| Geant4 Cross Reference |
1 // 1 //
2 // ******************************************* 2 // ********************************************************************
3 // * License and Disclaimer 3 // * License and Disclaimer *
4 // * 4 // * *
5 // * The Geant4 software is copyright of th 5 // * The Geant4 software is copyright of the Copyright Holders of *
6 // * the Geant4 Collaboration. It is provided 6 // * the Geant4 Collaboration. It is provided under the terms and *
7 // * conditions of the Geant4 Software License 7 // * conditions of the Geant4 Software License, included in the file *
8 // * LICENSE and available at http://cern.ch/ 8 // * LICENSE and available at http://cern.ch/geant4/license . These *
9 // * include a list of copyright holders. 9 // * include a list of copyright holders. *
10 // * 10 // * *
11 // * Neither the authors of this software syst 11 // * Neither the authors of this software system, nor their employing *
12 // * institutes,nor the agencies providing fin 12 // * institutes,nor the agencies providing financial support for this *
13 // * work make any representation or warran 13 // * work make any representation or warranty, express or implied, *
14 // * regarding this software system or assum 14 // * regarding this software system or assume any liability for its *
15 // * use. Please see the license in the file 15 // * use. Please see the license in the file LICENSE and URL above *
16 // * for the full disclaimer and the limitatio 16 // * for the full disclaimer and the limitation of liability. *
17 // * 17 // * *
18 // * This code implementation is the result 18 // * This code implementation is the result of the scientific and *
19 // * technical work of the GEANT4 collaboratio 19 // * technical work of the GEANT4 collaboration. *
20 // * By using, copying, modifying or distri 20 // * By using, copying, modifying or distributing the software (or *
21 // * any work based on the software) you ag 21 // * any work based on the software) you agree to acknowledge its *
22 // * use in resulting scientific publicati 22 // * use in resulting scientific publications, and indicate your *
23 // * acceptance of all terms of the Geant4 Sof 23 // * acceptance of all terms of the Geant4 Software license. *
24 // ******************************************* 24 // ********************************************************************
25 // 25 //
26 // This example is provided by the Geant4-DNA 26 // This example is provided by the Geant4-DNA collaboration
27 // Any report or published results obtained us 27 // Any report or published results obtained using the Geant4-DNA software
28 // shall cite the following Geant4-DNA collabo 28 // shall cite the following Geant4-DNA collaboration publication:
29 // Med. Phys. 37 (2010) 4692-4708 29 // Med. Phys. 37 (2010) 4692-4708
30 // Delage et al. PDB4DNA: implementation of DN 30 // Delage et al. PDB4DNA: implementation of DNA geometry from the Protein Data
31 // Bank (PDB) description for 31 // Bank (PDB) description for Geant4-DNA Monte-Carlo
32 // simulations (submitted to 32 // simulations (submitted to Comput. Phys. Commun.)
33 // The Geant4-DNA web site is available at htt 33 // The Geant4-DNA web site is available at http://geant4-dna.org
34 // 34 //
35 // ------------------------------------------- 35 // --------------------------------------------------------------
36 // Authors: E. Delage 36 // Authors: E. Delage
37 // november 2013 37 // november 2013
38 // ------------------------------------------- 38 // --------------------------------------------------------------
39 // 39 //
40 // 40 //
41 /// \file PDBbarycenter.hh 41 /// \file PDBbarycenter.hh
42 /// \brief Definition of the Barycenter class 42 /// \brief Definition of the Barycenter class
43 43
44 //....oooOO0OOooo........oooOO0OOooo........oo 44 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
45 45
46 #ifndef BARY_H 46 #ifndef BARY_H
47 # define BARY_H << 47 #define BARY_H
48 48
49 //! Molecule Class 49 //! Molecule Class
50 /*! 50 /*!
51 * This Class define Molecule model ... << 51 * This Class define Molecule model ...
