BALL  1.5.0
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
13 # include <BALL/CONCEPT/composite.h>
14 #endif
15 
16 #include <vector>
17 
18 namespace BALL
19 {
20  class SecondaryStructure;
21 
39  : public UnaryProcessor<Composite>
40  {
41  public:
42 
48 
51  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
BALL::SecondaryStructureProcessor::setSecondaryStructureType_
char setSecondaryStructureType_(SecondaryStructure *ss, char type)
BALL::SecondaryStructureProcessor::changeAllXToY_
void changeAllXToY_(char X, char Y, String &target)
BALL_EXPORT
#define BALL_EXPORT
Definition: COMMON/global.h:50
BALL::SecondaryStructureProcessor::threeturn_
String threeturn_
Definition: secondaryStructureProcessor.h:79
BALL::SecondaryStructureProcessor::testString2_
bool testString2_(const String &s, Size offset)
BALL::SecondaryStructure
Definition: secondaryStructure.h:31
BALL::SecondaryStructureProcessor::posbridges_
std::vector< std::vector< int > > posbridges_
Definition: secondaryStructureProcessor.h:74
BALL::String
Definition: string.h:57
BALL::SecondaryStructureProcessor::fiveturn_
String fiveturn_
Definition: secondaryStructureProcessor.h:77
BALL
Definition: constants.h:13
BALL::SecondaryStructureProcessor::summary_
String summary_
Definition: secondaryStructureProcessor.h:80
BALL::SecondaryStructureProcessor::fourturn_
String fourturn_
Definition: secondaryStructureProcessor.h:78
BALL::SecondaryStructureProcessor::insertTurn_
void insertTurn_(int turn, int position)
BALL::SecondaryStructureProcessor::testString_
bool testString_(const String &s, Size offset, Size offset_2)
BALL::Composite
Definition: composite.h:74
BALL_SIZE_TYPE
BALL::UnaryProcessor
Definition: processor.h:60
composite.h
BALL::SecondaryStructureProcessor::HBonds_
std::vector< std::vector< Position > > HBonds_
Definition: secondaryStructureProcessor.h:71
common.h
BALL::SecondaryStructureProcessor
Secondary structure extraction from 3D structure.
Definition: secondaryStructureProcessor.h:40
BALL::SecondaryStructureProcessor::compute_
void compute_()
Compute the secondary structure.
BALL::Processor::Result
int Result
Definition: processor.h:36
BALL::SecondaryStructureProcessor::testString3_
bool testString3_(const String &s, Size offset, char x)
BALL::SecondaryStructureProcessor::sheet_
String sheet_
Definition: secondaryStructureProcessor.h:76