source: src/Fragmentation/Fragmentation.hpp@ d21933

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Last change on this file since d21933 was fe0cb8, checked in by Frederik Heber <heber@…>, 11 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: 2.3 KB
Line 
1/*
2 * Fragmentation.hpp
3 *
4 * Created on: Oct 18, 2011
5 * Author: heber
6 */
7
8#ifndef FRAGMENTATION_HPP_
9#define FRAGMENTATION_HPP_
10
11
12#ifdef HAVE_CONFIG_H
13#include <config.h>
14#endif
15
16#include "Fragmentation/fragmentation_helpers.hpp"
17#include "Fragmentation/Graph.hpp"
18#include "Fragmentation/HydrogenSaturation_enum.hpp"
19#include "Graph/ListOfLocalAtoms.hpp"
20#include "types.hpp"
21
22#include <map>
23#include <string>
24#include <vector>
25
26#include <boost/bimap.hpp>
27
28class atom;
29class AtomMask_t;
30class AdjacencyList;
31class KeySet;
32class molecule;
33
34class Fragmentation
35{
36 // some typedefs for intermediat global id <-> local id bimap
37 typedef atomId_t global_t;
38 typedef atomId_t local_t;
39 typedef boost::bimap< global_t, local_t > Global_local_bimap_t;
40 typedef Global_local_bimap_t::value_type idpair_t;
41public:
42 Fragmentation(
43 molecule *_mol,
44 AdjacencyList &_FileChecker,
45 const enum HydrogenTreatment _treatment);
46 ~Fragmentation();
47
48 int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, const std::string &prefix, const Graph &ParsedFragmentList);
49
50 const Graph& getGraph() const {
51 return TotalGraph;
52 }
53
54private:
55
56 void FragmentBOSSANOVA(molecule *mol, Graph &FragmentList, KeyStack &RootStack);
57 int GuesstimateFragmentCount(int order);
58
59 // order at site
60 bool CheckOrderAtSite(AtomMask_t &AtomMask, const Graph &GlobalKeySetList, int Order, const std::string &path, bool LoopDoneAlready);
61 bool StoreOrderAtSiteFile(const std::string &path);
62 bool ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, const std::string &path, const Global_local_bimap_t &global_local_bimap);
63
64 // storing fragments
65 void FillRootStackForSubgraphs(KeyStack &RootStack, const AtomMask_t &AtomMask);
66 bool AssignKeySetsToFragment(const Graph &KeySetList, ListOfLocalAtoms_t &ListOfLocalAtoms, Graph &FragmentList, bool FreeList = false);
67 void TranslateIndicesToGlobalIDs(Graph &FragmentList, int &TotalNumberOfKeySets, Graph &TotalGraph);
68
69private:
70 //!> pointer to molecule that is fragmented
71 molecule *mol;
72 //!> whether to treat hydrogen special
73 const enum HydrogenTreatment treatment;
74 //!> reference to an external adjacency for comparison
75 AdjacencyList &FileChecker;
76 //!> Resulting Graph with all keysets
77 Graph TotalGraph;
78};
79
80
81#endif /* FRAGMENTATION_HPP_ */
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