Import Geant4 11.3.0 source tree
This commit is contained in:
Gabriele Cosmo
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//
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// ********************************************************************
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// * License and Disclaimer *
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// * *
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// * The Geant4 software is copyright of the Copyright Holders of *
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// * the Geant4 Collaboration. It is provided under the terms and *
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// * conditions of the Geant4 Software License, included in the file *
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// * LICENSE and available at http://cern.ch/geant4/license . These *
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// * include a list of copyright holders. *
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// * *
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// * Neither the authors of this software system, nor their employing *
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// * institutes,nor the agencies providing financial support for this *
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// * work make any representation or warranty, express or implied, *
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// * regarding this software system or assume any liability for its *
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// * use. Please see the license in the file LICENSE and URL above *
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// * for the full disclaimer and the limitation of liability. *
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// * *
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// * This code implementation is the result of the scientific and *
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// * technical work of the GEANT4 collaboration. *
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// * By using, copying, modifying or distributing the software (or *
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// * any work based on the software) you agree to acknowledge its *
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// * use in resulting scientific publications, and indicate your *
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// * acceptance of all terms of the Geant4 Software license. *
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// ********************************************************************
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//
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//
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#ifndef MOLECULAR_ANALYSIS_MANAGER_HH
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#define MOLECULAR_ANALYSIS_MANAGER_HH
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#include "G4AnalysisManager.hh"
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#include "G4Electron_aq.hh"
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#include "G4Hydrogen.hh"
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#include "G4OH.hh"
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#include "G4RootAnalysisManager.hh"
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#include "G4ThreeVector.hh"
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#include "globals.hh"
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#include <map>
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#include <vector>
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class ChromosomeHit;
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class DNAHit;
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class AnalysisMessenger;
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class DNAGeometry;
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struct BasePairDamageRecord
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{
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G4double fStrand1Energy = 0;
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G4double fStrand2Energy = 0;
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G4double fBp1Energy = 0;
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G4double fBp2Energy = 0;
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G4bool fBp1IndirectDmg = false;
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G4bool fBp2IndirectDmg = false;
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G4bool fStrand1IndirectDmg = false;
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G4bool fStrand2IndirectDmg = false;
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G4bool fBp1IndirectEvt = false;
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G4bool fBp2IndirectEvt = false;
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G4bool fStrand1IndirectEvt = false;
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G4bool fStrand2IndirectEvt = false;
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G4bool fbp1DirectDmg = false;
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G4bool fbp2DirectDmg = false;
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G4bool fStrand1DirectDmg = false;
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G4bool fStrand2DirectDmg = false;
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G4bool fbp1InducedBreak = false;
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G4bool fbp2InducedBreak = false;
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};
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// exp
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enum complexityEnum
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{
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SSB,
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SSBplus,
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twoSSB,
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DSB,
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DSBplus,
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DSBplusplus,
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NoneComplexity
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};
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enum sourceEnum
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{
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SSBd,
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SSBi,
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SSBm,
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DSBh,
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DSBm,
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DSBd,
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DSBi,
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undefined
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};
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//
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struct DamageClassification
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{
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complexityEnum fComplexity = NoneComplexity;
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sourceEnum fSource = undefined;
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G4int fbaseDmg = 0;
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G4int fStrandDmg = 0;
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G4int fDirectBreaks = 0;
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G4int fIndirectBreaks = 0;
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G4int fInducedBreaks = 0;
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};
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class DamageRecord
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{
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public:
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DamageRecord(const G4String&, int64_t, G4int, G4int); // dousatsu
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~DamageRecord();
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void AddBasePairDamage(BasePairDamageRecord* bp, const G4ThreeVector& pos)
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{
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fDamageRecords.push_back(bp);
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fPositions.push_back(pos);
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};
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void AddEmptyBPDamage(int64_t ii);
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void AddStrandHit(const G4MoleculeDefinition* mol);