52 */ 52 */
53 class Barycenter 53 class Barycenter
54 { 54 {
55 public: << 55 public:
56 //! First constructor << 56 //! First constructor
57 Barycenter(); << 57 Barycenter();
58 //! Second constructor << 58 //! Second constructor
59 Barycenter(int bNum, double x, double y, d << 59 Barycenter(int bNum,double x,double y, double z,//Nucleotide bar. coordinates
60 double Bx, double By, double Bz << 60 double Bx,double By, double Bz, //Base bar. coordinates
61 double Sx, double Sy, double Sz << 61 double Sx,double Sy, double Sz, //Sugar bar. coordinates
62 double Px, double Py, double Pz << 62 double Px,double Py, double Pz);//Phosphate bar. coordinates
63 //! Destructor << 63 //! Destructor
64 ~Barycenter() {}; << 64 ~Barycenter() {};
65 << 65
66 //! Get the next Barycenter << 66 //! Get the next Barycenter
67 Barycenter* GetNext(); << 67 Barycenter *GetNext();
68 //! Get the first << 68 //! Get the first
69 // Residue *GetFirst(); << 69 //Residue *GetFirst();
70 //! Get number Barycenter << 70 //! Get number Barycenter
71 int GetID(); << 71 int GetID();
72 //! Set the next Barycenter << 72 //! Set the next Barycenter
73 void SetNext(Barycenter*); << 73 void SetNext(Barycenter *);
74 //! Set the distance between atom i and nu << 74 //! Set the distance between atom i and nucleotide barycenter
75 void SetDistance(int i, double); << 75 void SetDistance(int i, double);
76 //! Get the distance between atom i and nu << 76 //! Get the distance between atom i and nucleotide barycenter
77 double GetDistance(int i); << 77 double GetDistance(int i);
78 //! Set the distance between the farther a << 78 //! Set the distance between the farther atom and nucleotide barycenter
79 void SetRadius(double); << 79 void SetRadius(double );
80 //! Get the distance between the farther a << 80 //! Get the distance between the farther atom and nucleotide barycenter
81 double GetRadius(); << 81 double GetRadius();
82 << 82
83 int fBaryNum; //!< Barycenter number << 83 int fBaryNum;//!< Barycenter number
84 double fDistanceTab[33]; //!< distance ta << 84 double fDistanceTab[33];//!< distance table [0..32] (11 hydrogens!)
85 double fRadius; << 85 double fRadius;
86 << 86
87 double fCenterX; //!< "X coordinate" of t << 87 double fCenterX; //!< "X coordinate" of this nucelotide Barycenter
88 double fCenterY; //!< "Y coordinate" of t << 88 double fCenterY; //!< "Y coordinate" of this nucelotide Barycenter
89 double fCenterZ; //!< "Z coordinate" of t << 89 double fCenterZ; //!< "Z coordinate" of this nucelotide Barycenter
90 << 90
91 double fCenterBaseX; //!< "X coordinate" << 91 double fCenterBaseX; //!< "X coordinate" of this Base Barycenter
92 double fCenterBaseY; //!< "Y coordinate" << 92 double fCenterBaseY; //!< "Y coordinate" of this Base Barycenter
93 double fCenterBaseZ; //!< "Z coordinate" << 93 double fCenterBaseZ; //!< "Z coordinate" of this Base Barycenter
94 << 94
95 double fCenterSugarX; //!< "X coordinate" << 95 double fCenterSugarX; //!< "X coordinate" of this Sugar Barycenter
96 double fCenterSugarY; //!< "Y coordinate" << 96 double fCenterSugarY; //!< "Y coordinate" of this Sugar Barycenter
97 double fCenterSugarZ; //!< "Z coordinate" << 97 double fCenterSugarZ; //!< "Z coordinate" of this Sugar Barycenter
98 << 98
99 double fCenterPhosphateX; //!< "X coordin << 99 double fCenterPhosphateX; //!< "X coordinate" of this Phosphate Barycenter
100 double fCenterPhosphateY; //!< "Y coordin << 100 double fCenterPhosphateY; //!< "Y coordinate" of this Phosphate Barycenter
101 double fCenterPhosphateZ; //!< "Z coordin << 101 double fCenterPhosphateZ; //!< "Z coordinate" of this Phosphate Barycenter
102 102
103 private: << 103 private:
104 Barycenter* fpNext; //!< Header of the ne << 104 Barycenter *fpNext; //!< Header of the next Molecule (usage before vector)
105 }; 105 };
106 #endif 106 #endif
107 107
108 //....oooOO0OOooo........oooOO0OOooo........oo 108 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
>> 109
109 110