source: src/Graph/CyclicStructureAnalysis.hpp@ b760bc3

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Last change on this file since b760bc3 was 88c8ec, checked in by Frederik Heber <heber@…>, 13 years ago

REFACTOR: Replaced all "bond *" appearances by bond::ptr.

  • this is preparatory for making bond::ptr a boost::shared_ptr of bond.
  • NOTE: We had to remove a const prefix at four or five places and forward declarations had to be replaced by the true inclusion of bond.hpp at tne or so files. Apart from that, the replacement has been very smooth.
  • Property mode set to 100644
File size: 1.7 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
19#include "Bond/bond.hpp"
20#include "Bond/GraphEdge.hpp"
21#include "Fragmentation/HydrogenSaturation_enum.hpp"
22#include "Helpers/defs.hpp"
23#include "types.hpp"
24
25class atom;
26class molecule;
27
28class CyclicStructureAnalysis
29{
30public:
31 explicit CyclicStructureAnalysis(const enum HydrogenSaturation _saturation);
32 ~CyclicStructureAnalysis();
33
34 void Reset();
35 void operator()(std::deque<bond::ptr > * BackEdgeStack);
36
37 const std::map<atomId_t, int >& getMinimumRingSize() const;
38
39private:
40 // init or reset
41 void InitNode(atomId_t atom_id);
42 void CleanAllTouched();
43 void InitializeToRoot(atom *&Walker);
44 // performing tasks
45 void CyclicBFSFromRootToRoot(bond::ptr &BackEdge);
46 void RetrieveCycleMembers(atom *&OtherAtom, bond::ptr &BackEdge, int &MinRingSize);
47 void BFSToNextCycle(atom *&Root, atom *&Walker);
48 void AssignRingSizetoNonCycleMembers(int &MinRingSize, int &NumCycles);
49 // output
50 void OutputAlreadyVisited(int *list);
51
52 std::map<atomId_t, atom *> PredecessorList;
53 std::map<atomId_t, int > ShortestPathList;
54 std::map<atomId_t, enum GraphEdge::Shading> ColorList;
55 std::map<atomId_t, int > MinimumRingSize;
56 std::deque<atom *> BFSStack;
57 std::deque<atom *> TouchedStack;
58 int BondOrder;
59 atom *Root;
60
61 //!> whether to treat hydrogen special or not
62 const enum HydrogenSaturation saturation;
63
64 bool BackStepping;
65 int CurrentGraphNr;
66 int ComponentNr;
67};
68
69#endif /* CYCLICSTRUCTUREANALYSIS_HPP_ */
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