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void AddBaseHit(const G4MoleculeDefinition* mol);
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void PrintRecord(const G4String&, const G4double& dsbDistance = 10);
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DamageClassification* GetClassification(const G4double& dsbDistance = 10);
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inline const G4String& GetName() const { return fName; };
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int64_t GetSize() const { return fDamageRecords.size(); }; // dousatsu
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inline G4int GetOHBaseHits() const { return fOHBase; };
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inline G4int GetEaqBaseHits() const { return fEaqBase; };
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inline G4int GetHBaseHits() const { return fHBase; };
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inline G4int GetOHStrandHits() const { return fOHStrand; };
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inline G4int GetEaqStrandHits() const { return fEaqStrand; };
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inline G4int GetHStrandHits() const { return fHStrand; };
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inline G4int GetPlacementIdx() const { return fStartPlacement; };
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inline G4int GetChainIdx() const { return fChainIdx; };
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inline G4int GetStrandIdx() const { return fStrandIdx; };
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inline int64_t GetStartBPIdx() const { return fStartIndex; }; // dousatsu
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void AddTestDamage(G4int, G4int, G4int, G4int);
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G4ThreeVector GetMeanPosition() const;
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G4double GetMeanDistance() const;
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G4double GetEnergy() const;
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private:
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G4String fName;
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int64_t fStartIndex;
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G4int fStartPlacement, fChainIdx, fStrandIdx = 0;
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G4int fOHBase = 0, fOHStrand = 0, fHBase = 0, fHStrand = 0, fEaqBase = 0, fEaqStrand = 0;
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std::vector<BasePairDamageRecord*> fDamageRecords;
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std::vector<G4ThreeVector> fPositions;
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const G4MoleculeDefinition* fOH = G4OH::Definition();
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const G4MoleculeDefinition* fe_aq = G4Electron_aq::Definition();
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const G4MoleculeDefinition* fH = G4Hydrogen::Definition();
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static const char* fDirectDamageChar;
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static const char* fIndirectDamageChar;
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static const char* fHitNoDamageChar;
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static const char* fNotHitChar;
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static const char* fBothDamageChar;
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const char* GetChar(const G4bool&, const G4bool&, const G4double&);
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};
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struct Node
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{
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int64_t fkey;
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DNAHit* fdata;
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Node* fleft;
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Node* fright;
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Node* fparent;
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};
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// A binary tree is used to order the DNA hit objects
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// It creates internal copies of all DNA Hits passed to it and then
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// deletes them
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class BinaryTree
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{
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public:
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BinaryTree();
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virtual ~BinaryTree();
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void Insert(const DNAHit*);
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DNAHit* Search(int64_t);
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void Destroy_tree();
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// return left-most node
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DNAHit* First() const;
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// Return next node with higher key
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DNAHit* Next(const DNAHit*) const;
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private:
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void Destroy_tree_(Node*);
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void Insert_(DNAHit*, Node*);
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DNAHit* Search_(int64_t, Node*);
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DNAHit* First_(Node*) const;
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DNAHit* Next_(int64_t, Node*) const;
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Node* fRoot;
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};
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class AnalysisManager
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{
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public:
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AnalysisManager();
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virtual ~AnalysisManager();
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void Initialize();
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void ProcessDNAHitsVector(const std::vector<const DNAHit*>&);
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void ProcessChromosomeHitMap(const std::map<uint32_t, ChromosomeHit*>&);
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void ProcessPrimary(const G4ThreeVector&, const G4double&, const G4double&);
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void ProcessCellEdep(const G4double&); // dousatsu
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void Close();
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inline void SetSaveStrands(const G4bool strand) { fSaveStrands = strand; };
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inline void SetStrandDirectory(const G4String& dir) { fStrandDirectory = dir; };
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inline void SetFragmentGap(G4int gap) { fFragmentGap = gap; };
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inline void SetDSBDistance(G4int gap) { fDSBDistance = gap; };
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inline void SetChainToSave(G4int i) { fChainToSave = i; };
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inline void SetFileName(const G4String& name) { fFileName = name; };
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void TestClassification();
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private:
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G4AnalysisManager* fAnalysisManager;
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G4bool fSaveStrands = false;
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G4String fStrandDirectory = "./";
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G4String fFileName = "molecular-dna";
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G4int fFragmentGap = 100;
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G4int fDSBDistance = 10;
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G4int fChainToSave = -1;
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DNAGeometry* fpDNAGeometry = nullptr;
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AnalysisMessenger* fpAnalysisMessenger;
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};
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#endif // MOLECULAR_ANALYSIS_MANAGER_HH
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