| [246e13] | 1 | /*
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| 2 | * Fragmentation.hpp
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| 3 | *
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| 4 | * Created on: Oct 18, 2011
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| 5 | * Author: heber
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| 6 | */
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| 7 |
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| 8 | #ifndef FRAGMENTATION_HPP_
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| 9 | #define FRAGMENTATION_HPP_
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| 10 |
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| 11 |
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| 12 | #ifdef HAVE_CONFIG_H
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| 13 | #include <config.h>
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| 14 | #endif
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| 15 |
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| 16 | #include "Graph/DepthFirstSearchAnalysis.hpp"
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| 17 |
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| [ba94c5] | 18 | #include "Fragmentation/fragmentation_helpers.hpp"
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| [ca8bea] | 19 | #include "Fragmentation/Graph.hpp"
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| 20 | #include "Fragmentation/HydrogenSaturation_enum.hpp"
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| [d4d7a1] | 21 | #include "types.hpp"
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| [dadc74] | 22 |
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| [d4d7a1] | 23 | #include <map>
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| [99b0dc] | 24 | #include <string>
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| 25 | #include <vector>
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| 26 |
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| [246e13] | 27 | class atom;
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| [f96874] | 28 | class AtomMask_t;
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| [0fad93] | 29 | class AdjacencyList;
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| [f0674a] | 30 | class KeySet;
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| [246e13] | 31 | class molecule;
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| 32 |
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| 33 | class Fragmentation
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| 34 | {
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| 35 | public:
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| [9291d04] | 36 | Fragmentation(
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| 37 | molecule *_mol,
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| 38 | AdjacencyList &_FileChecker,
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| 39 | const enum HydrogenTreatment _treatment);
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| [246e13] | 40 | ~Fragmentation();
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| 41 |
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| [bfbd4a] | 42 | int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, const std::string &prefix, DepthFirstSearchAnalysis &DFS, const Graph &ParsedFragmentList);
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| [99b0dc] | 43 |
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| [ca8bea] | 44 | const Graph& getGraph() const {
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| 45 | return TotalGraph;
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| 46 | }
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| [246e13] | 47 |
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| 48 | private:
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| 49 |
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| [339910] | 50 | void FragmentBOSSANOVA(molecule *mol, Graph &FragmentList, KeyStack &RootStack);
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| [246e13] | 51 | int GuesstimateFragmentCount(int order);
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| 52 |
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| 53 | // order at site
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| [e71325] | 54 | bool CheckOrderAtSite(AtomMask_t &AtomMask, const Graph &GlobalKeySetList, int Order, const std::string &path, bool LoopDoneAlready);
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| 55 | bool StoreOrderAtSiteFile(const std::string &path);
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| 56 | bool ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, const std::string &path);
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| [246e13] | 57 |
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| 58 | // storing fragments
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| [339910] | 59 | void FillRootStackForSubgraphs(KeyStack &RootStack, const AtomMask_t &AtomMask);
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| [bfbd4a] | 60 | bool AssignKeySetsToFragment(const Graph &KeySetList, ListOfLocalAtoms_t &ListOfLocalAtoms, Graph &FragmentList, bool FreeList = false);
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| [339910] | 61 | void TranslateIndicesToGlobalIDs(Graph &FragmentList, int &TotalNumberOfKeySets, Graph &TotalGraph);
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| [246e13] | 62 |
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| 63 | private:
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| [99b0dc] | 64 | //!> pointer to molecule that is fragmented
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| [246e13] | 65 | molecule *mol;
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| [9291d04] | 66 | //!> whether to treat hydrogen special
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| 67 | const enum HydrogenTreatment treatment;
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| [9511c7] | 68 | //!> reference to an external adjacency for comparison
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| [0fad93] | 69 | AdjacencyList &FileChecker;
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| [ca8bea] | 70 | //!> Resulting Graph with all keysets
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| 71 | Graph TotalGraph;
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| [246e13] | 72 | };
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| 73 |
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| 74 |
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| 75 | #endif /* FRAGMENTATION_HPP_ */
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