| 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 "Fragmentation/fragmentation_helpers.hpp"
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| 17 | #include "Fragmentation/Graph.hpp"
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| 18 | #include "Fragmentation/HydrogenSaturation_enum.hpp"
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| 19 | #include "Graph/ListOfLocalAtoms.hpp"
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| 20 | #include "types.hpp"
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| 21 |
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| 22 | #include <map>
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| 23 | #include <string>
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| 24 | #include <vector>
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| 25 |
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| 26 | #include <boost/bimap.hpp>
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| 27 |
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| 28 | class atom;
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| 29 | class AtomMask_t;
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| 30 | class AdjacencyList;
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| 31 | class KeySet;
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| 32 | class molecule;
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| 33 |
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| 34 | class Fragmentation
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| 35 | {
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| 36 | // some typedefs for intermediat global id <-> local id bimap
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| 37 | typedef atomId_t global_t;
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| 38 | typedef atomId_t local_t;
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| 39 | typedef boost::bimap< global_t, local_t > Global_local_bimap_t;
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| 40 | typedef Global_local_bimap_t::value_type idpair_t;
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| 41 | public:
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| 42 | Fragmentation(
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| 43 | molecule *_mol,
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| 44 | AdjacencyList &_FileChecker,
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| 45 | const enum HydrogenTreatment _treatment);
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| 46 | ~Fragmentation();
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| 47 |
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| 48 | int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, const std::string &prefix, const Graph &ParsedFragmentList, const bool _ParseStateFile);
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| 49 |
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| 50 | const Graph& getGraph() const {
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| 51 | return TotalGraph;
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| 52 | }
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| 53 |
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| 54 | private:
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| 55 |
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| 56 | void FragmentBOSSANOVA(molecule *mol, Graph &FragmentList, KeyStack &RootStack);
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| 57 | int GuesstimateFragmentCount(int order);
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| 58 |
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| 59 | // order at site
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| 60 | bool CheckOrderAtSite(AtomMask_t &AtomMask, const Graph &GlobalKeySetList, int Order, const std::string &path, bool LoopDoneAlready);
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| 61 | bool StoreOrderAtSiteFile(const std::string &path);
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| 62 | bool ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, const std::string &path, const Global_local_bimap_t &global_local_bimap);
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| 63 |
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| 64 | // storing fragments
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| 65 | void FillRootStackForSubgraphs(KeyStack &RootStack, const AtomMask_t &AtomMask);
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| 66 | bool AssignKeySetsToFragment(const Graph &KeySetList, ListOfLocalAtoms_t &ListOfLocalAtoms, Graph &FragmentList, bool FreeList = false);
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| 67 | void TranslateIndicesToGlobalIDs(Graph &FragmentList, int &TotalNumberOfKeySets, Graph &TotalGraph);
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| 68 |
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| 69 | private:
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| 70 | //!> pointer to molecule that is fragmented
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| 71 | molecule *mol;
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| 72 | //!> whether to treat hydrogen special
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| 73 | const enum HydrogenTreatment treatment;
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| 74 | //!> reference to an external adjacency for comparison
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| 75 | AdjacencyList &FileChecker;
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| 76 | //!> Resulting Graph with all keysets
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| 77 | Graph TotalGraph;
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| 78 | };
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| 79 |
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| 80 |
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| 81 | #endif /* FRAGMENTATION_HPP_ */
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