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