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1 //
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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 PDBatom.hh
42 /// \brief Definition of the Atom class
43
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45
46 #ifndef ATOM_H
47 # define ATOM_H
48
49 # include <string>
50
51 //! Atom Class
52 /*!
53 * This Class define Atom model ...
54 */
55 class Atom
56 {
57 public:
58 //! constructor with initialization
59 Atom(int serial, const std::string& name, const std::string& resName, int numInRes, int resSeq,
60 double xInit, double yInit, double zInit, double radius, double occupancy,
61 double tempFactor, const std::string& element);
62
63 //! Empty destructor
64 ~Atom() {};
65
66 //! Returns the next Atom
67 Atom* GetNext();
68 //! Return the X position for the Atom
69 double GetX();
70 //! Return the Y position for the Atom
71 double GetY();
72 //! Return the Z position for the Atom
73 double GetZ();
74 //! Return the Atom's ID
75 int GetID();
76 //! Return name of the atom
77 const std::string& GetName();
78 //! Return name of the element
79 const std::string& GetElementName();
80 //! Return name of the atom
81 double GetVanDerWaalsRadius();
82 //! Set the next atom
83 void SetNext(Atom*);
84
85 int fSerial; //!< its serial number
86 int fNumInRes; //!< its number in residue sequence
87 std::string fName; //!< Atom name
88 std::string fResName; //!< Residue name
89 int fResSeq; //!< Residue sequence number
90 double fX; //!< X orthogonal coordinates in Angstroms
91 double fY; //!< Y orthogonal coordinates in Angstroms
92 double fZ; //!< Z orthogonal coordinates in Angstroms
93 double fVdwRadius; // Vand der Waals Radius in Angstrom
94 double fOccupancy; //!< Occupancy for the Atom
95 std::string fElement; //!< Element symbol extracted from 'atom name'
96 double fTempFactor; //!< Temperature factor for the Atom
97
98 private:
99 Atom* fpNext; //!< Pointer to the next Atom
100 };
101 #endif
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104