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1 //
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4 // * *
5 // * The Geant4 software is copyright of the Copyright Holders of *
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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 *
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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 PDBlib.hh
42 /// \brief Definition of the PDBlib class
43
44 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
45
46 #ifndef PDBlib_h
47 # define PDBlib_h 1
48
49 # include "PDBbarycenter.hh"
50 # include "PDBmolecule.hh"
51
52 //! PDBlib Class
53 /*!
54 * This Class define Molecule model ...
55 */
56 class PDBlib
57 {
58 public:
59 //! First constructor
60 PDBlib();
61 //! Destructor
62 ~PDBlib() {};
63
64 //! Load PDB file into memory
65 Molecule* Load(const std::string& filename, unsigned short int& isDNA,
66 unsigned short int verbose);
67
68 // All declarations below are 'DNA specific'
69 // Just comment those lines if you need to use this code elsewhere.
70
71 //! Compute nucleotide barycenter from memory
72 Barycenter* ComputeNucleotideBarycenters(Molecule* moleculeListTemp);
73
74 //! Compute the corresponding bounding volume parameters
75 void ComputeBoundingVolumeParams(Molecule* moleculeListTemp, double& dX, double& dY,
76 double& dZ, // Dimensions for bounding volume
77 double& tX, double& tY,
78 double& tZ); // Translation for bounding volume
79
80 //! Compute number of nucleotide per strand
81 void ComputeNbNucleotidsPerStrand(Molecule* moleculeListTemp);
82
83 //! Compute if energy is deposited in per atom
84 unsigned short int ComputeMatchEdepDNA(Barycenter*, Molecule*, double x, double y, double z,
85 int& numStrand, int& numNucleotid, int& codeResidue);
86
87 private:
88 //! return distance between two 3D points
89 double DistanceTwo3Dpoints(double xA, double xB, double yA, double yB, double zA, double zB);
90
91 //! Number of nucleotid per strand
92 int fNbNucleotidsPerStrand;
93 };
94
95 #endif
96
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98