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secondaryStructureProcessor.h
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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#ifndef BALL_STRUCTURE_SECONDARYSTRUCTUREPROCESSOR_H
#define BALL_STRUCTURE_SECONDARYSTRUCTUREPROCESSOR_H
#ifndef BALL_COMMON_H
#include <BALL/common.h>
#endif
#ifndef BALL_CONCEPT_COMPOSITE_H
# include <BALL/CONCEPT/composite.h>
#endif
#include <vector>
namespace BALL
{
class SecondaryStructure;
class BALL_EXPORT SecondaryStructureProcessor
: public UnaryProcessor<Composite>
{
public:
SecondaryStructureProcessor();
virtual Processor::Result operator() (Composite& composite);
protected:
void compute_();
// helper function for finish()
char setSecondaryStructureType_(SecondaryStructure* ss, char type);
bool testString_(const String& s, Size offset, Size offset_2);
bool testString2_(const String& s, Size offset);
bool testString3_(const String& s, Size offset, char x);
void insertTurn_(int turn, int position);
void changeAllXToY_(char X, char Y, String& target);
// matrix to save the possible HBondPairs
std::vector<std::vector<Position> > HBonds_;
//vector to save the bridges
std::vector<std::vector<int> > posbridges_;
String sheet_;
String fiveturn_;
String fourturn_;
String threeturn_;
String summary_;
};
} //namespace BALL
#endif // BALL_STRUCTURE_SECONDARYSTRUCTUREPROCESSOR_H
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
BALL::Composite
Definition composite.h:74
BALL::Processor::Result
int Result
Definition processor.h:36
BALL::SecondaryStructureProcessor::sheet_
String sheet_
Definition secondaryStructureProcessor.h:76
BALL::SecondaryStructureProcessor::insertTurn_
void insertTurn_(int turn, int position)
BALL::SecondaryStructureProcessor::testString_
bool testString_(const String &s, Size offset, Size offset_2)
BALL::SecondaryStructureProcessor::changeAllXToY_
void changeAllXToY_(char X, char Y, String &target)
BALL::SecondaryStructureProcessor::SecondaryStructureProcessor
SecondaryStructureProcessor()
BALL::SecondaryStructureProcessor::summary_
String summary_
Definition secondaryStructureProcessor.h:80
BALL::SecondaryStructureProcessor::testString3_
bool testString3_(const String &s, Size offset, char x)
BALL::SecondaryStructureProcessor::compute_
void compute_()
Compute the secondary structure.
BALL::SecondaryStructureProcessor::setSecondaryStructureType_
char setSecondaryStructureType_(SecondaryStructure *ss, char type)
BALL::SecondaryStructureProcessor::HBonds_
std::vector< std::vector< Position > > HBonds_
Definition secondaryStructureProcessor.h:71
BALL::SecondaryStructureProcessor::threeturn_
String threeturn_
Definition secondaryStructureProcessor.h:79
BALL::SecondaryStructureProcessor::fiveturn_
String fiveturn_
Definition secondaryStructureProcessor.h:77
BALL::SecondaryStructureProcessor::testString2_
bool testString2_(const String &s, Size offset)
BALL::SecondaryStructureProcessor::fourturn_
String fourturn_
Definition secondaryStructureProcessor.h:78
BALL::SecondaryStructureProcessor::posbridges_
std::vector< std::vector< int > > posbridges_
Definition secondaryStructureProcessor.h:74
BALL::SecondaryStructure
Definition secondaryStructure.h:31
BALL::String
Definition string.h:57
BALL::UnaryProcessor< Composite >::UnaryProcessor
UnaryProcessor()
Definition processor.h:69
common.h
composite.h
BALL
Definition constants.h:13
BALL::Size
BALL_SIZE_TYPE Size
Definition COMMON/global.h:114