source: src/Fragmentation/Fragmentation.hpp@ 0cd8cf

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Last change on this file since 0cd8cf was 9291d04, checked in by Frederik Heber <heber@…>, 12 years ago

Split saturation with hydrogen of treatment of hydrogen.
  • Property mode set to 100644
File size: 2.0 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 "Graph/DepthFirstSearchAnalysis.hpp"
17
18#include "Fragmentation/fragmentation_helpers.hpp"
19#include "Fragmentation/Graph.hpp"
20#include "Fragmentation/HydrogenSaturation_enum.hpp"
21#include "types.hpp"
22
23#include <map>
24#include <string>
25#include <vector>
26
27class atom;
28class AtomMask_t;
29class AdjacencyList;
30class KeySet;
31class molecule;
32
33class Fragmentation
34{
35public:
36 Fragmentation(
37 molecule *_mol,
38 AdjacencyList &_FileChecker,
39 const enum HydrogenTreatment _treatment);
40 ~Fragmentation();
41
42 int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, const std::string &prefix, DepthFirstSearchAnalysis &DFS, const Graph &ParsedFragmentList);
43
44 const Graph& getGraph() const {
45 return TotalGraph;
46 }
47
48private:
49
50 void FragmentBOSSANOVA(molecule *mol, Graph &FragmentList, KeyStack &RootStack);
51 int GuesstimateFragmentCount(int order);
52
53 // order at site
54 bool CheckOrderAtSite(AtomMask_t &AtomMask, const Graph &GlobalKeySetList, int Order, const std::string &path, bool LoopDoneAlready);
55 bool StoreOrderAtSiteFile(const std::string &path);
56 bool ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, const std::string &path);
57
58 // storing fragments
59 void FillRootStackForSubgraphs(KeyStack &RootStack, const AtomMask_t &AtomMask);
60 bool AssignKeySetsToFragment(const Graph &KeySetList, ListOfLocalAtoms_t &ListOfLocalAtoms, Graph &FragmentList, bool FreeList = false);
61 void TranslateIndicesToGlobalIDs(Graph &FragmentList, int &TotalNumberOfKeySets, Graph &TotalGraph);
62
63private:
64 //!> pointer to molecule that is fragmented
65 molecule *mol;
66 //!> whether to treat hydrogen special
67 const enum HydrogenTreatment treatment;
68 //!> reference to an external adjacency for comparison
69 AdjacencyList &FileChecker;
70 //!> Resulting Graph with all keysets
71 Graph TotalGraph;
72};
73
74
75#endif /* FRAGMENTATION_HPP_ */
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