BALL::SideChainPlacementProcessor Class Reference

#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
Constant Definitions
	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
Options	options
	options More...
String	mutated_sequence_
	Sequence in OneLetterCode with mutated residues. More...
bool	valid_
bool	readOptions_ ()

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< ArgumentType, ResultType >
typedef ResultType	result_type
typedef ArgumentType	argument_type
typedef ArgumentType &	argument_reference
typedef const ArgumentType &	const_argument_reference
typedef ArgumentType *	argument_pointer
typedef const ArgumentType *	const_argument_pointer

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

SideChainPlacementProcessor() [1/2]

BALL::SideChainPlacementProcessor::SideChainPlacementProcessor

(

)

Default Constructor.

SideChainPlacementProcessor() [2/2]

BALL::SideChainPlacementProcessor::SideChainPlacementProcessor

(

const SideChainPlacementProcessor &

scpp

)

Copy Construcor.

~SideChainPlacementProcessor()

virtual BALL::SideChainPlacementProcessor::~SideChainPlacementProcessor ( )

virtual

Destructor.

Member Function Documentation

BALL_CREATE()

BALL::SideChainPlacementProcessor::BALL_CREATE

(

SideChainPlacementProcessor

)

clear()

void BALL::SideChainPlacementProcessor::clear

(

)

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

finish()

virtual bool BALL::SideChainPlacementProcessor::finish ( )

virtual

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

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

getMutations() [1/2]

String BALL::SideChainPlacementProcessor::getMutations ( )

inline

Get the mutated sequence.

Definition at line 189 of file sideChainPlacementProcessor.h.

getMutations() [2/2]

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

inline

Get the mutated sequence.

Definition at line 185 of file sideChainPlacementProcessor.h.

operator()()

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 >.

operator=()

SideChainPlacementProcessor& BALL::SideChainPlacementProcessor::operator=

(

const SideChainPlacementProcessor &

scpp

)

assignment operator

readOptions_()

bool BALL::SideChainPlacementProcessor::readOptions_ ( )

protected

Reads, checks and stores the options.

Returns

bool - false if one of the options got an invalid value.

bool - true otherwise

setDefaultOptions()

void BALL::SideChainPlacementProcessor::setDefaultOptions

(

)

Resets the options to default values.

setMutations()

void BALL::SideChainPlacementProcessor::setMutations ( String  mutated_seq )

inline

Set the mutation indicating sequence.

Definition at line 181 of file sideChainPlacementProcessor.h.

start()

virtual bool BALL::SideChainPlacementProcessor::start ( )

virtual

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

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

Member Data Documentation

mutated_sequence_

String BALL::SideChainPlacementProcessor::mutated_sequence_

protected

Sequence in OneLetterCode with mutated residues.

Definition at line 218 of file sideChainPlacementProcessor.h.

options

Options BALL::SideChainPlacementProcessor::options

options

Definition at line 205 of file sideChainPlacementProcessor.h.

valid_

bool BALL::SideChainPlacementProcessor::valid_

protected

Definition at line 221 of file sideChainPlacementProcessor.h.