#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. More...

	SideChainPlacementProcessor (const SideChainPlacementProcessor &scpp)
	Copy Construcor. More...

virtual	~SideChainPlacementProcessor ()
	Destructor. More...

Processor-related methods
virtual bool	start ()
	Processor method which is called before the operator()-call. More...

void	clear ()

virtual Processor::Result	operator() (AtomContainer &ac)

virtual bool	finish ()
	Processor method which is called after the operator()-call. More...

Accessors
void	setDefaultOptions ()

void	setMutations (String mutated_seq)

const String &	getMutations () const

String	getMutations ()

Assignment
SideChainPlacementProcessor &	operator= (const SideChainPlacementProcessor &scpp)
	assignment operator More...

Public Member Functions inherited from BALL::UnaryProcessor< AtomContainer >
	UnaryProcessor ()

	UnaryProcessor (const UnaryProcessor &)

virtual	~UnaryProcessor ()

Public Attributes
Public Attributes
Options	options
	options More...

Protected Member Functions
bool	readOptions_ ()

Protected Attributes
String	mutated_sequence_
	Sequence in OneLetterCode with mutated residues. More...

bool	valid_

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< AtomContainer, Processor::Result >
typedef Processor::Result	result_type

typedef AtomContainer	argument_type

typedef AtomContainer &	argument_reference

typedef const AtomContainer &	const_argument_reference

typedef AtomContainer *	argument_pointer

typedef const AtomContainer *	const_argument_pointer

Detailed Description

Side Chain Placement ProcessorPlacement 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 >.

const String& BALL::SideChainPlacementProcessor::getMutations ( ) const

inline

Get the mutated sequence.

Definition at line 185 of file sideChainPlacementProcessor.h.

String BALL::SideChainPlacementProcessor::getMutations ( )

inline

Get the mutated sequence.

Definition at line 189 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