOptions() to clear the options.

virtual bool BALL::SideChainPlacementProcessor::finish ( ) [virtual]

Processor method which is called after the operator()-call.

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

String BALL::SideChainPlacementProcessor::getMutations ( ) [inline]

Get the mutated sequence.

Definition at line 189 of file sideChainPlacementProcessor.h.

const String& BALL::SideChainPlacementProcessor::getMutations ( ) const [inline]

Get the mutated sequence.

Definition at line 185 of file sideChainPlacementProcessor.h.

virtual Processor::Result BALL::SideChainPlacementProcessor::operator() ( AtomContainer & ac ) [virtual]

Operator () for the processor

Called with Default-options the processor assigns side chain torsion angles to residues.

The processor can be applied to a system, a protein, or a chain. The selection mechanism can be used to restrict the processor to certain residues. If no selection is given all side chains are considered. The option Option::MUTATE_SELECTED_SIDE_CHAINS can be used to mutate selected amino acids as specified in the member mutated_sequence_ (see setMutations(String mutationed_seq) .

Parameters:

ac

the AtomContainer to which the processor is applied.

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

SideChainPlacementProcessor& BALL::SideChainPlacementProcessor::operator= ( const SideChainPlacementProcessor & scpp )

assignment operator

bool BALL::SideChainPlacementProcessor::readOptions_ ( ) [protected]

Reads, checks and stores the options.