source: src/Fragmentation/Fragmentation.hpp@ dda3e8

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Last change on this file since dda3e8 was bfbd4a, checked in by Frederik Heber <heber@…>, 13 years ago

Storing KeySet file with global ids now.

  • We now parse in key set file in FragmentationAction::performCall().
  • new function Graph::getLocalGraph() which sorts out all keysets local to a given molecule.
  • this local graph is passed on to Fragmentation::FragmentMolecule().
  • Fragmentation::AssignKeySetsToFragment() now has const Graph ref as param.
  • Property mode set to 100644
File size: 2.0 KB
RevLine 
[246e13]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
[ba94c5]18#include "Fragmentation/fragmentation_helpers.hpp"
[ca8bea]19#include "Fragmentation/Graph.hpp"
20#include "Fragmentation/HydrogenSaturation_enum.hpp"
[d4d7a1]21#include "types.hpp"
[dadc74]22
[d4d7a1]23#include <map>
[99b0dc]24#include <string>
25#include <vector>
26
[246e13]27class atom;
[f96874]28class AtomMask_t;
[0fad93]29class AdjacencyList;
[f0674a]30class KeySet;
[246e13]31class molecule;
32
33class Fragmentation
34{
35public:
[0fad93]36 Fragmentation(molecule *_mol, AdjacencyList &_FileChecker, const enum HydrogenSaturation _saturation);
[246e13]37 ~Fragmentation();
38
[bfbd4a]39 int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, const std::string &prefix, DepthFirstSearchAnalysis &DFS, const Graph &ParsedFragmentList);
[99b0dc]40
[ca8bea]41 const Graph& getGraph() const {
42 return TotalGraph;
43 }
[246e13]44
45private:
46
[339910]47 void FragmentBOSSANOVA(molecule *mol, Graph &FragmentList, KeyStack &RootStack);
[246e13]48 int GuesstimateFragmentCount(int order);
49
50 // order at site
[e71325]51 bool CheckOrderAtSite(AtomMask_t &AtomMask, const Graph &GlobalKeySetList, int Order, const std::string &path, bool LoopDoneAlready);
52 bool StoreOrderAtSiteFile(const std::string &path);
53 bool ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, const std::string &path);
[246e13]54
55 // storing fragments
[339910]56 void FillRootStackForSubgraphs(KeyStack &RootStack, const AtomMask_t &AtomMask);
[bfbd4a]57 bool AssignKeySetsToFragment(const Graph &KeySetList, ListOfLocalAtoms_t &ListOfLocalAtoms, Graph &FragmentList, bool FreeList = false);
[339910]58 void TranslateIndicesToGlobalIDs(Graph &FragmentList, int &TotalNumberOfKeySets, Graph &TotalGraph);
[246e13]59
60private:
[99b0dc]61 //!> pointer to molecule that is fragmented
[246e13]62 molecule *mol;
[07a47e]63 //!> whether to saturate dangling bonds with hydrogen and hence treat hydrogen special
64 const enum HydrogenSaturation saturation;
[9511c7]65 //!> reference to an external adjacency for comparison
[0fad93]66 AdjacencyList &FileChecker;
[ca8bea]67 //!> Resulting Graph with all keysets
68 Graph TotalGraph;
[246e13]69};
70
71
72#endif /* FRAGMENTATION_HPP_ */
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