BALL  1.4.1
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Classes | Public Member Functions | Protected Member Functions | Protected Attributes
BALL::SideChainPlacementProcessor Class Reference

#include <BALL/STRUCTURE/sideChainPlacementProcessor.h>

Inheritance diagram for BALL::SideChainPlacementProcessor:
BALL::UnaryProcessor< AtomContainer > BALL::UnaryFunctor< AtomContainer, Processor::Result >

List of all members.

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 StringgetMutations () const
String getMutations ()
Assignment
SideChainPlacementProcessoroperator= (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

Default Constructor.

Copy Construcor.

Destructor.


Member Function Documentation

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

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

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

Get the mutated sequence.

Definition at line 185 of file sideChainPlacementProcessor.h.

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:
acthe AtomContainer to which the processor is applied.

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

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

assignment operator

Reads, checks and stores the options.

Returns:
bool - false if one of the options got an invalid value.
bool - true otherwise

Resets the options to default values.

Set the mutation indicating sequence.

Definition at line 181 of file sideChainPlacementProcessor.h.

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

Reimplemented from BALL::UnaryProcessor< AtomContainer >.


Member Data Documentation

Sequence in OneLetterCode with mutated residues.

Definition at line 218 of file sideChainPlacementProcessor.h.

options

Definition at line 205 of file sideChainPlacementProcessor.h.

Definition at line 221 of file sideChainPlacementProcessor.h.

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