source: src/Graph/CyclicStructureAnalysis.hpp@ 0588e9

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Last change on this file since 0588e9 was fe0cb8, checked in by Frederik Heber <heber@…>, 12 years ago

Added option DoCyclesFull to FragmentationAction.

  • FIX: Fragmentation::Fragmentation() has no need for a ref to DFS anymore.
  • DFS in FragmentationAction is now used for Cycle detection only.
  • CyclicStructureAnalysis::RetrieveCycleMembers() also fills internal vector with all found cycles (as KeySet's), with a getter.
  • Property mode set to 100644
File size: 2.1 KB
Line 
1/*
2 * CyclicStructureAnalysis.hpp
3 *
4 * Created on: Feb 16, 2011
5 * Author: heber
6 */
7
8#ifndef CYCLICSTRUCTUREANALYSIS_HPP_
9#define CYCLICSTRUCTUREANALYSIS_HPP_
10
11// include config.h
12#ifdef HAVE_CONFIG_H
13#include <config.h>
14#endif
15
16#include <deque>
17#include <map>
18#include <vector>
19
20#include "Bond/bond.hpp"
21#include "Bond/GraphEdge.hpp"
22#include "Fragmentation/KeySet.hpp"
23#include "Fragmentation/HydrogenSaturation_enum.hpp"
24#include "Helpers/defs.hpp"
25#include "types.hpp"
26
27class atom;
28class molecule;
29
30class CyclicStructureAnalysis
31{
32public:
33 //!> typedef for specifying a cycle
34 typedef KeySet cycle_t;
35 //!> typedef for specifying many cycles
36 typedef std::vector< cycle_t > cycles_t;
37
38 explicit CyclicStructureAnalysis(const enum HydrogenTreatment _treatment);
39 ~CyclicStructureAnalysis();
40
41 void Reset();
42 void operator()(std::deque<bond::ptr > * BackEdgeStack);
43
44 const std::map<atomId_t, int >& getMinimumRingSize() const;
45
46 /** Getter for all found cycles.
47 *
48 */
49 cycles_t getAllCycles() const {
50 return allcycles;
51 }
52
53private:
54
55 // init or reset
56 void InitNode(atomId_t atom_id);
57 void CleanAllTouched();
58 void InitializeToRoot(atom *&Walker);
59 // performing tasks
60 void CyclicBFSFromRootToRoot(atom *&OtherAtom, bond::ptr &BackEdge);
61 void RetrieveCycleMembers(atom *&OtherAtom, bond::ptr &BackEdge, int &MinRingSize, int &NumCycles);
62 void BFSToNextCycle(atom *Walker);
63 void AssignRingSizetoNonCycleMembers(const int MinRingSize, const int NumCycles);
64 // output
65 void OutputAlreadyVisited(int *list);
66
67 std::map<atomId_t, atom *> PredecessorList;
68 std::map<atomId_t, int > ShortestPathList;
69 std::map<atomId_t, enum GraphEdge::Shading> ColorList;
70 std::map<atomId_t, int > MinimumRingSize;
71 std::deque<atom *> BFSStack;
72 std::deque<atom *> TouchedStack;
73 int BondOrder;
74 atom *Root;
75
76 //!> container for all found cycles, note that these are global ids
77 cycles_t allcycles;
78
79 //!> whether to treat hydrogen special or not
80 const enum HydrogenTreatment treatment;
81
82 bool BackStepping;
83 int CurrentGraphNr;
84 int ComponentNr;
85};
86
87#endif /* CYCLICSTRUCTUREANALYSIS_HPP_ */
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