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sideChainPlacementProcessor.h
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#ifndef BALL_STRUCTURE_SIDECHAINPLACEMENTPROCESSOR_H
#define BALL_STRUCTURE_SIDECHAINPLACEMENTPROCESSOR_H
#ifndef BALL_CONCEPT_PROCESSOR_H
#include <BALL/CONCEPT/processor.h>
#endif
#ifndef BALL_KERNEL_ATOMCONTAINER_H
#include <BALL/KERNEL/atomContainer.h>
#endif
#ifndef BALL_DATATYPE_OPTIONS_H
# include <BALL/DATATYPE/options.h>
#endif
namespace BALL
{
class BALL_EXPORT SideChainPlacementProcessor
: public UnaryProcessor<AtomContainer>
{
public:
struct BALL_EXPORT Option
{
static const char* METHOD;
static const char* SCWRL_BINARY_PATH;
static const char* SCWRL_INPUT_FILE;
static const char* SCWRL_SEQUENCE_FILE;
static const char* SCWRL_OUTPUT_FILE;
static const char* MUTATE_SELECTED_SIDE_CHAINS;
};
struct BALL_EXPORT Default
{
static const String METHOD;
static const String SCWRL_BINARY_PATH;
static const bool MUTATE_SELECTED_SIDE_CHAINS;
static const String SCWRL_INPUT_FILE;
static const String SCWRL_SEQUENCE_FILE;
static const String SCWRL_OUTPUT_FILE;
};
struct BALL_EXPORT Method
{
static const String SCWRL_4_0;
//static const String SCWRL_SERVER;
//static const String ILP;
};
BALL_CREATE(SideChainPlacementProcessor);
SideChainPlacementProcessor();
SideChainPlacementProcessor(const SideChainPlacementProcessor& scpp);
virtual ~SideChainPlacementProcessor();
virtual bool start();
void clear();
virtual Processor::Result operator ()(AtomContainer& ac);
virtual bool finish();
void setDefaultOptions();
void setMutations(String mutated_seq) {mutated_sequence_ = mutated_seq;}
const String& getMutations() const {return mutated_sequence_;}
String getMutations() {return mutated_sequence_;}
SideChainPlacementProcessor& operator = (const SideChainPlacementProcessor& scpp);
Options options;
protected:
bool readOptions_();
String mutated_sequence_;
// The processor state.
bool valid_;
};
} // namespace BALL
#endif // BALL_STRUCTURE_SIDECHAINPLACEMENTPROCESSOR_H
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
atomContainer.h
BALL::AtomContainer
Definition atomContainer.h:32
BALL::Options
Definition options.h:48
BALL::Processor::Result
int Result
Definition processor.h:36
BALL::SideChainPlacementProcessor::setMutations
void setMutations(String mutated_seq)
Definition sideChainPlacementProcessor.h:181
BALL::SideChainPlacementProcessor::mutated_sequence_
String mutated_sequence_
Sequence in OneLetterCode with mutated residues.
Definition sideChainPlacementProcessor.h:218
BALL::SideChainPlacementProcessor::start
virtual bool start()
Processor method which is called before the operator()-call.
BALL::SideChainPlacementProcessor::getMutations
String getMutations()
Definition sideChainPlacementProcessor.h:189
BALL::SideChainPlacementProcessor::readOptions_
bool readOptions_()
BALL::SideChainPlacementProcessor::valid_
bool valid_
Definition sideChainPlacementProcessor.h:221
BALL::SideChainPlacementProcessor::options
Options options
options
Definition sideChainPlacementProcessor.h:205
BALL::SideChainPlacementProcessor::SideChainPlacementProcessor
SideChainPlacementProcessor(const SideChainPlacementProcessor &scpp)
Copy Construcor.
BALL::SideChainPlacementProcessor::setDefaultOptions
void setDefaultOptions()
BALL::SideChainPlacementProcessor::finish
virtual bool finish()
Processor method which is called after the operator()-call.
BALL::SideChainPlacementProcessor::clear
void clear()
BALL::SideChainPlacementProcessor::getMutations
const String & getMutations() const
Definition sideChainPlacementProcessor.h:185
BALL::SideChainPlacementProcessor::~SideChainPlacementProcessor
virtual ~SideChainPlacementProcessor()
Destructor.
BALL::SideChainPlacementProcessor::SideChainPlacementProcessor
SideChainPlacementProcessor()
Default Constructor.
BALL::SideChainPlacementProcessor::BALL_CREATE
BALL_CREATE(SideChainPlacementProcessor)
BALL::String
Definition string.h:57
BALL::UnaryProcessor< AtomContainer >::UnaryProcessor
UnaryProcessor()
Definition processor.h:69
BALL
Definition constants.h:13
options.h
processor.h
BALL::SideChainPlacementProcessor::Default
Default values for options.
Definition sideChainPlacementProcessor.h:100
BALL::SideChainPlacementProcessor::Default::SCWRL_BINARY_PATH
static const String SCWRL_BINARY_PATH
Definition sideChainPlacementProcessor.h:102
BALL::SideChainPlacementProcessor::Default::MUTATE_SELECTED_SIDE_CHAINS
static const bool MUTATE_SELECTED_SIDE_CHAINS
Definition sideChainPlacementProcessor.h:103
BALL::SideChainPlacementProcessor::Default::SCWRL_INPUT_FILE
static const String SCWRL_INPUT_FILE
Definition sideChainPlacementProcessor.h:104
BALL::SideChainPlacementProcessor::Default::SCWRL_SEQUENCE_FILE
static const String SCWRL_SEQUENCE_FILE
Definition sideChainPlacementProcessor.h:105
BALL::SideChainPlacementProcessor::Default::METHOD
static const String METHOD
Definition sideChainPlacementProcessor.h:101
BALL::SideChainPlacementProcessor::Default::SCWRL_OUTPUT_FILE
static const String SCWRL_OUTPUT_FILE
Definition sideChainPlacementProcessor.h:106
BALL::SideChainPlacementProcessor::Method
Definition sideChainPlacementProcessor.h:110
BALL::SideChainPlacementProcessor::Method::SCWRL_4_0
static const String SCWRL_4_0
Definition sideChainPlacementProcessor.h:114
BALL::SideChainPlacementProcessor::Option
Option names.
Definition sideChainPlacementProcessor.h:56
BALL::SideChainPlacementProcessor::Option::METHOD
static const char * METHOD
Definition sideChainPlacementProcessor.h:59
BALL::SideChainPlacementProcessor::Option::SCWRL_BINARY_PATH
static const char * SCWRL_BINARY_PATH
Definition sideChainPlacementProcessor.h:63
BALL::SideChainPlacementProcessor::Option::SCWRL_SEQUENCE_FILE
static const char * SCWRL_SEQUENCE_FILE
Definition sideChainPlacementProcessor.h:79
BALL::SideChainPlacementProcessor::Option::SCWRL_INPUT_FILE
static const char * SCWRL_INPUT_FILE
Definition sideChainPlacementProcessor.h:71
BALL::SideChainPlacementProcessor::Option::SCWRL_OUTPUT_FILE
static const char * SCWRL_OUTPUT_FILE
Definition sideChainPlacementProcessor.h:90
BALL::SideChainPlacementProcessor::Option::MUTATE_SELECTED_SIDE_CHAINS
static const char * MUTATE_SELECTED_SIDE_CHAINS
Definition sideChainPlacementProcessor.h:94