BALL 1.5.0
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secondaryStructureProcessor.h
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1// -*- Mode: C++; tab-width: 2; -*-
2// vi: set ts=2:
3//
4
5#ifndef BALL_STRUCTURE_SECONDARYSTRUCTUREPROCESSOR_H
6#define BALL_STRUCTURE_SECONDARYSTRUCTUREPROCESSOR_H
7
8#ifndef BALL_COMMON_H
9#include <BALL/common.h>
10#endif
11
12#ifndef BALL_CONCEPT_COMPOSITE_H
14#endif
15
16#include <vector>
17
18namespace BALL
19{
20 class SecondaryStructure;
21
39 : public UnaryProcessor<Composite>
40 {
41 public:
42
48
52 virtual Processor::Result operator() (Composite& composite);
54
55 protected:
56
58 void compute_();
59
60 // helper function for finish()
62
63 bool testString_(const String& s, Size offset, Size offset_2);
64 bool testString2_(const String& s, Size offset);
65 bool testString3_(const String& s, Size offset, char x);
66
67 void insertTurn_(int turn, int position);
68 void changeAllXToY_(char X, char Y, String& target);
69
70 // matrix to save the possible HBondPairs
71 std::vector<std::vector<Position> > HBonds_;
72
73 //vector to save the bridges
74 std::vector<std::vector<int> > posbridges_;
75
81 };
82
83} //namespace BALL
84
85#endif // BALL_STRUCTURE_SECONDARYSTRUCTUREPROCESSOR_H
Secondary structure extraction from 3D structure.
void insertTurn_(int turn, int position)
bool testString_(const String &s, Size offset, Size offset_2)
void changeAllXToY_(char X, char Y, String &target)
bool testString3_(const String &s, Size offset, char x)
void compute_()
Compute the secondary structure.
char setSecondaryStructureType_(SecondaryStructure *ss, char type)
std::vector< std::vector< Position > > HBonds_
bool testString2_(const String &s, Size offset)
std::vector< std::vector< int > > posbridges_
#define BALL_EXPORT